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 3.4.21.4.
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 http://ribosoft.fungalgenomics.ca/ribosoft/.
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: http://www.genevue.com/A_Books/DNA_2.html (First entry on page) 25$ including shipping with in the U.S. sks at monitor.net ...
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. ...
LOC FOR DETECTION OF HYBRIDIZATION OF NUCLEIC ACID SEQUENCES WITH PRIMER-LINKED STEM-AND-LOOP PROBES - diagram, schematic, and image 20 ...
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).
5.6.2 designates the enzyme further as being capable of altering nucleic acid, or DNA, conformations. Lastly, the full ... "EC 5.6.2 Enzymes altering nucleic acid conformation". IUBMB Enzyme Nomenclature. International Union of Biochemistry and ... However, when present, both ions are found near the binding site for nucleic acids. It is thought that these zinc fingers play ... The structure of the enzyme includes both a helicase domain, which is responsible for separating nucleic acids, and a ...
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". fbio.uh.cu. 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. Wikimedia Commons has media related to ... 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. Vol. 1654. ... 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 ...
Two typical alternative conformations for nucleic acids" (PDF). Curr. Sci. 45: 779-783. Sasisekharan, V.; Pattabiraman, N. ( ... two typical alternative conformations for nucleic acids". Current Science. 45: 779-783. Sasisekharan, V.; Pattabiraman, N.; ... Protein-nucleic acid interactions • Catalysis and regulation. 47: 1-8. doi:10.1016/j.sbi.2017.03.006. ISSN 0959-440X. PMID ... The discovery of topoisomerases and gyrases, enzymes that can change the linking number of circular nucleic acids and thus " ...
The crRNA-foreign nucleic acid complex is then cleaved, however if there are mismatches between the spacer and the target DNA, ... One representing a conformation of Cas9 in the apo state, and two representing Cas9 in the DNA bound state. In sgRNA-Cas9 ... Free energy changes of nucleic acids are also highly relevant in defining cleavage activity. Guide RNAs that bind to the DNA ... Alkan F, Wenzel A, Anthon C, Havgaard JH, Gorodkin J (October 2018). "CRISPR-Cas9 off-targeting assessment with nucleic acid ...
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, ...
Nucleic Acids Research. 44 (W1): W410-W415. doi:10.1093/nar/gkw348. ISSN 0305-1048. PMC 4987908. PMID 27131380. Chou, Peter Y ... Fasman, Gerald D. (1974-01-15). "Prediction of protein conformation". Biochemistry. 13 (2): 222-245. doi:10.1021/bi00699a002. ... The first isoform has a non-repeating proline-rich region from amino acids 12 to 80. The function of the region is not well ... The unmodified protein has 358 amino acids, predicted molecular weight of 40kDa, charge of -11, and isoelectric point of 5. 44 ...
... 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) ...
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 ...
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 ...
Krstić I, Hänsel R, Romainczyk O, Engels JW, Dötsch V, Prisner TF (2011). "Long-range distance measurements on nucleic acids in ... In this way, first unambiguous evidence was provided for an exclusive all-trans retinal conformation in the dark state and a ... To control proteins and nucleic acids by light CEF scientists have designed and applied a range of photoswitchable tethers, ... Wavelength-selective light-triggering was established for nucleic acids as well as three-dimensional control of DNA ...
The mimics are typically composed of locked nucleic acids (LNA), 2'-OMe, or 2'-F modified bases. LNA sequences are RNA ... analogues "locked" into an ideal Watson-Crick base pairing conformation. Gapmers often utilize nucleotides modified with ... LNAs, 2'-OMe, or 2'-F modified bases are chemical analogs of natural RNA nucleic acids. These modifications allow for an ... "Ribonuclease H1-dependent hepatotoxicity caused by locked nucleic acid-modified gapmer antisense oligonucleotides". Scientific ...
Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots. The base pairing in ... Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. ... In a non-biological context, secondary structure is a vital consideration in the nucleic acid design of nucleic acid structures ... "Paradigms for computational nucleic acid design". Nucleic Acids Research. 32 (4): 1392-1403. doi:10.1093/nar/gkh291. PMC 390280 ...
... 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 ... In: Current protocols in nucleic acid chemistry. (John Wiley & Sons, Inc.) (2013), Chapter 3, Unit 3.1., pp. 3.1.1-3.1.60. doi: ...
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 ...
The bridged ribose conformation enhances base stacking and pre-organizes the backbone of the oligonucleotide significantly ... Current Protocols in Nucleic Acid Chemistry. Current Protocols in Nucleic Acid Chemistry. Vol. Chapter 4. pp. 4.12.1-4.12.16. ... C-ethylene-bridged nucleic acids (ENA) with nuclease-resistance and high affinity for RNA". Nucleic Acids Research. Supplement ... A bridged nucleic acid (BNA) is a modified RNA nucleotide. They are sometimes also referred to as constrained or inaccessible ...
Watson JD, Crick FH (April 1953). "Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid". Nature. 171 ... Smith AB, Maxwell A (2006). "A strand-passage conformation of DNA gyrase is required to allow the bacterial toxin, CcdB, to ... Baker NM, Rajan R, Mondragón A (February 2009). "Structural studies of type I topoisomerases". Nucleic Acids Research. 37 (3): ... Nucleic Acids Research. 39 (15): 6327-6339. doi:10.1093/nar/gkr258. PMC 3159449. PMID 21525132. McKie SJ, Desai PR, Seol Y, ...
