The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
DNA analogs containing neutral amide backbone linkages composed of aminoethyl glycine units instead of the usual phosphodiester linkage of deoxyribose groups. Peptide nucleic acids have high biological stability and higher affinity for complementary DNA or RNA sequences than analogous DNA oligomers.
The characteristic three-dimensional shape of a molecule.
Nucleic acid which complements a specific mRNA or DNA molecule, or fragment thereof; used for hybridization studies in order to identify microorganisms and for genetic studies.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.
Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
The parts of a macromolecule that directly participate in its specific combination with another molecule.
A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).
A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
The rate dynamics in chemical or physical systems.
A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.
Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)
The homogeneous mixtures formed by the mixing of a solid, liquid, or gaseous substance (solute) with a liquid (the solvent), from which the dissolved substances can be recovered by physical processes. (From Grant & Hackh's Chemical Dictionary, 5th ed)
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.
NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
Measurement of the intensity and quality of fluorescence.
Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.
The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.
A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
A computer simulation developed to study the motion of molecules over a period of time.
Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.
A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Ribonucleic acid that makes up the genetic material of viruses.
The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
Determination of the spectra of ultraviolet absorption by specific molecules in gases or liquids, for example Cl2, SO2, NO2, CS2, ozone, mercury vapor, and various unsaturated compounds. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
An isothermal in-vitro nucleotide amplification process. The process involves the concomitant action of a RNA-DIRECTED DNA POLYMERASE, a ribonuclease (RIBONUCLEASES), and DNA-DIRECTED RNA POLYMERASES to synthesize large quantities of sequence-specific RNA and DNA molecules.
A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.
A group of 13 or more deoxyribonucleotides in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).
Computer-based representation of physical systems and phenomena such as chemical processes.
The scattering of x-rays by matter, especially crystals, with accompanying variation in intensity due to interference effects. Analysis of the crystal structure of materials is performed by passing x-rays through them and registering the diffraction image of the rays (CRYSTALLOGRAPHY, X-RAY). (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Deoxyribonucleic acid that makes up the genetic material of viruses.
The process by which two molecules of the same chemical composition form a condensation product or polymer.
The characteristic 3-dimensional shape of a carbohydrate.
Proteins prepared by recombinant DNA technology.
The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
Disruption of the non-covalent bonds and/or disulfide bonds responsible for maintaining the three-dimensional shape and activity of the native protein.
The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.
Double-stranded nucleic acid molecules (DNA-DNA or DNA-RNA) which contain regions of nucleotide mismatches (non-complementary). In vivo, these heteroduplexes can result from mutation or genetic recombination; in vitro, they are formed by nucleic acid hybridization. Electron microscopic analysis of the resulting heteroduplexes facilitates the mapping of regions of base sequence homology of nucleic acids.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
The accumulation of an electric charge on a object
Nucleotide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
Agents that emit light after excitation by light. The wave length of the emitted light is usually longer than that of the incident light. Fluorochromes are substances that cause fluorescence in other substances, i.e., dyes used to mark or label other compounds with fluorescent tags.
The branch of science that deals with the geometric description of crystals and their internal arrangement. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
Higher-order DNA and RNA structures formed from guanine-rich sequences. They are formed around a core of at least 2 stacked tetrads of hydrogen-bonded GUANINE bases. They can be formed from one two or four separate strands of DNA (or RNA) and can display a wide variety of topologies, which are a consequence of various combinations of strand direction, length, and sequence. (From Nucleic Acids Res. 2006;34(19):5402-15)
Proteins found in any species of bacterium.
A clear, odorless, tasteless liquid that is essential for most animal and plant life and is an excellent solvent for many substances. The chemical formula is hydrogen oxide (H2O). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.
Established cell cultures that have the potential to propagate indefinitely.
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Analysis of the intensity of Raman scattering of monochromatic light as a function of frequency of the scattered light.
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
Liquids that dissolve other substances (solutes), generally solids, without any change in chemical composition, as, water containing sugar. (Grant & Hackh's Chemical Dictionary, 5th ed)
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.
The process of cleaving a chemical compound by the addition of a molecule of water.
A type of FLUORESCENCE SPECTROSCOPY using two FLUORESCENT DYES with overlapping emission and absorption spectra, which is used to indicate proximity of labeled molecules. This technique is useful for studying interactions of molecules and PROTEIN FOLDING.
Purine or pyrimidine bases attached to a ribose or deoxyribose. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
The most common form of DNA found in nature. It is a right-handed helix with 10 base pairs per turn, a pitch of 0.338 nm per base pair and a helical diameter of 1.9 nm.
Agents that are capable of inserting themselves between the successive bases in DNA, thus kinking, uncoiling or otherwise deforming it and therefore preventing its proper functioning. They are used in the study of DNA.
A metallic element that has the atomic symbol Mg, atomic number 12, and atomic weight 24.31. It is important for the activity of many enzymes, especially those involved in OXIDATIVE PHOSPHORYLATION.
The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals.
A basic science concerned with the composition, structure, and properties of matter; and the reactions that occur between substances and the associated energy exchange.
An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.
The phenomenon whereby compounds whose molecules have the same number and kind of atoms and the same atomic arrangement, but differ in their spatial relationships. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 5th ed)
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
The thermodynamic interaction between a substance and WATER.
A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
The composition, conformation, and properties of atoms and molecules, and their reaction and interaction processes.
A group of atoms or molecules attached to other molecules or cellular structures and used in studying the properties of these molecules and structures. Radioactive DNA or RNA sequences are used in MOLECULAR GENETICS to detect the presence of a complementary sequence by NUCLEIC ACID HYBRIDIZATION.
A group of 13 or more ribonucleotides in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.
Sequential operating programs and data which instruct the functioning of a digital computer.
Scattering of a beam of electromagnetic or acoustic RADIATION, or particles, at small angles by particles or cavities whose dimensions are many times as large as the wavelength of the radiation or the de Broglie wavelength of the scattered particles. Also know as low angle scattering. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Small angle scattering (SAS) techniques, small angle neutron (SANS), X-ray (SAXS), and light (SALS, or just LS) scattering, are used to characterize objects on a nanoscale.
A spectroscopic technique in which a range of wavelengths is presented simultaneously with an interferometer and the spectrum is mathematically derived from the pattern thus obtained.
Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.
The modification of the reactivity of ENZYMES by the binding of effectors to sites (ALLOSTERIC SITES) on the enzymes other than the substrate BINDING SITES.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
Proteins obtained from ESCHERICHIA COLI.
A representation, generally small in scale, to show the structure, construction, or appearance of something. (From Random House Unabridged Dictionary, 2d ed)
A purine base and a fundamental unit of ADENINE NUCLEOTIDES.
Molecules of DNA that possess enzymatic activity.
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
Chemical groups containing the covalent disulfide bonds -S-S-. The sulfur atoms can be bound to inorganic or organic moieties.
The study of CHEMICAL PHENOMENA and processes in terms of the underlying PHYSICAL PHENOMENA and processes.
Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.
Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
Presence of warmth or heat or a temperature notably higher than an accustomed norm.
The physical phenomena describing the structure and properties of atoms and molecules, and their reaction and interaction processes.
Short fragments of DNA or RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.
A series of heterocyclic compounds that are variously substituted in nature and are known also as purine bases. They include ADENINE and GUANINE, constituents of nucleic acids, as well as many alkaloids such as CAFFEINE and THEOPHYLLINE. Uric acid is the metabolic end product of purine metabolism.
Proteins found in any species of virus.
A purine nucleoside that has guanine linked by its N9 nitrogen to the C1 carbon of ribose. It is a component of ribonucleic acid and its nucleotides play important roles in metabolism. (From Dorland, 28th ed)
Stable elementary particles having the smallest known positive charge, found in the nuclei of all elements. The proton mass is less than that of a neutron. A proton is the nucleus of the light hydrogen atom, i.e., the hydrogen ion.
The study of PHYSICAL PHENOMENA and PHYSICAL PROCESSES as applied to living things.
Reagents with two reactive groups, usually at opposite ends of the molecule, that are capable of reacting with and thereby forming bridges between side chains of amino acids in proteins; the locations of naturally reactive areas within proteins can thereby be identified; may also be used for other macromolecules, like glycoproteins, nucleic acids, or other.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.
An isoform of DNA that occurs in an environment rich in SODIUM and POTASSIUM ions. It is a right-handed helix with 11 base pairs per turn, a pitch of 0.256 nm per base pair and a helical diameter of 2.3 nm.
A pyrimidine base that is a fundamental unit of nucleic acids.
The measurement of the quantity of heat involved in various processes, such as chemical reactions, changes of state, and formations of solutions, or in the determination of the heat capacities of substances. The fundamental unit of measurement is the joule or the calorie (4.184 joules). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A pentose active in biological systems usually in its D-form.
The property of emitting radiation while being irradiated. The radiation emitted is usually of longer wavelength than that incident or absorbed, e.g., a substance can be irradiated with invisible radiation and emit visible light. X-ray fluorescence is used in diagnosis.
Microscopy using an electron beam, instead of light, to visualize the sample, thereby allowing much greater magnification. The interactions of ELECTRONS with specimens are used to provide information about the fine structure of that specimen. In TRANSMISSION ELECTRON MICROSCOPY the reactions of the electrons that are transmitted through the specimen are imaged. In SCANNING ELECTRON MICROSCOPY an electron beam falls at a non-normal angle on the specimen and the image is derived from the reactions occurring above the plane of the specimen.
The use of devices which use detector molecules to detect, investigate, or analyze other molecules, macromolecules, molecular aggregates, or organisms.
The reformation of all, or part of, the native conformation of a nucleic acid molecule after the molecule has undergone denaturation.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
A family of cellular proteins that mediate the correct assembly or disassembly of polypeptides and their associated ligands. Although they take part in the assembly process, molecular chaperones are not components of the final structures.
MOLECULAR BIOLOGY techniques used in the diagnosis of disease.
The ability of a protein to retain its structural conformation or its activity when subjected to physical or chemical manipulations.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
Compounds formed by the joining of smaller, usually repeating, units linked by covalent bonds. These compounds often form large macromolecules (e.g., BIOPOLYMERS; PLASTICS).
The sum of the weight of all the atoms in a molecule.
RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.
The physical characteristics and processes of biological systems.
The molecular designing of drugs for specific purposes (such as DNA-binding, enzyme inhibition, anti-cancer efficacy, etc.) based on knowledge of molecular properties such as activity of functional groups, molecular geometry, and electronic structure, and also on information cataloged on analogous molecules. Drug design is generally computer-assisted molecular modeling and does not include pharmacokinetics, dosage analysis, or drug administration analysis.
A non-aqueous co-solvent that serves as tool to study protein folding. It is also used in various pharmaceutical, chemical and engineering applications.
Spectrophotometry in the infrared region, usually for the purpose of chemical analysis through measurement of absorption spectra associated with rotational and vibrational energy levels of molecules. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Substances produced from the reaction between acids and bases; compounds consisting of a metal (positive) and nonmetal (negative) radical. (Grant & Hackh's Chemical Dictionary, 5th ed)
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.
DNA or RNA bound to a substrate thereby having fixed positions.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.
Polydeoxyribonucleotides made up of deoxyadenine nucleotides and thymine nucleotides. Present in DNA preparations isolated from crab species. Synthetic preparations have been used extensively in the study of DNA.
Elements of limited time intervals, contributing to particular results or situations.
Topical antiseptic used mainly in wound dressings.
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Measurement of the polarization of fluorescent light from solutions or microscopic specimens. It is used to provide information concerning molecular size, shape, and conformation, molecular anisotropy, electronic energy transfer, molecular interaction, including dye and coenzyme binding, and the antigen-antibody reaction.
Stable carbon atoms that have the same atomic number as the element carbon, but differ in atomic weight. C-13 is a stable carbon isotope.
A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.
Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.
Positively charged atoms, radicals or groups of atoms which travel to the cathode or negative pole during electrolysis.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.
Proteins produced from GENES that have acquired MUTATIONS.
Peptides composed of between two and twelve amino acids.
A serine endopeptidase that is formed from TRYPSINOGEN in the pancreas. It is converted into its active form by ENTEROPEPTIDASE in the small intestine. It catalyzes hydrolysis of the carboxyl group of either arginine or lysine. EC
Small proteinaceous infectious particles which resist inactivation by procedures that modify NUCLEIC ACIDS and contain an abnormal isoform of a cellular protein which is a major and necessary component. The abnormal (scrapie) isoform is PrPSc (PRPSC PROTEINS) and the cellular isoform PrPC (PRPC PROTEINS). The primary amino acid sequence of the two isoforms is identical. Human diseases caused by prions include CREUTZFELDT-JAKOB SYNDROME; GERSTMANN-STRAUSSLER SYNDROME; and INSOMNIA, FATAL FAMILIAL.
The measurement of the amplitude of the components of a complex waveform throughout the frequency range of the waveform. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
A method of generating a large library of randomized nucleotides and selecting NUCLEOTIDE APTAMERS by iterative rounds of in vitro selection. A modified procedure substitutes AMINO ACIDS in place of NUCLEOTIDES to make PEPTIDE APTAMERS.
A site on an enzyme which upon binding of a modulator, causes the enzyme to undergo a conformational change that may alter its catalytic or binding properties.
Layers of lipid molecules which are two molecules thick. Bilayer systems are frequently studied as models of biological membranes.
Characteristics or attributes of the outer boundaries of objects, including molecules.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
The art or process of comparing photometrically the relative intensities of the light in different parts of the spectrum.
Substances used for the detection, identification, analysis, etc. of chemical, biological, or pathologic processes or conditions. Indicators are substances that change in physical appearance, e.g., color, at or approaching the endpoint of a chemical titration, e.g., on the passage between acidity and alkalinity. Reagents are substances used for the detection or determination of another substance by chemical or microscopical means, especially analysis. Types of reagents are precipitants, solvents, oxidizers, reducers, fluxes, and colorimetric reagents. (From Grant & Hackh's Chemical Dictionary, 5th ed, p301, p499)
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
A biosensing technique in which biomolecules capable of binding to specific analytes or ligands are first immobilized on one side of a metallic film. Light is then focused on the opposite side of the film to excite the surface plasmons, that is, the oscillations of free electrons propagating along the film's surface. The refractive index of light reflecting off this surface is measured. When the immobilized biomolecules are bound by their ligands, an alteration in surface plasmons on the opposite side of the film is created which is directly proportional to the change in bound, or adsorbed, mass. Binding is measured by changes in the refractive index. The technique is used to study biomolecular interactions, such as antigen-antibody binding.
A non-essential amino acid that is synthesized from GLUTAMIC ACID. It is an essential component of COLLAGEN and is important for proper functioning of joints and tendons.
The phenomenon whereby certain chemical compounds have structures that are different although the compounds possess the same elemental composition. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 5th ed)
The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.
A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).
The deductive study of shape, quantity, and dependence. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
The study of the structure, growth, function, genetics, and reproduction of viruses, and VIRUS DISEASES.
RNA, usually prepared by transcription from cloned DNA, which complements a specific mRNA or DNA and is generally used for studies of virus genes, distribution of specific RNA in tissues and cells, integration of viral DNA into genomes, transcription, etc. Whereas DNA PROBES are preferred for use at a more macroscopic level for detection of the presence of DNA/RNA from specific species or subspecies, RNA probes are preferred for genetic studies. Conventional labels for the RNA probe include radioisotope labels 32P and 125I and the chemical label biotin. RNA probes may be further divided by category into plus-sense RNA probes, minus-sense RNA probes, and antisense RNA probes.
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
A group of guanine ribonucleotides in which the phosphate residues of each guanine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
The chemical and physical integrity of a pharmaceutical product.
An atom or group of atoms that have a positive or negative electric charge due to a gain (negative charge) or loss (positive charge) of one or more electrons. Atoms with a positive charge are known as CATIONS; those with a negative charge are ANIONS.

