Nucleic acid conformation. Medical search

The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.

The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).

DNA analogs containing neutral amide backbone linkages composed of aminoethyl glycine units instead of the usual phosphodiester linkage of deoxyribose groups. Peptide nucleic acids have high biological stability and higher affinity for complementary DNA or RNA sequences than analogous DNA oligomers.

The characteristic three-dimensional shape of a molecule.

Nucleic acid which complements a specific mRNA or DNA molecule, or fragment thereof; used for hybridization studies in order to identify microorganisms and for genetic studies.

A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).

Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.

Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.

Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.

The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.

Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)

The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)

The parts of a macromolecule that directly participate in its specific combination with another molecule.

A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.

The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.

Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).

A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)

The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.

The rate dynamics in chemical or physical systems.

A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.

Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)

The homogeneous mixtures formed by the mixing of a solid, liquid, or gaseous substance (solute) with a liquid (the solvent), from which the dissolved substances can be recovered by physical processes. (From Grant & Hackh's Chemical Dictionary, 5th ed)

The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.

Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.

NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.

A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.

Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.

The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.

The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.

Measurement of the intensity and quality of fluorescence.

Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.

The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.

A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)

Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.

In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.

A computer simulation developed to study the motion of molecules over a period of time.

Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.

A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.

Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.

Ribonucleic acid that makes up the genetic material of viruses.

The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)

Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.

Determination of the spectra of ultraviolet absorption by specific molecules in gases or liquids, for example Cl2, SO2, NO2, CS2, ozone, mercury vapor, and various unsaturated compounds. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

An isothermal in-vitro nucleotide amplification process. The process involves the concomitant action of a RNA-DIRECTED DNA POLYMERASE, a ribonuclease (RIBONUCLEASES), and DNA-DIRECTED RNA POLYMERASES to synthesize large quantities of sequence-specific RNA and DNA molecules.

A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.

A group of 13 or more deoxyribonucleotides in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.

The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).

Computer-based representation of physical systems and phenomena such as chemical processes.

The scattering of x-rays by matter, especially crystals, with accompanying variation in intensity due to interference effects. Analysis of the crystal structure of materials is performed by passing x-rays through them and registering the diffraction image of the rays (CRYSTALLOGRAPHY, X-RAY). (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

Deoxyribonucleic acid that makes up the genetic material of viruses.

The process by which two molecules of the same chemical composition form a condensation product or polymer.

The characteristic 3-dimensional shape of a carbohydrate.

Proteins prepared by recombinant DNA technology.

The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)

Disruption of the non-covalent bonds and/or disulfide bonds responsible for maintaining the three-dimensional shape and activity of the native protein.

The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.

Double-stranded nucleic acid molecules (DNA-DNA or DNA-RNA) which contain regions of nucleotide mismatches (non-complementary). In vivo, these heteroduplexes can result from mutation or genetic recombination; in vitro, they are formed by nucleic acid hybridization. Electron microscopic analysis of the resulting heteroduplexes facilitates the mapping of regions of base sequence homology of nucleic acids.

Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.

The accumulation of an electric charge on a object

Nucleotide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.

Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.

Agents that emit light after excitation by light. The wave length of the emitted light is usually longer than that of the incident light. Fluorochromes are substances that cause fluorescence in other substances, i.e., dyes used to mark or label other compounds with fluorescent tags.

The branch of science that deals with the geometric description of crystals and their internal arrangement. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.

Higher-order DNA and RNA structures formed from guanine-rich sequences. They are formed around a core of at least 2 stacked tetrads of hydrogen-bonded GUANINE bases. They can be formed from one two or four separate strands of DNA (or RNA) and can display a wide variety of topologies, which are a consequence of various combinations of strand direction, length, and sequence. (From Nucleic Acids Res. 2006;34(19):5402-15)

Proteins found in any species of bacterium.

A clear, odorless, tasteless liquid that is essential for most animal and plant life and is an excellent solvent for many substances. The chemical formula is hydrogen oxide (H2O). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)

Deoxyribonucleic acid that makes up the genetic material of bacteria.

Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.

Established cell cultures that have the potential to propagate indefinitely.

The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.

The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.

Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.

The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.

The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.

Analysis of the intensity of Raman scattering of monochromatic light as a function of frequency of the scattered light.

Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.

Liquids that dissolve other substances (solutes), generally solids, without any change in chemical composition, as, water containing sugar. (Grant & Hackh's Chemical Dictionary, 5th ed)

Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.

The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.

The process of cleaving a chemical compound by the addition of a molecule of water.

A type of FLUORESCENCE SPECTROSCOPY using two FLUORESCENT DYES with overlapping emission and absorption spectra, which is used to indicate proximity of labeled molecules. This technique is useful for studying interactions of molecules and PROTEIN FOLDING.

Purine or pyrimidine bases attached to a ribose or deoxyribose. (From King & Stansfield, A Dictionary of Genetics, 4th ed)

The most common form of DNA found in nature. It is a right-handed helix with 10 base pairs per turn, a pitch of 0.338 nm per base pair and a helical diameter of 1.9 nm.

Agents that are capable of inserting themselves between the successive bases in DNA, thus kinking, uncoiling or otherwise deforming it and therefore preventing its proper functioning. They are used in the study of DNA.

A metallic element that has the atomic symbol Mg, atomic number 12, and atomic weight 24.31. It is important for the activity of many enzymes, especially those involved in OXIDATIVE PHOSPHORYLATION.

The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals.

A basic science concerned with the composition, structure, and properties of matter; and the reactions that occur between substances and the associated energy exchange.

An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter.

Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.

Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.

The phenomenon whereby compounds whose molecules have the same number and kind of atoms and the same atomic arrangement, but differ in their spatial relationships. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 5th ed)

Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.

The thermodynamic interaction between a substance and WATER.

A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.

The composition, conformation, and properties of atoms and molecules, and their reaction and interaction processes.

A group of atoms or molecules attached to other molecules or cellular structures and used in studying the properties of these molecules and structures. Radioactive DNA or RNA sequences are used in MOLECULAR GENETICS to detect the presence of a complementary sequence by NUCLEIC ACID HYBRIDIZATION.

A group of 13 or more ribonucleotides in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.

Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.

Sequential operating programs and data which instruct the functioning of a digital computer.

Scattering of a beam of electromagnetic or acoustic RADIATION, or particles, at small angles by particles or cavities whose dimensions are many times as large as the wavelength of the radiation or the de Broglie wavelength of the scattered particles. Also know as low angle scattering. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Small angle scattering (SAS) techniques, small angle neutron (SANS), X-ray (SAXS), and light (SALS, or just LS) scattering, are used to characterize objects on a nanoscale.

A spectroscopic technique in which a range of wavelengths is presented simultaneously with an interferometer and the spectrum is mathematically derived from the pattern thus obtained.

Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.

Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.

The modification of the reactivity of ENZYMES by the binding of effectors to sites (ALLOSTERIC SITES) on the enzymes other than the substrate BINDING SITES.

The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.

Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.

Proteins obtained from ESCHERICHIA COLI.