The bridge "locks" the ribose in the 3'-endo (North) conformation, which is often found in the A-form duplexes. This structure ... A locked nucleic acid (LNA), also known as bridged nucleic acid (BNA), and often referred to as inaccessible RNA, is a modified ... Kurreck, J. (2002-05-01). "Design of antisense oligonucleotides stabilized by locked nucleic acids". Nucleic Acids Research. 30 ... C-Ethylene-bridged nucleic acids (ENA) with nuclease-resistance and high affnity for RNA". Nucleic Acids Symposium Series. 1 (1 ...
proteins, nucleic acids, phospholipids and oligosaccharides). They are made up of chiral building blocks that are put together ... in space in handed conformations. These biological targets function as receptors for the drug enantiomers. So, at the binding ... Amino acids exist in two mirror-image versions (D- and L- configurations). Several D-amino acids, like D-methionine, D-proline ... 2-Arylpropionic acid nonsteroidal anti-inflammatory drugs (NSAIDs) provide one of the best pharmaceutical examples of chiral ...
Applications To Docking and Structure Prediction From The Distorted Native Conformation , journal=J. Comput. Chem. ,volume=15 , ... "Modeling unusual nucleic acid structures". Molecular Modeling of Nucleic Acids: 379-393. Petr Šulc; Flavio Romano; Thomas E. ... This is a list of notable computer programs that are used for nucleic acids simulations. Min - Optimization MD - Molecular ... Nucleic Acids Research. 44 (W1): W315-W319. doi:10.1093/nar/gkw279. ISSN 0305-1048. PMC 4987879. PMID 27095203. v t e (CS1 ...
... 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, ... RNA thermometer - Another class of mRNA regulatory segments which change conformation in response to temperature fluctuations, ... 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 ...
... acid design is the process of generating a set of nucleic acid base sequences that will associate into a desired conformation. ... Thus, in nucleic acids the sequence determines the pattern of binding and thus the overall structure. Nucleic acid design is ... Nucleic acid design encompasses all levels of nucleic acid structure: Primary structure-the raw sequence of nucleobases of each ... Nucleic acid design can be considered the inverse of nucleic acid structure prediction. In structure prediction, the structure ...
Folding, including the secondary and tertiary structure of biopolymers (nucleic acids and proteins). Akamptisomerism - due to ... the anti-conformation (left-most, below) and the gauche conformation (right-most, below). Both conformations are free of ... Ring conformation Cyclohexane conformations, including with chair and boat conformations among others. Cycloalkane ... The staggered conformation is more stable by 12.5 kJ/mol than the eclipsed conformation, which is the energy maximum for ethane ...
Progress in Nucleic Acid Research and Molecular Biology. Vol. 53. pp. 1-78. doi:10.1016/s0079-6603(08)60142-7. ISBN ... Traut TW, Payne RC (Dec 1980). "Dependence of the catalytic activities on the aggregation and conformation states of uridine 5 ... Traut TW, Jones ME (1996). Uracil metabolism--UMP synthesis from orotic acid or uridine and conversion of uracil to beta- ... Traut TW, Payne RC, Jones ME (Dec 1980). "Dependence of the aggregation and conformation states of uridine 5'-phosphate ...
Some of these are believed to affect the shape of nucleic acids (see for example RNA self-splicing), but this is only sometimes ... "An approach to detection of protein structural motifs using an encoding scheme of backbone conformations" (PDF). Pacific ... "Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical ... Biology portal Biomolecular structure Mammalian Motif Finder MochiView Multiple EM for Motif Elicitation Nucleic acid sequence ...
Nucleic Acids Research. 42 (21): 13134-49. doi:10.1093/nar/gku1051. PMC 4245941. PMID 25378325. Ishida T, Akimitsu N, Kashioka ... Filling of the sites changes origin conformation from its native state. It is hypothesized that DNA stretching by DnaA bound to ... Nucleic Acids Research. 43 (19): 9262-9275. doi:10.1093/nar/gkv804. PMC 4627069. PMID 26253742. (Wikipedia articles needing ...
Kozlowski, LP (26 October 2016). "Proteome-pI: proteome isoelectric point database". Nucleic Acids Research. 45 (D1): D1112- ... Upon absorption of a photon, retinal changes its conformation, causing a conformational change in the bacterioopsin protein, as ... Amino acids are the main source of chemical energy for H. salinarum, particularly arginine and aspartate, though they are able ... Vreeland, H; Rosenzweig, W D; Lowenstein, T; Satterfield, C; Ventosa, A (December 2006). "Fatty acid and DNA analyses of ...
Nucleic Acids Research. 48 (17): 9550-9570. doi:10.1093/nar/gkaa671. PMC 7515708. PMID 32810208. Trinklein ND, Aldred SF, ... A promoter is induced in response to changes in abundance or conformation of regulatory proteins in a cell, which enable ...
Nucleic Acids Research. Archived from the original on 16 October 2016. Retrieved 24 November 2015. (Articles with short ... These are highly involved in condensing chromatin from the beads-on-a-string conformation to a 30-nm fiber. Similar to other ... Histone H2B is a lightweight structural protein made of 126 amino acids. Many of these amino acids have a positive charge at ... All variants of histone H2B contain the same number of amino acids, and the variations in sequence are few in number. Only two ...
"Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification". Nucleic Acids Res. ... Single Strand Conformation Analysis) effectively identify SNPs and small insertions and deletions. MLPA, however, is one of the ... "Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification". Nucleic Acids ... The method was first described in 2002 in the scientific journal Nucleic Acid Research. The first applications included the ...
