Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Protein Conformation: 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).Peptide Nucleic Acids: 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.Molecular Conformation: The characteristic three-dimensional shape of a molecule.Nucleic Acid Probes: 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.DNA: 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).Molecular Sequence Data: 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.Nucleic Acid Amplification Techniques: Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.Nucleic Acid Denaturation: 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.Amino Acid Sequence: 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.Nucleic Acid Hybridization: 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)Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)RNA: 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)Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Circular Dichroism: 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)Protein Structure, Secondary: 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.Protein Binding: 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.Magnetic Resonance Spectroscopy: 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).Thermodynamics: 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)Protein Structure, Tertiary: 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.Kinetics: The rate dynamics in chemical or physical systems.Hydrogen Bonding: 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.Oligonucleotides: 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)Solutions: 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)Structure-Activity Relationship: 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.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.Nuclear Magnetic Resonance, Biomolecular: 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.Escherichia coli: 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.Mutation: 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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Temperature: 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.Spectrometry, Fluorescence: Measurement of the intensity and quality of fluorescence.Models, Chemical: Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.Molecular Structure: 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.Ligands: 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)Peptides: 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.Polymerase Chain Reaction: 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.Molecular Dynamics Simulation: A computer simulation developed to study the motion of molecules over a period of time.Polymorphism, Single-Stranded Conformational: 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.Oligodeoxyribonucleotides: 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.Proteins: 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.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Hydrogen-Ion Concentration: 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)Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.Spectrophotometry, Ultraviolet: 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)Self-Sustained Sequence Replication: 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.DNA, Single-Stranded: A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.Polydeoxyribonucleotides: 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.Protein Structure, Quaternary: The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.X-Ray Diffraction: 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)DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.Carbohydrate Conformation: The characteristic 3-dimensional shape of a carbohydrate.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Nucleotides: 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)Protein Denaturation: Disruption of the non-covalent bonds and/or disulfide bonds responsible for maintaining the three-dimensional shape and activity of the native protein.Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.Nucleic Acid Heteroduplexes: 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.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Static Electricity: The accumulation of an electric charge on a objectAptamers, Nucleotide: Nucleotide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Fluorescent Dyes: 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.Crystallography: 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)Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.G-Quadruplexes: 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)Bacterial Proteins: Proteins found in any species of bacterium.Water: 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)GuanineSensitivity and Specificity: 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)DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.DNA Probes: 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.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Amino Acid Substitution: 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.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Sequence Alignment: 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.Spectrum Analysis, Raman: Analysis of the intensity of Raman scattering of monochromatic light as a function of frequency of the scattered light.Cattle: 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.Solvents: 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)DNA Primers: 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.Protein Multimerization: The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.Hydrolysis: The process of cleaving a chemical compound by the addition of a molecule of water.PolynucleotidesFluorescence Resonance Energy Transfer: 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.Nucleosides: Purine or pyrimidine bases attached to a ribose or deoxyribose. (From King & Stansfield, A Dictionary of Genetics, 4th ed)DNA, B-Form: 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.Intercalating Agents: 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.Magnesium: 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.Crystallization: The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Tryptophan: 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.Chemistry: A basic science concerned with the composition, structure, and properties of matter; and the reactions that occur between substances and the associated energy exchange.Adenosine Triphosphate: 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.Plasmids: 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.Macromolecular Substances: 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.Stereoisomerism: 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, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Hydrophobic and Hydrophilic Interactions: The thermodynamic interaction between a substance and WATER.Oligoribonucleotides: 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.Chemical Phenomena: The composition, conformation, and properties of atoms and molecules, and their reaction and interaction processes.Molecular Probes: 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.Polyribonucleotides: 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.Ribonucleases: Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Scattering, Small Angle: 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.Spectroscopy, Fourier Transform Infrared: 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.Oligonucleotide Probes: 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.Amino Acid Motifs: 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.Allosteric Regulation: 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.Cloning, Molecular: 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, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Models, Structural: A representation, generally small in scale, to show the structure, construction, or appearance of something. (From Random House Unabridged Dictionary, 2d ed)Adenine: A purine base and a fundamental unit of ADENINE NUCLEOTIDES.DNA, Catalytic: Molecules of DNA that possess enzymatic activity.Point Mutation: 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.Disulfides: Chemical groups containing the covalent disulfide bonds -S-S-. The sulfur atoms can be bound to inorganic or organic moieties.UridineChemistry, Physical: The study of CHEMICAL PHENOMENA and processes in terms of the underlying PHYSICAL PHENOMENA and processes.Amino Acids: 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.Viruses: 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.DNA-Binding Proteins: 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.Hot Temperature: Presence of warmth or heat or a temperature notably higher than an accustomed norm.Physicochemical Phenomena: The physical phenomena describing the structure and properties of atoms and molecules, and their reaction and interaction processes.Oligonucleotides, Antisense: Short fragments of DNA or RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.Purines: 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.Viral Proteins: Proteins found in any species of virus.Guanosine: 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)Protons: 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.Biophysics: The study of PHYSICAL PHENOMENA and PHYSICAL PROCESSES as applied to living things.Cross-Linking Reagents: 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.Sequence Homology, Nucleic Acid: 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.Models, Biological: 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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Cysteine: A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.DNA, A-Form: 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.Cytosine: A pyrimidine base that is a fundamental unit of nucleic acids.Calorimetry: 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)Ribose: A pentose active in biological systems usually in its D-form.Fluorescence: 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, Electron: 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.Molecular Probe Techniques: The use of devices which use detector molecules to detect, investigate, or analyze other molecules, macromolecules, molecular aggregates, or organisms.Nucleic Acid Renaturation: The reformation of all, or part of, the native conformation of a nucleic acid molecule after the molecule has undergone denaturation.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Molecular Chaperones: 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 Diagnostic Techniques: MOLECULAR BIOLOGY techniques used in the diagnosis of disease.Protein Stability: The ability of a protein to retain its structural conformation or its activity when subjected to physical or chemical manipulations.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Polymers: Compounds formed by the joining of smaller, usually repeating, units linked by covalent bonds. These compounds often form large macromolecules (e.g., BIOPOLYMERS; PLASTICS).Molecular Weight: The sum of the weight of all the atoms in a molecule.RNA, Catalytic: 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.Biophysical Phenomena: The physical characteristics and processes of biological systems.Drug Design: 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.Trifluoroethanol: 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, Infrared: 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)Salts: 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)RNA, Transfer: 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.Structural Homology, Protein: 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.Immobilized Nucleic Acids: DNA or RNA bound to a substrate thereby having fixed positions.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.HIV-1: The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.Poly dA-dT: 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.UracilTime Factors: Elements of limited time intervals, contributing to particular results or situations.Proflavine: Topical antiseptic used mainly in wound dressings.Databases, Nucleic Acid: 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, Messenger: 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.Fluorescence Polarization: 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.Carbon Isotopes: 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.Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.Deoxyribonucleases: Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.Cations: Positively charged atoms, radicals or groups of atoms which travel to the cathode or negative pole during electrolysis.Conserved Sequence: 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.Binding, Competitive: 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.ThymineMutant Proteins: Proteins produced from GENES that have acquired MUTATIONS.Oligopeptides: Peptides composed of between two and twelve amino acids.Trypsin: 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.Prions: 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.Spectrum Analysis: 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)SELEX Aptamer Technique: 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.Allosteric Site: 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.Lipid Bilayers: Layers of lipid molecules which are two molecules thick. Bilayer systems are frequently studied as models of biological membranes.Surface Properties: Characteristics or attributes of the outer boundaries of objects, including molecules.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Spectrophotometry: The art or process of comparing photometrically the relative intensities of the light in different parts of the spectrum.Indicators and Reagents: 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)Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Surface Plasmon Resonance: 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.Proline: 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.Isomerism: 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)Cell Membrane: The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.Oxidation-Reduction: 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).Mathematics: The deductive study of shape, quantity, and dependence. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Virology: The study of the structure, growth, function, genetics, and reproduction of viruses, and VIRUS DISEASES.RNA Probes: 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 Fusion Proteins: 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.Poly G: 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.Drug Stability: The chemical and physical integrity of a pharmaceutical product.