A representation, generally small in scale, to show the structure, construction, or appearance of something. (From Random House Unabridged Dictionary, 2d ed)

A purine base and a fundamental unit of ADENINE NUCLEOTIDES.

Molecules of DNA that possess enzymatic activity.

A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.

Chemical groups containing the covalent disulfide bonds -S-S-. The sulfur atoms can be bound to inorganic or organic moieties.

The study of CHEMICAL PHENOMENA and processes in terms of the underlying PHYSICAL PHENOMENA and processes.

Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.

Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells.

Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.

Presence of warmth or heat or a temperature notably higher than an accustomed norm.

The physical phenomena describing the structure and properties of atoms and molecules, and their reaction and interaction processes.

Short fragments of DNA or RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.

A series of heterocyclic compounds that are variously substituted in nature and are known also as purine bases. They include ADENINE and GUANINE, constituents of nucleic acids, as well as many alkaloids such as CAFFEINE and THEOPHYLLINE. Uric acid is the metabolic end product of purine metabolism.

Proteins found in any species of virus.

A purine nucleoside that has guanine linked by its N9 nitrogen to the C1 carbon of ribose. It is a component of ribonucleic acid and its nucleotides play important roles in metabolism. (From Dorland, 28th ed)

Stable elementary particles having the smallest known positive charge, found in the nuclei of all elements. The proton mass is less than that of a neutron. A proton is the nucleus of the light hydrogen atom, i.e., the hydrogen ion.

The study of PHYSICAL PHENOMENA and PHYSICAL PROCESSES as applied to living things.

Reagents with two reactive groups, usually at opposite ends of the molecule, that are capable of reacting with and thereby forming bridges between side chains of amino acids in proteins; the locations of naturally reactive areas within proteins can thereby be identified; may also be used for other macromolecules, like glycoproteins, nucleic acids, or other.

The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.

Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.

A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.

A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.

An isoform of DNA that occurs in an environment rich in SODIUM and POTASSIUM ions. It is a right-handed helix with 11 base pairs per turn, a pitch of 0.256 nm per base pair and a helical diameter of 2.3 nm.

A pyrimidine base that is a fundamental unit of nucleic acids.

The measurement of the quantity of heat involved in various processes, such as chemical reactions, changes of state, and formations of solutions, or in the determination of the heat capacities of substances. The fundamental unit of measurement is the joule or the calorie (4.184 joules). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

A pentose active in biological systems usually in its D-form.

The property of emitting radiation while being irradiated. The radiation emitted is usually of longer wavelength than that incident or absorbed, e.g., a substance can be irradiated with invisible radiation and emit visible light. X-ray fluorescence is used in diagnosis.

Microscopy using an electron beam, instead of light, to visualize the sample, thereby allowing much greater magnification. The interactions of ELECTRONS with specimens are used to provide information about the fine structure of that specimen. In TRANSMISSION ELECTRON MICROSCOPY the reactions of the electrons that are transmitted through the specimen are imaged. In SCANNING ELECTRON MICROSCOPY an electron beam falls at a non-normal angle on the specimen and the image is derived from the reactions occurring above the plane of the specimen.

The use of devices which use detector molecules to detect, investigate, or analyze other molecules, macromolecules, molecular aggregates, or organisms.

The reformation of all, or part of, the native conformation of a nucleic acid molecule after the molecule has undergone denaturation.

The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.

A family of cellular proteins that mediate the correct assembly or disassembly of polypeptides and their associated ligands. Although they take part in the assembly process, molecular chaperones are not components of the final structures.

MOLECULAR BIOLOGY techniques used in the diagnosis of disease.

The ability of a protein to retain its structural conformation or its activity when subjected to physical or chemical manipulations.

A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.

Compounds formed by the joining of smaller, usually repeating, units linked by covalent bonds. These compounds often form large macromolecules (e.g., BIOPOLYMERS; PLASTICS).

The sum of the weight of all the atoms in a molecule.

RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.

The physical characteristics and processes of biological systems.

The molecular designing of drugs for specific purposes (such as DNA-binding, enzyme inhibition, anti-cancer efficacy, etc.) based on knowledge of molecular properties such as activity of functional groups, molecular geometry, and electronic structure, and also on information cataloged on analogous molecules. Drug design is generally computer-assisted molecular modeling and does not include pharmacokinetics, dosage analysis, or drug administration analysis.

A non-aqueous co-solvent that serves as tool to study protein folding. It is also used in various pharmaceutical, chemical and engineering applications.

Spectrophotometry in the infrared region, usually for the purpose of chemical analysis through measurement of absorption spectra associated with rotational and vibrational energy levels of molecules. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

Substances produced from the reaction between acids and bases; compounds consisting of a metal (positive) and nonmetal (negative) radical. (Grant & Hackh's Chemical Dictionary, 5th ed)

The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.

The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.

DNA or RNA bound to a substrate thereby having fixed positions.

Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.

The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.

Polydeoxyribonucleotides made up of deoxyadenine nucleotides and thymine nucleotides. Present in DNA preparations isolated from crab species. Synthetic preparations have been used extensively in the study of DNA.

Elements of limited time intervals, contributing to particular results or situations.

Topical antiseptic used mainly in wound dressings.

Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.

RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.

Measurement of the polarization of fluorescent light from solutions or microscopic specimens. It is used to provide information concerning molecular size, shape, and conformation, molecular anisotropy, electronic energy transfer, molecular interaction, including dye and coenzyme binding, and the antigen-antibody reaction.

Stable carbon atoms that have the same atomic number as the element carbon, but differ in atomic weight. C-13 is a stable carbon isotope.

A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.

Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.

Positively charged atoms, radicals or groups of atoms which travel to the cathode or negative pole during electrolysis.

A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.

The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.

Proteins produced from GENES that have acquired MUTATIONS.

Peptides composed of between two and twelve amino acids.

A serine endopeptidase that is formed from TRYPSINOGEN in the pancreas. It is converted into its active form by ENTEROPEPTIDASE in the small intestine. It catalyzes hydrolysis of the carboxyl group of either arginine or lysine. EC 3.4.21.4.

Small proteinaceous infectious particles which resist inactivation by procedures that modify NUCLEIC ACIDS and contain an abnormal isoform of a cellular protein which is a major and necessary component. The abnormal (scrapie) isoform is PrPSc (PRPSC PROTEINS) and the cellular isoform PrPC (PRPC PROTEINS). The primary amino acid sequence of the two isoforms is identical. Human diseases caused by prions include CREUTZFELDT-JAKOB SYNDROME; GERSTMANN-STRAUSSLER SYNDROME; and INSOMNIA, FATAL FAMILIAL.

The measurement of the amplitude of the components of a complex waveform throughout the frequency range of the waveform. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)

A method of generating a large library of randomized nucleotides and selecting NUCLEOTIDE APTAMERS by iterative rounds of in vitro selection. A modified procedure substitutes AMINO ACIDS in place of NUCLEOTIDES to make PEPTIDE APTAMERS.

A site on an enzyme which upon binding of a modulator, causes the enzyme to undergo a conformational change that may alter its catalytic or binding properties.

Layers of lipid molecules which are two molecules thick. Bilayer systems are frequently studied as models of biological membranes.