... is a molecular cytogenetic technique that uses fluorescent probes that bind to only particular parts of a nucleic acid sequence ... 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. 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 ...
Zhabinskaya D, Benham CJ (November 2013). "Competitive superhelical transitions involving cruciform extrusion". Nucleic Acids ... The conformation formed here has symmetry, unlike the folded conformation formed at high sodium ion concentrations. Lastly, the ... When DNA is faced with significant stress, a negative supercoiled conformation is adopted. A negative supercoiled conformation ... Nucleic Acids Research. 15 (23): 9641-54. doi:10.1093/nar/15.23.9641. PMC 306521. PMID 3697079. Horwitz MS, Loeb LA (August ...
... nucleic acid - nucleic acid regulatory sequence - nucleic acid repetitive sequence - nucleic acid sequence homology - nucleon ... conformation - chemical element - chemical equilibrium - chemical formula - chemical nomenclature - chemical property - ... amino acid - amino acid receptor - amino acid sequence - amino acid sequence homology - aminobutyric acid - ammonia - AMPA ... It deals with the structure and function of cellular components such as proteins, carbohydrates, lipids, nucleic acids and ...
Nucleic Acids Research. 48 (14): 7609-7622. doi:10.1093/nar/gkaa438. PMC 7641302. PMID 32476018. Abelson J, Trotta CR, Li H ( ... takes on a rectangular parallelepiped conformation consisting of four α subunits of 179 amino acids each. Each α subunit is ... Nucleic Acids Research. 37 (17): 5793-5802. doi:10.1093/nar/gkp537. PMC 761253. PMID 19578064. Tocchini-Valentini GD, ... All four structures feature at least two active sites made of three amino acids (tyrosine, histidine, and lysine) that catalyze ...
Nucleic Acids Research. 19 (9): 2315-2320. doi:10.1093/nar/19.9.2315. ISSN 0305-1048. PMC 329436. PMID 1710353. Tocchini- ... This puts the molecule in the bulge-helix-bulge conformation, and cleavage occurs in this formation, resulting in cleavage ... Dependence of DNA Continuity and Conformation". Proceedings of the National Academy of Sciences of the United States of America ...
Nucleic Acids Research. 46 (10): 4991-5000. doi:10.1093/nar/gky207. ISSN 0305-1048. PMC 6007630. PMID 29850895. Jha, Narendra ... Kar, Rajesh Kumar; Kharerin, Hungyo; Padinhateeri, Ranjith; Bhat, Paike Jayadeva (6 January 2017). "Multiple Conformations of ...
Nucleic Acids Research. 25 (10): 1903-12. doi:10.1093/nar/25.10.1903. PMC 146682. PMID 9115356. Rual, Jean-François; Venkatesan ... Agonist ligands work by inducing a conformation of the receptor which favors coactivator binding (see upper half of the figure ... Some of these receptors such as FXR, LXR, and PPAR bind a number of metabolic intermediates such as fatty acids, bile acids and ... Two putative orphan receptors, HNF4 and USP were found, via structural and mass spectrometry analysis, to bind fatty acids and ...
A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is ... Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots. The structural ... Pleij CW, Rietveld K, Bosch L (1985). "A new principle of RNA folding based on pseudoknotting". Nucleic Acids Res. 13 (5): 1717 ... Dirks, R.M. Pierce N.A. (2004) An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. "J ...
... instead of in nucleic acids. Several prion-forming proteins have been identified in fungi, primarily in the yeast Saccharomyces ... The amyloid conformation is self-propagating and represents the prion state. Amazingly distinct prion states exist for the ... The structure is based on the stacking of the prion domains in an in-register and parallel beta sheet conformation. An ... This makes prions a metastable, dominant mechanism for inheritance that relies solely on the conformation of the protein. Many ...
August 1987). ""Homology" in proteins and nucleic acids: a terminology muddle and a way out of it". Cell. 50 (5): 667. doi: ... different probes are generally applied with the goal being to obtain a large number of different protein-probe conformations. ... Information may come from nucleic acid sequence homology, gene expression profiles, protein domain structures, text mining of ... Okuda S, Yoshizawa AC (January 2011). "ODB: a database for operon organizations, 2011 update". Nucleic Acids Research. 39 ( ...
"Transmembrane Domain Peptide/Peptide Nucleic Acid Hybrid as a Model of a SNARE Protein in Vesicle Fusion". Angewandte Chemie ... Holopainen, Juha M.; Lehtonen, Jukka Y.A.; Kinnunen, Paavo K.J. (1999). "Evidence for the Extended Phospholipid Conformation in ... and one negatively charged glutamic acids called peptide E). Interestingly, it was discovered that not only the coiled-coil ... "Divalent Cation Induced Fusion and Lipid Lateral Segregation in Phosphatidylcholine-Phosphatidic Acid Vesicles". Biochemistry. ...
The B reader loop is further thought to stabilise NTPs in the active site and, due to its flexibility, allow the nucleic acids ... The open and closed conformations refer to the state of the DNA and whether the template strand has been separated from the non ... TFIIB is a single 33kDa polypeptide consisting of 316 amino acids. TFIIB is made up of four functional regions: the C-terminal ... Although TFIIB keeps a similar structure in both conformations some of the intramolecular interactions between the core and the ...
... fit a sequence of amino acids in alpha helix conformation into density. Place strand here - fit a sequence of amino acids in ... typically of proteins or nucleic acids, using 3D computer graphics. It is primarily focused on building and validation of ... Pukka puckers - check for unusual DNA/RNA conformations. Coot is built upon a number of libraries. Crystallographic tools ... check for unusual protein side-chain conformations. Density fit analysis - identify parts of the model which don't fit the ...