Evidence on the conformation of HeLa-cell 5.8S ribosomal ribonucleic acid from the reaction of specific cytidine residues with sodium bisulphite. (1/22440)

The reaction of HeLa-cell 5.8S rRNA with NaHSO3 under conditions in which exposed cytidine residues are deaminated to uridine was studied. It was possible to estimate the reactivities of most of the 46 cytidine residues in the nucleotide sequence by comparing 'fingerprints' of the bisulphite-treated RNA with those of untreated RNA. The findings were consistent with the main features of the secondary-structure model for mammalian 5.85S rRNA proposed by Nazar, Sitz, & Busch [J. Biol. Chem (1975) 250, 8591--8597]. Five out of six regions that are depicted in the model as single-stranded loops contain cytidine residues that are reactive towards bisulphite at 25 degrees C (the other loop contains no cytidine). The cytidine residue nearest to the 3'-terminus is also reactive. Several cytidines residues that are internally located within proposed double-helical regions show little or no reactivity towards bisulphite, but the cytidine residues of several C.G pairs at the ends of helical regions show some reactivity, and one of the proposed loops appears to contain six nucleotides, rather than the minimum of four suggested by the primary structure. Two cytidine residues that are thought to be 'looped out' by small helix imperfections also show some reactivity.  (+info)

Four dimers of lambda repressor bound to two suitably spaced pairs of lambda operators form octamers and DNA loops over large distances. (2/22440)

Transcription factors that are bound specifically to DNA often interact with each other over thousands of base pairs [1] [2]. Large DNA loops resulting from such interactions have been observed in Escherichia coli with the transcription factors deoR [3] and NtrC [4], but such interactions are not, as yet, well understood. We propose that unique protein complexes, that are not present in solution, may form specifically on DNA. Their uniqueness would make it possible for them to interact tightly and specifically with each other. We used the repressor and operators of coliphage lambda to construct a model system in which to test our proposition. lambda repressor is a dimer at physiological concentrations, but forms tetramers and octamers at a hundredfold higher concentration. We predict that two lambda repressor dimers form a tetramer in vitro when bound to two lambda operators spaced 24 bp apart and that two such tetramers interact to form an octamer. We examined, in vitro, relaxed circular plasmid DNA in which such operator pairs were separated by 2,850 bp and 2,470 bp. Of these molecules, 29% formed loops as seen by electron microscopy (EM). The loop increased the tightness of binding of lambda repressor to lambda operator. Consequently, repression of the lambda PR promoter in vivo was increased fourfold by the presence of a second pair of lambda operators, separated by a distance of 3,600 bp.  (+info)

Tight binding of the 5' exon to domain I of a group II self-splicing intron requires completion of the intron active site. (3/22440)

Group II self-splicing requires the 5' exon to form base pairs with two stretches of intronic sequence (EBS1 and EBS2) which also bind the DNA target during retrotransposition of the intron. We have used dimethyl sulfate modification of bases to obtain footprints of the 5' exon on intron Pl.LSU/2 from the mitochondrion of the alga Pylaiella littoralis, as well as on truncated intron derivatives. Aside from the EBS sites, which are part of the same subdomain (ID) of ribozyme secondary structure, three distant adenines become either less or more sensitive to modification in the presence of the exon. Unexpectedly, one of these adenines in subdomain IC1 is footprinted only in the presence of the distal helix of domain V, which is involved in catalysis. While the loss of that footprint is accompanied by a 100-fold decrease in the affinity for the exon, both protection from modification and efficient binding can be restored by a separate domain V transcript, whose binding results in its own, concise footprint on domains I and III. Possible biological implications of the need for the group II active site to be complete in order to observe high-affinity binding of the 5' exon to domain I are discussed.  (+info)

Structural basis for the specificity of the initiation of HIV-1 reverse transcription. (4/22440)

Initiation of human immunodeficiency virus type 1 (HIV-1) reverse transcription requires specific recognition of the viral genome, tRNA3Lys, which acts as primer, and reverse transcriptase (RT). The specificity of this ternary complex is mediated by intricate interactions between HIV-1 RNA and tRNA3Lys, but remains poorly understood at the three-dimensional level. We used chemical probing to gain insight into the three-dimensional structure of the viral RNA-tRNA3Lys complex, and enzymatic footprinting to delineate regions interacting with RT. These and previous experimental data were used to derive a three-dimensional model of the initiation complex. The viral RNA and tRNA3Lys form a compact structure in which the two RNAs fold into distinct structural domains. The extended interactions between these molecules are not directly recognized by RT. Rather, they favor RT binding by preventing steric clashes between the nucleic acids and the polymerase and inducing a viral RNA-tRNA3Lys conformation which fits perfectly into the nucleic acid binding cleft of RT. Recognition of the 3' end of tRNA3Lys and of the first template nucleotides by RT is favored by a kink in the template strand promoted by the short junctions present in the previously established secondary structure.  (+info)

Pseudouridine mapping in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (snRNAs) reveals that pseudouridine synthase pus1p exhibits a dual substrate specificity for U2 snRNA and tRNA. (5/22440)

Pseudouridine (Psi) residues were localized in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (UsnRNAs) by using the chemical mapping method. In contrast to vertebrate UsnRNAs, S. cerevisiae UsnRNAs contain only a few Psi residues, which are located in segments involved in intermolecular RNA-RNA or RNA-protein interactions. At these positions, UsnRNAs are universally modified. When yeast mutants disrupted for one of the several pseudouridine synthase genes (PUS1, PUS2, PUS3, and PUS4) or depleted in rRNA-pseudouridine synthase Cbf5p were tested for UsnRNA Psi content, only the loss of the Pus1p activity was found to affect Psi formation in spliceosomal UsnRNAs. Indeed, Psi44 formation in U2 snRNA was abolished. By using purified Pus1p enzyme and in vitro-produced U2 snRNA, Pus1p is shown here to catalyze Psi44 formation in the S. cerevisiae U2 snRNA. Thus, Pus1p is the first UsnRNA pseudouridine synthase characterized so far which exhibits a dual substrate specificity, acting on both tRNAs and U2 snRNA. As depletion of rRNA-pseudouridine synthase Cbf5p had no effect on UsnRNA Psi content, formation of Psi residues in S. cerevisiae UsnRNAs is not dependent on the Cbf5p-snoRNA guided mechanism.  (+info)

Comparative sequence analysis of human minisatellites showing meiotic repeat instability. (6/22440)

The highly variable human minisatellites MS32 (D1S8), MS31A (D7S21), and CEB1 (D2S90) all show recombination-based repeat instability restricted to the germline. Mutation usually results in polar interallelic conversion or occasionally in crossovers, which, at MS32 at least, extend into DNA flanking the repeat array, defining a localized recombination hotspot and suggesting that cis-acting elements in flanking DNA can influence repeat instability. Therefore, comparative sequence analysis was performed to search for common flanking elements associated with these unstable loci. All three minisatellites are located in GC-rich DNA abundant in dispersed and tandem repetitive elements. There were no significant sequence similarities between different loci upstream of the unstable end of the repeat array. Only one of the three loci showed clear evidence for putative coding sequences near the minisatellite. No consistent patterns of thermal stability or DNA secondary structure were shared by DNA flanking these loci. This work extends previous data on the genomic environment of minisatellites. In addition, this work suggests that recombinational activity is not controlled by primary or secondary characteristics of the DNA sequence flanking the repeat array and is not obviously associated with gene promoters as seen in yeast.  (+info)

Specificity from steric restrictions in the guanosine binding pocket of a group I ribozyme. (7/22440)

The 3' splice site of group I introns is defined, in part, by base pairs between the intron core and residues just upstream of the splice site, referred to as P9.0. We have studied the specificity imparted by P9.0 using the well-characterized L-21 Scal ribozyme from Tetrahymena by adding residues to the 5' end of the guanosine (G) that functions as a nucleophile in the oligonucleotide cleavage reaction: CCCUCUA5 (S) + NNG <--> CCCUCU + NNGA5. UCG, predicted to form two base pairs in P9.0, reacts with a (kcat/KM) value approximately 10-fold greater than G, consistent with previous results. Altering the bases that form P9.0 in both the trinucleotide G analog and the ribozyme affects the specificity in the manner predicted for base-pairing. Strikingly, oligonucleotides incapable of forming P9.0 react approximately 10-fold more slowly than G, for which the mispaired residues are simply absent. The observed specificity is consistent with a model in which the P9.0 site is sterically restricted such that an energetic penalty, not present for G, must be overcome by G analogs with 5' extensions. Shortening S to include only one residue 3' of the cleavage site (CCCUCUA) eliminates this penalty and uniformly enhances the reactions of matched and mismatched oligonucleotides relative to guanosine. These results suggest that the 3' portion of S occupies the P9.0 site, sterically interfering with binding of G analogs with 5' extensions. Similar steric effects may more generally allow structured RNAs to avoid formation of incorrect contacts, thereby helping to avoid kinetic traps during folding and enhancing cooperative formation of the correct structure.  (+info)

The influence of junction conformation on RNA cleavage by the hairpin ribozyme in its natural junction form. (8/22440)

In the natural form of the hairpin ribozyme the two loop-carrying duplexes that comprise the majority of essential bases for activity form two adjacent helical arms of a four-way RNA junction. In the present work we have manipulated the sequence around the junction in a way known to perturb the global folding properties. We find that replacement of the junction by a different sequence that has the same conformational properties as the natural sequence gives closely similar reaction rate and Arrhenius activation energy for the substrate cleavage reaction. By comparison, rotation of the natural sequence in order to alter the three-dimensional folding of the ribozyme leads to a tenfold reduction in the kinetics of cleavage. Replacement with the U1 four-way junction that is resistant to rotation into the antiparallel structure required to allow interaction between the loops also gives a tenfold reduction in cleavage rate. The results indicate that the conformation of the junction has a major influence on the catalytic activity of the ribozyme. The results are all consistent with a role for the junction in the provision of a framework by which the loops are presented for interaction in order to create the active form of the ribozyme.  (+info)