Characteristics or attributes of the outer boundaries of objects, including molecules.

The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.

The art or process of comparing photometrically the relative intensities of the light in different parts of the spectrum.

Substances used for the detection, identification, analysis, etc. of chemical, biological, or pathologic processes or conditions. Indicators are substances that change in physical appearance, e.g., color, at or approaching the endpoint of a chemical titration, e.g., on the passage between acidity and alkalinity. Reagents are substances used for the detection or determination of another substance by chemical or microscopical means, especially analysis. Types of reagents are precipitants, solvents, oxidizers, reducers, fluxes, and colorimetric reagents. (From Grant & Hackh's Chemical Dictionary, 5th ed, p301, p499)

Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.

A biosensing technique in which biomolecules capable of binding to specific analytes or ligands are first immobilized on one side of a metallic film. Light is then focused on the opposite side of the film to excite the surface plasmons, that is, the oscillations of free electrons propagating along the film's surface. The refractive index of light reflecting off this surface is measured. When the immobilized biomolecules are bound by their ligands, an alteration in surface plasmons on the opposite side of the film is created which is directly proportional to the change in bound, or adsorbed, mass. Binding is measured by changes in the refractive index. The technique is used to study biomolecular interactions, such as antigen-antibody binding.

A non-essential amino acid that is synthesized from GLUTAMIC ACID. It is an essential component of COLLAGEN and is important for proper functioning of joints and tendons.

The phenomenon whereby certain chemical compounds have structures that are different although the compounds possess the same elemental composition. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 5th ed)

The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.

A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).

The deductive study of shape, quantity, and dependence. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)

The study of the structure, growth, function, genetics, and reproduction of viruses, and VIRUS DISEASES.

RNA, usually prepared by transcription from cloned DNA, which complements a specific mRNA or DNA and is generally used for studies of virus genes, distribution of specific RNA in tissues and cells, integration of viral DNA into genomes, transcription, etc. Whereas DNA PROBES are preferred for use at a more macroscopic level for detection of the presence of DNA/RNA from specific species or subspecies, RNA probes are preferred for genetic studies. Conventional labels for the RNA probe include radioisotope labels 32P and 125I and the chemical label biotin. RNA probes may be further divided by category into plus-sense RNA probes, minus-sense RNA probes, and antisense RNA probes.

Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.

A group of guanine ribonucleotides in which the phosphate residues of each guanine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.

The chemical and physical integrity of a pharmaceutical product.

An atom or group of atoms that have a positive or negative electric charge due to a gain (negative charge) or loss (positive charge) of one or more electrons. Atoms with a positive charge are known as CATIONS; those with a negative charge are ANIONS.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

5.6.2 designates the enzyme further as being capable of altering nucleic acid, or DNA, conformations. Lastly, the full ... "EC 5.6.2 Enzymes altering nucleic acid conformation". IUBMB Enzyme Nomenclature. International Union of Biochemistry and ... However, when present, both ions are found near the binding site for nucleic acids. It is thought that these zinc fingers play ... The structure of the enzyme includes both a helicase domain, which is responsible for separating nucleic acids, and a ...

https://en.wikipedia.org/wiki/Reverse_gyrase

Evaluation of periodicity using endogenous and exogenous nucleases". Biochimica et Biophysica Acta (BBA) - Nucleic Acids and ... Wingert L, Von Hippel PH (March 1968). "The conformation dependent hydrolysis of DNA by micrococcal nuclease". Biochimica et ... Nucleic Acids and Protein Synthesis. 157 (1): 114-26. doi:10.1016/0005-2787(68)90270-0. PMID 4296058. Hiwasa T, Segawa M, ...

https://en.wikipedia.org/wiki/MNase-seq

Wrede P, Rich A (November 1979). "Stability of the unique anticodon loop conformation of E.coli tRNAfMet". Nucleic Acids ... contains three glycans bound to the amino acid asparagine via N-glycosylation two Disulphide bridges between cysteine residues ...

https://en.wikipedia.org/wiki/Nuclease_S1

"Impact of modified ribose sugars on nucleic acid conformation and function". Heterocyclic Communications. 23 (3): 155-165. doi: ... "Nucleic acid architecture". fbio.uh.cu. Retrieved 8 October 2019. Neidle, Stephen (2008). "The Building-Blocks of DNA and RNA ... The secondary structure of a nucleic acid is determined by the rotation of its 7 torsion angles. Having a large amount of ... Levene, P. A.; Jacobs, W. A. (1909). "Über die Pentose in den Nucleinsäuren" [About the pentose in the nucleic acids]. Berichte ...

https://en.wikipedia.org/wiki/Ribose

Nucleic Acids Research. 39 (8): e52. doi:10.1093/nar/gkr035. PMC 3082908. PMID 21297115. Wikimedia Commons has media related to ... Wienken CJ, Baaske P, Duhr S, Braun D (2011). "Thermophoretic melting curves quantify the conformation and stability of RNA and ... a general method for the synthesis of pure 2-arylpropionic acids. 2-Phenylpropionic acid". Organic Syntheses. 76: 169. doi: ... Protein methylation typically takes place on arginine or lysine amino acid residues in the protein sequence. Arginine can be ...

https://en.wikipedia.org/wiki/Methylation

"Thermophoretic melting curves quantify the conformation and stability of RNA and DNA". Nucleic Acids Res. 39 (8): e52. doi: ... A Rapid and Precise Method to Quantify Protein-Nucleic Acid Interactions in Solution. Methods in Molecular Biology. Vol. 1654. ... A Rapid and Precise Method to Quantify Protein-Nucleic Acid Interactions in Solution". MicroScale Thermophoresis: ... The fluorescence of a target molecule can be extrinsic or intrinsic (aromatic amino acids) and is altered in temperature ...

https://en.wikipedia.org/wiki/Microscale_thermophoresis

Alternative stable conformation capable of protein misinteraction links tRNA synthetase to peripheral neuropathy. Nucleic Acids ... Nucleic Acids Research. 45 (13): 8091-8104. doi:10.1093/nar/gkx455. ISSN 0305-1048. PMC 5737801. PMID 28531329. Mo, Zhongying; ... Two conformations of a crystalline human tRNA synthetase-tRNA complex: implications for protein synthesis. EMBO J. 2006;25(12): ... CMT disease severity correlates with mutation-induced open conformation of histidyl-tRNA synthetase, not aminoacylation loss, ...

https://en.wikipedia.org/wiki/Xiang-Lei_Yang

"Mitochondrial DNA deletions are associated with non-B DNA conformations". Nucleic Acids Research. 40 (16): 7606-21. doi:10.1093 ... Damas J, Carneiro J, Amorim A, Pereira F (January 2014). "MitoBreak: the mitochondrial DNA breakpoints database". Nucleic Acids ... Nucleic Acids Research. 47 (D1): D29-D32. doi:10.1093/nar/gky843. PMC 6324066. PMID 30247677. Gu Z, Li J, Gao S, Gong M, Wang J ... Nucleic Acids Research. 44 (D1): D1262-5. doi:10.1093/nar/gkv1187. PMC 4702847. PMID 26590258. Damas J, Carneiro J, Gonçalves J ...