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.. ...
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 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 ...
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 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
The solution structure of a human immunodeficiency virus type-1 (HIV-1) Rev peptide bound to stem-loop IIB of the Rev response element (RRE) RNA was solved by nuclear magnetic resonance spectroscopy. The Rev peptide has an α-helical conformation and binds in the major groove of the RNA near a purine-rich internal loop. Several arginine side chains make base-specific contacts, and an asparagine residue contacts a G·A base pair. The phosphate backbone adjacent to a G·G base pair adopts an unusual structure that allows the peptide to access a widened major groove. The structure formed by the two purine-purine base pairs of the RRE creates a distinctive binding pocket that the peptide can use for specific recognition.. ...
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
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
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 ...
... 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.
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 ...
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.. ...
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 ...
Basepairs involving Hoogsteen(H) edge of Adenine and WatsonCrick(W) edge of Guanine is shown. Highlighted examples are found from RNA crystal structures obtained from PDB. Base pairs stabilized by N-H...N/O type hydrogen bonds ...
NUPARM-Plus :: DESCRIPTION NUPARM-Plus is a program for analysis of sequence dependent variations in nucleic apdb_id (DNA & RNA) double helices ::DEVELOPER Prof. Manju Bansal Lab, MBU, IISc, Bangalore, Ind
Buy The Double Helix Mini DNA Models, Let Students Build A Human DNA Strand With Free UK Delivery On Orders Over 50. A Wide Range Of Biology Aids Available.
Decoding and Targeting RNA Machines in Living Cells RNA molecules fold into structures and intermolecular interactions to execute a second layer of genetic instructions beyond encoding proteins. Functions of RNA structures are pervasive and diverse, including many levels of gene regulation, guiding, scaffolding and catalysis. RNA molecules are directly involved in a variety of human…
DNA molecule. Computer artwork of a molecule of DNA (deoxyribonucleic acid). DNA is composed of two strands (outside) twisted into a double helix. Each strand consists of a sugar-phosphate backbone attached to nucleotide bases (spheres). There are four bases: adenine, cytosine, guanine and thymine. The bases are joined together by hydrogen bonds (rods between spheres). DNA contains sections called genes that encode the bodys genetic information. - Stock Image G110/1050
HB plot is the hydrogen-bonding network of a protein (see the reference on the HBplot tab; Bikadi et al., 2007). The axis represent the amino acid residues of the protein, a dot indicates if a hydrogen bond is present connecting two residues. From the HB plot secondary structure can be easily visualized. Moreover, bonds that contribute to 3D stability can be simply spotted as well. Amino acid residues that interact with the docked ligand are indicated on the right panel and on the plot as well ...
HB plot is the hydrogen-bonding network of a protein (see the reference on the HBplot tab; Bikadi et al., 2007). The axis represent the amino acid residues of the protein, a dot indicates if a hydrogen bond is present connecting two residues. From the HB plot secondary structure can be easily visualized. Moreover, bonds that contribute to 3D stability can be simply spotted as well. Amino acid residues that interact with the docked ligand are indicated on the right panel and on the plot as well ...
DNA molecule. Computer artwork of the structure of deoxyribonucleic acid (DNA). DNA is composed of two strands twisted into a double helix. Each strand consists of a sugar-phosphate backbone (on outside of helix) attached to nucleotide bases (between strands). There are four different bases: guanine, cytosine, thymine and adenine. DNA contains sections called genes, which encode the bodys genetic information. - Stock Image G110/1024
One of the ways to improve formability of Advanced High Strength Steel grades is by modifying the surface during downstream production process. In this study, Galvannealed DP980 grade was selected to understand the impact of a change in the annealing furnace atmosphere before hot-dip coating on product attributes such as diffusible hydrogen content in the steel, bendability, etc. Results showed that an increase in the dew point in the furnace resulted in an increase in surface decarburization which correlates with an improvement in bendability. Along with a decarburized layer, changes in diffusible hydrogen amounts were also observed with furnace atmosphere changes. This paper will also discuss the relationship between hydrogen diffusivity and delayed fracture (DF) susceptibility associated with the presence or absence of a decarburized layer.. ...
Professor Horst Klump, Department of Molecular and Cell Biology, will lecture on the thermodynamics and kinetics of protein folding and ligand binding and will discuss the structures of nucleic acid structures including, DNA, RNA and ribozymes. Professor Klump is internationally renowned for his work on DNA triple helices.. ...
That morning, Watson and Crick knew, although still in mind only, the entire structure: it had emerged from the shadow of billions of years, absolute and simple, and was seen and understood for the first time. Twenty angstrom units in diameter, seventy-none billionths of an inch. Two chains twinning coaxially, clockwise, one up the other down, a complete turn the screw in 34 angstroms. The bases flat in their pairs in the middle, 3.4 angstroms and a tenth of a revolution separating a pair from the one above or below. The chains held by the pairing closer to each other around the circumference one way than the other, by an eighth of a turn, one groove up the outside narrow, the other wide. A melody for the eye of the intellect, not a note wasted. In itself, physically, structure carried the means of replication-positive to negative, complementary. As the strands unwound, at double template was there in the base pairing, so that only complementary nucleotides could form bonds and drop into place ...
Ive read some of the responses dealing with 5 RACE, but didnt see anything about possible secondary structure. Ive been having problems getting anything on my gels for 5 RACE (even using touchdown pcr). I think that it may be due to 2* structure. Does anyone have any protocols for relaxing the 2 ...