Abstract : Nucleotide analog interference mapping (NAIM) is a combinatorial approach that probes individual atoms and functional groups in an RNA molecule and identifies those that are important for a specific biochemical function. Here, we show how NAIM can be adapted to reveal functionally important atoms and groups on RNA substrates of helicases. We explain how NAIM can be used to investigate translocation and unwinding mechanisms of helicases and discuss the advantages and limitations of this powerful chemogenetic approach.. ...
Although interferon (IFN) signaling induces genes that limit viral infection, many pathogenic viruses overcome this host response. As an example, 2-O methylation of the 5′ cap of viral RNA subverts mammalian antiviral responses by evading restriction of Ifit1, an IFN-stimulated gene that regulates protein synthesis. However, alphaviruses replicate efficiently in cells expressing Ifit1 even though their genomic RNA has a 5′ cap lacking 2-O methylation. We show that pathogenic alphaviruses use secondary structural motifs within the 5′ untranslated region (UTR) of their RNA to alter Ifit1 binding and function. Mutations within the 5′-UTR affecting RNA structural elements enabled restriction by or antagonism of Ifit1 in vitro and in vivo. These results identify an evasion mechanism by which viruses use RNA structural motifs to avoid immune restriction.. ...
An improved dynamic programming algorithm is reported for RNA secondary structure prediction by free energy minimization. Thermodynamic parameters for the stabilities of secondary structure motifs are revised to include expanded sequence dependence as revealed by recent experiments. Additional algor …
Disclosed is a method for detecting a nucleic acid target sequence by formation of triple helix nucleic acid structures. The method may, but need not, involve amplifying the nucleic acid in vitro using cycles of denaturation and amplification to yield product duplexes, and detecting the product duplexes by hybridizing a third strand of nucleic acid to the product duplexes without denaturation. The triple helix-forming duplex sequences may be endogenous to the target sequence being detected, or they may be introduced in the probes used during amplification.
A miRNA-inhibiting RNA complex has a double-stranded structure, in which at least one RNA strand that includes a miRNA-binding sequence is linked to the two strands at at least one end of the double-stranded structure. The complex can efficiently inhibit miRNAs. In particular, RNAs in which two RNAs containing a miRNA binding sequence are positioned between two double-stranded structures were able to strongly inhibit miRNA. These RNAs can be expressed from, for example, a PolIII promoter, and by integration into a vector, miRNAs can be stably inhibited for a long period of time.
The existence and functional importance of RNA secondary structure in the replication of positive-stranded RNA viruses is increasingly recognized. We applied several computational methods to detect RNA secondary structure in the coding region of hepatitis C virus (HCV), including thermodynamic prediction, calculation of free energy on folding, and a newly developed method to scan sequences for covariant sites and associated secondary structures using a parsimony-based algorithm. Each of the prediction methods provided evidence for complex RNA folding in the core- and NS5B-encoding regions of the genome. The positioning of covariant sites and associated predicted stem-loop structures coincided with thermodynamic predictions of RNA base pairing, and localized precisely in parts of the genome with marked suppression of variability at synonymous sites. Combined, there was evidence for a total of six evolutionarily conserved stem-loop structures in the NS5B-encoding region and two in the core gene. The virus
The RNA shapes studio comprises four RNA secondary structure prediction tools, which make heavy use of shape abstraction. An abstract shape is a mathematically well defined coarse grained view of an RNA structure, supporting the user to focus only on interesting structural features. RNAshapes and pKiss operate on single sequence inputs. Their counterparts RNAalishapes and pAliKiss take an multiple sequence alignment as input. RNAshapes and RNAalishapes predict purely nested secondary structures. pKiss and pAliKiss additionally consider H-type pseudoknots and kissing hairpins. KnotInFrame - KnotInFrame is a pipeline to predict ribosomal -1 frameshift sites with a simple pseudoknot as secondary structure in DNA and RNA sequences.. pAliKiss - pAliKiss is a tool for secondary structure prediction including kissing hairpin motifs.. pKiss - pKiss is a tool for secondary structure prediction including kissing hairpin motifs.. pknotsRG - RNA folding and thermodynamic matching RapidShapes - Computes a ...
A common problem for researchers working with RNA is to determine the three-dimensional structure of the molecule. However, in the case of RNA much of the final structure is determined by the secondary structure or intra-molecular base-pairing interactions of the molecule. This is shown by the high conservation of base-pair across diverse species. One of the first attempts to predict RNA secondary structure was made by Ruth Nussinov and co-workers who used dynamic programming method for maximising the number of base-pairs [1]. However, there are several issues with this approach, most importantly the solution is not unique. Nussinov et al published an adaptation of their approach to use a simple nearest-neighbour energy model in 1980 [2]. Michael Zuker and Patrick Stiegler in 1981 proposed using a slightly refined dynamic programming approach that models nearest neighbour energy interactions that directly incorporates stacking into the prediction [3]. The energies that are minimized by the ...
The mechanism of RNA cleavage by the hammerhead ribozyme and the sequence specific recognition of RNA by bacteriophage coat proteins will be studied by biochemical and biophysical methods. The two projects were chosen because they allow a detailed study of RNA function in a situation where the biologically relevant activity is contained with an RNA sufficiently small that variants can easily be synthesized by chemical or embryological methods. The availability of several X-ray crystal structures and quantitative assays for both systems permits the design of sophisticated experiments to refine our concepts of how RNA works. Experiments on the hammerhead will focus on obtaining additional evidence that the X-ray structure and the major solution conformation are not in a catalytically active conformation. A nucleotide analogue interference approach will be used to identify essential functional groups and attempt to identify revertants of hammerhead base mutations. Hammerhead modifications that ...
Since the famous discovery of the structure of the DNA double helix, referred to as the canonical, right-handed B-form DNA by Watson and Crick, experimental evidence has revealed the existence of more than a dozen alternative (or non-B) DNA secondary structures. These include, among others, stem-loops (also known as cruciforms or hairpins), triplexes or H-DNA, quadruplexes or G4 DNA, A-DNA, and Z-DNA The important role of DNA secondary structures in various genomic processes is documented experimentally in genomes of many organisms from bacteria to humans. It was shown that stem-loop structures can function as terminators, attenuators, promoter and recognition elements, while cruciform structures play roles in DNA replication, and genetic instability. Triplexes (H-DNA) have been shown to play roles in transcriptional repression, recombination, and genetic instability. Quadruplexes can regulate DNA replication, gene expression, and telomere maintenance. A-DNA can play an essential role in
One focus of our research is to further our understanding of the physico-chemical properties of non-canonical nucleic acid structures. In this work, DNA hairpins are used to mimic a common motif present in RNA, i.e., a stem-loop motif with a bulge or inte
The structure of noncoding RNAs largely determines their functions. With the rapid growth of experimental data on the RNA secondary structures, the task of predicting its spatial structure becomes the most urgent task of RNA bioinformatics. The ability to predict tertiary base pairs from data on the secondary structure could significantly reduce the operating time and improve the quality of the RNA spatial structure prediction algorithms. In this work, we applied the machine learning algorithm for the problem of RNA tertiary base pairs prediction from data on the RNA sequence and secondary structure. A group of local base pairs was identified that can be predicted with high quality (80% precision, 80% recall). It was also shown that more than 70% of all long-range noncanonical base pairs in RNA are the base pairs of geometric classes Sugar-Edge/Sugar-Edge and Sugar-Edge/Watson-Crick-Edge that correspond to ribose zipper and A-minor tertiary motifs. ...
This unit documents how to use the Vienna RNA package for RNA secondary structure analysis. Possible tasks include structure prediction for single sequences, prediction of consensus structures, prediction of RNA-RNA interactions, and sequence design.
The initial interaction between the ColE1 plasmid specific transcripts RNA I and RNA II, which function as antisense regulators of plasmid replication, comprises a transient complex between complementary loops found within the RNA secondary structures. Multidimensional heteronuclear magnetic resonance spectroscopy was used to characterize complexes formed between model RNA hairpins having seven nucleotide complementary loops. Seven base pairs are formed in the loop-loop helix, with continuous helical stacking of the loop residues on the 3 side of their helical stems. A sharp bend in the loop-loop helix, documented by gel electrophoresis, narrows the major groove and allows bridging of the phosphodiester backbones across the major groove in order to close the hairpin loops at their 5-ends. The bend is further enhanced by the binding of Rom, a ColE1 encoded protein that regulates replication. ...
Dodecamer d-AGATCTAGATCT and a Homologous Hairpin form Triplex in the Presence of Peptide REWER. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Functional RNAs (fRNAs) are being recognized as an important regulatory component in biological processes. Interestingly, recent computational studies suggest that the number and biological significance of functional RNAs within coding regions (coding fRNAs) may have been underestimated. We hypothesized that such coding fRNAs will impose additional constraint on sequence evolution because the DNA primary sequence has to simultaneously code for functional RNA secondary structures on the messenger RNA in addition to the amino acid codons for the protein sequence. To test this prediction, we first utilized computational methods to predict conserved fRNA secondary structures within multiple species alignments of Saccharomyces sensu strico genomes. We predict that as much as 5% of the genes in the yeast genome contain at least one functional RNA secondary structure within their protein-coding region. We then analyzed the impact of coding fRNAs on the evolutionary rate of protein-coding genes because a
RNA viruses infecting vertebrates differ fundamentally in their ability to establish persistent infections with markedly different patterns of transmission, disease mechanisms and evolutionary relationships with their hosts. Although interactions with host innate and adaptive responses are complex and persistence mechanisms likely multi-factorial, we previously observed associations between bioinformatically predicted RNA secondary formation in genomes of positive-stranded RNA viruses with their in vivo fitness and persistence. To analyse this interactions functionally, we transfected fibroblasts with non-replicating, non-translated RNA transcripts from RNA viral genomes with differing degrees of genome-scale ordered RNA structure (GORS). Single-stranded RNA transcripts induced interferon-β mediated though RIG-I and PKR activation, the latter associated with rapid induction of antiviral stress granules. A striking inverse correlation was observed between induction of both cellular responses with
A complex secondary structure in U1A pre-mRNA that binds two molecules of U1A protein is required for regulation of polyadenylation.: The human U1A protein-U1A
TY - JOUR. T1 - Correlation of RNA Secondary Structure Statistics with Thermodynamic Stability and Applications to Folding. AU - Wu, Johnny C.. AU - Gardner, David P.. AU - Ozer, Stuart. AU - Gutell, Robin R.. AU - Ren, Pengyu. PY - 2009/8/28. Y1 - 2009/8/28. N2 - The accurate prediction of the secondary and tertiary structure of an RNA with different folding algorithms is dependent on several factors, including the energy functions. However, an RNA higher-order structure cannot be predicted accurately from its sequence based on a limited set of energy parameters. The inter- and intramolecular forces between this RNA and other small molecules and macromolecules, in addition to other factors in the cell such as pH, ionic strength, and temperature, influence the complex dynamics associated with transition of a single stranded RNA to its secondary and tertiary structure. Since all of the factors that affect the formation of an RNAs 3D structure cannot be determined experimentally, statistically ...
Does very low or very high free energy ensure a successful design?. No. In nature, RNA does not always adopt its minimum free energy structure. Furthermore, the tools used to predict the minimum free energy structure are imperfect.. What is the optimal free energy?. No specific value of free energy is ideal. Most successful lab designs do not attempt achieve the maximum or minimum value of free energy possible for a given secondary structure.. Why shouldnt I use all GC pairs in a lab design?. GC-rich sequences are difficult to synthesize and prone to being caught in folding traps. Furthermore, the use of only one type of base pair increases the likelihood of undesired pairing.. Why shouldnt I use all AU or GU pairs in a lab design?. AU and GU pairs are weaker than GC pairs. Alone, they are unlikely to hold an RNA molecule in a specific structure. Furthermore, the use of only one type of base pair increases the likelihood of undesired pairing.. What is the optimal balance of AU, GU, and ...
The secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids. Secondary structure was predicted by using the programs PSIPRED and ALB. The residues predicted as helical are marked by H by PSIPRED and by H and & by ALB, and those predicted as -structural are marked by E by PSIPRED and by S and B by ALB ...
The RNA hairpin loops represent important RNA motifs with nominally unpaired single strand segment folded on itself to terminate an A-RNA double helix. The most frequently observed hairpin loops with indispensable biological functions are tetraloops (TLs)
Note that the one of the principle extrinsic curvatures at any point on the two-dimensional infinite standard cylinder of some radius r would be by definition 1/r, while the intrinsic curvature would be zero (There is no distortion in the parallel transport of a vector on a closed curve embedded in the cylinder). The intrinsic curvature is non-zero on a sphere, where parallel-transport of a vector on a closed curve does result in a disagreement. The motivation is that one does not need to reference an external space or embedding in order to measure the intrinsic curvature of a manifold (ie., measuring the 4-dimensional curvature of spacetime ...
Unusual DNA Structures Associated With Germline Genetic Activity in Caenorhabditis elegans: We describe a surprising long-range periodicity that underlies a sub
TY - JOUR. T1 - Fe-bleomycin as a probe of RNA conformation. AU - Holmes, Chris E.. AU - Abraham, Anil T.. AU - Hecht, Sidney M.. AU - Florentz, Catherine. AU - Giegé, Richard. N1 - Funding Information: We thank Dr Anne Théobald-Dietrich for purified tRNAAsp and Dr Philippe Dumas for providing us with the crystallographic coordinates of form A of mature yeast tRNAAsp. We thank Mr Steven Sucheck and Dr Richard Manderville for assistance with the molecular graphics and Mr Michael Morgan for carrying out some tRNA cleavage experiments. This study was supported at the University of Virginia by research grant CA53913 from the National Cancer Institute and at IBMC, Strasbourg, by a grant from the CNRS.. PY - 1996. Y1 - 1996. N2 - Two crystallographically defined tRNAs, yeast tRNA(Asp) and tRNA(Phe), were used as substrates for oxidative cleavage by Fe bleomycin to facilitate definition at high resolution of the structural elements in RNAs conducive to bleomycin binding and cleavage. Yeast tRNA(Asp) ...
In living cells, two major classes of ribonucleic acid (RNA) molecules can be found. The first class called the messenger RNA (mRNA) contains the genetic information that allows the ribosome to read and translate it into proteins. The second class called non-coding RNA (ncRNA), do not code for proteins and are involved with key cellular processes, such as gene expression regulation, splicing, differentiation and development. NcRNAs fold into an ensemble of thermodynamically stable secondary structures, which will eventually lead the molecule to fold into a specific 3D structure. It is widely known that ncRNAs carry their functions via their 3D structure as well as their molecular composition. The secondary structure of ncRNAs is composed of different types of structural elements (motifs) such as stacking base pairs, internal loops, hairpin loops and pseudoknots. Pseudoknots are specifically difficult to model, are abundant in nature and known to stabilize the functional form of the molecule. Due ...
The Alternative Structure Browser creates an interactive graphical representation of the Bill of Materials (BOM) with advanced visualization.
Local variations in B-DNA helix structure are compared among three decamers and eight dodecamers, which contain examples of all ten base-pair step types. All pairwise combinations of helix parameters are compared by linear regression analysis, in a search for internal relationships as well as correlations with base sequence. The primary conclusions are: (1) Three-center hydrogen bonds between base-pairs occur frequently in the major groove at C-C, C-A, A-A and A-C steps, but are less convincing at C-C and C-T steps in the minor groove. The requirements for large base-pair propeller are (1) that the base-pair should be A.T rather than G.C, and (2) that it be involved in a major groove three-center hydrogen bond with the following base-pair. Either condition alone is insufficient. Hence, a large propeller is expected at the leading base-pair of A-A and A-C steps, but not at A-T, T-A, C-A or C-C steps. (2) A systematic and quantitative linkage exists between helix variables twist, rise, cup and roll, of
Three-way helical junctions (3WJs) arise in genetic processing, and they have architectural and functional roles in structured nucleic acids. An internal bulge at the junction core allows the helical domains to become oriented into two possible, coaxially stacked conformers. Here, the helical stacking arrangements for a series of bulged, DNA 3WJs were examined using ensemble…
The initial version was coded after several unfruitful attempts at finding a RNA secondary structure drawing software to be used inside of a webserver. Indeed, it seemed at the time that most of the webservers dedicated to the secondary structure of RNA offered rather clumsy renderings (Mostly static, cgi-bin generated, PS or PNG files). In 2008, I (Yann Ponty) was unable to find a tool that would be at the same time available, easy to install and still running (SStructView was no longer tolerated by latest Java plugins security policies; RNAMLViews goal was rather to display a projection of the 3D structure, and RNAMovies was more tailored towards animations...). Therefore, I coded a basic software from scratch, initially using a radial layout strategy adopted by the software RNAViz, later to be extended to other classic algorithms such that NAView, a classic Feynman-diagram representation and a linear one, hoping it would be useful to some... VARNA development team was subsequently joined by ...
CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm is particularly fast in the vicinity of the minimum free energy. This enables the efficient approximation of statistical quantities, such as the partition function or measures for structural diversity. The density of states at low energies and its associated structures are crucial in assessing from a thermodynamic point of view how well-defined the ground state is. We demonstrate this by exploring the role of base modification in tRNA secondary structures, both at the level of individual sequences from Escherichia coli and by comparing artificially generated ensembles of modified and unmodified sequences with the same tRNA structure. The two major conclusions are that (1) base modification considerably sharpens the definition of the ground state structure by
Dna Double Helix software free downloads. Dna Double Helix shareware, freeware, demos: OnScreen DNA By-the-Day by OnScreen Science Inc, OnScreen DNA Model by OnScreen Science Inc, RC-AirSim by Fabricated Reality etc...