https://en.wikipedia.org/wiki/Mitochondrial_DNA

Two typical alternative conformations for nucleic acids" (PDF). Curr. Sci. 45: 779-783. Sasisekharan, V.; Pattabiraman, N. ( ... two typical alternative conformations for nucleic acids". Current Science. 45: 779-783. Sasisekharan, V.; Pattabiraman, N.; ... Protein-nucleic acid interactions • Catalysis and regulation. 47: 1-8. doi:10.1016/j.sbi.2017.03.006. ISSN 0959-440X. PMID ... The discovery of topoisomerases and gyrases, enzymes that can change the linking number of circular nucleic acids and thus " ...

https://en.wikipedia.org/wiki/Obsolete_models_of_DNA_structure

The crRNA-foreign nucleic acid complex is then cleaved, however if there are mismatches between the spacer and the target DNA, ... One representing a conformation of Cas9 in the apo state, and two representing Cas9 in the DNA bound state. In sgRNA-Cas9 ... Free energy changes of nucleic acids are also highly relevant in defining cleavage activity. Guide RNAs that bind to the DNA ... Alkan F, Wenzel A, Anthon C, Havgaard JH, Gorodkin J (October 2018). "CRISPR-Cas9 off-targeting assessment with nucleic acid ...

https://en.wikipedia.org/wiki/Cas9

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, ...

https://en.wikipedia.org/wiki/George_B._Johnson

Nucleic Acids Research. 44 (W1): W410-W415. doi:10.1093/nar/gkw348. ISSN 0305-1048. PMC 4987908. PMID 27131380. Chou, Peter Y ... Fasman, Gerald D. (1974-01-15). "Prediction of protein conformation". Biochemistry. 13 (2): 222-245. doi:10.1021/bi00699a002. ... The first isoform has a non-repeating proline-rich region from amino acids 12 to 80. The function of the region is not well ... The unmodified protein has 358 amino acids, predicted molecular weight of 40kDa, charge of -11, and isoelectric point of 5. 44 ...

https://en.wikipedia.org/wiki/C19orf67

... two typical alternative conformations for nucleic acids" (PDF). Current Science. 45: 779-783. Sasisekharan, V.; Pattabiraman, N ... Later in his career, part of Sasisekharan's work focused on the structure of nucleic acids. He and his coworkers demonstrated ... Ramachandran plot G. N. Ramachandran Nucleic acid double helix India portal Biology portal Sasisekharan, V (1962). Ramanathan, ... He introduced the use of torsion angles to describe polypeptide and protein conformation, a central principle of the (φ, ψ) ...

https://en.wikipedia.org/wiki/V._Sasisekharan

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 ...

https://en.wikipedia.org/wiki/KH_domain

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 ...

https://en.wikipedia.org/wiki/Influenza_A_segment_7_splice_site

Krstić I, Hänsel R, Romainczyk O, Engels JW, Dötsch V, Prisner TF (2011). "Long-range distance measurements on nucleic acids in ... In this way, first unambiguous evidence was provided for an exclusive all-trans retinal conformation in the dark state and a ... To control proteins and nucleic acids by light CEF scientists have designed and applied a range of photoswitchable tethers, ... Wavelength-selective light-triggering was established for nucleic acids as well as three-dimensional control of DNA ...

https://en.wikipedia.org/wiki/Cluster_of_Excellence_Frankfurt_Macromolecular_Complexes

The mimics are typically composed of locked nucleic acids (LNA), 2'-OMe, or 2'-F modified bases. LNA sequences are RNA ... analogues "locked" into an ideal Watson-Crick base pairing conformation. Gapmers often utilize nucleotides modified with ... LNAs, 2'-OMe, or 2'-F modified bases are chemical analogs of natural RNA nucleic acids. These modifications allow for an ... "Ribonuclease H1-dependent hepatotoxicity caused by locked nucleic acid-modified gapmer antisense oligonucleotides". Scientific ...

https://en.wikipedia.org/wiki/Gapmer

Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots. The base pairing in ... Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. ... In a non-biological context, secondary structure is a vital consideration in the nucleic acid design of nucleic acid structures ... "Paradigms for computational nucleic acid design". Nucleic Acids Research. 32 (4): 1392-1403. doi:10.1093/nar/gkh291. PMC 390280 ...

https://en.wikipedia.org/wiki/Nucleic_acid_secondary_structure

... conformation and stability". Nucleic Acids Res. 18 (21): 6353-6359. doi:10.1093/nar/18.21.6353. PMC 332506. PMID 2243780. ... Nucleic acids Nucleic acid analogues Peptide nucleic acid Bridged Nucleic Acids Beaucage, S. L.; Iyer, R. P. (1992). "Advances ... The DMT group is removed with a solution of an acid, such as 2% trichloroacetic acid (TCA) or 3% dichloroacetic acid (DCA), in ... In: Current protocols in nucleic acid chemistry. (John Wiley & Sons, Inc.) (2013), Chapter 3, Unit 3.1., pp. 3.1.1-3.1.60. doi: ...

https://en.wikipedia.org/wiki/Oligonucleotide_synthesis

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 ...

https://en.wikipedia.org/wiki/Transcription_factor

The bridged ribose conformation enhances base stacking and pre-organizes the backbone of the oligonucleotide significantly ... Current Protocols in Nucleic Acid Chemistry. Current Protocols in Nucleic Acid Chemistry. Vol. Chapter 4. pp. 4.12.1-4.12.16. ... C-ethylene-bridged nucleic acids (ENA) with nuclease-resistance and high affinity for RNA". Nucleic Acids Research. Supplement ... A bridged nucleic acid (BNA) is a modified RNA nucleotide. They are sometimes also referred to as constrained or inaccessible ...

https://en.wikipedia.org/wiki/Bridged_nucleic_acid

Watson JD, Crick FH (April 1953). "Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid". Nature. 171 ... Smith AB, Maxwell A (2006). "A strand-passage conformation of DNA gyrase is required to allow the bacterial toxin, CcdB, to ... Baker NM, Rajan R, Mondragón A (February 2009). "Structural studies of type I topoisomerases". Nucleic Acids Research. 37 (3): ... Nucleic Acids Research. 39 (15): 6327-6339. doi:10.1093/nar/gkr258. PMC 3159449. PMID 21525132. McKie SJ, Desai PR, Seol Y, ...

https://en.wikipedia.org/wiki/Topoisomerase

The bridge "locks" the ribose in the 3'-endo (North) conformation, which is often found in the A-form duplexes. This structure ... A locked nucleic acid (LNA), also known as bridged nucleic acid (BNA), and often referred to as inaccessible RNA, is a modified ... Kurreck, J. (2002-05-01). "Design of antisense oligonucleotides stabilized by locked nucleic acids". Nucleic Acids Research. 30 ... C-Ethylene-bridged nucleic acids (ENA) with nuclease-resistance and high affnity for RNA". Nucleic Acids Symposium Series. 1 (1 ...