Jeffers M, Paciucci R, Pellicer A (Oct 1990). "Characterization of unr; a gene closely linked to N-ras". Nucleic Acids Res. 18 ... 2003). "The Apaf-1 internal ribosome entry segment attains the correct structural conformation for function via interactions ... 2006). "The LIFEdb database in 2006". Nucleic Acids Res. 34 (Database issue): D415-8. doi:10.1093/nar/gkj139. PMC 1347501. PMID ... Nucleic Acids Res. 33 (10): 3095-108. doi:10.1093/nar/gki611. PMC 1142345. PMID 15928332. Patel GP, Ma S, Bag J (2006). "The ...
Krogh A, Mian IS, Haussler D (1994). "A hidden Markov model that finds genes in E. coli DNA". Nucleic Acids Res. 22 (22): 4768- ... Hamelryck T, Kent JT, Krogh A (2006). "Sampling Realistic Protein Conformations Using Local Structural Bias". PLOS Comput. Biol ... Nucleic Acids Res. 36 (Database issue): D102-6. doi:10.1093/nar/gkm955. PMC 2238834. PMID 18006571. Lindow M, Jacobsen A, ... Probabilistic Models of Proteins and Nucleic Acids (1st ed.), Cambridge, New York: Cambridge University Press, ISBN 0-521-62971 ...
Nucleic Acids Research. 16 (7): 3109. doi:10.1093/nar/16.7.3109. PMC 336462. PMID 3368322. MacLeod AR, Houlker C, Reinach FC, ... which adopt a bent coiled coil conformation to wrap around the seven actin molecules in a functional unit of muscle. It is ... β-tropomyosin is roughly 32 kDa in molecular weight (284 amino acids), but multiple splice variants exist. Tropomysin is a ... which is one amino acid away from the C-terminus. β-tropomyosin also has a Serine residue at position 283, thus, it is likely ...
Momand J, Jung D, Wilczynski S, Niland J (August 1998). "The MDM2 gene amplification database". Nucleic Acids Research. 26 (15 ... K29-, K33-, K63- and M1-linked chains have a fairly linear conformation; they are known as open-conformation chains. K6-, K11 ... In contrast, the closed conformation chains have interfaces with interacting residues. Altering the chain conformations exposes ... Journal of Nucleic Acids. 2010: 1-8. doi:10.4061/2010/761217. PMC 2935186. PMID 20847899. Jackson SP, Durocher D (March 2013 ...
Nucleic Acids Res. 31 (6): 1633-9. doi:10.1093/nar/gkg273. PMC 152875. PMID 12626704. This article incorporates text from the ... Polosina YY, Cupples CG (2009). "Changes in the conformation of the Vsr endonuclease amino-terminal domain accompany DNA ...
Some RNA sequences have more than one biologically active conformation (i.e., riboswitches) For this reason, the ability to ... "Modeling Unusual Nucleic Acid Structures". Modeling unusual nucleic acid structures. In Molecular Modeling of Nucleic Acids. ... Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its ... Zuker M (2003). "Mfold web server for nucleic acid folding and hybridization prediction". Nucleic Acids Research. 31 (13): 3406 ...
The conformation of the DNA and the interactions of the nucleic acid with the protein in a complex of human immunodeficiency ... The conformation of the DNA and the interactions of the nucleic acid with the protein in a complex of human immunodeficiency ... Protein-nucleic acid interactions and DNA conformation in a complex of human immunodeficiency virus type 1 reverse ... The interactions between the dsDNA and protein primarily involve the sugar-phosphate backbone of the nucleic acid and ...
AP2 bound to heparin in the closed conformation ... Nucleic Acid Database. *wwPDB Partners. *RCSB PDB. *PDBe. *PDBj ... Muniscin-engaged AP2 is primed to rearrange into the vesicle-competent conformation on binding the tyrosine cargo ... AP2 bound to heparin in the closed conformation. *PDB DOI: 10.2210/pdb7RW8/pdb ...
They can adopt several distinctive conformations. G4s have been shown to form in the herpes simplex virus-1 (HSV-1) genome ... are four-stranded nucleic acid structures abundant at gene promoters. ... are four-stranded nucleic acid structures abundant at gene promoters. They can adopt several distinctive conformations. G4s ... A catalytic and selective scissoring molecular tool for quadruplex nucleic acids. J. Am. Chem. Soc. 140, 14528-14532 (2018). ...
Nucleic acids dynamics, interactions and recognition. This project concerns a number of fundamental problems, some of which ... A stretched conformation of DNA with a biological role? Author: Niklas Bosaeus; Anna Reymer; Tamas Beke-Somfai; T. Brown; M. ... The sialic acid-dependent nematocyst discharge process in relation to its physical-chemical properties is a role model for ... primed by earlier discoveries in our laboratory related to the structure and biological function of nucleic... ...
5.6 Isomerases altering macromolecular conformation. 5.6.2 Enzymes altering nucleic acid conformation. 5.6.2.4 DNA 3-5 ... 5.6 Isomerases altering macromolecular conformation. 5.6.2 Enzymes altering nucleic acid conformation. 5.6.2.4 DNA 3-5 ... 5.6 Isomerases altering macromolecular conformation. 5.6.2 Enzymes altering nucleic acid conformation. 5.6.2.4 DNA 3-5 ...
Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions ... Nucleic Acids Res. 2016;44(W1):W160-5. https://doi.org/10.1093/nar/gkw257. ... Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions ... Nucleic Acids Res. 2014;42(18):e143. https://doi.org/10.1093/nar/gku738. ...
Additional topics may include: nucleic acid conformation, DNA/protein interactions, signal transduction and transport phenomena ... These tools will be used to study some class of specific structures, (such as membrane, nucleic acid binding, regulatory, ... We will explore how bonding plays a central role in assembling simple biological building blocks such as sugars, amino acids, ... Protein conformation, enzymatic mechanisms and selected metabolic pathways will be analyzed. ...
31P Chemical Shift Tensors for Canonical and Non-Canonical Nucleic Acid Conformations: DFT Calculations and NMR Implications. ... Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations PŘECECHTĚLOVÁ Jana ... Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations ...
Potential plot of all furanose ring conformations (p. 771) , html , pdf , *Fig. 23.4.2.6. Plot of observed sugar conformations ... Nucleic acids. Contents. *23.4. Nucleic acids (pp. 766-799) , html , pdf , chapter contents , R. E. Dickerson ... Glycosyl conformation and chain sense (p. 777) , html , pdf , *Fig. 23.4.3.5. The role of the C2′-OH in RNA helix geometry (p. ... Sugar ring conformations (p. 775) , html , pdf , *23.4.3.4. Helical twist and rise, and propeller twist (pp. 775-777) , html , ...
"Measuring significant changes in chromatin conformation with ACCOST." Nucleic Acids Research. 48(5):2303-2311, 2020. ... "MEME Suite: tools for motif discovery and searching." Nucleic Acids Research. 37(Web server issue):W202-208, 2009.. MEME. ... "Accurate identification of centromere locations in yeast genomes using Hi-C." Nucleic Acids Research. 43(11):5331-5339, 2015. ... "On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements." Nucleic Acids ...
DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability. Nucleic Acids Res 2018;46:W350- ... Nucleic Acids Res 2019;47:D607-13.doi:10.1093/nar/gky1131 pmid:30476243 ... thus affecting chromatin conformation and gene expression. In addition, amino acids 1-333, which include the JmjC domain, have ... Nucleic Acids Res 2018;46:3339-50.doi:10.1093/nar/gky080 pmid:http://www.ncbi.nlm.nih.gov/pubmed/29425303 ...
Nucleic acids are characterized by a vast structural variability. Secondary structural conformations include the main ... Goobes R., Cohen O. & Minsky A. (2002) Nucleic Acids Research. 30, 10, p. 2154-2161 Abstract Triple-stranded DNA structures can ... Nucleic acids are characterized by a predominant right-handed helical configuration that derives from the chirality of the ... In biological systems nucleic acids are invariably found in highly compact forms. These rather intricate forms raise questions ...
Nucleic Acids Research (London) 49 (14), S. 7954 - 7965 (2021). MPG.PuRe ... Steuer, J.; Kukharenko, O.; Riedmiller, K.; Hartig, J. S.; Peter, C.: Guanidine-II aptamer conformations and ligand binding ... Kahlen, J.; Salimi, L.; Sulpizi, M.; Peter, C.; Donadio, D.: Interaction of Charged Amino-Acid Side Chains with Ions: An ...
... not perturb the DNA conformation could have valuable applications for the study of the structure and dynamics of nucleic acid ... The NMR structure determination of the self-complementary sequence 5-CTC(tC)ACGTGGAG shows a DNA conformation consistent with ... CD spectra are practically identical for modified and unmodified sequences, indicating an unperturbed B-DNA conformation. ... without distorting the DNA backbone conformation. This first example of an artificial, highly fluorescent DNA base that does ...
Incorporate locked nucleic acid monomers to increase PCR probe Tm, heighten target specificity, impart nuclease resistance, ... endo conformation. ... What are locked nucleic acids?. Locked nucleic acids are ... As with locked nucleic acid qPCR probes, hybridization Tm can be manipulated by the number of locked nucleic acid bases ... Manage sequence Tm using locked nucleic acid bases. Because of the afforded increase in Tm, locked nucleic acid qPCR probes can ...
Probing the impact of chromatin conformation on genome editing tools. *Xiaoyu Chen, Marrit Rinsma, J. Janssen, Jin Liu, I. ... Nucleic acids research. *2011. TLDR. The combination of high nuclease activity with reduced cytotoxicity and the simple design ...
Nucleic Acids Res. 37(13):4453-63. *Cupples CG (2009) DNA Repair, Encyclopedia of Microbiology, pp 99-112, Elsevier. ... 2009) Changes in the conformation of the Vsr endonuclease amino-terminal domain accompany DNA cleavage. J. Biochem. 146(4):523- ...
... which bind to nucleic acids in the Z-conformation. However, the specific role of these Zα domains in orchestrating ZBP1 ... Z-DNA-binding protein 1 (ZBP1) is an innate immune sensor of nucleic acids that regulates host defense responses and ... Fatty acid-binding protein 4 (FABP4) is predominantly expressed in adipocytes and macrophages and regulates metabolic and ... Most paramyxoviruses enter epithelial cells of the airway using sialic acid as a receptor and cause only mild disease. However ...
... to expunge heat-induced modifications of nucleic acids; (d) metabolic enzymes, to reorganize and stabilize the vigour fund of ... which assist other proteins exchange to their native conformation; (b) components of the proteolytic system, to degrade irre- ... In individual, dissection of IL-1 and IL-1Ra mRNAs after systemic injection of kainic acid in rats has shown that these ... Rosenson, RS, Tangney, CC, and Casey, LC (1999) gastritis acid reflux diet. Such a simple mould of attention was updated in the ...