During DNA replication, nucleotides are specifically matched to their complementary base pair. According to PBS, DNA resembles a long spiraling ladder consisting of a sugar-phosphate backbone and...
Two polynucleotide strands join together to form a double-helix. - The nucleotides join up between the phosphate group of one nucleotide and the sugar of another, creating a sugar-phospahte backbone.. - Two DNA polynucleotide starnds join together by hydrogen bonds between the bases.. - Each base can only join with one particular partner- this is called specific base pairing.. - Adenine always pairs with Thymine and Guanine always pairs with Cytosine. - The two strands wind up to form the DNA double helix.. ...
A simple physical energy function, which uses electrostatics, solvation, hydrogen bonds and atom-packing terms to model direct readout and sequence-specific DNA conformational energy to model indirect readout of DNA sequence …
1. Both have three components - sugar, phosphate and a nitrogenous base - which form nucleotide units that are connected by covalent bonds to form a linear molecule with 3 and 5 ends, with the nitrogenous bases perpendicular to the sugar-phosphate backbone ...
1JTN: Crystal Structures of a T4-lysozyme Duplication-extension Mutant Demonstrate that the Highly Conserved beta-Sheet Region has Low Intrinsic Folding Propensity
Eternabot 2.0 is a set of rules developed by the Eterna project (eternagame.org) to predict sequences for a target RNA secondary structure
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I am fascinated by a fundamental question in biology; How is regulation of gene expression as a response to external stimulus achieved? My laboratory
In this activity, students build a paper model of DNA and use their model to explore key structural features of the DNA double helix. This activity can be used to complement the short film The Double Helix.. ...
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What is the structure of DNA? Five amazing facts about the molecular structure of DNA. Find out more about the DNA molecule and the structure of DNA.
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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. ...
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
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 ...
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
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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.. ...
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
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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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. ...
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 ...
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.
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 ...
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 ...
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 ...
Get your students communicating their knowledge of DNA structure and function through their analysis of a variety of DNA models! Plan your 60 minutes lesson in Science or DNA Structure and Function with helpful tips from Maria Laws
We use "Riboswitch" as our speedy switch, which can control translation. It is divided into two parts: a sensor and an actuator. Before the discovery of RNA regulatory system , the only way to induce reaction in a cell was through inducible promoters. By turning these promoters on or off, we could control the transcription of the downstream DNA into RNA thus also controlling the translation of RNA to Protein. However, with only promoters we traditionally skip the RNA system involved in the pathway of protein synthesis. By inserting a "switch" between the DNA and RNA system we can make a thorough inspection into the individual mechanism of both systems and the cross-effect between their regulatory factors. The discovery of the riboswitch was based on data which described conserved mRNA secondary structure found on 5-untranslated regions and the creation of small-molecule binding mRNA, sensors. The function of these riboswitches is similar to the function of inducible promoters in that they both ...
In early physical studies of DNA, a variety of experiments indicated that DNA molecules occur in long helixes with each helix being formed from two or more polynucleotide chains bound side by side. Chemical analyses also demonstrated that the phosphate groups were on the outside of the helix and that the number of A and T residues in DNA were always equal, as were those of G and C. With these facts in mind, Watson and Crick in 1953 proposed that the DNA molecule actually consists of two polynucleotide chains coiled around the same axis to form a double helix (Figure 3). In this model, the hydrophilic sugar-phosphate groups follow the outer edges of the molecule where they can interact with water. The hydrophobic bases face inward toward each other in the molecules center and thus avoid contact with water. The two polynucleotide strands run in opposite directions (they are anti- parallel) and are held together primarily by hydrogen and hydrophobic bonding between the bases, where A is always ...
The effects of the lesions induced by single, site-specific 1,2-GG or 1,3-GTG intrastrand adducts of cis-diamminedichloroplatinum(II) formed in oligodeoxyribonucleotide duplexes on energetics of DNA were examined by means of differential scanning calorimetry. These effects were correlated with affinity of these duplexes for damaged-DNA binding-proteins XPA and RPA; this affinity was examined by gel electrophoresis. The results confirm that rigid DNA bending is the specific determinant responsible for high-affinity interactions of XPA with damaged DNA, but that an additional important factor, which affects affinity of XPA to damaged DNA, is a change of thermodynamic stability of DNA induced by the damage. In addition, the results also confirm that RPA preferentially binds to DNA distorted so that hydrogen bonds between complementary bases are interrupted. RPA also binds to nondenaturational distortions in double-helical DNA, but affinity of RPA to these distortions is insensitive to alterations ...
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The pairing of complementary nucleotide bases (adenine and thymine, guanine and cytosine) to each other via hydrogen bonds from opposite strands of a double stranded nucleic acid (such as DNA or RNA), thereby holding the double-stranded nucleic acid together ...
RNA secondary structure analysis often requires searching for potential helices in large sequence data. We present a utility program that efficiently locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs. It accepts a target and a query set of sequences, and determines all exact matches under RNA rules between target and query sequences that exceed a specified length.. If you need to create larger output than we permit for online use, or want to incorporate into your own pipeline, please download the program from the BiBiServ download department.. ...
RNA secondary structure analysis often requires searching for potential helices in large sequence data. We present a utility program that efficiently locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs. It accepts a target and a query set of sequences, and determines all exact matches under RNA rules between target and query sequences that exceed a specified length.. If you need to create larger output than we permit for online use, or want to incorporate into your own pipeline, please download the program from the BiBiServ download department.. ...
The last in a set of units by the same authors, this unit addresses some important remaining questions about molecular modeling of nucleic acids
Recently, nucleic acid secondary structures, G-quadruplexes in particular, have received much attention. G-quadruplexes are non-canonical nucleic acid secondary structures that are formed from G-rich sequences. These sequences consist of four stretches of G residues (each stretch with two or more G residues) interspersed by sequences of variable composition that form the loops. The formation of G-quadruplexes is induced and stabilized by monovalent cations like potassium and sodium. The presence of G-quadruplexes was first reported in telomeres and subsequently in the promoter region of several genes, 5′UTR (untranslated regions) and 3′UTRs [1-6]. G-quadruplexes function as regulatory elements and can influence key biological processes including transcription [3], translation [4] and splicing [7]. Recently, G-quadruplexes were also reported to be enriched at certain positions of eukaryotic retrotransposons, which correspond to regulatory regions of genes and viruses [8, 9]. Genome-wide ...