https://en.wikipedia.org/wiki/Locked_nucleic_acid

proteins, nucleic acids, phospholipids and oligosaccharides). They are made up of chiral building blocks that are put together ... in space in handed conformations. These biological targets function as receptors for the drug enantiomers. So, at the binding ... Amino acids exist in two mirror-image versions (D- and L- configurations). Several D-amino acids, like D-methionine, D-proline ... 2-Arylpropionic acid nonsteroidal anti-inflammatory drugs (NSAIDs) provide one of the best pharmaceutical examples of chiral ...

https://en.wikipedia.org/wiki/Chiral_inversion

Applications To Docking and Structure Prediction From The Distorted Native Conformation , journal=J. Comput. Chem. ,volume=15 , ... "Modeling unusual nucleic acid structures". Molecular Modeling of Nucleic Acids: 379-393. Petr Šulc; Flavio Romano; Thomas E. ... This is a list of notable computer programs that are used for nucleic acids simulations. Min - Optimization MD - Molecular ... Nucleic Acids Research. 44 (W1): W315-W319. doi:10.1093/nar/gkw279. ISSN 0305-1048. PMC 4987879. PMID 27095203. v t e (CS1 ...

https://en.wikipedia.org/wiki/Comparison_of_nucleic_acid_simulation_software

... to stabilize essential compounds like amino acids, nucleic acids and lipids to target age-related diseases. Cantor held ... Cantor co-authored Biophysical Chemistry with Paul Schimmel, which was published in three volumes: Part 1, The Conformation of ... Cantor, C. R.; Katz, L. (1971). "Nucleic Acids". Annual Review of Physical Chemistry. 22: 25-46. Bibcode:1971ARPC...22...25C. ... Cantor's reviews include one on the physical chemistry of nucleic acids. ...

https://en.wikipedia.org/wiki/Charles_Cantor

Circuit topology of Proteins and nucleic acids, Structure 22(9):1227-1237 (2014) Conformation Activity Relationships: Why Do ... The Mashaghi group, LACDR, Leiden University "A Rubik's cube at the nanoscale: proteins puzzle with amino acid chains". ...

https://en.wikipedia.org/wiki/Alireza_Mashaghi

Nucleic Acids Research. 33 (Web Server issue): W690-2. doi:10.1093/nar/gki445. PMC 1160206. PMID 15980564. Chang TH, Huang HD, ... RNA thermometer - Another class of mRNA regulatory segments which change conformation in response to temperature fluctuations, ... Nucleic Acids Research. 35 (14): 4809-4819. doi:10.1093/nar/gkm487. PMC 1950547. PMID 17621584. Weinberg Z, Wang JX, Bogue J, ... Nucleic Acids Research. 36 (18): 5955-5969. doi:10.1093/nar/gkn601. PMC 2566862. PMID 18812398. Loh E, Dussurget O, Gripenland ...

https://en.wikipedia.org/wiki/Riboswitch

... acid design is the process of generating a set of nucleic acid base sequences that will associate into a desired conformation. ... Thus, in nucleic acids the sequence determines the pattern of binding and thus the overall structure. Nucleic acid design is ... Nucleic acid design encompasses all levels of nucleic acid structure: Primary structure-the raw sequence of nucleobases of each ... Nucleic acid design can be considered the inverse of nucleic acid structure prediction. In structure prediction, the structure ...

https://en.wikipedia.org/wiki/Nucleic_acid_design

Folding, including the secondary and tertiary structure of biopolymers (nucleic acids and proteins). Akamptisomerism - due to ... the anti-conformation (left-most, below) and the gauche conformation (right-most, below). Both conformations are free of ... Ring conformation Cyclohexane conformations, including with chair and boat conformations among others. Cycloalkane ... The staggered conformation is more stable by 12.5 kJ/mol than the eclipsed conformation, which is the energy maximum for ethane ...

https://en.wikipedia.org/wiki/Conformational_isomerism

Progress in Nucleic Acid Research and Molecular Biology. Vol. 53. pp. 1-78. doi:10.1016/s0079-6603(08)60142-7. ISBN ... Traut TW, Payne RC (Dec 1980). "Dependence of the catalytic activities on the aggregation and conformation states of uridine 5 ... Traut TW, Jones ME (1996). Uracil metabolism--UMP synthesis from orotic acid or uridine and conversion of uracil to beta- ... Traut TW, Payne RC, Jones ME (Dec 1980). "Dependence of the aggregation and conformation states of uridine 5'-phosphate ...

https://en.wikipedia.org/wiki/Uridine_monophosphate_synthase

Some of these are believed to affect the shape of nucleic acids (see for example RNA self-splicing), but this is only sometimes ... "An approach to detection of protein structural motifs using an encoding scheme of backbone conformations" (PDF). Pacific ... "Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical ... Biology portal Biomolecular structure Mammalian Motif Finder MochiView Multiple EM for Motif Elicitation Nucleic acid sequence ...

https://en.wikipedia.org/wiki/Sequence_motif

Nucleic Acids Research. 42 (21): 13134-49. doi:10.1093/nar/gku1051. PMC 4245941. PMID 25378325. Ishida T, Akimitsu N, Kashioka ... Filling of the sites changes origin conformation from its native state. It is hypothesized that DNA stretching by DnaA bound to ... Nucleic Acids Research. 43 (19): 9262-9275. doi:10.1093/nar/gkv804. PMC 4627069. PMID 26253742. (Wikipedia articles needing ...

https://en.wikipedia.org/wiki/Prokaryotic_DNA_replication

Kozlowski, LP (26 October 2016). "Proteome-pI: proteome isoelectric point database". Nucleic Acids Research. 45 (D1): D1112- ... Upon absorption of a photon, retinal changes its conformation, causing a conformational change in the bacterioopsin protein, as ... Amino acids are the main source of chemical energy for H. salinarum, particularly arginine and aspartate, though they are able ... Vreeland, H; Rosenzweig, W D; Lowenstein, T; Satterfield, C; Ventosa, A (December 2006). "Fatty acid and DNA analyses of ...

https://en.wikipedia.org/wiki/Halobacterium_salinarum

Nucleic Acids Research. 48 (17): 9550-9570. doi:10.1093/nar/gkaa671. PMC 7515708. PMID 32810208. Trinklein ND, Aldred SF, ... A promoter is induced in response to changes in abundance or conformation of regulatory proteins in a cell, which enable ...

https://en.wikipedia.org/wiki/Promoter_(genetics)

Nucleic Acids Research. Archived from the original on 16 October 2016. Retrieved 24 November 2015. (Articles with short ... These are highly involved in condensing chromatin from the beads-on-a-string conformation to a 30-nm fiber. Similar to other ... Histone H2B is a lightweight structural protein made of 126 amino acids. Many of these amino acids have a positive charge at ... All variants of histone H2B contain the same number of amino acids, and the variations in sequence are few in number. Only two ...

https://en.wikipedia.org/wiki/Histone_H2B

"Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification". Nucleic Acids Res. ... Single Strand Conformation Analysis) effectively identify SNPs and small insertions and deletions. MLPA, however, is one of the ... "Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification". Nucleic Acids ... The method was first described in 2002 in the scientific journal Nucleic Acid Research. The first applications included the ...