Decomposition of pseudoknotted secondary structures into components has generally not been explained explicitly, although a number of authors have already used it implicitly. In particular, the word pseudoknot is used both for the entire non-orthodox secondary structure, and for the subset of bonds that actually form the knot, though it is generally quite clear from the context which is meant.. One common and natural definition is that the pseudoknot contains the minimal sets of knotted ladders. In the semi-circle representation of ladders, this means that semi-circles that cross are grouped together. This causes the ladders to be partitioned in a unique way into what I call the knot-components. In an orthodox structure, all knot-components are just a single ladder; otherwise, there is at least one knot-component with knotted ladders, and these are the ones I call pseudoknots.. The orthodox secondary structure has a natural tree-representation as two ladders are either nested (one semi-circle ...
UNAFold is a comprehensive software package for nucleic acid folding and hybridization prediction. The name is derived from Unified Nucleic Acid Folding. Folding of single-stranded RNA or DNA, or hybridization between two single-strands, is accomplished in a variety of ways. Partition functions can be computed to derive base pair probabilities and stochastic samples of foldings or hybridizations. Energy minimization methods compute minimum free energy foldings or hybridizations, and can also compute suboptimal foldings that mimic the performance of the famous mfold software. ...
The non-coding RNA (ncRNA) elements in the 3 untranslated regions (3-UTRs) are known to participate in the genes post-transcriptional regulation, such as their stability, translation efficiency, and subcellular localization. Inferring co-expression patterns of the genes by clustering their 3-UTR ncRNA elements will provide invaluable knowledge for further studies of their functionalities and interactions under specific physiological processes. In this work, we propose an improved RNA structural clustering pipeline that takes into account the length-dependent distribution of the structural similarity measure. Benchmark of the proposed pipeline on Rfam data clearly demonstrates over 10% performance gain, when compared to a traditional hierarchical clustering pipeline. By applying the proposed clustering pipeline to Drosophila melanogaster s 3-UTRs, we have successfully identified 184 ncRNA clusters, of which 91.3% appear to be true RNA structural elements, based on RNAzs prediction. Among ...
Secondary structure formation of FRA16B DNA following denaturation and re-annealing (reduplexing) reaction. (A) Gel electrophoresis analysis of re-annealed FRA1
Interacting selectively and non-covalently with DNA containing secondary structure elements such as four-way junctions, bubbles, loops, Y-form DNA, or double-strand/single-strand junctions.
Cα to N substitution in aza-amino acids imposes local conformational constraints, changes in hydrogen bonding properties, and leads to adaptive chirality at the nitrogen atom. These properties can be exploited in mimicry and stabilization of peptide secondary structures and self-assembly. Here, the effect of a single aza-amino acid incorporation located in the upper β-strand at a hydrogen-bonded (HB) site of a β-hairpin model peptide (H-Arg-Tyr-Val-Glu-Val-d-Pro-Gly-Orn-Lys-Ile-Leu-Gln-NH2) is reported. Specifically, analogs in which valine3 was substituted for aza-valine3 or aza-glycine3 were synthesized, and their β-hairpin stabilities were examined using Nuclear Magnetic Resonance (NMR) spectroscopy. The azapeptide analogs were found to destabilize β-hairpin formation compared to the parent peptide. The aza-valine3 residue was more disruptive of β-hairpin geometry than its aza-glycine3 counterpart.
Restriction enzymes (restriction endonuclease) cut through the DNA at certain points. Their restriction sites where they cut through a specific sequence are about 10 bases long. They catalyse a hydrolysis reaction that breaks the sugar-phosphate backbone of the DNA double helix which gives a staggered cut or sticky end (short run of unpaired, exposed bases that can anneal to other complementary sticky ends). When separate fragments of DNA need to be stuck together, DNA ligase catalyses the condensation reaction that joins the sugar-phosphate backbone.. In order to join fragments they mustve been cut by the same restriction enzyme as this makes them complementary and allows the bases to pair up and anneal. DNA ligase seals the backbone.. DNA formed this way is called recombinant DNA (combining DNA from different sources in a single organism).. ...
Many processes in genetics require that proteins be able to recognize and bind to specific sequences of basepairs in double-stranded DNA. Since the bases are only accessible via the grooves, this is generally accomplished by H-bond and apolar contacts between the protein and certain features on the major and minor groove edges of the basepairs. In this view, the H-bond acceptors in the grooves have been colored yellow, while the H-bond donors have been colored green. The thymine methyl groups (the main surfaces in the grooves available for apolar contact with proteins) have been colored magenta. All a protein can sense when it is searching for a particular sequence is the spatial arrangement of these various H-bonding and apolar groups. Carefully examine the major and minor grooves at various points along the length of the molecule to get a feel for what it is that a protein sees when it is attempting to recognize a specific DNA sequence ...
Figure 6. Each group of bars represents folding accuracy of (from left to right) tRNA, eukaryotic 5 S rRNA, bacterial 5 S rRNA, and bacterial 16 S rRNA. Within each group, each bar represents (from left to right) unmodified Mfold, base-pair stack, hairpin flank, and internal loop SEs derived using tRNA, eukaryotic 5 S rRNA, bacterial 5 S rRNA, bacterial 16 S rRNA, and all-sequence dataset ...
The Masters will cover the following topics: fundamental aspects of RNA functions in cellular metabolism; RNA molecules as targets and therapeutic tools; strategies for recombinant DNA cloning and RNA and recombinant protein production; transcriptome analysis by high-throughput technologies and bioinformatics; RNA structure analysis and studies of RNA modification and RNA-protein interactions; methods for studying and engineering enzymes; biotechnology and the impact of enzyme on the health sciences. Teaching modules. COMMON COURSES and optional teaching depending on the specialty chosen by the student (e.g. RNA Sciences or ENZYMES Sciences) Options RNA and ENZYMES are almost exclusive due to rather tight schedule during the autumn semester. Please contact us if you envisage to take cources from BOTH options. Please take into account that a total of EXACTLY 60 ECTS for the year is required to get a Diploma.. ...
The stability and structure of nylon nucleic acid duplexes with complementary DNA and RNA strands was examined. Thermal denaturing studies of a series of oligonucleotides that contained nylon nucleic acids (1-5 amide linkages) revealed that the amide linkage significantly enhanced the binding affinity of nylon nucleic acids towards both complementary DNA (up to 26°C) increase in the thermal transition temperature (Tm) for five linkages) and RNA (around 15°C increase in Tm for five linkages) compared with nonamide linked precursor strands. For both DNA and RNA complements, increasing derivatization decreased the melting temperatures of uncoupled molecules relative to unmodified strands; by contrast, increasing lengths of coupled copolymer raised Tm from less to slightly greater than Tm of unmodified strands. Thermodynamic data extracted from melting curves and CD spectra of nylon nucleic acid duplexes were consistent with loss of stability due to incorporation of pendent groups on the 2-position of
Other articles where Double helix is discussed: James Watson: …a molecular model for DNA-a double helix, which can be likened to a spiraling staircase or a twisting ladder. The DNA double helix consists of two intertwined sugar-phosphate chains, with the flat base pairs forming the steps between them. Watson and Cricks model also shows how the DNA molecule could…
The asymmetrical spacing of the sugar-phosphate backbones generates major grooves (where the backbone is far apart) and minor grooves (where the backbone is close together).
Genetic information is written by a variation in sequence on the one hand, and the physical stability of the double-stranded structure is determined by the base composition on the other hand. … DNA...
This thesis is based on ten publications (Papers I-X). The phosphodiester backbone makes DNA or RNA to behave as polyelectrolyte, the pentose sugar gives the flexibility, and the aglycones promote the self-assembly or the ligand-binding process. The hydrogen bonding, stacking, stereoelectronics and hydration are few of the important non-covalent forces dictating the self-assembly of DNA/RNA. The pH-dependent thermodynamics clearly show (Papers I and II) that a change of the electronic character of aglycone modulates the conformation of the sugar moiety by the tunable interplay of stereoelectronic anomeric and gauche effects, which are further transmitted to steer the sugar-phosphate backbone conformation in a cooperative manner. 3-anthraniloyl adenosine (a mimic of 3-teminal CCAOH of the aminoacyl-tRNAPhe) binds to EF-Tu*GTP in preference over 2-anthraniloyl adenosine, thereby showing (Paper III) that the 2-endo sugar conformation is a more suitable mimic of the transition state geometry ...
This thesis is based on ten publications (Papers I-X). The phosphodiester backbone makes DNA or RNA to behave as polyelectrolyte, the pentose sugar gives the flexibility, and the aglycones promote the self-assembly or the ligand-binding process. The hydrogen bonding, stacking, stereoelectronics and hydration are few of the important non-covalent forces dictating the self-assembly of DNA/RNA. The pH-dependent thermodynamics clearly show (Papers I and II) that a change of the electronic character of aglycone modulates the conformation of the sugar moiety by the tunable interplay of stereoelectronic anomeric and gauche effects, which are further transmitted to steer the sugar-phosphate backbone conformation in a cooperative manner. 3-anthraniloyl adenosine (a mimic of 3-teminal CCAOH of the aminoacyl-tRNAPhe) binds to EF-Tu*GTP in preference over 2-anthraniloyl adenosine, thereby showing (Paper III) that the 2-endo sugar conformation is a more suitable mimic of the transition state geometry ...
Introduction] Cooperative binding by proteins to DNA results in higher sequence specificity as well as greater sensitivity to concentration changes. We recently reported cooperative binding of two oligonucleotides at abutting sites by triple helix formation on double helical DNA. However, the enhanced binding observed was modest (a factor of 3.5) and likely due to favorable basestacking interactions between adjacent oligonucleotides and/or induced conformational changes propagated to adjacent binding sites. Thus, the issue arises whether cooperativity in oligonucleotide-directed triple helix formation can be enhanced by the addition of discrete dimerization domains. We report here the binding properties of oligonucleotides that dimerize by Watson-Crick hydrogen bonds and bind neighboring sites on double helical DNA by triple helix formation. ...
RNA secondary structure prediction by energy minimization is the central computational tool for the analysis of structural non-coding RNAs and their interactions. Sparsification has been successfully applied to improve the time efficiency of various structure prediction algorithms while guaranteeing the same result; however, for many such folding problems, space efficiency is of even greater concern, particularly for long RNA sequences. So far, space-efficient sparsified RNA folding with fold reconstruction was solved only for simple base-pair-based pseudo-energy models. Here, we revisit the problem of space-efficient free energy minimization. Whereas the space-efficient minimization of the free energy has been sketched before, the reconstruction of the optimum structure has not even been discussed. We show that this reconstruction is not possible in trivial extension of the method for simple energy models. Then, we present the time- and space-efficient sparsified free energy minimization algorithm
A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982. Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots. The structural configuration of pseudoknots does not lend itself well to bio-computational detection due to its context-sensitivity or overlapping nature. The base pairing in pseudoknots is not well nested; that is, base pairs occur that overlap one another in sequence position. This makes the presence of pseudoknots in RNA sequences more difficult to predict by the standard method of dynamic programming, which use a recursive scoring system to identify paired stems and consequently, most cannot detect non-nested base pairs. The newer method of stochastic context-free grammars suffers from the same problem. Thus, popular secondary ...
Circular dichroism (CD) spectroscopy is an optical technique that measures the difference in the absorption of left and right circularly polarized light. This technique has been widely employed in the studies of nucleic acids structures and the use of it to monitor conformational polymorphism of DNA has grown tremendously in the past few decades. DNA may undergo conformational changes to B-form, A-form, Z-form, quadruplexes, triplexes and other structures as a result of the binding process to different compounds. Here we review the recent CD spectroscopic studies of the induction of DNA conformational changes by different ligands, which includes metal derivative complex of aureolic family drugs, actinomycin D, neomycin, cisplatin, and polyamine. It is clear that CD spectroscopy is extremely sensitive and relatively inexpensive, as compared with other techniques. These studies show that CD spectroscopy is a powerful technique to monitor DNA conformational changes resulting from drug binding and also
Filip CHIRALEU, Maria MAGANU and Călin DELEANU. Pyridines with long alkyl substituents as ligands in oligomerization of isopropene. Download Art 19 (PDF). Key words: pyridines; ligands; homogeneous catalysts; terpenes. 20. Camelia HULUBEI and Maria BRUMĂ. Maleimide type polymers based on N-(3-acetoxy-4-carboxy-phenyl)maleimide. Download Art 20 (PDF). Key words: maleimide copolymers; azobenzene; metal complexes; crosslinked networks. 21. Ion SAVA. Influence of conformational parameters on physical properties of some poly(amide-ester)s. Download Art 21 (PDF). Key words: poly(amide-ester)s; isopropylidene; benzonitrile; Monte Carlo; conformational parameters. 22. Ion SAVA and Corneliu HAMCIUC. Polyisophthalamides with pendent acetoxybenzamide or imide groups. Download Art 22 (PDF). Key words: polyisophthalamides; pendent; tetrachlorophthalimide; acetoxybenzamide; conformational parameters. 23. Elena HAMCIUC, Maria BRUMĂ, Corneliu HAMCIUC and Ramona LUNGU. Aromatic polyimides containing polar ...
Filip CHIRALEU, Maria MAGANU and Călin DELEANU. Pyridines with long alkyl substituents as ligands in oligomerization of isopropene. Download Art 19 (PDF). Key words: pyridines; ligands; homogeneous catalysts; terpenes. 20. Camelia HULUBEI and Maria BRUMĂ. Maleimide type polymers based on N-(3-acetoxy-4-carboxy-phenyl)maleimide. Download Art 20 (PDF). Key words: maleimide copolymers; azobenzene; metal complexes; crosslinked networks. 21. Ion SAVA. Influence of conformational parameters on physical properties of some poly(amide-ester)s. Download Art 21 (PDF). Key words: poly(amide-ester)s; isopropylidene; benzonitrile; Monte Carlo; conformational parameters. 22. Ion SAVA and Corneliu HAMCIUC. Polyisophthalamides with pendent acetoxybenzamide or imide groups. Download Art 22 (PDF). Key words: polyisophthalamides; pendent; tetrachlorophthalimide; acetoxybenzamide; conformational parameters. 23. Elena HAMCIUC, Maria BRUMĂ, Corneliu HAMCIUC and Ramona LUNGU. Aromatic polyimides containing polar ...
Our results establish that the extent of stable DNA wrapping in RPo depends on the sequence of the promoter and, in particular, on sequence determinants in the upstream region of the promoter (UP elements). The presence of αCTD and an intact α‐linker is required to maintain extensive stable DNA wrapping. Our results further indicate that the sequence of the upstream region of the promoter can affect DNA wrapping even in the absence of αCTD and thus even in the absence of αCTD-DNA interactions. For example, RPo prepared using ΔαCTDI/ΔαCTDII RNAP shows an apparent DNA compaction of 13±0.6 nm at lacUV5(UPfull) but only 4±0.8 nm at lacUV5(ICAP) (Fig 3E,F). We infer that the sequence of the upstream region of the promoter can affect compaction not only through effects on αCTD-DNA interaction but also through other effects. We suggest that these other effects involve intrinsic DNA curvature, noting that UP‐element subsites and UP elements are A/T‐rich sequences (Fig 1A; Ross et al, ...
The dimerization initiation site (DIS) stem-loop within the HIV-1 RNA genome is vital for the production of infectious virions in T-cell lines but not in primary cells. In comparison to peripheral blood mononuclear cells (PBMCs), which can support the replication of both wild type and HIV-1 DIS RNA mutants, we have found that DIS RNA mutants are up to 100 000-fold less infectious than wild-type HIV-1 in T-cell lines. We have also found that the cell-type-dependent replication of HIV-1 DIS RNA mutants is largely producer cell-dependent, with mutants displaying a greater defect in viral cDNA synthesis when viruses were not derived from PBMCs. While many examples exist of host pathogen interplays that are mediated via proteins, analogous examples which rely on nucleic acid triggers are limited. Our data provide evidence to illustrate that primary T-lymphocytes rescue, in part, the replication of HIV-1 DIS RNA mutants through mediating the reverse transcription process in a cell-type-dependent ...
We present a new publicly accessible web-service, RiboSoft, which implements a comprehensive hammerhead ribozyme design procedure. It accepts as input a target sequence (and some design parameters) then generates a set of ranked hammerhead ribozymes, which target the input sequence. This paper describes the implemented procedure, which takes into consideration multiple objectives leading to a multi-objective ranking of the computer-generated ribozymes. Many ribozymes were assayed and validated, including four ribozymes targeting the transcript of a disease-causing gene (a mutant version of PABPN1). These four ribozymes were successfully tested in vitro and in vivo, for their ability to cleave the targeted transcript. The wet-lab positive results of the test are presented here demonstrating the real-world potential of both hammerhead ribozymes and RiboSoft. RiboSoft is freely available at the website
A hammerhead ribozyme was demonstrated to be a metalloenzyme. By controlling the metal-binding ability of the hammerhead ribozyme in the presence or absence of a specific sequence of interest, we engineered an allosterically controllable ribozyme, designated the maxizyme. Hybrid ribozymes were then constructed by coupling the site-specific cleavage activity of a hammerhead ribozyme with the unwinding activity of an endogenous RNA helicase. This leads to extremely efficient cleavage of target mRNA, not only in vitro, but also in vivo, and eliminates one of the major problems arising in the application of ribozymes for cleavage of mRNA in vivo: that many target sites on the RNA were previously inaccessible to cleavage owing to secondary and/or tertiary structure formation. Since hybrid ribozymes can efficiently attack target sites within mRNA, libraries were made of hybrid ribozymes with randomized binding arms, which were then introduced into cells. This procedure made it possible to readily ...
The invention is directed to an expandable self-expanding stent for implantation in a body lumen, such as an artery. The stent is made with a plurality of cylindrical elements which are interconnected by a plurality of interconnecting members which connect adjacent cylindrical elements, some of the interconnecting members have one or more bending points formed therein for promoting the bendability of the interconnecting member. The bending point can be formed by reducing the strut wall thickness of the interconnecting member to promote the bending of the strut or it can be formed by reducing the strut width of the interconnecting member, or a combination of both. The bending points on the interconnecting member enhances the bendability and flexibility of the composite stent device by creating mechanical hinges which help to bend the stent as it is delivered through the tortuous anatomy of the patient or conforms to a curved portion of a body vessel, where the stent may be implanted.
TY - JOUR. T1 - She2p is a novel RNA binding protein with a basic helical hairpin motif. AU - Niessing, Dierk. AU - Hüttelmaier, Stefan. AU - Zenklusen, Daniel. AU - Singer, Robert H.. AU - Burley, Stephen K.. PY - 2004/11/12. Y1 - 2004/11/12. N2 - Selective transport of mRNAs in ribonucleoprotein particles (mRNP) ensures asymmetric distribution of information within and among eukaryotic cells. Actin-dependent transport of ASH1 mRNA in yeast represents one of the best-characterized examples of mRNP translocation. Formation of the ASH1 mRNP requires recognition of zip code elements by the RNA binding protein She2p. We determined the X-ray structure of She2p at 1.95 Å resolution. She2p is a member of a previously unknown class of nucleic acid binding proteins, composed of a single globular domain with a five α helix bundle that forms a symmetric homodimer. After demonstrating potent, dimer-dependent RNA binding in vitro, we mapped the RNA binding surface of She2p to a basic helical hairpin in ...