View Notes - Lecture8 from BIOC 100A at UCSC. 25 26 The hammerhead ribozyme (plant virus) Martick & Scott, Cell 2006 27 Group I intron ribozyme Golden et al, and cech Science (1998) 28 Acid-Base
RNALogo: a new approach to display structural RNA alignment - Regulatory RNAs play essential roles in many essential biological processes, ranging from gene regulation to protein synthesis. This work presents a web-based tool, RNALogo, to create a new graphical representation of the patterns in a multiple RNA sequence alignment with a consensus structure. The RNALogo graph can indicate significant features within an RNA sequence alignment and its consensus RNA secondary structure. RNALogo extends Sequence logos, and specifically incorporates RNA secondary structures and mutual information of base-paired regions into the graphical representation. Each RNALogo graph is composed of stacks of letters, with one stack for each position in the consensus RNA secondary structure. RNALogo provides a convenient and high configurable logo generator. An RNALogo graph is generated for each RNA family in Rfam, and these generated logos are accumulated into a gallery of RNALogo. Users can search or browse RNALogo
The 69 nucleotide left-terminal domain (T(L)) of the potato spindle tuber RNA viroid (PSTVd) constitutes one of its five structural elements. Due to a twofold complementary sequence repeat, two possible conformations are proposed for the T(L) secondary structure; an elongated-rod and a bifurcated form. In the present study, two T(L) mutants were designed that remove the symmetry of the sequence repeats and ensure that either the bifurcated or the elongated-rod conformation is thermodynamically favored. Imino 1H and 15N resonances were assigned for both mutants and the native T(L) domain based on 1H-1H NOESY and heteronuclear 1H-15N HSQC high-resolution NMR spectra. The NMR secondary structure analysis of all constructs establishes unambiguously the elongated-rod form as the secondary structure of the native T(L) domain. Temperature-gradient gel electrophoresis and UV melting experiments corroborate these results. A combined secondary structure and sequence analysis of T(L) domains of other ...
The B. subtilis trp operon is regulated by transcription attenuation in response to changes in the intracellular level of tryptophan by the mtrB gene product, TRAP. TRAP interaction with the 11 (G/U)AG repeats present within the nascenttrp leader transcript promotes formation of the intrinsic terminator by blocking formation of the overlapping antiterminator structure (Fig. 1). An essentially identical transcription attenuation mechanism was shown to regulate expression of the B. pumilus trp operon (20). In addition, the trp operon leaders of B. caldotenax and B. stearothermophilus contain multiple triplet repeats, as well as overlapping antiterminator and terminator structures. Thus, it appears that all four of these bacilli regulate trp operon expression by a conserved attenuation mechanism.. In this study, the function of an RNA secondary structure predicted to form at the 5′ end of the B. subtilis trp leader transcript was examined. The conservation of similar structures in thetrp operon ...
DExD/H-box proteins are a diverse class of proteins that are implicated in RNA and RNP remodeling. They have sequence homology to DNA helicases and share conserved ATPase domains, suggesting that they use the energy of ATP binding and hydrolysis to mediate conformational rearrangements in RNAs. In the past, the action of DExD/H-box proteins has been characterized primarily on simple model substrates such as small RNA duplexes. It is not known how DExD/H-box proteins manipulate structured RNA, what determines target specificity and what molecular events follow their action. Here, using the well-characterized Tetrahymena group I intron ribozyme, I performed kinetic and thermodynamic studies to understand the mechanism of CYT-19 and related DExD/Hbox proteins. CYT-19 has been shown previously to facilitate the folding of several group I and group II introns. I demonstrated that CYT-19 acts as a chaperone, accelerating the re-folding of a long-lived misfolded species of the Tetrahymena group I ...
Viroids are a unique class of noncoding RNAs: composed of only a circular, single-stranded molecule of 246-401 nt, they manage to replicate, move, circumvent host defenses, and frequently induce disease in higher plants. Viroids replicate through an RNA-to-RNA rolling-circle mechanism consisting of transcription of oligomeric viroid RNA intermediates, cleavage to unit-length strands, and circularization. Though the host RNA polymerase II (redirected to accept RNA templates) mediates RNA synthesis and a type-III RNase presumably cleavage of Potato spindle tuber viroid (PSTVd) and closely related members of the family Pospiviroidae, the host enzyme catalyzing the final circularization step, has remained elusive. In this study we propose that PSTVd subverts host DNA ligase 1, converting it to an RNA ligase, for the final step. To support this hypothesis, we show that the tomato (Solanum lycopersicum L.) DNA ligase 1 specifically and efficiently catalyzes circularization of the genuine PSTVd ...
"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. Methods in ... The fluorescence of a target molecule can be extrinsic or intrinsic (aromatic amino acids) and is altered in temperature ...
Nucleic Acid Res. Mol. Biol.. - 1990. - Т. Progress in Nucleic Acid Research and Molecular Biology. - С. 37-89. - ISBN 978-0-12 ... Protein structure and conformations of the pure (Na+ +K+)-ATPase (англ.) // Biochim. Biophys. Acta (англ.)русск. : journal. - ...
Wrede, Paul; Alexander Rich (1979). "Stability of the unique anticodon loop conformation of E.Col tRNAMetf". Nucleic Acids ...
Nucleic Acids Research. 39 (8): e52-e52. doi:10.1093/nar/gkr035. PMC 3082908 . PMID 21297115. deltaMasses Detection of ... 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 ...
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, ...
The nucleic acid is bound in an extended conformation across one side of the domain. The binding occurs in a cleft formed ... An evolutionarily conserved sequence of around 70 amino acids, the KH domain is present in a wide variety of nucleic acid- ... Grishin NV (February 2001). "KH domain: one motif, two folds". Nucleic Acids Res. 29 (3): 638-43. doi:10.1093/nar/29.3.638. PMC ... Valverde and colleagues note that, "Nucleic acid base-to-protein aromatic side chain stacking interactions which are prevalent ...
Nucleic Acids Research. 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, a predicted molecular weight of 40kDa, a charge of -11, and an isoelectric point of ...
satellites (nucleic acid molecules with or without a capsid that require a helper virus for infection and reproduction), and ... proteins that can exist in a pathological conformation that induces other prion molecules to assume that same conformation).[3] ... The most useful and most widely used classification system distinguishes viruses according to the type of nucleic acid they use ...
Folding, including the secondary and tertiary structure of biopolymers (nucleic acids and proteins). ... The gauche conformation on the right is a conformer, while the eclipsed conformation on the left is a transition state between ... Conformation-dependent reactions[edit]. Reaction rates are highly dependent on the conformation of the reactants. This theme is ... The staggered conformation includes the gauche (±60°) and anti (180°) conformations, depending on the spatial orientations of ...
pseudoknot Non-coding RNA Nucleic acid secondary structure Moss WN, Priore SF, Turner DH (June 2011). "Identification of ... The hairpin conformation was predicted using RNAalifold, while the pseudoknot was predicted with DotKnot. Segment 7 encodes the ... Initial models of the secondary structure were based on computational methods for Nucleic acid structure prediction. ... Nucleic Acids Res. 38 (7): e103. doi:10.1093/nar/gkq021. PMC 2853144 . PMID 20123730. Moss WN, Dela-Moss LI, Kierzek E, Kierzek ...