https://en.wikipedia.org/wiki/Multiplex_ligation-dependent_probe_amplification

... is a molecular cytogenetic technique that uses fluorescent probes that bind to only particular parts of a nucleic acid sequence ... The extended conformation of the chromosomes allows dramatically higher resolution - even down to a few kilobases. The ... The hybridization signals for each probe when a nucleic abnormality is detected. Each probe for the detection of mRNA and ... or adopting a chromosome territory conformation, as in interphase FISH. This is accomplished by applying mechanical shear along ...

https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization

Zhabinskaya D, Benham CJ (November 2013). "Competitive superhelical transitions involving cruciform extrusion". Nucleic Acids ... The conformation formed here has symmetry, unlike the folded conformation formed at high sodium ion concentrations. Lastly, the ... When DNA is faced with significant stress, a negative supercoiled conformation is adopted. A negative supercoiled conformation ... Nucleic Acids Research. 15 (23): 9641-54. doi:10.1093/nar/15.23.9641. PMC 306521. PMID 3697079. Horwitz MS, Loeb LA (August ...

https://en.wikipedia.org/wiki/Cruciform_DNA

... nucleic acid - nucleic acid regulatory sequence - nucleic acid repetitive sequence - nucleic acid sequence homology - nucleon ... conformation - chemical element - chemical equilibrium - chemical formula - chemical nomenclature - chemical property - ... amino acid - amino acid receptor - amino acid sequence - amino acid sequence homology - aminobutyric acid - ammonia - AMPA ... It deals with the structure and function of cellular components such as proteins, carbohydrates, lipids, nucleic acids and ...

https://en.wikipedia.org/wiki/Index_of_biochemistry_articles

Nucleic Acids Research. 48 (14): 7609-7622. doi:10.1093/nar/gkaa438. PMC 7641302. PMID 32476018. Abelson J, Trotta CR, Li H ( ... takes on a rectangular parallelepiped conformation consisting of four α subunits of 179 amino acids each. Each α subunit is ... Nucleic Acids Research. 37 (17): 5793-5802. doi:10.1093/nar/gkp537. PMC 761253. PMID 19578064. Tocchini-Valentini GD, ... All four structures feature at least two active sites made of three amino acids (tyrosine, histidine, and lysine) that catalyze ...

https://en.wikipedia.org/wiki/TRNA-intron_endonuclease

Nucleic Acids Research. 19 (9): 2315-2320. doi:10.1093/nar/19.9.2315. ISSN 0305-1048. PMC 329436. PMID 1710353. Tocchini- ... This puts the molecule in the bulge-helix-bulge conformation, and cleavage occurs in this formation, resulting in cleavage ... Dependence of DNA Continuity and Conformation". Proceedings of the National Academy of Sciences of the United States of America ...

https://en.wikipedia.org/wiki/Glauco_Tocchini-Valentini

Nucleic Acids Research. 46 (10): 4991-5000. doi:10.1093/nar/gky207. ISSN 0305-1048. PMC 6007630. PMID 29850895. Jha, Narendra ... Kar, Rajesh Kumar; Kharerin, Hungyo; Padinhateeri, Ranjith; Bhat, Paike Jayadeva (6 January 2017). "Multiple Conformations of ...

https://en.wikipedia.org/wiki/Ranjith_Padinhateeri

Nucleic Acids Research. 25 (10): 1903-12. doi:10.1093/nar/25.10.1903. PMC 146682. PMID 9115356. Rual, Jean-François; Venkatesan ... Agonist ligands work by inducing a conformation of the receptor which favors coactivator binding (see upper half of the figure ... Some of these receptors such as FXR, LXR, and PPAR bind a number of metabolic intermediates such as fatty acids, bile acids and ... Two putative orphan receptors, HNF4 and USP were found, via structural and mass spectrometry analysis, to bind fatty acids and ...

https://en.wikipedia.org/wiki/Nuclear_receptor

A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is ... Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots. The structural ... Pleij CW, Rietveld K, Bosch L (1985). "A new principle of RNA folding based on pseudoknotting". Nucleic Acids Res. 13 (5): 1717 ... Dirks, R.M. Pierce N.A. (2004) An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. "J ...

https://en.wikipedia.org/wiki/Pseudoknot

... instead of in nucleic acids. Several prion-forming proteins have been identified in fungi, primarily in the yeast Saccharomyces ... The amyloid conformation is self-propagating and represents the prion state. Amazingly distinct prion states exist for the ... The structure is based on the stacking of the prion domains in an in-register and parallel beta sheet conformation. An ... This makes prions a metastable, dominant mechanism for inheritance that relies solely on the conformation of the protein. Many ...

https://en.wikipedia.org/wiki/Fungal_prion

August 1987). ""Homology" in proteins and nucleic acids: a terminology muddle and a way out of it". Cell. 50 (5): 667. doi: ... different probes are generally applied with the goal being to obtain a large number of different protein-probe conformations. ... Information may come from nucleic acid sequence homology, gene expression profiles, protein domain structures, text mining of ... Okuda S, Yoshizawa AC (January 2011). "ODB: a database for operon organizations, 2011 update". Nucleic Acids Research. 39 ( ...

https://en.wikipedia.org/wiki/Protein_function_prediction

"Transmembrane Domain Peptide/Peptide Nucleic Acid Hybrid as a Model of a SNARE Protein in Vesicle Fusion". Angewandte Chemie ... Holopainen, Juha M.; Lehtonen, Jukka Y.A.; Kinnunen, Paavo K.J. (1999). "Evidence for the Extended Phospholipid Conformation in ... and one negatively charged glutamic acids called peptide E). Interestingly, it was discovered that not only the coiled-coil ... "Divalent Cation Induced Fusion and Lipid Lateral Segregation in Phosphatidylcholine-Phosphatidic Acid Vesicles". Biochemistry. ...

https://en.wikipedia.org/wiki/Lipid_bilayer_fusion

The B reader loop is further thought to stabilise NTPs in the active site and, due to its flexibility, allow the nucleic acids ... The open and closed conformations refer to the state of the DNA and whether the template strand has been separated from the non ... TFIIB is a single 33kDa polypeptide consisting of 316 amino acids. TFIIB is made up of four functional regions: the C-terminal ... Although TFIIB keeps a similar structure in both conformations some of the intramolecular interactions between the core and the ...

https://en.wikipedia.org/wiki/Transcription_factor_II_B

... fit a sequence of amino acids in alpha helix conformation into density. Place strand here - fit a sequence of amino acids in ... typically of proteins or nucleic acids, using 3D computer graphics. It is primarily focused on building and validation of ... Pukka puckers - check for unusual DNA/RNA conformations. Coot is built upon a number of libraries. Crystallographic tools ... check for unusual protein side-chain conformations. Density fit analysis - identify parts of the model which don't fit the ...

https://en.wikipedia.org/wiki/Coot_(software)