This chapter relates the intricate architecture of the L11-RNA complex to previous studies that delineated crucial features of the RNA tertiary structure and protein-RNA interface. In describing the structure, it is interesting to note how conservation and variation of different nucleotides and amino acids serve as a guide to critical features of the complex, and the authors use the extreme conservation of some bases to speculate about functional surfaces of the rRNA domain. Lastly, the chapter discusses the possibility that the functional role of L11-C76 is to promote a correct RNA tertiary fold. Relatively few RNA structures that have noncanonical interactions have been determined at atomic resolution, and of these only tRNA and the P4-P6 domain of group I intron have extensive tertiary structure. From nuclear magnetic resonance (NMR) studies of the free L11 RNA binding domain (L11-C76), it was known that the protein folds into three α-helices that are superimposable on the α-helices of the
The T:G mismatched base pair is associated with many genetic mutations. Understanding its biological consequences may be aided by studying the structural perturbation of DNA caused by a T:G base pair and by specific probing of the mismatch using small molecular ligands. We have shown previously that AR-1-144, a tri-imidazole (Im-Im-Im) minor groove binder, recognizes the sequence CCGG. NMR structural analysis of the symmetric 2:1 complex of AR-1-144 and GAACCGGTTC revealed that each AR-1-144 binds to four base pairs with the guanine N2 amino group forming a bifurcated hydrogen bond to a side-by-side Im/Im pair. We predicted that the free G-N2 amino group in a T:G wobble base pair can form two individual hydrogen bonds to a side-by-side Im/Im pair. Thus an Im/Im pair may be a good recognition motif for a T:G base pair in DNA. Cooperative and tight binding of an AR-1-144 homodimer to GAACTGGTTC permits a detailed structural analysis by 2D NOE NMR refinement and the refined structure confirms our ...
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Speaker: Alexander Grosberg (New York University). Each cell of our body contains about two meters worth of DNA packed in a cell nucleus with diameter about 5 micrometers. Moreover, each piece of DNA remains accessible for manipulations by the cell machinery. Recent experiments confirmed the 20 years old theoretical idea as to how DNA can be both densely packed and manageable. In this lecture, these experiments will be reviewed along with the renewed theoretical efforts to understand the genome folding quantitatively ...
Despite often being referred to as the inactive storage medium of genetic information DNA is of very dynamic and polymorphic nature adopting a variety of alternative secondary structures. In particular evidence for G-quadruplexes (GQPs), four-stranded helical complexes that are assembled from multiple stacked guanine tetrads, as important components in cellular processes has been increasing in recent years. These transiently formed alternative DNA structures have been shown to perform regulative roles in close to all integral biological processes such as recombination, replication, transcription and translation. In addition their polymorphic structure and high stability makes them attractive building blocks to be used in DNA nanoarchitectures and nanodevices.,br /,,br /,In the first part of this thesis the GQP folding properties of the DNA sequence (G,sub,4,/sub,CT),sub,3,/sub,G,sub,4,/sub, were characterized. The G-rich sequence was recently identified as a potential quadruplex-forming sequence ...
We have used laser tweezers to unfold single RNA molecules at room temperature and in physiological-type solvents. The forces necessary to unfold the RNAs are over the range 10-20 pN, forces that can be generated by cellular enzymes. The Gibbs free energy for the unfolding of TAR (transactivation-responsive) RNA from HIV was found to be increased after the addition of argininamide; the TAR hairpin was stabilized. The rate of unfolding was decreased and the rate of folding was increased by argininamide.. ...
The function of a noncoding RNA sequence is mainly determined by its secondary structure and therefore a family of noncoding RNA sequences is much more conserved on the structural level than on the sequence level. Understanding the function of noncoding RNA sequence families requires two things: a hand-crafted or hand-improved alignment and detailed analyses of the secondary structures. There are several tools available that help performing these tasks, but all of them are specialized and focus on only one aspect, editing the alignment or plotting the secondary structure. The problem is both these tasks need to be performed simultaneously. 4SALE is designed to handle sequence and secondary structure information of RNAs synchronously. By including a complete new method of simultaneous visualization and editing RNA sequences and secondary structure information, 4SALE enables to improve and understand RNA sequence and secondary structure evolution much more easily. 4SALE is a step further for
A method apparatus for a radially expandable stent for implantation within a body vessel, comprising a first wire formed winding and a second wire formed winding. The first wire formed winding has a hollow cylindrical shape including a preformed pattern such as a sinusoidal wave form and being wound into a continuous helix the length of the stent. The second wire formed winding has a hollow cylindrical shape including a preformed pattern such as a sinusoidal wave form and being wound into a continuous helix the length of the stent. The second winding helix is opposite that of the first winding helix. The second winding has a greater inner diameter than the outer diameter of the first winding. The second winding is coaxial with the first winding, the pattern of the first winding symmetrically intersects with the pattern of the second winding to form a uniform series of crossings thereby permitting even expansion of the first and second windings. The proximal end of the first winding may be attached to
12/10-Helical beta-Peptide with Dynamic Folding Propensity: Coexistence of Right- and Left-Handed Helices in an Enantiomeric ...
We investigate the empirical complexity of the RNA secondary structure design problem, that is, the scaling of the typical difficulty of the design task for various classes of RNA structures as the size of the target structure is increased. The purpose of this work is to understand better the factors that make RNA structures hard to design for existing, high-performance algorithms. Such understanding provides the basis for improving the performance of one of the best algorithms for this problem, RNA-SSD, and for characterising its limitations. To gain insights into the practical complexity of the problem, we present a scaling analysis on random and biologically motivated structures using an improved version of the RNA-SSD algorithm, and also the RNAinverse algorithm from the Vienna package. Since primary structure constraints are relevant for designing RNA structures, we also investigate the correlation between the number and the location of the primary structure constraints when designing structures
RNA structure is important for RNA function and regulation, and there is growing interest in determining the RNA structure of many transcripts. Here we provide a detailed protocol for the parallel analysis of RNA structure (PARS) for probing RNA secondary structures genome-wide. In this method, enzymatic footprinting is coupled to high-throughput sequencing to provide secondary structure data for thousands of RNAs simultaneously. The entire experimental protocol takes ∼5 d to complete, and sequencing and data analysis take an additional 6-8 d. PARS was developed using the yeast genome as proof of principle, but its approach should be applicable to probing RNA structures from different transcriptomes and structural dynamics under diverse solution conditions. Nat Protoc 2013 May; 8(5):849-69.
Provides the folding functions as used in the ViennaRNA package. Here, they are in Haskell form to be used by Haskell programs.. ...
Aligning homologous non-coding RNAs (ncRNAs) correctly in terms of sequence and structure is an unresolved problem, due to both mathematical complexity and imperfect scoring functions. High quality alignments, however, are a prerequisite for most consensus structure prediction approaches, homology searches, and tools for phylogeny inference. Automatically created ncRNA alignments often need manual corrections, yet this manual refinement is tedious and error-prone. We present an extended version of CONSTRUCT, a semi-automatic, graphical tool suitable for creating RNA alignments correct in terms of both consensus sequence and consensus structure. To this purpose CONSTRUCT combines sequence alignment, thermodynamic data and various measures of covariation. One important feature is that the user is guided during the alignment correction step by a consensus dotplot, which displays all thermodynamically optimal base pairs and the corresponding covariation. Once the initial alignment is corrected, optimal and
Borodavka A, Singaram SW, Stockley PG, Gelbart WM, Ben-Shaul A, Tuma R. Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures. BIOPHYSICAL JOURNAL. 2016;111 :2077-2085.
Some sequences of DNA that possess certain guanine or cytosine-riched stretches are capable of associating into four-stranded DNA structures, namely G-quadruplex and i-motif respectively. It has been suggested that some of these quadruplex structures could exist in some biologically important regions of DNA such as at the end of chromosomes and in the regulatory regions of oncogenes. In addition, due to their distinctive structural characteristics, quadruplex structures of DNA have been widely used as building blocks in various nanotechnological applications. With the aim of exploring new properties and applications of quadruplex DNA, we have (1) constructed i-motif DNA-based molecular devices that are operable through variations of their surrounding pH values; (2) developed certain fluorescence-tagged circular G-quadruplexes to be used as molecular probes; and (3) investigated the factors that affect the G-quadruplex that could undergo self-cleavage reactions. Finally, we have designed and ...
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For sale: Principles of Nucleic Acid Structure by Wolfram Saenger. Publisher Springer-Verlag. Softcover in very good condition. For more info see: (First entry on page) 25$ including shipping with in the U.S. sks at ...
An R-loop is a three-stranded nucleic acid structure, composed of a DNA:RNA hybrid and the associated non-template single-stranded DNA. R-loops may be formed in a variety of circumstances, and may be tolerated or cleared by cellular components. The term R-loop was given to reflect the similarity of these structures to D-loops; the R in this case represents the involvement of an RNA moiety. In the laboratory, R-loops may also be created by the hybridization of mature mRNA with double-stranded DNA under conditions favoring the formation of a DNA-RNA hybrid; in this case, the intron regions (which have been spliced out of the mRNA) form single-stranded loops, as they cannot hybridize with complementary sequence in the mRNA. ...
Hammerhead ribozyme, molecular model. Ribozymes are RNA (ribonucleic acid) molecules that catalyse certain biochemical reactions. Until their discovery in the 1980s, it was thought only proteins had this ability. Most ribozymes catalyse their own cleavage, or that of other RNAs, but some also have roles within ribosomes, the location of protein synthesis. - Stock Image F009/6228
Yeast tRNA (m(7)G46) methyltransferase contains two protein subunits (Trm8 and Trm82). To address the RNA recognition mechanism of the Trm8-Trm82 complex, we investigated methyl acceptance activities of eight truncated yeast tRNA(Phe) transcripts. Both the D-stem and T-stem structures were required for efficient methyl-transfer. To clarify the role of the D-stem structure, we tested four mutant transcripts, in which tertiary base pairs were disrupted. The tertiary base pairs were important but not essential for the methyl-transfer to yeast tRNA(Phe) transcript, suggesting that these base pairs support the induced fit of the G46 base into the catalytic pocket ...
PubMed journal article: RNA secondary structures in the proximal 3UTR of Indonesian Dengue 1 virus strains. Download Prime PubMed App to iPhone, iPad, or Android
This web site contains information about the software system eXtended Dynalign (X-Dynalign for short). This program takes as input three RNA sequences and produces a three-way sequence alignment, as well as a common secondary structure. The objective function consists of a linear combination of the free-energy of each sequence, given the common secondary structure, and an empirical term for gap penalties ...
Although some polypeptides exist as linear chains, most are twisted or folded into more complex secondary structures that form when bonding occurs between amino acids with different properties at different regions of the polypeptide. The most common secondary structure is a spiral called an alpha-helix. If you were to take a length of string and simply twist it into a spiral, it would not hold the shape. Similarly, a strand of amino acids could not maintain a stable spiral shape without the help of hydrogen bonds, which create bridges between different regions of the same strand (see [link]b). Less commonly, a polypeptide chain can form a beta-pleated sheet, in which hydrogen bonds form bridges between different regions of a single polypeptide that has folded back upon itself, or between two or more adjacent polypeptide chains.. The secondary structure of proteins further folds into a compact three-dimensional shape, referred to as the proteins tertiary structure (see [link]c). In this ...
User:Catherine I. Mortensen,Catherine I. Mortensen]] 13:46, 1 March 2013 (EST): The presence of a polyuracil region is not dependent on whether or not the hairpin forms. A polymerase will transcribe through a polyuracil region but the speed at which it does this decreases because something about the chemistry of uracil (possibly due to the fact that uracil can only form 2 hydrogen bonds instead of 3 like guanine and cytosine can) slightly destabilizes the polymerase. When the hairpin forms, the polymerase becomes too unstable to hold onto the polyuracil region. Its as if the polymerase runs over a bump and loses control Id say ...
Probes and processes for their use for specific recognition and/or cleavage of double-stranded DNA or RNA at sequence specific desired loci through the intermediacy of a triple helix are disclosed. These probes may also be used as diagnostic chemotherapeutic agents through incorporation of a radiolabeled, fluorescing, or otherwise detectable molecule. Preferred assay conditions are also provided for recognition of homopurine-homopyrimidine double-helical tracts within large DNA by triple helix formation under physiological conditions. Hybridization probes for double-stranded recognition with binding site sizes that range |8 base pairs are also provided.
To identify DNA under a microscope or even a picture, you should know some of its key structural features. When you browse through the array of different DNA pictures, you will find different types of illustrations that represent the DNA molecule.. Each will be different in quality and color; however, they all will depict the same pattern of the structure. In medical terminology, the structure is a double helix, in which two strands of the DNA are intertwining and forming a twisting ladder.. For a simpler representation, you can unwind the double-stranded structure and look at the two strands separately. Each strand consists of individual units or Nucleotides. Each Nucleotide consists of a nitrogenous base, phosphate, and sugar.. All the nucleotides in each strand join because of the bond between the two nitrogenous bases on each strand. Every nucleotide has one of four different nitrogenous bases in the body that are compatible with their suited pairs.. Holding these pairs of A, G, T, and C are ...
The decay of eukaryotic mRNA is triggered mainly by deadenylation, which leads to decapping and degradation from the 5 end of an mRNA. Poly(A)-binding protein has been proposed to inhibit the decapping process and to stabilize mRNA by blocking the recruitment of mRNA to the P-bodies where mRNA degradation takes place after stimulation of translation initiation. In contrast, several lines of evidence show that poly(A)-binding protein (Pab1p) has distinct functions in mRNA decay and translation in yeast. To address the translation-independent function of Pab1p in inhibition of decapping, we examined the contribution of Pab1p to the stability of non-translated mRNAs, an AUG codon-less mRNA or an mRNA containing a stable stem-loop structure at the 5-UTR. Tethering of Pab1p stabilized non-translated mRNAs, and this stabilization did not require either the eIF4G-interacting domain of Pab1p or the Pab1p-interacting domain of eIF4G. In a ski2Δ mutant in which 3 to 5 mRNA degradation activity is ...
TY - JOUR. T1 - UAP56/DDX39B is a major cotranscriptional RNA-DNA helicase that unwinds harmful R loops genome-wide. AU - Pérez-Calero, Carmen. AU - Bayona-Feliu, Aleix. AU - Xue, Xiaoyu. AU - Barroso, Sonia I.. AU - Muñoz, Sergio. AU - González-Basallote, Víctor M.. AU - Sung, Patrick. AU - Aguilera, Andrés. PY - 2020/7. Y1 - 2020/7. N2 - Nonscheduled R loops represent a major source of DNA damage and replication stress. Cells have different ways to prevent R-loop accumulation. One mechanism relies on the conserved THO complex in association with cotranscriptional RNA processing factors including the RNA-dependent ATPase UAP56/DDX39B and histone modifiers such as the SIN3 deacetylase in humans. We investigated the function of UAP56/DDX39B in R-loop removal. We show that UAP56 depletion causes R-loop accumulation, R-loop-mediated genome instability, and replication fork stalling. We demonstrate an RNA-DNA helicase activity in UAP56 and show that its overexpression suppresses R loops and ...
An analysis of the base pair doublet geometries in available crystal structures indicates that the often reported intrinsic curvature of DNA containing oligo-(d(A).d(T)) tracts may also depend on the nature of the flanking sequences. The presence of CA/TG doublet in particular at the 5 end of these tracts is expected to enhance their intrinsic bending property. To test this proposition, three oligonucleotides, d(GAAAAACCCCCC), d(CCCCCCAAAAAG), d(GAAAAATTTTTC), and their complementary sequences were synthesized to study the effect of various flanking sequences, at the 5 and 3 ends of the A-tracts, on the curvature of DNA in solution. An analysis of the polyacrylamide gel electrophoretic mobilities of these sequences under different conditions of salts and temperatures (below their melting points) clearly showed that the oligomer with CA/TG sequence in the center was always more retarded than the oligomer with AC/GT sequence, as well as the oligomer with AT/AT sequence. Hydroxyl radical probing ...
The kinetic theory of replication has been extended to include dual mechanisms for conversion of self-annealed single-strand RNA to double-strand molecules, which do not replicate. An analysis of experimental results established that the replicate-template annealing reaction during transcription significantly retarded replication in vitro among three RNA variants copied by Qβ replicase. Annealing between complementary RNA strands free in solution had far less significance. The finding that an RNA variant can be replicated in a multiple hairpin configuration, but not as its single, long hairpin conformer, the correlation between stability of strand secondary structure and replicative fitness, and a lack of homology in the internal sequence of RNA variants copied by Qβ replicase support the conclusion that template competence depends on strand configuration, independent of most of the underlying base sequence. Occurrence of self-annealed strands in the Qβ replicase system was attributed to its ...
Using in silico analysis tools, we compiled Arabidopsis nuclear mRNA poly(A) signals from two independently produced 3′-UTR datasets covering about 17,000 independent genes. Beyond confirming the previous working model on the NUE and FUE, we revealed complex nucleotide distribution patterns around the CS and poly(A) site. The signal surrounding the CS is named CE here. A set of prevailing, although not highly conserved, patterns that are potentially poly(A) signals for each of the three elements are presented. Conserved secondary structures surrounding the CSs were also predicted using the RNA secondary structure prediction program, mFold. Using data from the literature, it is confirmed that these structures are important for the functionality of the signals because only those mutations that altered secondary structures had impact on the efficiency of the signals. These findings should serve as a new starting point for plant poly(A) signal study, e.g. the basis for mutagenesis tests of CE, the ...
Secondary structure prediction and consensus sequence of PelD and PleD. A. Secondary structure predication was made using the web-based ProteinPredict program h