Nucleic Acids Research, 36 (S2): 185-. Kittichotirat W, M Guerquin, RE Bumgarner, and R Samudrala (2009) "Protinfo PPC: a web ... Esmaielbeiki, R; Nebel, J-C (2014). "Scoring docking conformations using predicted protein interfaces". BMC Bioinformatics. 15 ... Nucleic Acids Research, 37 (Web Server issue): 519-25. Shoemaker, BA; Zhang, D; Thangudu, RR; Tyagi, M; Fong, JH; Marchler- ... Nucleic Acids Res. 38: D518-24. doi:10.1093/nar/gkp842. PMC 2808861 . PMID 19843613. ...
... conformation and stability". Nucleic Acids Res. 18 (21): 6353-6359. doi:10.1093/nar/18.21.6353. PMC 332506 . PMID 2243780. ... Nucleic acids Nucleic acid analogues Peptide nucleic acid Bridged Nucleic Acids Beaucage, S. L.; Iyer, R. P. (1992). "Advances ... The DMT group is removed with a solution of an acid, such as 2% trichloroacetic acid (TCA) or 3% dichloroacetic acid (DCA), in ... Nucleic Acid Chem. 46 (16): 4.1.1-4.1.22. doi:10.1002/0471142700.nc0401s46. Pease A. C.; Solas D.; Sullivan E. J.; Cronin M. T ...
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). Proc. of 2nd ... "Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical ... Bailey TL, Williams N, Misleh C, Li WW (2006). "MEME: discovering and analyzing DNA and protein sequence motifs". Nucleic Acids ...
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 ...
Nucleic Acids Research. 34 (Web Server issue): W529-33. doi:10.1093/nar/gkl212. PMC 1538886. PMID 16845064.. ... protein complex that occupies the promoter DNA and the amino acid sequence of the cofactor determine its spatial conformation. ... "Nucleic Acids Research. 42 (Database issue): D1182-7. doi:10.1093/nar/gkt1016. PMC 3965000. PMID 24174544.. ... "Nucleic Acids Research. 34 (Database issue): D108-10. doi:10.1093/nar/gkj143. PMC 1347505. PMID 16381825.. ...
Nucleic Acids Research. 31 (18): 5449-5460. doi:10.1093/nar/gkg732. PMC 203317 . PMID 12954782. Sternberg N, Hamilton D (Aug ... "Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative ... The carboxy terminal domain of the enzyme consists of amino acids 132-341 and it harbours the active site of the enzyme. The ... Cre recombinase consists of 343 amino acids that form two distinct domains. The amino terminal domain encompasses residues 20- ...
"Sfold web server for statistical folding and rational design of nucleic acids". Nucleic Acids Res. 32 (Web Server issue): W135- ... G Rodrigo G & A Jaramillo (2014). "RiboMaker: computational design of conformation-based riboregulation". Bioinformatics. 30 ( ... software to identify motifs and short-range interactions in trajectories of nucleic acids". Nucleic Acids Research. 43 (17): ... Wilm A, Higgins DG, Notredame C (May 2008). "R-Coffee: a method for multiple alignment of non-coding RNA". Nucleic Acids Res. ...
Nucleic Acids Res. 27: 795-802. doi:10.1093/nar/27.3.795. Mathews, D.; Sabina, J.; Zuker, M.; Turner, D. (1999). "Expanded ... The upstream inhibitory -24/-15 stretch from the aforementioned inhibitory conformation is now sequestered in a hairpin P(-1) ... 2010). "A 1.9 Å Crystal Structure of the HDV Ribozyme Precleavage Suggests both Lewis Acid and General Acid Mechanisms ... Nucleic Acids Res. 39 (18): 8065-8077. doi:10.1093/nar/gkr478. PMC 3185411 . PMID 21724615. Sánchez-Luque, FJ; López MC; Macias ...
Circuit topology of Proteins and nucleic acids, Structure 22(9):1227-1237 (2014) Conformation Activity Relationships: Why Do ... proteins puzzle with amino acid chains Universal clamping protein stabilizes folded proteins: New insight into how the ...
Nucleic Acid Res. Mol. Biol. Progress in Nucleic Acid Research and Molecular Biology. 38: 37-89. doi:10.1016/S0079-6603(08) ... Protein structure and conformations of the pure (Na+ +K+)-ATPase". Biochim. Biophys. Acta. 694 (1): 27-68. doi:10.1016/0304- ...
Nucleic Acids Res. 29 (16): 3424-32. PMID 11504880. doi:10.1093/nar/29.16.3424. ... 2001). "X-ray structure of the orphan nuclear receptor RORbeta ligand-binding domain in the active conformation.". Embo J. 20 ( ... 2003). "All-trans retinoic acid is a ligand for the orphan nuclear receptor ROR beta.". Nat. Struct. Biol. 10 (10): 820-5. PMID ...
"Nucleic acid NMR" is the use of NMR spectroscopy to obtain information about the structure and dynamics of polynucleic acids, ... It is now a common tool for the determination of Conformation Activity Relationships where the structure before and after ... Nucleic acids[edit]. Main article: Nuclear magnetic resonance spectroscopy of nucleic acids ... Nucleic acid and protein NMR spectroscopy are similar but differences exist. Nucleic acids have a smaller percentage of ...
Nucleic Acids Res. 29 (16): 3424-32. doi:10.1093/nar/29.16.3424. PMC 55847 . PMID 11504880. Stehlin C, Wurtz JM, Steinmetz A, ... "X-ray structure of the orphan nuclear receptor RORbeta ligand-binding domain in the active conformation". EMBO J. 20 (21): 5822 ... "All-trans retinoic acid is a ligand for the orphan nuclear receptor ROR beta". Nat. Struct. Biol. 10 (10): 820-5. doi:10.1038/ ...
Coaxial stacking is the tendency of nucleic acid blunt ends to bind to each other, by interactions between the exposed bases. ... a perpendicular stacked conformation at moderate concentrations, and rotate into a parallel stacked conformation at low ... A Holliday junction is a branched nucleic acid structure that contains four double-stranded arms joined together. These arms ... In the 1990s, crystallography and nucleic acid NMR methods became available, as well as computational molecular modelling tools ...
In its lifetime, NCp7 facilitates the unwinding of tRNA, acts as a primer for reverse transcription, chaperones nucleic acids ... They react with the cysteine residues on the zinc finger of the NCp7 and cause a covalent conformation change which ejects the ... Nucleic Acids Research. 34 (2): 472-484. doi:10.1093/nar/gkj442. PMC 1351370 . PMID 16434700. Musah, Rabi Ann (2004). "The HIV- ... These motifs contain two peptide units of Cys-X2-Cys-X4-His-X4-Cys (CCHC), where the X represents a substituted amino acid, ...