Jeffers M, Paciucci R, Pellicer A (Oct 1990). "Characterization of unr; a gene closely linked to N-ras". Nucleic Acids Res. 18 ... 2003). "The Apaf-1 internal ribosome entry segment attains the correct structural conformation for function via interactions ... 2006). "The LIFEdb database in 2006". Nucleic Acids Res. 34 (Database issue): D415-8. doi:10.1093/nar/gkj139. PMC 1347501. PMID ... Nucleic Acids Res. 33 (10): 3095-108. doi:10.1093/nar/gki611. PMC 1142345. PMID 15928332. Patel GP, Ma S, Bag J (2006). "The ...

https://en.wikipedia.org/wiki/CSDE1

Krogh A, Mian IS, Haussler D (1994). "A hidden Markov model that finds genes in E. coli DNA". Nucleic Acids Res. 22 (22): 4768- ... Hamelryck T, Kent JT, Krogh A (2006). "Sampling Realistic Protein Conformations Using Local Structural Bias". PLOS Comput. Biol ... Nucleic Acids Res. 36 (Database issue): D102-6. doi:10.1093/nar/gkm955. PMC 2238834. PMID 18006571. Lindow M, Jacobsen A, ... Probabilistic Models of Proteins and Nucleic Acids (1st ed.), Cambridge, New York: Cambridge University Press, ISBN 0-521-62971 ...

https://en.wikipedia.org/wiki/Anders_Krogh

Nucleic Acids Research. 16 (7): 3109. doi:10.1093/nar/16.7.3109. PMC 336462. PMID 3368322. MacLeod AR, Houlker C, Reinach FC, ... which adopt a bent coiled coil conformation to wrap around the seven actin molecules in a functional unit of muscle. It is ... β-tropomyosin is roughly 32 kDa in molecular weight (284 amino acids), but multiple splice variants exist. Tropomysin is a ... which is one amino acid away from the C-terminus. β-tropomyosin also has a Serine residue at position 283, thus, it is likely ...

https://en.wikipedia.org/wiki/TPM2

Momand J, Jung D, Wilczynski S, Niland J (August 1998). "The MDM2 gene amplification database". Nucleic Acids Research. 26 (15 ... K29-, K33-, K63- and M1-linked chains have a fairly linear conformation; they are known as open-conformation chains. K6-, K11 ... In contrast, the closed conformation chains have interfaces with interacting residues. Altering the chain conformations exposes ... Journal of Nucleic Acids. 2010: 1-8. doi:10.4061/2010/761217. PMC 2935186. PMID 20847899. Jackson SP, Durocher D (March 2013 ...

https://en.wikipedia.org/wiki/Ubiquitin

Nucleic Acids Res. 31 (6): 1633-9. doi:10.1093/nar/gkg273. PMC 152875. PMID 12626704. This article incorporates text from the ... Polosina YY, Cupples CG (2009). "Changes in the conformation of the Vsr endonuclease amino-terminal domain accompany DNA ...

https://en.wikipedia.org/wiki/Very_short_patch_repair

Some RNA sequences have more than one biologically active conformation (i.e., riboswitches) For this reason, the ability to ... "Modeling Unusual Nucleic Acid Structures". Modeling unusual nucleic acid structures. In Molecular Modeling of Nucleic Acids. ... Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its ... Zuker M (2003). "Mfold web server for nucleic acid folding and hybridization prediction". Nucleic Acids Research. 31 (13): 3406 ...

https://en.wikipedia.org/wiki/Nucleic_acid_structure_prediction

The conformation of the DNA and the interactions of the nucleic acid with the protein in a complex of human immunodeficiency ... The conformation of the DNA and the interactions of the nucleic acid with the protein in a complex of human immunodeficiency ... Protein-nucleic acid interactions and DNA conformation in a complex of human immunodeficiency virus type 1 reverse ... The interactions between the dsDNA and protein primarily involve the sugar-phosphate backbone of the nucleic acid and ...

https://pubmed.ncbi.nlm.nih.gov/9354757/

AP2 bound to heparin in the closed conformation ... Nucleic Acid Database. *wwPDB Partners. *RCSB PDB. *PDBe. *PDBj ... Muniscin-engaged AP2 is primed to rearrange into the vesicle-competent conformation on binding the tyrosine cargo ... AP2 bound to heparin in the closed conformation. *PDB DOI: 10.2210/pdb7RW8/pdb ...

https://www.rcsb.org/structure/7RW8

They can adopt several distinctive conformations. G4s have been shown to form in the herpes simplex virus-1 (HSV-1) genome ... are four-stranded nucleic acid structures abundant at gene promoters. ... are four-stranded nucleic acid structures abundant at gene promoters. They can adopt several distinctive conformations. G4s ... A catalytic and selective scissoring molecular tool for quadruplex nucleic acids. J. Am. Chem. Soc. 140, 14528-14532 (2018). ...

https://www.nature.com/articles/s42003-021-02035-y?error=cookies_not_supported&code=8e82e0f5-f7c5-42ec-bc4b-6dfdc9aa6576

Nucleic acids dynamics, interactions and recognition. This project concerns a number of fundamental problems, some of which ... A stretched conformation of DNA with a biological role? Author: Niklas Bosaeus; Anna Reymer; Tamas Beke-Somfai; T. Brown; M. ... The sialic acid-dependent nematocyst discharge process in relation to its physical-chemical properties is a role model for ... primed by earlier discoveries in our laboratory related to the structure and biological function of nucleic... ...

http://www.chalmers.se/en/staff/pages/bengt-norden.aspx

5.6 Isomerases altering macromolecular conformation. 5.6.2 Enzymes altering nucleic acid conformation. 5.6.2.4 DNA 3-5 ... 5.6 Isomerases altering macromolecular conformation. 5.6.2 Enzymes altering nucleic acid conformation. 5.6.2.4 DNA 3-5 ... 5.6 Isomerases altering macromolecular conformation. 5.6.2 Enzymes altering nucleic acid conformation. 5.6.2.4 DNA 3-5 ...

https://www.genome.jp/entry/sma:SAVERM_3072+sma:SAVERM_3076+sma:SAVERM_3463

Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions ... Nucleic Acids Res. 2016;44(W1):W160-5. https://doi.org/10.1093/nar/gkw257. ... Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions ... Nucleic Acids Res. 2014;42(18):e143. https://doi.org/10.1093/nar/gku738. ...