... rebuilding and visualization of three-dimensional nucleic acid structures, Nucleic Acids Res.31(17), 5108-21.. Xiang-Jun Lu & ... The above values were obtained using first alternate conformation only and calculated by 3DNA program. Xiang-Jun Lu & Wilma K. ... A Portal for Three-dimensional Structural Information about Nucleic Acids. As of 23-Nov-2022 number of released structures: ... [email protected] ©1995-2022 The Nucleic Acid Database Project , Rutgers, The State University of New Jersey ...
... conformation and stability. Nucleic Acid Res. 18, 6353-6359 (1990). ... Nucleic Acids Res. 29, 2437-2447 (2001). Alseth, I. et al. Inosine in DNA and RNA. Cur. Opi. Genetics and Dev. 26, 116-123 ( ... Nucleic Acids Res. 26, 4309-4314 (1998).. Chiu, Y. and Rana, T. M. siRNA function in RNAi: a chemical modification analysis. ... Nucleic Acids Res. 38, 1415-1430 (2010). Squires, J. E. et al. Widespread occurrence of 5-methylcytosine in human coding and ...
Nucleic Acid Conformation, Protein Binding, Protein Conformation, Recombinant Proteins chemistry, Recombinant Proteins ... Nucleic acids research. [Nucleic Acids Res] 2019 Jul 26; Vol. 47 (13), pp. 7118-7129. ... Amino Acid Motifs genetics, Amino Acid Sequence, Bacteriophage P22 genetics, Bacteriophage P22 metabolism, Crystallography, X- ... Ray, Models, Molecular, Podoviridae genetics, Protein Conformation, Sequence Homology, Amino Acid, Viral Tail Proteins genetics ...
This reaction is sterically prohibited for the B form DNA conformation. If, however, the nucleic acid structure is deformed, ... It was not possible to uniquely identify the preferred transition-state complex with respect to nucleic acid structure or ... In one, I was located "outside" the nucleic acid structure; in the other geometry, I was intercalated between adjacent base ... Terms: DNA or Deoxyribonucleic acid OR DNA or Deoxyribonucleic acid 574 - 574 of 583 Bibliographic entries ...
En: Nucleic Acids Research. 1989. Vol. 17. N m. 16. Pag. 6669-6680 Fern ndez Bola os Vazquez, Jose Manuel, Iglesias Guerra, ... Conformations in Crystals and Solutions of D(Cacgtg), D(Ccgcgg) and D(Ggcgcc) Studied by Vibrational Spectroscopy. ... Serinol-Based Benzoic Acid Esters as New Scaffolds for the Development of Adenovirus Infection Inhibitors: Design, Synthesis, ... Preparation of Crayfish Chitin by in Situ Lactic Acid Production. En: Process Biochemistry. 2001. Vol. 37. N m. 3. Pag. 229-234 ...
CADB: Conformation Angles DataBase of Proteins. ," Nucleic Acids Res.. 0305-1048, 31 ... Protofold: A Successive Kinetostatic Compliance Method for Protein Conformation Prediction J. Mech. Des (July,2005) ... between the resultant conformation and the PDB data is minimized to yield the best values for the bond length and bond angles ...
... and decreased electronegativity of the thio-group leads to cytotoxicity by altering the hydrogen bonds between nucleic acid ... duplexes, resulting in the disruption the conformation of the DNA thus inhibiting replication and transcription. Through NMR ... THREE CEREAL GRAIN PROTEINS,TAABF, TAWD40, AND AFN1, HAVE PUTATIVE ROLES IN THE ABSCISIC ACID-MEDIATED GENE EXPRESSION PATHWAY ... The amino acid sequence is left unchanged when the mutation is synonymous and it is affected when the mutation is non- ...
A C-C mismatch usually confers substantial destabilization to nucleic-acid structure, and disrupts helices and tertiary ... Translation-competent conformations of the tRNA, mRNA, and decoding center demonstrate how the ribosomal P site helps to ... arranging the cytosine-cytosine pair into a nearly planar conformation, resembling a Watson-Crick base pair formed by ...
Nucleic Acid Conformation G2.111.570.790.486 G2.111.570.820.486 Nucleotide Motifs G2.111.570.790.486.662 G2.111.570.820.486.662 ... Nucleic Acid L1.700.508.300.188.400.300.500 L1.313.500.750.300.188.400.300.500 L1.700.508.300.188.400.325.630 L1.313.500.750. ... Arachidonic Acid D10.251.355.96.100 Arachidonic Acids D10.251.355.96 Arachis hypogaea J2.500.850.500.77 (Replaced for 2015 by ... Fusidic Acid D10.570.938.515 Fuzzy Logic L1.224.65.250 L1.224.50.375.250 G-Quadruplexes G2.111.570.790.486.550 G2.111.570.820. ...
Diekmann, S.; Zarling, D. A.: Unique poly(dA).poly(dT) B-conformation in cellular and synthetic DNAs. Nucleic Acids Research ... In: Nucleic acids and molecular biology, Vol. 1, pp. 1138 - 156 (Ed. Eckstein, F.). Springer, Berlin (1987) ...