... nucleic acids, and polysaccharides to fold into well-defined conformations, such as helices and β-sheets. The structure of a ... β-peptides are composed of amino acids containing an additional CH 2 unit between the amine and carboxylic acid. They are more ... Using a heteroligopeptide consisting of α-amino acids and cis-β-aminocyclopropanecarboxulic acids (cis-β-ACCs) they found the ... while nucleotidomimetic foldamers are based on the interactions in nucleic acids. Abiotic foldamers are stabilized by aromatic ...
... nucleic acid constituents, carbohydrates and ionophore complexes.[218]. Lithium naturally only occurs in traces in biological ... The heavier alkali metals also favour the sterically congested conformation.[142] Several crystal structures of organopotassium ... Sodium salts of fatty acids are used as soap.[197] Pure sodium metal also has many applications, including use in sodium-vapour ... Indeed, transferring of protons between chemicals is the basis of acid-base chemistry.[10]:43 Also unique is hydrogen's ability ...
... particularly protein and nucleic acids such as DNA and RNA. In fact, the double-helical structure of DNA was deduced from ... X-ray crystallography is the primary method for determining the molecular conformations of biological macromolecules, ...
... ... Here, a protein probe that could specifically bind to Z-conformation was used to map the Z-DNA distribution in the human genome ... Besides the common right-handed B- or A- structures, the alternate Z-conformation, which is left-handed, can be formed in both ... However, formation of Z-conformation in living organisms and its biological significance remains largely elusive. ...
... have been used to study the effect of different ions on the stability and conformation of PNA-DNA, PNA-PNA, and DNA-DNA ... Peptide nucleic acid (PNA) is a DNA analogue in which the negatively charged sugar phosphate backbone has been substituted by ... Ionic effects on the stability and conformation of peptide nucleic acid complexes Artikel i vetenskaplig tidskrift, 1996 ... Peptide nucleic acid (PNA) is a DNA analogue in which the negatively charged sugar phosphate backbone has been substituted by ...
HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANSPORT ATP- BINDING PROTEIN (1G6H:A) * Nucleotide Binding ... CRYSTAL STRUCTURE OF THE ADP CONFORMATION OF MJ1267, AN ATP-BINDING CASSETTE OF AN ABC TRANSPORTER. ...
... conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4 ... Nucleic Acid Database. *wwPDB Partners. *RCSB PDB. *PDBe. *PDBj. *BMRB. RCSB PDB (citation) is hosted by ... Diheteromeric NMDA receptor GluN1/GluN2A in the 1-Knuckle conformation, in complex with glycine and glutamate, in the ... we use cryoelectron microscopy to elucidate the structure of the GluN1/GluN2A NMDAR in a large ensemble of conformations under ...
ATP-PEPTIDE CONJUGATEPROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1Magnesium IonThiophosphoric Acid O-((Adenosyl-Phospho)phospho)- ... "MMDB and VAST+: tracking structural similarities between macromolecular complexes.Nucleic Acids Res. 2014 Jan; 42(Database ... 2G1T: A Src-Like Inactive Conformation In The Abl Tyrosine Kinase Domain. ...
Molecular conformation (1). * Nucleic acids (1). Date ​ Choose a date option to show results from those dates only. * Today ...
Nucleic Acids Res 34: W596-W599.. *CrossRef,. *PubMed,. *CAS,. *Web of Science® Times Cited: 58 ... Catalano FA, Meador-Parton J, Popham DL & Driks A (2001) Amino acids in the Bacillus subtilis morphogenetic protein SpoIVA with ... An autoinhibitory conformation of the Bacillus subtilis spore coat protein SpoIVA prevents its premature ATP-independent ... An autoinhibitory conformation of the Bacillus subtilis spore coat protein SpoIVA prevents its premature ATP-independent ...
Nucleic Acids Res 38:W540-544.. OpenUrlAbstract/FREE Full Text. *↵. *Schueler-Furman O, ... 4). For the split-fusion PCNA-Ub, the χ2 fit went from 23.8 to 4.35 for the best ensemble of three conformations. For the cross ... E113G and G178S, two key amino acid substitutions in PCNA that disrupt TLS, are located at the subunit-subunit interface and ... Based on the representation of each conformation in solution, we calculated the frequency in which the ubiquitin would have ...
Protein Conformation. Repetitive Sequences, Nucleic Acid*. RNA Polymerase II. Unique Identifier: 86302779. Chemical Identifiers ...
IPD-the Immuno Polymorphism Database. Nucleic Acids Res. 38: D863-D869.. OpenUrlAbstract/FREE Full Text ... 2C). The binding specificity of mAb 177407 was recently shown to be sensitive to the folding conformation of KIR3DL1 (28). ... Antigenic properties and amino acid sequences around the site of glycosylation. J. Biol. Chem. 252: 7555-7567. ... The intracellular retention of KIR3DL1*004 depends on two amino acid substitutions, Leu86 and Ser182, respectively, in the D0 ...
Thanks to this multi-layer approach, we focus on the interplay of chromatin conformation and cancer mutations in different ... Thanks to this multi-layer approach, we focus on the interplay of chromatin conformation and cancer mutations in different ... In particular, the integration of data about cancer mutations, gene functional annotations, genome conformation, epigenetic ... In particular, the integration of data about cancer mutations, gene functional annotations, genome conformation, epigenetic ...
Holm, L. & Rosenström, P. (2010). Nucleic Acids Res. 38, W545-W549. Web of Science CrossRef CAS PubMed. Hunter, R. L., Olsen, M ... Cantarel, B. L., Coutinho, P. M., Rancurel, C., Bernard, T., Lombard, V. & Henrissat, B. (2009). Nucleic Acids Res. 37, D233- ... Open and closed TS conformations. The crystal structure of MtTS showed two conformations (Roy et al., 2013. ). In one ... However, the apo D. radiodurans AS (DrAS) showed a strikingly different conformation in which the β2-α2 loop is disordered and ...
Morikawa, N. (2006). Nucleic Acids Res. 34, W239-W242. Web of Science PubMed. Mosca, R., Brannetti, B. & Schneider, T. R. (2008 ... Structural comparison of nucleic acids. Local comparative analysis of the P-site and E-site fMet-tRNA models from a 70S ... ProSMART structural comparison of a sialic acid-binding protein (PDB entry 2cex chain A) and a sodium α-keto acid-binding ... such as nucleic acids (Fig. 6. ). Such analyses may be performed using models derived using various techniques (e.g. MX or EM; ...