Riboadenosine, or adenosine (rA) is a purine ribonucleoside, and is one of the four standard ribonucleosides that compose an RNA molecule. The presence of the OH group at the 2 -position of the ribose results in RNA being less stable to DNA (which lacks OH groups at this position), because this 2 -hydroxyl group can chemically attack the adjacent phosphodiester bond in the sugar-phosphate backbone of RNA, leading to cleavage of the backbone structure. rA forms a Watson-Crick base pair with rU (ribouridine/uridine) in RNA duplexes, and dT (deoxythymidine) in RNA-DNA duplexes.. - riboadenosine rA. ...
This is an almost verbatim copy of a press release from the London Centre for nanotechnology.When Watson, Crick and Wilkins discovered the DNA double helix nearly sixty years ago, they based their structure on an X-ray diffraction image (courtesy of Franklin) averaged over millions of DNA molecules (derived from squid sperm, I understand).
Evaluation of periodicity using endogenous and exogenous nucleases". Biochimica et Biophysica Acta (BBA) - Nucleic Acids and ... Wingert L, Von Hippel PH (March 1968). "The conformation dependent hydrolysis of DNA by micrococcal nuclease". Biochimica et ... Nucleic Acids and Protein Synthesis. 157 (1): 114-26. doi:10.1016/0005-2787(68)90270-0. PMID 4296058. Hiwasa T, Segawa M, ...
Wrede P, Rich A (November 1979). "Stability of the unique anticodon loop conformation of E.coli tRNAfMet". Nucleic Acids ... contains three glycans bound to the amino acid asparagine via N-glycosylation two Disulphide bridges between cysteine residues ...
"Impact of modified ribose sugars on nucleic acid conformation and function". Heterocyclic Communications. 23 (3): 155-165. doi: ... "Nucleic acid architecture". Retrieved 8 October 2019. Neidle, Stephen (2008). "The Building-Blocks of DNA and RNA ... The secondary structure of a nucleic acid is determined by the rotation of its 7 torsion angles. Having a large amount of ... Levene, P. A.; Jacobs, W. A. (1909). "Über die Pentose in den Nucleinsäuren" [About the pentose in the nucleic acids]. Berichte ...
Nucleic Acids Research. 39 (8): e52. doi:10.1093/nar/gkr035. PMC 3082908. PMID 21297115. deltaMasses Detection of Methylations ... Wienken CJ, Baaske P, Duhr S, Braun D (2011). "Thermophoretic melting curves quantify the conformation and stability of RNA and ... a general method for the synthesis of pure 2-arylpropionic acids. 2-Phenylpropionic acid". Organic Syntheses. 76: 169. doi: ... Protein methylation typically takes place on arginine or lysine amino acid residues in the protein sequence. Arginine can be ...
"Thermophoretic melting curves quantify the conformation and stability of RNA and DNA". Nucleic Acids Res. 39 (8): e52. doi: ... A Rapid and Precise Method to Quantify Protein-Nucleic Acid Interactions in Solution. Methods in Molecular Biology. 1654. pp. ... A Rapid and Precise Method to Quantify Protein-Nucleic Acid Interactions in Solution". MicroScale Thermophoresis: ... The fluorescence of a target molecule can be extrinsic or intrinsic (aromatic amino acids) and is altered in temperature ...
Alternative stable conformation capable of protein misinteraction links tRNA synthetase to peripheral neuropathy. Nucleic Acids ... Nucleic Acids Research. 45 (13): 8091-8104. doi:10.1093/nar/gkx455. ISSN 0305-1048. PMC 5737801. PMID 28531329. Mo, Zhongying; ... Two conformations of a crystalline human tRNA synthetase-tRNA complex: implications for protein synthesis. EMBO J. 2006;25(12): ... CMT disease severity correlates with mutation-induced open conformation of histidyl-tRNA synthetase, not aminoacylation loss, ...
"Mitochondrial DNA deletions are associated with non-B DNA conformations". Nucleic Acids Research. 40 (16): 7606-21. doi:10.1093 ... Damas J, Carneiro J, Amorim A, Pereira F (January 2014). "MitoBreak: the mitochondrial DNA breakpoints database". Nucleic Acids ... Nucleic Acids Research. 47 (D1): D29-D32. doi:10.1093/nar/gky843. PMC 6324066. PMID 30247677. Gu Z, Li J, Gao S, Gong M, Wang J ... Nucleic Acids Research. 44 (D1): D1262-5. doi:10.1093/nar/gkv1187. PMC 4702847. PMID 26590258. Damas J, Carneiro J, Gonçalves J ...
Abstract: Genetics 86: s33, (1977) Genetically controlled variation in conformation of enzymes, 1979, Prog. Nucleic Acid Res. ... 233-234 Purification and characterization of glutamic acid dehydrogenase from Escherichia coli strain K-12. Master's thesis, ...
... two typical alternative conformations for nucleic acids" (PDF). Current Science. 45: 779-783. Sasisekharan, V.; Pattabiraman, N ... Later in his career, part of Sasisekharan's work focused on the structure of nucleic acids. He and his coworkers demonstrated ... Ramachandran plot G. N. Ramachandran Nucleic acid double helix India portal Biology portal Sasisekharan, V (1962). Ramanathan, ... He introduced the use of torsion angles to describe polypeptide and protein conformation, a central principle of the (φ, ψ) ...
To control proteins and nucleic acids by light CEF scientists have designed and applied a range of photoswitchable tethers, ... In this way, first unambiguous evidence was provided for an exclusive all-trans retinal conformation in the dark state and a ... Wavelength-selective light-triggering was established for nucleic acids as well as three-dimensional control of DNA ... Furthermore, light-activatable interaction of DNA nanoarchitectures, light-dependent conformational changes in nucleic acids, ...
The nucleic acid is bound in an extended conformation across one side of the domain. The binding occurs in a cleft formed ... An evolutionarily conserved sequence of around 70 amino acids, the KH domain is present in a wide variety of nucleic acid- ... Grishin NV (February 2001). "KH domain: one motif, two folds". Nucleic Acids Res. 29 (3): 638-43. doi:10.1093/nar/29.3.638. PMC ... Valverde and colleagues note that, "Nucleic acid base-to-protein aromatic side chain stacking interactions which are prevalent ...
Nucleic Acids Research, 36 (S2): 185-. Kittichotirat W, M Guerquin, RE Bumgarner, and R Samudrala (2009) "Protinfo PPC: a web ... Esmaielbeiki, R; Nebel, J-C (2014). "Scoring docking conformations using predicted protein interfaces". BMC Bioinformatics. 15 ... For example, if we had the amino acid sequences of proteins A and B and the amino acid sequences of all proteins in a certain ... Nucleic Acids Research, 37 (Web Server issue): 519-25. Shoemaker, BA; Zhang, D; Thangudu, RR; Tyagi, M; Fong, JH; Marchler- ...
pseudoknot Non-coding RNA Nucleic acid secondary structure Moss WN, Priore SF, Turner DH (June 2011). "Identification of ... The hairpin conformation was predicted using RNAalifold, while the pseudoknot was predicted with DotKnot. Segment 7 encodes the ... Initial models of the secondary structure were based on computational methods for Nucleic acid structure prediction. ... Nucleic Acids Res. 38 (7): e103. doi:10.1093/nar/gkq021. PMC 2853144. PMID 20123730. Moss WN, Dela-Moss LI, Kierzek E, Kierzek ...
Nucleic Acid Res. Mol. Biol.. - 1990. - Т. Progress in Nucleic Acid Research and Molecular Biology. - С. 37-89. - ISBN 978-0-12 ... Protein structure and conformations of the pure (Na+ +K+)-ATPase (англ.) // Biochim. Biophys. Acta (англ.)русск. : journal. - ...
Folding, including the secondary and tertiary structure of biopolymers (nucleic acids and proteins). ... The gauche conformation on the right is a conformer, while the eclipsed conformation on the left is a transition state between ... Conformation-dependent reactions[edit]. Reaction rates are highly dependent on the conformation of the reactants. This theme is ... The staggered conformation includes the gauche (±60°) and anti (180°) conformations, depending on the spatial orientations of ...
... conformation and stability". Nucleic Acids Res. 18 (21): 6353-6359. doi:10.1093/nar/18.21.6353. PMC 332506. PMID 2243780. ... Nucleic acids Nucleic acid analogues Peptide nucleic acid Bridged Nucleic Acids Beaucage, S. L.; Iyer, R. P. (1992). "Advances ... The DMT group is removed with a solution of an acid, such as 2% trichloroacetic acid (TCA) or 3% dichloroacetic acid (DCA), in ... Nucleic Acid Chem. 46 (16): 4.1.1-4.1.22. doi:10.1002/0471142700.nc0401s46. ISBN 978-0471142706. PMID 21901670. Pease A. C.; ...
Nucleic Acids Research. 34 (Web Server issue): W529-33. doi:10.1093/nar/gkl212. PMC 1538886. PMID 16845064. Wenta N, Strauss H ... protein complex that occupies the promoter DNA and the amino acid sequence of the cofactor determine its spatial conformation. ... Nucleic Acids Research. 42 (Database issue): D1182-7. doi:10.1093/nar/gkt1016. PMC 3965000. PMID 24174544. Matys V, Kel- ... Nucleic Acids Research. 37 (17): 5641-55. doi:10.1093/nar/gkp610. PMC 2761276. PMID 19625488. Teif VB, Rippe K (October 2010 ...
Dear, PH; Cook, PR (September 1989). "Happy mapping: a proposal for linkage mapping the human genome". Nucleic Acids Res. 17 ( ... It overcomes some limitations of Chromosome conformation capture (3C), as these methods have a reliance on digestion and ... "The statistical-mechanics of chromosome conformation capture". Nucleus. 4 (5): 390-8. doi:10.4161/nucl.26513. PMC 3899129. PMID ...
satellites (nucleic acid molecules with or without a capsid that require a helper virus for infection and reproduction), and ... proteins that can exist in a pathological conformation that induces other prion molecules to assume that same conformation).[3] ... The most useful and most widely used classification system distinguishes viruses according to the type of nucleic acid they use ...
... to stabilize essential compounds like amino acids, nucleic acids and lipids to target age-related diseases. Cantor held ... Cantor co-authored Biophysical Chemistry with Paul Schimmel, which was published in three volumes: Part 1, The Conformation of ... Cantor, C. R.; Katz, L. (1971). "Nucleic Acids". Annual Review of Physical Chemistry. 22: 25-46. Bibcode:1971ARPC...22...25C. ... Cantor's reviews include one on the physical chemistry of nucleic acids. ...
Circuit topology of Proteins and nucleic acids, Structure 22(9):1227-1237 (2014) Conformation Activity Relationships: Why Do ... The Mashaghi group, LACDR, Leiden University "A Rubik's cube at the nanoscale: proteins puzzle with amino acid chains". ...
Nucleic Acids Research. 33 (Web Server issue): W690-2. doi:10.1093/nar/gki445. PMC 1160206. PMID 15980564. Chang TH, Huang HD, ... "Computational identification of riboswitches based on RNA conserved functional sequences and conformations". RNA. 15 (7): 1426- ... Nucleic Acids Research. 35 (14): 4809-4819. doi:10.1093/nar/gkm487. PMC 1950547. PMID 17621584. Weinberg Z, Wang JX, Bogue J, ... Nucleic Acids Research. 36 (18): 5955-5969. doi:10.1093/nar/gkn601. PMC 2566862. PMID 18812398. Loh E, Dussurget O, Gripenland ...
Progress in Nucleic Acid Research and Molecular Biology. 61. pp. 181-209. doi:10.1016/S0079-6603(08)60827-2. ISBN 978-0-12- ... Monovalent cations have been shown to activate IMPDH enzymes and may serve to stabilize the conformation of the active-site ... IMPDH has also been shown to bind nucleic acids, and this function can be impaired by mutations that are located in the ... Magasanik B, Moyed HS, Gehring LB (May 1957). "Enzymes essential for the biosynthesis of nucleic acid guanine; inosine 5'- ...
Nucleic Acids Research. 31 (18): 5449-5460. doi:10.1093/nar/gkg732. PMC 203317. PMID 12954782. Sternberg N, Hamilton D (Aug ... "Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative ... The carboxy terminal domain of the enzyme consists of amino acids 132-341 and it harbours the active site of the enzyme. The ... Cre recombinase consists of 343 amino acids that form two distinct domains. The amino terminal domain encompasses residues 20- ...
Nucleic Acids Research. 27 (3): 795-802. doi:10.1093/nar/27.3.795. PMC 148249. PMID 9889275. Mathews DH, Sabina J, Zuker M, ... The upstream inhibitory -24/-15 stretch from the aforementioned inhibitory conformation is now sequestered in a hairpin P(-1) ... Nucleic Acids Research. 18 (23): 6821-6827. doi:10.1093/nar/18.23.6821. PMC 332737. PMID 2263447. Perrotta AT, Been MD (April ... Nucleic Acids Research. 32 (3): 39e-39. doi:10.1093/nar/gnh037. PMC 373431. PMID 14973333. Page for Hepatitis delta virus ...
Nucleic Acids Res. 29 (16): 3424-32. doi:10.1093/nar/29.16.3424. PMC 55847. PMID 11504880. Stehlin C, Wurtz JM, Steinmetz A, ... "X-ray structure of the orphan nuclear receptor RORbeta ligand-binding domain in the active conformation". EMBO J. 20 (21): 5822 ... "All-trans retinoic acid is a ligand for the orphan nuclear receptor ROR beta". Nat. Struct. Biol. 10 (10): 820-5. doi:10.1038/ ...
This can be used to: detect if two labelled protein or nucleic acids come into contact or a doubly labelled single molecules is ... Fluorescence has been used to study the structure and conformations of DNA and proteins with techniques such as Fluorescence ... nucleic acids, lipids or small molecules can be "labelled" with an extrinsic fluorophore, a fluorescent dye which can be a ... DNA detection: the compound ethidium bromide, when free to change its conformation in solution, has very little fluorescence. ...
Nucleic Acids Research. 34 (Web Server issue): W529-33. doi:10.1093/nar/gkl212. PMC 1538886. PMID 16845064.. ... protein complex that occupies the promoter DNA and the amino acid sequence of the cofactor determine its spatial conformation. ... "Nucleic Acids Research. 42 (Database issue): D1182-7. doi:10.1093/nar/gkt1016. PMC 3965000. PMID 24174544.. ... "Nucleic Acids Research. 34 (Database issue): D108-10. doi:10.1093/nar/gkj143. PMC 1347505. PMID 16381825.. ...
Thomas J, Lea K, Zucker-Aprison E, Blumenthal T (May 1990). "The spliceosomal snRNAs of Caenorhabditis elegans". Nucleic Acids ... "Cwc2 and its human homologue RBM22 promote an active conformation of the spliceosome catalytic centre". The EMBO Journal. 31 (6 ... Zwieb C (January 1997). "The uRNA database". Nucleic Acids Research. 25 (1): 102-3. doi:10.1093/nar/25.1.102. PMC 146409. PMID ...
... nucleic acid constituents, carbohydrates and ionophore complexes.[218]. Lithium naturally only occurs in traces in biological ... The heavier alkali metals also favour the sterically congested conformation.[142] Several crystal structures of organopotassium ... Sodium salts of fatty acids are used as soap.[197] Pure sodium metal also has many applications, including use in sodium-vapour ... Indeed, transferring of protons between chemicals is the basis of acid-base chemistry.[10]:43 Also unique is hydrogen's ability ...
... is a molecular cytogenetic technique that uses fluorescent probes that bind to only those parts of a nucleic acid sequence with ... The extended conformation of the chromosomes allows dramatically higher resolution - even down to a few kilobases. The ... The hybridization signals for each probe when a nucleic abnormality is detected.[9] Each probe for the detection of mRNA and ... or adopting a chromosome territory conformation, as in interphase FISH. This is accomplished by applying mechanical shear along ...
"Nucleic Acids Research. 34 (9): 2653-62. doi:10.1093/nar/gkl338. PMC 1464108. PMID 16714444.. ... The most basic such formation is the 10 nm fiber or beads on a string conformation. This involves the wrapping of DNA around ... The single-letter amino acid abbreviation (e.g., K for Lysine) and the amino acid position in the protein ... compared amino acid compositions in the same histone from different organisms, and compared amino acid sequences of the same ...
... and sugar pucker conformations. The presence or absence of imino proton resonances, or of coupling between 15N atoms across a ... Nucleic acid NMR uses techniques similar to those of protein NMR, but has several differences. Nucleic acids have a smaller ... Because nucleic acids have a relatively large number of protons which are solvent-exchangeable, nucleic acid NMR is generally ... deoxyadenosine are incorporated into the nucleic acid strand, as natural nucleic acids do not contain any fluorine atoms.[2][4] ...
"for his fundamental studies of the biochemistry of nucleic acids, with particular regard to recombinant-DNA"[۲۹] ... especially concerning the connection between the amino acid sequence and the biologically active conformation"[۲۶] ... "for their contributions concerning the determination of base sequences in nucleic acids"[۲۹] ... his development of crystallographic electron microscopy and his structural elucidation of biologically important nucleic acid- ...
... pre-RNA nucleic acids have included peptide nucleic acid (PNA), threose nucleic acid (TNA) or glycol nucleic acid (GNA).[23][24 ... The hydroxyl group also forces the ribose into the C3'-endo sugar conformation unlike the C2'-endo conformation of the ... A candidate nucleic acid is peptide nucleic acid (PNA), which uses simple peptide bonds to link nucleobases.[89] PNA is more ... Threose nucleic acid (TNA) has also been proposed as a starting point, as has glycol nucleic acid (GNA), and like PNA, also ...
"Nucleic Acids Research. 42 (16): 10618-31. doi:10.1093/nar/gku734. PMC 4176335. PMID 25120263.. ... When the cytoplasmic receptors MDA5 and RIG-I recognize a virus the conformation between the caspase-recruitment domain (CARD) ... Sweat, desquamation, flushing,[2] organic acids[2] Gastrointestinal tract. Peristalsis, gastric acid, bile acids, digestive ... such as salicylic acid or jasmonic acid. Some of these travel through the plant and signal other cells to produce defensive ...
... amino acid chains) and polysaccharides (chains of monosaccharides/simple sugars) but lipids and nucleic acids become antigens ... Antigen specificity is due primarily to the side-chain conformations of the antigen. It is measurable and need not be linear or ... Lipids and nucleic acids are antigenic only when combined with proteins and polysaccharides.[citation needed] Non-microbial non ...
"Nucleic Acids Res. 29 (3): 753-758. doi:10.1093/nar/29.3.753. PMC 30388. PMID 11160898.. ... The conversion of PrPC to PrPSc conformation is the mechanism of transmission of fatal, neurodegenerative transmissible ... fatal familial insomnia - aspartic acid-178 is replaced by asparagine while methionine is present at amino acid 129[51] ... Creutzfeldt-Jakob disease - glutamic acid-200 is replaced by lysine while valine is present at amino acid 129 ...
"for his fundamental studies of the biochemistry of nucleic acids, with particular regard to recombinant-DNA"[72] ... especially concerning the connection between the amino acid sequence and the biologically active conformation"[64] ... "for their contributions concerning the determination of base sequences in nucleic acids"[72] ... "for their contributions to the development of the concept of conformation and its application in chemistry"[61] ...
டி.என்.ஏ (DNA) அல்லது தாயனை என்பது ஆக்சிசனற்ற ரைபோ கரு அமிலம் (Deoxyribonucleic acid அல்லது Deoxyribose nucleic acid - DNA) ... "Single-stranded adenine-rich DNA and RNA retain structural characteristics of their respective double-stranded conformations ... Saenger, Wolfram (1984). Principles of Nucleic Acid Structure. New York: Springer-Verlag. ISBN 0-387-90762-9. ... "A more unified picture for the thermodynamics of nucleic acid duplex melting: a characterization by calorimetric and volumetric ...
Nucleic Acids Research. 28 (1): 304-05. doi:10.1093/nar/28.1.304. PMC 102465. PMID 10592255. Archived from the original (PDF) ... which forces the CO-NH amide moiety into a fixed conformation.[1] The side chains of the standard amino acids, detailed in the ... "Nucleic Acids Research. 45 (D1): D1112-D1116. doi:10.1093/nar/gkw978. PMC 5210655. PMID 27789699.. ... Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and ...
"for his fundamental studies of the biochemistry of nucleic acids, with particular regard to recombinant-DNA"[79] ... especially concerning the connection between the amino acid sequence and the biologically active conformation"[71] ... "for their contributions concerning the determination of base sequences in nucleic acids"[79] ... "for their contributions to the development of the concept of conformation and its application in chemistry"[68] ...
Watson JD, Crick FH (1953). "Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid". Nature. 171 (4356 ... researchers in the Cambridge lab were attempting to determine the most stable helical conformation of amino acid chains in ... it cannot flow back to nucleic acids. In other words, the final step in the flow of information from nucleic acids to proteins ... He also explored the many theoretical possibilities by which short nucleic acid sequences might code for the 20 amino acids. ...
In its lifetime, NCp7 facilitates the unwinding of tRNA, acts as a primer for reverse transcription, chaperones nucleic acids ... They react with the cysteine residues on the zinc finger of the NCp7 and cause a covalent conformation change which ejects the ... Nucleic Acids Research. 34 (2): 472-484. doi:10.1093/nar/gkj442. PMC 1351370 . PMID 16434700. Musah, Rabi Ann (2004). "The HIV- ... These motifs contain two peptide units of Cys-X2-Cys-X4-His-X4-Cys (CCHC), where the X represents a substituted amino acid, ...
Kurt Wüthrich (1986). NMR of proteins and nucleic acids. New York: Wiley. ISBN 0-471-82893-9.. ... A set of conformations, determined by NMR or X-ray crystallography may be a better representation of the experimental data of a ... "Determination of three-dimensional structures of proteins and nucleic acids in solution". CRC Critical Reviews in Biochemistry ... and also nucleic acids, and their complexes. The field was pioneered by Richard R. Ernst and Kurt Wüthrich at the ETH,[1] and ...