  • Chymotrypsin -- A protease that catalyses the hydrolysis (the breakdown) of proteins into peptides or amino acids in the small intestine. (nih.gov)
  • Cysteine -- A sulfur-containing nonessential amino acid produced by the enzymatic or acid hydrolysis of proteins. (nih.gov)
  • Glutamic acid -- A nonessential amino acid occurring in proteins. (nih.gov)
  • Genetic Code Expansion (GCE) technology - the engineering of cellular translation to express proteins containing non-canonical amino acids - provides unprecedented ways to probe and manipulate macromolecular structure and function, analyze protein malfunctions in disease, engineer bioanalytical tools, and create precision biotherapeutics. (nih.gov)
  • Raman microscopy is a suitable technique for the studies of cells, tissues, biomolecules such as proteins and nucleic acids, as well as pharmacological formulations and microplastics. (photonics.com)
  • All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. (embl.de)
  • Ubiquitous in all life forms and central to any research or development program involving biomolecules, the interactions between proteins, nucleic acids, peptides and other biomacromolecules lie at the heart of biology, physiology, and medicine. (wyatt.com)
  • Amino acid residues from the polymerase active site region, including amino acid residues of the conserved Tyr-Met-Asp-Asp (YMDD) motif and the "primer grip," interact with 3'-terminal nucleotides of the primer strand and are involved in positioning the primer terminal nucleotide and its 3'-OH group at the polymerase active site. (nih.gov)
  • Amino acid residues of the "template grip" have close contacts with the template strand and aid in positioning the template strand near the polymerase active site. (nih.gov)
  • Amino acid residues of beta 1', alpha A', alpha B', and the loop containing His539 of the RNase H domain interact with the primer strand of the dsDNA. (nih.gov)
  • Proteome-wide identification of amino acid substitutions deleterious for protein function. (washington.edu)
  • The fourth domain of A561L is a 242 amino acid C-terminal domain, named A561LD4, with cell wall degrading activity. (weizmann.ac.il)
  • Interaction of Charged Amino-Acid Side Chains with Ions: An Optimization Strategy for Classical Force Fields. (mpg.de)
  • Through this process, Anfinsen could analyze the fragments of the three-dimensional amino acid chain. (nih.gov)
  • Our previous studies using gene-targeted mouse models of chronic wasting disease (CWD) demonstrated that Norway and North America cervids are infected with distinct prion strains that respond differently to naturally occurring amino acid variation at residue 226 of the prion protein. (cdc.gov)
  • Acetyl CoA transfer acetyl group to lysine amino acid with the presence of acetyltransferases enzymes. (avensonline.org)
  • Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions, and the adoption of ChIP techniques to 3C-based protocols makes it possible to identify long-range interactions. (biomedcentral.com)
  • A G-quadruplex (GQ) is a type of noncanonical nucleic acid structure that can form in regions of nucleic acids rich in guanine nucleotides. (vt.edu)
  • The conformation of the DNA and the interactions of the nucleic acid with the protein in a complex of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) and 19-mer/18-mer double-stranded DNA template-primer (dsDNA) are described. (nih.gov)
  • The interactions between the dsDNA and protein primarily involve the sugar-phosphate backbone of the nucleic acid and structural elements of the palm, thumb, and RNase H of p66, and are not sequence specific. (nih.gov)
  • The COMD/NMR Center develops advanced methods in NMR spectroscopy for studying conformation and dynamics of protein and nucleic acid during biological processes and makes these sophisticated methods accessible to a wider research community to facilitate applications to biomedical questions. (nih.gov)
  • Much of our work focuses on the viral nucleocapsid protein (NC), a nucleic acid chaperone that remodels nucleic acid structures so that the most thermodynamically stable conformations are formed-an activity that is critical for highly efficient and specific viral DNA synthesis. (nih.gov)
  • Selection of fully processed HIV-1 nucleocapsid protein is required for optimal nucleic acid chaperone activity in reverse transcription. (nih.gov)
  • Aberrant bcl-2 GQ conformations result in increased production of the BCL2 protein, which is an apoptosis inhibitor. (vt.edu)
  • Shortly after SARS-CoV emerged at the turn of the 21st century, the spike (S) protein (particularly in its native conformation) was identified as the immunodominant antigen of the virus3. (who.int)
  • Altogether, this suggests that tC works well as a cytosine analogue, i.e. it is situated in the base stack, forming hydrogen bonds with G in the complementary strand, without distorting the DNA backbone conformation. (chalmers.se)
  • G-quadruplexes (G4s) are four-stranded nucleic acid structures abundant at gene promoters. (nature.com)
  • Later, as they improved their understanding of the structures and the conformations ind the bases in the nucleic acids, they had more exact models machined from metal. (forextrading-madeeasy.com)
  • Using a dihedral angle metric and an affinity propagation technique, we have clustered the conformations of each CDR and unique loop length of antibody structures in the PDB, at this time, a total of 115 unique clusters [3] . (fccc.edu)
  • Dr. Duckett earned his PhD degree in Biochemistry from the University of Dundee under the mentorship of Professor David M. J. Lilley, a Member of Royal Society and the Director of the Cancer Research UK Nucleic Acid Structure Research Group, where Derek had a remarkable string of studies that defined the structures for DNA and RNA four-way helical junctions, and how these interact with resolving enzymes (Duckett, et al. (moffitt.org)
  • A C-C mismatch usually confers substantial destabilization to nucleic-acid structure, and disrupts helices and tertiary interactions. (umassmed.edu)
  • Unique poly(dA).poly(dT) B'-conformation in cellular and synthetic DNAs. (mpg.de)
  • DNA, or deoxyribonucleic acid -- The primary genetic material of all cellular organisms and the DNA viruses. (nih.gov)