Nucleic acids.- Proteins.- Acidic proteins.- Histones.- 4.2 Physico-Chemical Properties of Nucleohistones.- 4.2.1 Solubility.- ... 3.2.2 Analysis of the primary structure of histones for possible conformations.- 3.2.3 Physical studies of the conformations of ... Conformation of nucleohistones.- Anisotropy and orientation of chromophores.- Conformation of nucleoprotamines.- Ultraviolet ... 3.3 The Conformation of Nucleohistone.- 3.3.1 X-Ray diffraction studies of nucleohistones.- 3.3.2 Evidence for the "supercoiled ...
c) Each nucleic acid does exist as a single strand, however, DNA in its native state is found in. a double helix conformation. ... Amino acids are synthesized from other free amino acids and also from -keto acids by . ... a) Every amino acid residue has its own tRNA.. b) In a codon, the first two base pairs remain constant for a given amino acid ... d) Both nucleic acids are involved directly in the transcription process of protein synthesis. ...
... detecting DNA mismatches between heteroduplex strands produced between wildtype and mutation containing nucleic acid species. ... Nucleic Acids Res. 19: 879-895); single-strand conformation polymorphism (Orita et al., 1989, Proc. Natl. Acad. Sci. USA 86: ... for detecting genetic mutations and mismatches between nucleic acid heteroduplex strands in nucleic acids of all nucleic acid- ... Ganguly et al., Nucleic Acids Research 18 (13) : 3933-3939 (1990).. 15. *. Hongyo et al., 1993, Nucleic Acids Res. 21:3637 3642 ...
Purchase Advances in Nanomedicine for the Delivery of Therapeutic Nucleic Acids - 1st Edition. Print Book & E-Book. ISBN ... Locked nucleic acids: structure. *6.3. Locked nucleic acids: hybridization and conformation properties ... Therapeutic applications of locked nucleic acids. *6.7. Nanoparticle-mediated delivery of locked nucleic acid and locked ... for the Delivery of Therapeutic Nucleic Acids addresses several issues related to safe and effective delivery of nucleic acids ...
Nucleic Acid Res. Mol. Biol. 65:197-259. doi:10.1016/S0079-6603(00)65006-7. ... Systematic characterization of the conformation and dynamics of budding yeast chromosome XII. J. Cell Biol. 202:201-210. doi: ... Global reorganization of budding yeast chromosome conformation in different physiological conditions. Elisa Dultz, Harianto ... A single tether has local effects only. (A) Computational model of chr II conformation. Fraction of loci localized in ...
... allows characterising ground state conformations of flexible nucleobase aggregates that play a crucial role in nucleic acid ... From the themed collection: Photoinduced Processes in Nucleic Acids and Proteins The article was first published on 22 Mar 2018 ... From the themed collection: Photoinduced Processes in Nucleic Acids and Proteins The article was first published on 12 Mar 2018 ... From the themed collection: Photoinduced Processes in Nucleic Acids and Proteins The article was first published on 23 Jan 2018 ...
Once the nucleic acid is immobilized, the detectable non-nucleotide probe/target sequence complex, formed before or after the ... identification and/or quantitation of nucleic acids which are electrostatically immobilized to matrices using non-nucleotide ... either before or after the nucleic acid is bound to the matrix, in order to ... immobilization of the nucleic acid, can be detected, identified or quantitated under a wide range of assay conditions as a ...
Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature, 171(4356), 737-8. ... conformation and dynamics. Proceedings of the National Academy of Sciences, 78 (4), 2179-2183 DOI: 10.1073/pnas.78.4.2179 ... Its time for the annual blog about the annual Nucleic Acids Research (NAR) database issue. This is the 24th database issue for ... However, unlike last year, where the number of databases tracked by Nucleic Acids Research (NAR) dropped by… ...
Nucleic Acid Conformation. Restriction Mapping. Substrate Specificity. T-Phages / enzymology*, genetics. Chemical. ...
Nucleic Acid Conformation. RNA / chemistry*. Sequence Alignment / economics, methods*. Chemical. Reg. No./Substance: 63231-63-0 ...
Nucleic Acid Conformation * RNA, Bacterial / drug effects * RNA, Bacterial / genetics * RNA, Bacterial / metabolism* ...
Nucleic Acid Conformation * Nucleosomes / genetics * Nucleosomes / metabolism * Nucleotides / chemistry * Nucleotides / ... In one conformation the HSS binds flanking DNA, and in another conformation the HSS engages the nucleosome core. Based on these ...
  • 4. Mutein of any of claims 1 to 3, wherein at least one of the amino acid residues at sequence positions 70 to 74 of the natural amino acid sequence is mutated and/or wherein at least one of the amino acid residues at said sequence positions 70 to 74 is deleted. (freepatentsonline.com)
  • After a protease cleaves the RCL at the scissile bond between amino acid residues designated P1 and P1′, the serpin undergoes a large conformational change, and the protease is trapped with its active site distorted, resulting in its inactivation ( Gettins, 2007 ). (pubmedcentralcanada.ca)
  • A mutein of the invention is a C5a receptor antagonist wherein the amino acid residue naturally occurring at sequence position 69 is mutated. (freepatentsonline.com)
  • 2. Mutein of claim 1, wherein the amino acid residue at sequence position 69 is replaced by leucine or a positively charged amino acid residue. (freepatentsonline.com)
  • 3. Mutein of claim 1 or 2, wherein the amino acid residue naturally occurring at sequence position 67 is mutated. (freepatentsonline.com)
  • 5. Mutein of any of claims 1 to 4, wherein the positively charged amino acid residue at sequence position 69 is Arg or Lys. (freepatentsonline.com)
  • 6. Mutein of any of claim 1 to 5 which comprises at sequence position 67 an aromatic amino acid selected from the group consisting of Phe, Trp and Tyr. (freepatentsonline.com)
  • 7. Mutein of any of claims 1 to 6 which comprises a hydrophobic amino acid residue at sequence position 70. (freepatentsonline.com)
  • By labeling such complementary probe nucleic acids with some readily detectable chemical group, it was then made possible to detect the presence of any polynucleotide sequence of interest in a test medium containing sample nucleic acids in single stranded form. (google.ca)
  • We also demonstrated that locked nucleic acid (LNA) probes improved sensitivity approximately 4-fold compared to DNA probes of the same sequence. (nih.gov)
  • Nuclear magnetic resonance studies of an N2-guanine adduct derived from the tumorigen dibenzo[a,l]pyrene in DNA: impact of adduct stereochemistry, size, and local DNA sequence on solution conformations. (nyu.edu)
  • For proteins, a sequence motif is distinguished from a structural motif, a motif formed by the three-dimensional arrangement of amino acids which may not be adjacent. (wikipedia.org)
  • The fundamental idea behind all these notations is the matching principle, which assigns a meaning to a sequence of elements of the pattern notation: a sequence of elements of the pattern notation matches a sequence of amino acids if and only if the latter sequence can be partitioned into subsequences in such a way that each pattern element matches the corresponding subsequence in turn. (wikipedia.org)