... while proteins are built from up to twenty different amino acids with various functional groups, nucleic acids are built from ... the apparent lack of naturally occurring deoxyribozymes may also be due to the primarily double-stranded conformation of DNA in ... "Nucleic Acids Research. 33 (19): 6151-63. doi:10.1093/nar/gki930. PMC 1283523. PMID 16286368.. ... "Nucleic Acids Research. 31 (20): 5982-92. doi:10.1093/nar/gkg791. PMC 219472. PMID 14530446.. ...
Nucleic Acids Res. 29 (16): 3424-32. PMID 11504880. doi:10.1093/nar/29.16.3424. ... 2001). "X-ray structure of the orphan nuclear receptor RORbeta ligand-binding domain in the active conformation.". Embo J. 20 ( ... 2003). "All-trans retinoic acid is a ligand for the orphan nuclear receptor ROR beta.". Nat. Struct. Biol. 10 (10): 820-5. PMID ...
Nucleic acids and small molecules are sometimes considered antibody mimetics, but not artificial antibodies, antibody fragments ... Al-Lazikani B, Lesk AM, Chothia C (1997). "Standard conformations for the canonical structures of immunoglobulins". J Mol Biol ... α and γ contain approximately 450 amino acids, whereas μ and ε have approximately 550 amino acids.[2] ... They have sugar chains (glycans) added to conserved amino acid residues.[4][21] In other words, antibodies are glycoproteins.[4 ...
1999). Crystallization of Nucleic Acids and Proteins: A Practical Approach (2nd ed.). Oxford: Oxford University Press. ISBN 0- ... Disorder can take many forms but in general involves the coexistence of two or more species or conformations. Failure to ... "For their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in ... "For their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in ...
Nucleic acidsEdit. Nucleic acids have an important range of interactions with Mg2+. The binding of Mg2+ to DNA and RNA ... to either alter the conformation of the enzyme or take part in the chemistry of the catalytic reaction. In either case, because ... "Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes". Nucleic ... "Nucleic Acids Research. 11 (9): 2665-2679. doi:10.1093/nar/11.9.2665. PMC 325916 . PMID 6856472.. ...
J. A. McCammon, S. C. Harvey (1987) Dynamics of Proteins and Nucleic Acids. Cambridge University Press. ISBN 0-521-30750-3 ( ... It is not trivial to obtain a canonical ensemble distribution of conformations and velocities using these algorithms. How this ... About half the atoms in a protein or nucleic acid are non-polar hydrogens, so the use of united atoms can provide a substantial ... and nucleic acids. For example, instead of treating all four atoms of a CH3 methyl group explicitly (or all three atoms of CH2 ...
"Nucleic Acids Res. 39: D663-669. doi:10.1093/nar/gkq1022. PMC 3013650 . PMID 21051350.. CS1 maint: Explicit use of et al. (link ... Thus, all subunits must exist in the same conformation. The model further holds that, in the absence of any ligand (substrate ... For example, the GABAA receptor has two active sites that the neurotransmitter gamma-aminobutyric acid (GABA) binds, but also ... Thus, all enzyme subunits do not necessitate the same conformation. Moreover, the sequential model dictates that molecules of a ...
"for his fundamental studies of the biochemistry of nucleic acids, with particular regard to recombinant-DNA; for their ... especially concerning the connection between the amino acid sequence and the biologically active conformation; for their ... contributions concerning the determination of base sequences in nucleic acids". *^ "The Nobel Prize in Chemistry 1981". ... "for their contributions to the development of the concept of conformation and its application in chemistry". ...
"Nucleic Acids Research. 15 (16): 6733. doi:10.1093/nar/15.16.6733. PMC 306135 . PMID 2888085.. ... "The 14-3-3 protein affects the conformation of the regulatory domain of human tyrosine hydroxylase". Biochemistry. 47 (6): 1768 ... amino acid binding. • monooxygenase activity. • protein domain specific binding. Cellular component. • cytoplasm. • cytosol. • ... aromatic amino acid family metabolic process. • response to lipopolysaccharide. • cerebral cortex development. • response to ...
... lipids and nucleic acids.[22] These glycosylation products accumulate on the proteins of vessel wall collagen, forming an ... Conformation kidney biopsy should only be performed if non-diabetic kidney disease is suspected. ...
"Nucleic Acids Res. 26 (3): 847-53. doi:10.1093/nar/26.3.847. PMC 147327. PMID 9443979.. ... Both of these possibilities can occur in a single protein in a variety of different conformations.[33] The C-terminal BRCT ... In their unanimous decision on October 7, 2015 the "high court found that an isolated nucleic acid, coding for a BRCA1 protein ... fatty acid metabolic process. • positive regulation of gene expression. • negative regulation of histone H3-K4 methylation. • ...
"The physical basis of nucleic acid base stacking in water". Biophys J. 80 (1): 140-8. Bibcode:2001BpJ....80..140L. doi:10.1016/ ... The NMR chemical shifts of the two conformations were distinct and could be used to determine the ratio of the two states, ... and that the term should be specified for larger rings in stacked conformations which do seem to exhibit a cooperative pi ... which stack in a parallel displaced conformation, as a model system for pi stacking interactions. In their system, a methylene ...
"Nucleic Acids Research. 41 (13): 6729-6738. doi:10.1093/nar/gkt321. PMC 3711452 . PMID 23649835. Retrieved 23 November 2014.. ... The range of conformations adopted by tRNA as it transits the A/T through P/E sites on the ribosome. The Protein Data Bank (PDB ... "Nucleic Acids Research. 34 (21): 6137-6146. doi:10.1093/nar/gkl725. PMC 1693877 . PMID 17088292. Retrieved 23 November 2014.. ... Nucleic Acids Research. 10 (18): 5393-5406. doi:10.1093/nar/10.18.5393. PMC 320884 . PMID 6924209. Retrieved 23 November 2014. ...
... is a component in liquid/liquid phenol-chloroform extraction technique used in molecular biology for obtaining nucleic acids ... A recent in silico comparison of the gas phase acidities of the vinylogues of phenol and cyclohexanol in conformations that ... On page 69 of volume 31, Runge names phenol "Karbolsäure" (coal-oil-acid, carbolic acid). Runge characterizes phenol in: F. F. ... "Carbolic acid" redirects here. It is not to be confused with carbonic acid. ...
"Nucleic Acid Conformation" by people in this website by year, and whether "Nucleic Acid Conformation" was a major or minor ... "Nucleic Acid Conformation" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical ... Nucleic Acid Conformation*Nucleic Acid Conformation. *Conformation, Nucleic Acid. *Conformations, Nucleic Acid ... Below are the most recent publications written about "Nucleic Acid Conformation" by people in Profiles. ...
... ... Here, a protein probe that could specifically bind to Z-conformation was used to map the Z-DNA distribution in the human genome ... Besides the common right-handed B- or A- structures, the alternate Z-conformation, which is left-handed, can be formed in both ... However, formation of Z-conformation in living organisms and its biological significance remains largely elusive. ...
Effect of conformation, base composition and methylation of nucleic acids on the interaction with H1 and histone models and on ... Condensed states of nucleic acids. III. psi(+) and psi(-) conformational transitions of DNA induced by ethanol and salt. (opens ... Condensed states of nucleic acids. II. Effects of molecular size, base composition, and presence of intercalating agents on the ... Synthesis, conformation, and interaction with DNA of statistical copolymers (Lys x,Ala y)n. (opens in new tab) ...
... have been used to study the effect of different ions on the stability and conformation of PNA-DNA, PNA-PNA, and DNA-DNA ... Peptide nucleic acid (PNA) is a DNA analogue in which the negatively charged sugar phosphate backbone has been substituted by ... Ionic effects on the stability and conformation of peptide nucleic acid complexes Artikel i vetenskaplig tidskrift, 1996 ... Peptide nucleic acid (PNA) is a DNA analogue in which the negatively charged sugar phosphate backbone has been substituted by ...
ATP-PEPTIDE CONJUGATEPROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1Magnesium IonThiophosphoric Acid O-((Adenosyl-Phospho)phospho)- ... "MMDB and VAST+: tracking structural similarities between macromolecular complexes.Nucleic Acids Res. 2014 Jan; 42(Database ... 2G1T: A Src-Like Inactive Conformation In The Abl Tyrosine Kinase Domain. ...
Nucleic Acid Database. *wwPDB Partners. *RCSB PDB. *PDBe. *PDBj. *BMRB. RCSB PDB (citation) is hosted by ... and BCL-W adopts a conformation extremely similar to the ligand-free conformation of its closest relative BCL-XL in both ... Co-crystallization with conformation-specific designed ankyrin repeat proteins explains the conformational flexibility of BCL-W ... Co-Crystallization with Conformation-Specific Designed Ankyrin Repeat Proteins Explains the Conformational Flexibility of BCL-W ...
Nucleic Acid Database. *wwPDB Partners. *RCSB PDB. *PDBe. *PDBj. *BMRB. RCSB PDB (citation) is hosted by ... THE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC COMPLEXES: A COMPARISON OF THE CONFORMATION OF FIVE PEPTIDES PRESENTED BY HLA-A2. * ... The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2. ... the main chain and side chain conformations of each peptide are strikingly different in the center of the binding site, and ...
Nucleic Acids Res 34: W596-W599.. *CrossRef,. *PubMed,. *CAS,. *Web of Science® Times Cited: 58 ... Catalano FA, Meador-Parton J, Popham DL & Driks A (2001) Amino acids in the Bacillus subtilis morphogenetic protein SpoIVA with ... An autoinhibitory conformation of the Bacillus subtilis spore coat protein SpoIVA prevents its premature ATP-independent ... An autoinhibitory conformation of the Bacillus subtilis spore coat protein SpoIVA prevents its premature ATP-independent ...
Nucleic Acids Res 38:W540-544.. OpenUrlAbstract/FREE Full Text. *↵. *Schueler-Furman O, ... 4). For the split-fusion PCNA-Ub, the χ2 fit went from 23.8 to 4.35 for the best ensemble of three conformations. For the cross ... E113G and G178S, two key amino acid substitutions in PCNA that disrupt TLS, are located at the subunit-subunit interface and ... Based on the representation of each conformation in solution, we calculated the frequency in which the ubiquitin would have ...
Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303. ... 6KS7: TRiC at 0.1 mM ADP-AlFx, Conformation 1, 0.1-C1. PDB ID: ...
Molecular conformation (1). * Nucleic acids (1). Date ​ Choose a date option to show results from those dates only. * Today ...
We developed 4C technology (chromosome conformation capture (3C)-on-chip), which allows for an unbiased genome-wide search for ... Nucleic Acid Conformation* * Oligonucleotide Array Sequence Analysis / methods* Substances * Chromatin * DNA-Binding Proteins ... Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C) Nat ... We developed 4C technology (chromosome conformation capture (3C)-on-chip), which allows for an unbiased genome-wide search for ...
Nucleic Acid Conformation* * Organ Specificity * Polymorphism, Single Nucleotide / genetics * Promoter Regions, Genetic / ... Chromosome conformation elucidates regulatory relationships in developing human brain Nature. 2016 Oct 27;538(7626):523-527. ...
DNA fragment conformations in adducts with Kiteplatin Nicola Margiotta, Emanuele Petruzzella, James A. Platts, Shaun T. Mutter ... From the themed collection: Metal Interactions with Nucleic Acids The article was first published on 09 Feb 2015. Dalton Trans. ... From the themed collection: Metal Interactions with Nucleic Acids The article was first published on 31 Oct 2014. Dalton Trans. ... From the themed collection: Metal Interactions with Nucleic Acids The article was first published on 22 Oct 2014. Dalton Trans. ...
IPD-the Immuno Polymorphism Database. Nucleic Acids Res. 38: D863-D869.. OpenUrlAbstract/FREE Full Text ... 2C). The binding specificity of mAb 177407 was recently shown to be sensitive to the folding conformation of KIR3DL1 (28). ... Antigenic properties and amino acid sequences around the site of glycosylation. J. Biol. Chem. 252: 7555-7567. ... The intracellular retention of KIR3DL1*004 depends on two amino acid substitutions, Leu86 and Ser182, respectively, in the D0 ...
Thanks to this multi-layer approach, we focus on the interplay of chromatin conformation and cancer mutations in different ... Thanks to this multi-layer approach, we focus on the interplay of chromatin conformation and cancer mutations in different ... In particular, the integration of data about cancer mutations, gene functional annotations, genome conformation, epigenetic ... In particular, the integration of data about cancer mutations, gene functional annotations, genome conformation, epigenetic ...
Holm, L. & Rosenström, P. (2010). Nucleic Acids Res. 38, W545-W549. Web of Science CrossRef CAS PubMed. Hunter, R. L., Olsen, M ... Cantarel, B. L., Coutinho, P. M., Rancurel, C., Bernard, T., Lombard, V. & Henrissat, B. (2009). Nucleic Acids Res. 37, D233- ... Open and closed TS conformations. The crystal structure of MtTS showed two conformations (Roy et al., 2013. ). In one ... However, the apo D. radiodurans AS (DrAS) showed a strikingly different conformation in which the β2-α2 loop is disordered and ...
Holm, L. & Laakso, L. M. (2016). Nucleic Acids Res. 44, W351-W355. Web of Science CrossRef CAS PubMed Google Scholar. Jarrell, ... Buchan, D. W. A., Minneci, F., Nugent, T. C. O., Bryson, K. & Jones, D. T. (2013). Nucleic Acids Res. 41, W349-W357. Web of ... Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). Nucleic Acids Res. 25, 4876-4882. Web of ... as metabolites and nucleic acids), eventually yielded proteins that were suitable for biomolecular analysis and crystallization ...
Protein Conformation. Repetitive Sequences, Nucleic Acid*. RNA Polymerase II. Unique Identifier: 86302779. Chemical Identifiers ...
ANTI- AND SYN-CONFORMATIONS. Nucleic-acid bases can rotate about the glycosyl bond. The Watson-Crick hydrogen-bonding atoms ... and have the opposite orientation in the syn-conformation. Purines can form the syn-conformation more easily than pyrimidines. ... Left-handed Z-DNA in bands of acid-fixed polytene chromosomes. Proc. Natl Acad. Sci. USA 80, 4344-4348 (1983). ... Measures the vibrations of molecules that are usually influenced by the conformation of a molecule. This can be obtained from ...
Nucleic acids.- Proteins.- Acidic proteins.- Histones.- 4.2 Physico-Chemical Properties of Nucleohistones.- 4.2.1 Solubility.- ... 3.2.2 Analysis of the primary structure of histones for possible conformations.- 3.2.3 Physical studies of the conformations of ... Conformation of nucleohistones.- Anisotropy and orientation of chromophores.- Conformation of nucleoprotamines.- Ultraviolet ... 3.3 The Conformation of Nucleohistone.- 3.3.1 X-Ray diffraction studies of nucleohistones.- 3.3.2 Evidence for the "supercoiled ...
Nucleic Acid Res. Mol. Biol. 65:197-259. doi:10.1016/S0079-6603(00)65006-7. ... Systematic characterization of the conformation and dynamics of budding yeast chromosome XII. J. Cell Biol. 202:201-210. doi: ... Global reorganization of budding yeast chromosome conformation in different physiological conditions. Elisa Dultz, Harianto ... A single tether has local effects only. (A) Computational model of chr II conformation. Fraction of loci localized in ...
Simplifying Nucleic Acid Extraction and Cutting Down Waste. Simplifying Nucleic Acid Extraction and Cutting Down Waste ... Chromatin Conformation Computed. By manipulating DNA sequences that guide genome-folding, researchers confirm an existing model ...
c) Each nucleic acid does exist as a single strand, however, DNA in its native state is found in. a double helix conformation. ... Amino acids are synthesized from other free amino acids and also from -keto acids by . ... a) Every amino acid residue has its own tRNA.. b) In a codon, the first two base pairs remain constant for a given amino acid ... d) Both nucleic acids are involved directly in the transcription process of protein synthesis. ...
... detecting DNA mismatches between heteroduplex strands produced between wildtype and mutation containing nucleic acid species. ... Nucleic Acids Res. 19: 879-895); single-strand conformation polymorphism (Orita et al., 1989, Proc. Natl. Acad. Sci. USA 86: ... for detecting genetic mutations and mismatches between nucleic acid heteroduplex strands in nucleic acids of all nucleic acid- ... Ganguly et al., Nucleic Acids Research 18 (13) : 3933-3939 (1990).. 15. *. Hongyo et al., 1993, Nucleic Acids Res. 21:3637 3642 ...
Purchase Advances in Nanomedicine for the Delivery of Therapeutic Nucleic Acids - 1st Edition. Print Book & E-Book. ISBN ... Locked nucleic acids: structure. *6.3. Locked nucleic acids: hybridization and conformation properties ... Therapeutic applications of locked nucleic acids. *6.7. Nanoparticle-mediated delivery of locked nucleic acid and locked ... for the Delivery of Therapeutic Nucleic Acids addresses several issues related to safe and effective delivery of nucleic acids ...
Nucleic Acids Res. 20:6605-6611.. OpenUrlAbstract/FREE Full Text. *↵ Cobbe, N., and M.M. Heck. 2000. SMCs in the world of ... We propose that the "closed" conformation of condensin and the "open" conformation of cohesin are important structural ... Condensin and cohesin display different arm conformations with characteristic hinge angles. David E. Anderson, Ana Losada, ... 1 C, second row, last panel). This structural feature was also found in a holocomplex with the open-V conformation (Fig. 1 B, ...
Nucleic Acids Res. 2014; 42(7):4145-59.CrossRefGoogle Scholar. *. 16. ... Stable chromosome condensation revealed by chromosome conformation capture. Cell. 2015; 163(4):934-46.CrossRefGoogle Scholar ... These conformations can modulate the expression of genetic information by altering the frequency of interaction between a ... Here we apply dense neural networks (DNNs) to the problem of chromatin conformation. We show that using DNNs one is not only ...
... allows characterising ground state conformations of flexible nucleobase aggregates that play a crucial role in nucleic acid ... From the themed collection: Photoinduced Processes in Nucleic Acids and Proteins The article was first published on 22 Mar 2018 ... From the themed collection: Photoinduced Processes in Nucleic Acids and Proteins The article was first published on 12 Mar 2018 ... From the themed collection: Photoinduced Processes in Nucleic Acids and Proteins The article was first published on 23 Jan 2018 ...
e. Assessment of DNA conformation and nucleic acid-protein complex As discussed in the section of electrophoresis ... Nucleic Acid Electrophoresis Education › * Nucleic Acid Electrophoresis Applications-Preparative and Analytical Electrophoresis ... Nucleic Acid Electrophoresis Additional Considerations-7 Aspects › * Nucleic Acid Electrophoresis Applications-Preparative and ... 2. Preparative electrophoresis to purify nucleic acid samples In preparative applications of nucleic acid gel electrophoresis, ...
  • Biomolecular NMR Assignments provides a forum for publishing sequence-specific resonance assignments for proteins and nucleic acids as Assignment Notes. (
  • You'll get: Molecular, subcellular, physiological, anatomical, and environmental biophysics The laws of thermodynamics as they apply to biophysical systems Forces affecting conformation in biological molecules The composition and structure of carbohydrates, lipids, proteins, and nucleic acids The fluid mosaic model Simple enough for a beginner, but challenging enough for an advanced student, Biophysics Demystified makes this interdisciplinary subject easy to master. (
  • Thanks to this multi-layer approach, we focus on the interplay of chromatin conformation and cancer mutations in different pathways, such as metabolic processes, that are very important for tumor development. (
  • This suggests that specific interactions with chromatin binding factors are not required to maintain the global chromatin conformation observed in exponentially growing budding yeast cells. (
  • These simulations have been successful in corroborating that interactions between factors together with topological constraints may be responsible for driving chromatin conformation. (
  • Measuring significant changes in chromatin conformation with ACCOST. (
  • Welcome to the Dalton Transactions 'metal interactions with nucleic acids' themed issue. (
  • Furthermore, the Tlg2p N-peptide competes with the closed conformation for binding, suggesting a fundamental regulatory mechanism for SM-syntaxin interactions in SNARE assembly and membrane fusion. (
  • Additional topics may include: nucleic acid conformation, DNA/protein interactions, signal transduction and transport phenomena. (
  • Structure and conformation of nucleic acids and protein-nucleic acid interactions. (
  • Research on intra-chromosomal interactions was limited by inadequate techniques until 2002, when the lab of Job Dekker published the first biochemical approach for observing long-range chromatin interactions which he called chromosome conformation capture , or 3C for short. (
  • Chromosome conformation capture is a research method that allows researchers to observe interactions between genetic loci that are in close contact in the 3-dimensional structure of a chromosome but can be megabases apart in the linear sequence. (
  • r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data. (
  • In this report, we identify interactions and characteristics of nucleic acid probes that maximize BSI signal upon binding the respiratory syncytial virus nucleocapsid gene RNA biomarker. (