  • The replicative properties of prions stem from the capacity of PrP Sc to template its conformation on PrP C in a cyclical process resulting in exponential accumulation of prion infectivity ( 8 - 11 ). (cdc.gov)
  • Although they lack nucleic acids, prions exhibit heritable strain properties that influence disease outcomes, including the time between infection and disease onset (incubation period), clinical signs, patterns of neuronal degeneration and PrP Sc deposition in the central nervous system (CNS), and the ability to replicate in non-CNS tissues such as the lymphoreticular system and musculature ( 12 ). (cdc.gov)
  • Incorporation of locked nucleic acid bases increases sequence melting temperature. (idtdna.com)
  • When locked nucleic acid modified bases are incorporated into a DNA sequence (such as a qPCR probe), its duplex melting characteristics are changed, resulting in increased T m . (idtdna.com)
  • As with locked nucleic acid qPCR probes, hybridization T m can be manipulated by the number of locked nucleic acid bases incorporated. (idtdna.com)
  • Remarkably, the ribosome stabilizes the mismatched codon-anticodon helix, arranging the cytosine-cytosine pair into a nearly planar conformation, resembling a Watson-Crick base pair formed by complementary bases (e.g. (umassmed.edu)
  • The guanine bases form a square planar conformation via Hoogsteen hydrogen bonding. (vt.edu)
  • Molecular genetic tests for detecting drug-resistance are, in general, just a variation of nucleic acid amplification (NAA) tests and can reliably provide information on the presence of mutations associated with drug resistance in 1 to 2 days. (cdc.gov)
  • During examination at the HIV clinic, specimens were obtained from the pharynx, rectum, and urine for culture and a nucleic acid amplification test (NAAT). (cdc.gov)
  • It provides information about their chemical composition, the spatial distribution of the individual compounds, the conformation of the molecules, their crystallinity, and details of other properties. (photonics.com)
  • Gel electrophoresis is a standard laboratory procedure that is indispensable for nucleic acid visualization and purification. (integra-biosciences.com)
  • Nucleic acids research, 38, D105-110. (uib.no)
  • Through an optimization process, the structural error (root mean square deviation of all atoms) between the resultant conformation and the PDB data is minimized to yield the best values for the bond length and bond angles in the calibrated peptide unit. (asme.org)
  • The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape. (bvsalud.org)
  • Structural determinants of human APOBEC3A enzymatic and nucleic acid binding properties. (nih.gov)
  • When incorporated into an oligonucleotide probe, locked nucleic acid monomers impart heightened structural stability, resulting in increased hybridization melting temperature (T m ), both in vitro and in vivo (Figure 2). (idtdna.com)
  • Heritable strain information appears to be enciphered by distinct PrP Sc conformations that are faithfully propagated during prion replication ( 14 , 15 ). (cdc.gov)
  • The NMR structure determination of the self-complementary sequence 5'-CTC(tC)ACGTGGAG shows a DNA conformation consistent with B-form for the whole duplex. (chalmers.se)
  • Locked nucleic acid oligonucleotides are useful in template switching oligo designs and for strengthening target oligo binding in challenges sequence regions, such as AT-rich areas. (idtdna.com)
  • Cistron -- A basic unit of hereditary material, it is the smallest genetic unit that must be intact to function as a transmitter of genetic information, i.e., to determine the sequence of amino acids of one polypeptide chain. (nih.gov)
  • Improper GQ conformations can lead to improper regulation of gene expression, potentially resulting in genetic diseases or cancer. (vt.edu)
  • In most cases, addition of acetyl groups to histone tails causes gene activation by inducing and recruiting a euchromatin conformation and bromodomain containing transcription factors respectively for genes in close closeness to the acetylated histone [ 7,8 ]. (avensonline.org)
  • This first example of an artificial, highly fluorescent DNA base that does not perturb the DNA conformation could have valuable applications for the study of the structure and dynamics of nucleic acid systems. (chalmers.se)
  • If, however, the nucleic acid structure is deformed, such that the distance between two adjacent base pairs (one containing guanine and cytosine) is maximized, sterically allowed transition-state geometries can be identified. (cdc.gov)
  • It was not possible to uniquely identify the preferred transition-state complex with respect to nucleic acid structure or isomer of I. However, two types of general transition-state geometries were observed. (cdc.gov)
  • G-C). Translation-competent conformations of the tRNA, mRNA, and decoding center demonstrate how the ribosomal P site helps to establish and maintain the open reading frame. (umassmed.edu)
  • The enzyme crystallizes in two different conformations (open and closed). (embl.de)
  • Because of the afforded increase in T m , locked nucleic acid qPCR probes can be designed with shorter lengths than standard probes. (idtdna.com)
  • 16 this range (primarily cytochrome P-450 mediated oxidation to fatty acids and alcohols) is slow, while the aromatics are metabolized faster (oxidation of alkyl site and/or ring, sometimes with formation of reactive intermediates, and conjugation with glutathione, glucuronic acid, or glycine) (ATSDR 1999). (cdc.gov)
  • This reaction is sterically prohibited for the B form DNA conformation. (cdc.gov)
  • This induces migration towards the anode due to the negative charge of the nucleic acids, separating the individual components by size and/or conformation. (integra-biosciences.com)
  • Pioneering biocontainment systems used metabolic auxotrophy in which target cells could only grow in the presence of an exogenously supplied metabolite 7,8 , and the recent creation of an E. coli strain with an altered genetic code enabled production of synthetic auxotrophy strains in which an exogenous supply of non-natural amino acids is required for cell survival 9,10 . (justia.com)