  • Many chemical mutagens, such as chlorinated hydrocarbons and nitrites, owe their toxicity to the production of halides and nitrous acid during their metabolism in the body. (britannica.com)
  • Probes for specific nucleic acid sequences can be immobilized as arrays on solid phase surfaces for detection of multiple nucleic acid sequences simultaneously from electrophoresis gels and from aqueous solutions. (google.es)
  • These probes and methods for their use can be combined with known solid phases, particularly those used for plasmon surface detection and electron transfer detection of nucleic acid. (google.es)
  • Several binding sites were conserved between E. coli and human ribosomes, revealing that formation of Z-like RNA conformations might be a conserved property of the dynamic ribosome structure during translation. (ntu.edu.sg)
  • Here, we use cryoelectron microscopy to elucidate the structure of the GluN1/GluN2A NMDAR in a large ensemble of conformations under a range of physiologically relevant zinc and proton concentrations. (rcsb.org)
  • a structure for deoxyribose nucleic acid. (scienceblogs.com)
  • Structure of a B-DNA dodecamer: conformation and dynamics. (scienceblogs.com)
  • Chromatin structure-dependent conformations of the H1 CTD. (rochester.edu)
  • We start with an extensive article by T. P. Karpetsky, M. S. Boguski and C. C. Levy on the structure, properties and possible functions of polyadenylic acid. (google.com)
  • For the determinants of nucleic acid structure, we do not see the importance of a buried hydrophobic core. (bioinformatics.org)
  • Relative to deoxyribonucleic acids ( DNA 's), ribonucleic acids ( RNA 's) are short, and the single strand can fold back upon itself, forming the characteristic stem-loop secondary structure (e.g., loops, bulges and junctions). (bioinformatics.org)
  • Again, an RNA will take the conformation where the total energy of the final structure is minimized. (bioinformatics.org)
  • In particular, the 10 mer proved to have an unique structure as evidenced by NMR.At the present time, we are studying the binding ability of these new nucleic acid derivatives for target DNA or RNA fragmets. (nii.ac.jp)
  • Whilst there are many alignment tools that optimize a global superposition, there is a need for the development of methods that align macromolecular structures in a way that is independent of the global conformations of the compared chains. (iucr.org)
  • We present high-resolution structures of Deinococcus radiodurans (Dra)Nramp in multiple conformations to provide a thorough description of the Nramp transport cycle by identifying the key intramolecular rearrangements and changes to the metal coordination sphere. (elifesciences.org)
  • To define the conformation of the TPE:estrogen receptor (ER) complex, we employed a previously validated assay using the induction of transforming growth factor α (TGF α ) mRNA in situ in MDA-MB 231 cells stably transfected with wild-type ER (MC2) or D351G ER mutant (JM6). (aspetjournals.org)
  • wherein said matrix comprises charged functional groups that are suitable for binding nucleic acid under electrostatic binding conditions. (google.com)
  • 8. A method according to claim 6 , wherein said solid phase further comprises a nucleic acid comprising a quenching moiety. (google.es)
  • 11. A method according to claim 8 , wherein said solid phase comprises an array of discrete regions wherein each region contains a nucleic acid comprising a quenching moiety. (google.es)
  • 12. A method according to claim 11 , wherein said array comprises a plurality of different nucleic acids. (google.es)
  • 3. A zinc finger polypeptide according to claim 1 wherein said nucleic acid comprises single-stranded DNA. (patentgenius.com)
  • 6. A zinc finger polypeptide according to claim 1 wherein said nucleic acid comprises Hoogsteen base pairing. (patentgenius.com)
  • Orita M, Iwahana H, Kanazana H, Hayashi K and Sekiya T (1989) Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. (springer.com)
  • To make such analyses more accessible, the Procrustes Structural Matching Alignment and Restraints Tool ( ProSMART ) has been developed, which achieves a conformation-independent structural alignment, as well as providing such additional functionalities as the generation of restraints for use in the refinement of macromolecular models. (iucr.org)
  • The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. (osti.gov)
  • To prevent degradation by chemical and enzymatic processes, DNA is often stored as a precipitate in ethanol, at -80 °C. This increases nucleic acids stability, but means that the ethanol must be removed prior to use. (news-medical.net)
  • The A-to-B transition in DNA has also served as a prototype case for testing out and validating empirical energy functions and force fields used in molecular dynamics simulations on nucleic acids (2-4). (redorbit.com)
  • Nucleosome Histone Tail Conformation and Dynamics: Impacts of Lysine Acetylation and a Nearby Minor Groove Benzo[a]pyrene-Derived Lesion. (nyu.edu)
  • Structural modeling and in vitro experiments with recombinant human SIRT2 determined that propofol and [ 3 H]AziP m only bind specifically and competitively to the enzyme when co-equilibrated with other substrates, which suggests that the anesthetic site is either created or stabilized in enzymatic conformations that are induced by substrate binding. (pubmedcentralcanada.ca)
  • They were found to be resistant to acid and alkaline conditions as well as enzymatic digestion with spleen phosphodiesterase. (nii.ac.jp)
  • Further studies revealed that ZαADAR1 could bind to ribosomes and inhibit translation in both E. coli and mammalian systems in a Z-conformation dependent manner. (ntu.edu.sg)
  • This finding implied a degree of flexibility inherent in the Ub-PCNA complex that would allow it to transition into a conformation competent to bind the TLS polymerase. (pnas.org)
  • Ishibashi N, Tatematsu T, Shimamura S, Tomita M, Okonogi S. Effect of water activity on the viability of freeze-dried bifidobacteria and lactic acid bacteria. (springer.com)
  • Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow. (embl.de)
  • However, formation of Z-conformation in living organisms and its biological significance remains largely elusive. (ntu.edu.sg)
  • Light induced charge and energy transport in nucleic acids and proteins is the basis of fundamental biological processes such as photosynthesis, vision, DNA-photostability, DNA-photodamage and photosensing. (rsc.org)
  • We will explore how bonding plays a central role in assembling simple biological building blocks such as sugars, amino acids, and fatty acids to form complex carbohydrates, proteins, and membranes. (amherst.edu)
  • After two German chemists, Emil Fischer and Franz Hofmeister, independently stated in 1902 that proteins are essentially polypeptides consisting of many amino acids , an attempt was made to classify proteins according to their chemical and physical properties, because the biological function of proteins had not yet been established. (britannica.com)
  • Apart from revealing a general lack of appreciation of many important aspects of the chemical properties of poly adenylic acid, the literature also shows that there is a great gulf between those who study the biological role of polyadenylic acid. (google.com)