  • You will learn about the different composition and roles of nucleic acids in the cell, their interactions with each other and the use of ribozymes, aptamers, antisense and hybridization as tools in molecular research. (
  • Besides the common right-handed B- or A- structures, the alternate Z-conformation, which is left-handed, can be formed in both DNA and RNA molecules. (
  • 8. The composition of claim 1 , wherein the one or more nucleic acid molecules have been degraded except for that portion of the molecule or molecules that are protected from degradation by hybridization to the non-nucleotide probe. (
  • Stable isotope labeled nucleic acids play a significant rolein studying the links between the structure and dynamicsof the overall global conformation of RNA and DNA molecules. (
  • How does temperature impact the conformation of single DNA molecules below melting temperature? (
  • Crick first predicted the existence of Transfer RNA (tRNA) molecules that mediate the translation of messenger RNA (mRNA) codons into corresponding amino acids even before they were discovered [ 1 ]. (
  • He postulated that there must be "adaptor molecules" that would translate the RNA alphabet into a protein version to produce a polypeptide composed of the many different types of amino acids. (
  • In the simplest form, there would exist 20 adaptor molecules, one for each amino acid. (
  • prions ( proteins that can exist in a pathological conformation that induces other prion molecules to assume that same conformation). (
  • 10. A method according to claim 8 , wherein said oligonucleotide is indirectly linked to said solid phase by hybridization with said nucleic acid. (
  • Livak KJ, Flood SJ, Marmaro J, Giusti W and Deetz K (1995) Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic-acid hybridization. (
  • A nucleic acid hybridization assay employing an immobilized or immobilizable polynucleotide probe selected to form DNA.RNA or RNA.RNA hybrids with the particular polynucleotide sequence to be determined. (
  • No immobilization or labeling of sample nucleic acids is necessary and hybridization can be performed entirely in solution. (
  • This invention relates to nucleic acid hybridization assay methods and reagent systems for detecting specific polynucleotide sequences. (
  • The principle of nucleic acid hybridization assays was developed by workers in the recombinant DNA field as a means for determining and isolating particular polynucleotide base sequences of interest. (
  • Figure 2 ) and nucleic acid hybridization. (
  • While the peptide termini and their second and C-terminal anchor side chains are bound similarly in all five cases, the main chain and side chain conformations of each peptide are strikingly different in the center of the binding site, and these differences are accessible to direct TCR recognition. (
  • Peptide nucleic acid (PNA) is a DNA analogue in which the negatively charged sugar phosphate backbone has been substituted by uncharged N-(2-aminoethyl)glycine units. (
  • 6. The composition of claim 5 , wherein the non-nucleotide probe or probes are peptide nucleic acid. (
  • These modes include binding of the SM to a closed conformation of syntaxin, binding to the N-terminal peptide of syntaxin, binding to assembled SNARE complexes, and/or binding to nonsyntaxin SNAREs. (
  • Thus, the N-peptide interaction appears to be the most common mode of binding, and the closed conformation interaction has been hypothesized to be specific to the neuronal Munc18a ( 6 ). (
  • Pipkorn R, Wiessler M, Waldeck W, Hennrich U, Nokihara K, Beining M, Braun K. Improved Synthesis Strategy for Peptide Nucleic Acids (PNA) appropriate for Cell-specific Fluorescence Imaging. (
  • A search for the very first documentations of peptide nucleic acids (PNA) led to Miller's and Urey's experiments in the year 1953. (
  • Further, PNAs have applications in analysis of biosensor chips for identification of nucleic acids [ 22 ]. (
  • Here, a protein probe that could specifically bind to Z-conformation was used to map the Z-DNA distribution in the human genome. (
  • We find that both SMC protein complexes share the two-armed structure, but display different arm conformations with characteristic hinge angles. (
  • Tracking flavin conformations in protein crystal structures with Raman spectroscopy and QM/MM calculations. (
  • We conclude that propofol inhibits the mammalian deacetylase SIRT2 through a conformation-specific, allosteric protein site that is unique from the previously described binding sites of other inhibitors. (
  • Protein conformation, enzymatic mechanisms and selected metabolic pathways will be analyzed. (
  • Isolated, purified, and recombinant nucleic acids and proteins corresponding to the human GC6 gene and its mRNA and protein products, as well as peptides and antibodies corresponding to the GC6 protein can be used to identify. (
  • The problem becomes even more challenging due to the fact that a typical protein can contain several hundreds of amino acids or several thousands of atoms. (
  • Therefore, the search space made out of all possible conformations that a protein can assume is large and its enumeration is practically impossible. (
  • An Assignment Note generally will be considered for a protein of at least 100 amino acid residues in size based on data collected under non-denaturating conditions for the active form of the protein. (
  • An Assignment Note for a cooperatively folded protein of less than 100 amino acid residues or of unfolded/non-native states may be considered, provided that the authors present a convincing reason for publication of the data in the cover letter accompanying submission. (
  • Biomolecules and the forces that influence their structure and conformation are also covered, as are protein, nucleic acid, and membrane biophysics. (
  • 2010. Divalent Metal- and High Mobility Group N Protein-Dependent Nucleosome Stability and Conformation. (
  • Selection of zinc fingers that bind single-stranded telomeric DNA in the G-quadruplex conformation," Biochemistry, vol. 40, No. 3, Jan. 23, 2001, pp. 830-836. (
  • Antimicrobials that affect the synthesis and conformation of nucleic acids. (
  • It was concluded that formation and structure of complexes depend selectively on the DNA conformation and base composition. (
  • Recent applications of zinc( II ) complexes as fluorescent probes for nucleic acids are described highlighting their potential as diagnostic tools. (
  • Both complexes display the two-armed structure characteristic of SMC proteins, but their conformations are remarkably different. (
  • We classified the conformation of planar estrogens or angular TPE complexes as "estrogen-like" or "antiestrogen-like" complexes, respectively. (
  • This invention pertains to methods, kits and compositions suitable for the detection, identification and/or quantitation of nucleic acids which are electrostatically immobilized to matrices using non-nucleotide probes which sequence specifically hybridize to one or more target sequences of the nucleic. (
  • Once the nucleic acid is immobilized, the detectable non-nucleotide probe/target sequence complex, formed before or after the immobilization of the nucleic acid, can be detected, identified or quantitated under a wide range of assay conditions as a means to detect, identify or quantitate the target sequence in the sample. (
  • In particular, the integration of data about cancer mutations, gene functional annotations, genome conformation, epigenetic patterns, gene expression, and metabolic pathways in our multi-layer representation will allow a better interpretation of the mechanisms behind a complex disease such as cancer. (
  • Sarkar G, Yoon HS and Sommer SS (1992) Screening for mutations by RNA single strand conformation (rSSCP): comparison with DNA-SSCP. (
  • Optimization of the single-strand conformation polymorphism (SSCP) technique for detection of point mutations. (
  • The efficiency of detection of single base substitutions by single-stranded conformation polymorphism (SSCP) analysis was tested on 86 randomly distributed point mutations in a 193-bp-long DNA fragment of the mouse beta-globin gene. (
  • The fluorescence of a target molecule can be extrinsic or intrinsic (aromatic amino acids ) and is altered in temperature gradients due to two distinct effects. (
  • 7 . The method of claim 4 wherein said derivative comprises substitution of an oxygen molecule with a thiol, alkyl, carbonyl, amine, alcohol, aryl or an animo acid group. (
  • 1. An isolated nucleic acid molecule encoding an amino acid sequence as shown in SEQ ID No: 15. (
  • 2. A recombinant nucleic acid molecule comprising a promoter sequence operably linked to a nucleic acid molecule according to claim 1. (
  • 3. A recombinant nucleic acid vector comprising a nucleic acid molecule according to claim 1. (
  • 4. A host cell comprising a recombinant nucleic acid molecule according to claim 2. (
  • 6. An isolated nucleic acid molecule according to claim 1, wherein the molecule comprises the nucleic acid sequence shown in SEQ ID No: 16. (
  • The present invention relates to isolated or purified molecule(s) capable of binding to one or more of telomeric, G-quadruplex, or G-quartet nucleic acid(s). (
  • 1. An isolated Cys2 His2 zinc finger polypeptide that binds to a molecule selected from the group consisting of telomeric nucleic acid, G-quadruplex nucleic acid and G-quartetnucleic acid. (
  • All of the chromosome conformation capture assays (and their derivatives) share the same basic principles and to some degree, have overlapping methodologies. (
  • Below we discuss the basic methodology and applications for the most commonly used subset of chromosome conformation capture-based assays. (
  • Physico-chemical Properties of Nucleic Acids, Volume II basically deals with the structural studies on nucleic acids and other biopolymers. (
  • Crystal structures of the ligand binding-competent conformation exist for all anti-apoptotic family members, with the exception of BCL-W, due to the flexibility of the BCL-W groove region. (
  • We now determined two high-resolution crystal structures of human BCL-W in complex with different DARPins at resolutions 1.5 and 1.85Å, in which the structure of BCL-W is virtually identical, and BCL-W adopts a conformation extremely similar to the ligand-free conformation of its closest relative BCL-XL in both structures. (
  • We present high-resolution structures of Deinococcus radiodurans (Dra)Nramp in multiple conformations to provide a thorough description of the Nramp transport cycle by identifying the key intramolecular rearrangements and changes to the metal coordination sphere. (
  • This unit helps you understand the properties of nucleotides and how they contribute to secondary and tertiary structures of nucleic acids at the molecular level. (
  • Topology Links RNA Secondary Structurewith Global Conformation, Dynamics, and Adaptation. (
  • Belton JM, Dekker J. Randomized ligation control for chromosome conformation capture. (
  • Belton JM, Dekker J. Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast. (
  • We developed 4C technology (chromosome conformation capture (3C)-on-chip), which allows for an unbiased genome-wide search for DNA loci that contact a given locus in the nuclear space. (
  • What is Chromosome Conformation Capture? (
  • In fact, the sheer number of available chromosome conformation capture methods can be overwhelming at first glance. (
  • Chromosome conformation capture (3C) was the first chromatin structure assay on the scene in 2002. (
  • Chromosome conformation capture methods are being increasingly used to study three-dimensional genome architecture in multiple cell types and species. (
  • Many chemical mutagens, such as chlorinated hydrocarbons and nitrites, owe their toxicity to the production of halides and nitrous acid during their metabolism in the body. (
  • We show that single strand conformation polymorphism (SSCP) analysis, using the mutation detection enhancement (MDE TM ) matrix, is efficient at detecting sequence polymorphisms in PCR amplicons. (
  • Sheffield VC, Beck JS, Kwitek AE, Sandstrom DW and Stone EW (1993) The sensitivity of single-strand conformation polymorphism analysis for the detection of single base substitutions. (
  • The histone chaperones Nap1 and Vps75 bind histones H3 and H4 in a tetrameric conformation. (
  • Nucleosome Histone Tail Conformation and Dynamics: Impacts of Lysine Acetylation and a Nearby Minor Groove Benzo[a]pyrene-Derived Lesion. (
  • In this work, we propose a model for multi-omic data integration (i.e., genetic variations, gene expression, genome conformation, and epigenetic patterns), which exploits a multi-layer network approach to analyse, visualize, and obtain insights from such biological information, in order to use achieved results at a macroscopic level. (
  • In terms of nucleic acid packing, dsDNA viruses, which lack genome segmentation and intra-capsid transcriptional machinery, predominantly display single-spooled genome organizations. (
  • We find that in this group of viruses, RNA-dependent RNA polymerases do not direct genome ordering, and the dsRNA can adopt multiple conformations. (
  • We build a model that encompasses 90% of the genome, and use this to quantify variation in the packing density and to characterize the different liquid crystalline geometries that are exhibited by the tightly compacted nucleic acid. (
  • The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape. (
  • By labeling such complementary probe nucleic acids with some readily detectable chemical group, it was then made possible to detect the presence of any polynucleotide sequence of interest in a test medium containing sample nucleic acids in single stranded form. (
  • Exposure to acid causes the loss of purine residues, though specific enzymes exist in cells to repair these lesions. (
  • Nucleic acid electrophoresis is utilized in many research applications of molecular biology to examine experimental outcomes and, in some cases, to isolate and purify samples, before proceeding to a subsequent step. (
  • Therefore, applications of routine nucleic acid electrophoresis can be generally categorized as analytical or preparative, respectively, both of which rely on the technique to separate, resolve, and quantitate. (
  • The analytical applications of nucleic acid electrophoresis provide ways to examine experimental results of a prior step before continuing the workflow or another set of experiments. (
  • Probes for specific nucleic acid sequences can be immobilized as arrays on solid phase surfaces for detection of multiple nucleic acid sequences simultaneously from electrophoresis gels and from aqueous solutions. (
  • Orita M, Iwahana H, Kanazana H, Hayashi K and Sekiya T (1989) Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. (
  • UV and circular dichroism spectroscopy as well as isothermal titration calorimetry (ITC) have been used to study the effect of different ions on the stability and conformation of PNA-DNA, PNA-PNA, and DNA-DNA duplexes having the same base sequences. (
  • To prevent degradation by chemical and enzymatic processes, DNA is often stored as a precipitate in ethanol, at -80 °C. This increases nucleic acids stability, but means that the ethanol must be removed prior to use. (
  • A fluorescently labeled nucleic acid having a hairpin structure between the fluorophore label and a point of attachment to a solid phase is useful as a probe to detect nucleic acid from a sample. (
  • Resulting hybrids are detected by binding of an antibody reagent, preferably labeled with a detectable chemical group, selective for binding the hybrids in the presence of the single stranded sample and probe nucleic acids. (
  • Terbium(3+) as a probe of nucleic acids structure. (
  • Crystal structure of a membrane-bound l-amino acid deaminase from Proteus vulgaris. (
  • 9 . The method of claim 1 wherein said nucleic acid duplex is bound to a solid support. (
  • Histones , which are less alkaline, apparently occur only in cell nuclei , where they are bound to nucleic acids . (
  • contains three glycans bound to the amino acid asparagine via N-glycosylation two Disulphide bridges between cysteine residues. (
  • However, formation of Z-conformation in living organisms and its biological significance remains largely elusive. (
  • Light induced charge and energy transport in nucleic acids and proteins is the basis of fundamental biological processes such as photosynthesis, vision, DNA-photostability, DNA-photodamage and photosensing. (
  • After two German chemists, Emil Fischer and Franz Hofmeister, independently stated in 1902 that proteins are essentially polypeptides consisting of many amino acids , an attempt was made to classify proteins according to their chemical and physical properties, because the biological function of proteins had not yet been established. (
  • The present invention provides methods for specifically detecting DNA mismatches between heteroduplex strands produced between wildtype and mutation containing nucleic acid species. (
  • Several binding sites were conserved between E. coli and human ribosomes, revealing that formation of Z-like RNA conformations might be a conserved property of the dynamic ribosome structure during translation. (
  • a structure for deoxyribose nucleic acid. (
  • Structure of a B-DNA dodecamer: conformation and dynamics. (
  • Chromatin structure-dependent conformations of the H1 CTD. (
  • DNA is arranged in a helical stranded structure, but it can adopt different three-dimensional conformations. (
  • e) a detecting reagent for detecting specific binding of the immunological reagent to chemically modified mismatched heteroduplex nucleic acid. (
  • These probes and methods for their use can be combined with known solid phases, particularly those used for plasmon surface detection and electron transfer detection of nucleic acid. (
  • We also demonstrated that locked nucleic acid (LNA) probes improved sensitivity approximately 4-fold compared to DNA probes of the same sequence. (
  • To define the conformation of the TPE:estrogen receptor (ER) complex, we employed a previously validated assay using the induction of transforming growth factor α (TGF α ) mRNA in situ in MDA-MB 231 cells stably transfected with wild-type ER (MC2) or D351G ER mutant (JM6). (
  • DNA and RNA, such as obtained by denaturing their double stranded forms, will hybridize or recombine under appropriate conditions with complementary single stranded nucleic acids. (
  • Volume II begins with Chapter 10 as continuation of Volume I and discusses the infrared and Raman spectroscopy of nucleic acids and polynucleotides. (
  • The A-to-B transition in DNA has also served as a prototype case for testing out and validating empirical energy functions and force fields used in molecular dynamics simulations on nucleic acids (2-4). (
  • In addition, staining nucleic acids with a fluorescent dye that has high sensitivity and a wide dynamic range can further improve gel quantitation. (
  • Structural modeling and in vitro experiments with recombinant human SIRT2 determined that propofol and [ 3 H]AziP m only bind specifically and competitively to the enzyme when co-equilibrated with other substrates, which suggests that the anesthetic site is either created or stabilized in enzymatic conformations that are induced by substrate binding. (
  • These labeled nucleic acids help to improve NMR methodologies by enhancing experimental sensitivity and spectral resolution, as well as facilitating the measurement of local and long-range distance restraints. (
  • Deoxyribonucleic acid (DNA) carries the genetic information essential for the growth and functioning of living organisms, playing a significant role in life sciences research. (
  • The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. (
  • To capture its ligand binding-competent conformation by counteracting the conformational flexibility of the BCL-W groove, we had selected high-affinity groove-binding designed ankyrin repeat proteins (DARPins) using ribosome display. (
  • wherein said matrix comprises charged functional groups that are suitable for binding nucleic acid under electrostatic binding conditions. (
  • 8. A method according to claim 6 , wherein said solid phase further comprises a nucleic acid comprising a quenching moiety. (
  • 11. A method according to claim 8 , wherein said solid phase comprises an array of discrete regions wherein each region contains a nucleic acid comprising a quenching moiety. (
  • 12. A method according to claim 11 , wherein said array comprises a plurality of different nucleic acids. (
  • 3. A zinc finger polypeptide according to claim 1 wherein said nucleic acid comprises single-stranded DNA. (
  • 6. A zinc finger polypeptide according to claim 1 wherein said nucleic acid comprises Hoogsteen base pairing. (
  • The design and development of nucleic acid-based therapeutics for the treatment of diseases arising from genetic abnormalities has made significant progress over the past few years. (
  • These conformations can modulate the expression of genetic information by altering the frequency of interaction between a distant regulatory element such as an enhancer, and the corresponding target gene promoter. (
  • Deoxyribonucleic acid (DNA) is one of the most important macromolecules in cells, carrying the genetic information essential for the growth and functioning of living organisms. (
  • This finding implied a degree of flexibility inherent in the Ub-PCNA complex that would allow it to transition into a conformation competent to bind the TLS polymerase. (