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02597-4

Additional topics may include: nucleic acid conformation, DNA/protein interactions, signal transduction and transport phenomena ... These tools will be used to study some class of specific structures, (such as membrane, nucleic acid binding, regulatory, ... We will explore how bonding plays a central role in assembling simple biological building blocks such as sugars, amino acids, ... Protein conformation, enzymatic mechanisms and selected metabolic pathways will be analyzed. ...

https://www.amherst.edu/academiclife/departments/biology/courses/1415F?display=curriculum

31P Chemical Shift Tensors for Canonical and Non-Canonical Nucleic Acid Conformations: DFT Calculations and NMR Implications. ... Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations PŘECECHTĚLOVÁ Jana ... Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations ...

https://www.sci.muni.cz/o-nas/zamestnanci-fakulty/18691-marketa-munzarova/publikace?page=2

Research Synopsis: Theoretical studies of nucleic acid conformation, properties, and interactions *[email protected] ...

https://rutchem.rutgers.edu/research/faculty-research/interdisciplinary-research-areas/interdisciplinary-research-biomolecular-modeling-and-design

Potential plot of all furanose ring conformations (p. 771) , html , pdf , *Fig. 23.4.2.6. Plot of observed sugar conformations ... Nucleic acids. Contents. *23.4. Nucleic acids (pp. 766-799) , html , pdf , chapter contents , R. E. Dickerson ... Glycosyl conformation and chain sense (p. 777) , html , pdf , *Fig. 23.4.3.5. The role of the C2′-OH in RNA helix geometry (p. ... Sugar ring conformations (p. 775) , html , pdf , *23.4.3.4. Helical twist and rise, and propeller twist (pp. 775-777) , html , ...

https://it.iucr.org/Fb/ch23o4v0001/contents/

"Measuring significant changes in chromatin conformation with ACCOST." Nucleic Acids Research. 48(5):2303-2311, 2020. ... "MEME Suite: tools for motif discovery and searching." Nucleic Acids Research. 37(Web server issue):W202-208, 2009.. MEME. ... "Accurate identification of centromere locations in yeast genomes using Hi-C." Nucleic Acids Research. 43(11):5331-5339, 2015. ... "On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements." Nucleic Acids ...

https://noble.gs.washington.edu/pubs.html

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability. Nucleic Acids Res 2018;46:W350- ... Nucleic Acids Res 2019;47:D607-13.doi:10.1093/nar/gky1131 pmid:30476243 ... thus affecting chromatin conformation and gene expression. In addition, amino acids 1-333, which include the JmjC domain, have ... Nucleic Acids Res 2018;46:3339-50.doi:10.1093/nar/gky080 pmid:http://www.ncbi.nlm.nih.gov/pubmed/29425303 ...

https://jmg.bmj.com/content/59/7/644

Nucleic acids are characterized by a vast structural variability. Secondary structural conformations include the main ... Goobes R., Cohen O. & Minsky A. (2002) Nucleic Acids Research. 30, 10, p. 2154-2161 Abstract Triple-stranded DNA structures can ... Nucleic acids are characterized by a predominant right-handed helical configuration that derives from the chirality of the ... In biological systems nucleic acids are invariably found in highly compact forms. These rather intricate forms raise questions ...

http://www.weizmann.ac.il/CSB/minsky/publications

Nucleic Acids Research (London) 49 (14), S. 7954 - 7965 (2021). MPG.PuRe ... Steuer, J.; Kukharenko, O.; Riedmiller, K.; Hartig, J. S.; Peter, C.: Guanidine-II aptamer conformations and ligand binding ... Kahlen, J.; Salimi, L.; Sulpizi, M.; Peter, C.; Donadio, D.: Interaction of Charged Amino-Acid Side Chains with Ions: An ...

https://www.mpip-mainz.mpg.de/publication-search/125755?deactivate_global_blacklist=false&page=1&person=%2Fpersons%2Fresource%2Fpersons48575

... not perturb the DNA conformation could have valuable applications for the study of the structure and dynamics of nucleic acid ... The NMR structure determination of the self-complementary sequence 5-CTC(tC)ACGTGGAG shows a DNA conformation consistent with ... CD spectra are practically identical for modified and unmodified sequences, indicating an unperturbed B-DNA conformation. ... without distorting the DNA backbone conformation. This first example of an artificial, highly fluorescent DNA base that does ...

https://research.chalmers.se/en/publication/53928

Incorporate locked nucleic acid monomers to increase PCR probe Tm, heighten target specificity, impart nuclease resistance, ... endo conformation. ... What are locked nucleic acids?. Locked nucleic acids are ... As with locked nucleic acid qPCR probes, hybridization Tm can be manipulated by the number of locked nucleic acid bases ... Manage sequence Tm using locked nucleic acid bases. Because of the afforded increase in Tm, locked nucleic acid qPCR probes can ...

https://eu.idtdna.com/pages/technology/custom-dna-rna/locked-nucleic-acids

Probing the impact of chromatin conformation on genome editing tools. *Xiaoyu Chen, Marrit Rinsma, J. Janssen, Jin Liu, I. ... Nucleic acids research. *2011. TLDR. The combination of high nuclease activity with reduced cytotoxicity and the simple design ...

https://www.semanticscholar.org/paper/A-guide-to-genome-engineering-with-programmable-Kim-Kim/3744283196d8c1b423f5552894bc4453a4c302b6

Nucleic Acids Res. 37(13):4453-63. *Cupples CG (2009) DNA Repair, Encyclopedia of Microbiology, pp 99-112, Elsevier. ... 2009) Changes in the conformation of the Vsr endonuclease amino-terminal domain accompany DNA cleavage. J. Biochem. 146(4):523- ...

https://www.sfu.ca/mbbarchive/People/Cupples/

... which bind to nucleic acids in the Z-conformation. However, the specific role of these Zα domains in orchestrating ZBP1 ... Z-DNA-binding protein 1 (ZBP1) is an innate immune sensor of nucleic acids that regulates host defense responses and ... Fatty acid-binding protein 4 (FABP4) is predominantly expressed in adipocytes and macrophages and regulates metabolic and ... Most paramyxoviruses enter epithelial cells of the airway using sialic acid as a receptor and cause only mild disease. However ...

https://www.jbc.org/Microbiology?startPage=&KeywordRaw=infection

... to expunge heat-induced modifications of nucleic acids; (d) metabolic enzymes, to reorganize and stabilize the vigour fund of ... which assist other proteins exchange to their native conformation; (b) components of the proteolytic system, to degrade irre- ... In individual, dissection of IL-1 and IL-1Ra mRNAs after systemic injection of kainic acid in rats has shown that these ... Rosenson, RS, Tangney, CC, and Casey, LC (1999) gastritis acid reflux diet. Such a simple mould of attention was updated in the ...

https://www.daubnet.com/de/board/viewtopic.php?lang=de&p=9993

... rebuilding and visualization of three-dimensional nucleic acid structures, Nucleic Acids Res.31(17), 5108-21.. Xiang-Jun Lu & ... The above values were obtained using first alternate conformation only and calculated by 3DNA program. Xiang-Jun Lu & Wilma K. ... A Portal for Three-dimensional Structural Information about Nucleic Acids. As of 23-Nov-2022 number of released structures: ... [email protected] ©1995-2022 The Nucleic Acid Database Project , Rutgers, The State University of New Jersey ...

http://ndbserver.rutgers.edu/service/ndb/atlas/stfeatures?searchTarget=2B6G&ftrType=bpmsp&start=0&limit=50&type=html

... conformation and stability. Nucleic Acid Res. 18, 6353-6359 (1990). ... Nucleic Acids Res. 29, 2437-2447 (2001). Alseth, I. et al. Inosine in DNA and RNA. Cur. Opi. Genetics and Dev. 26, 116-123 ( ... Nucleic Acids Res. 26, 4309-4314 (1998).. Chiu, Y. and Rana, T. M. siRNA function in RNAi: a chemical modification analysis. ... Nucleic Acids Res. 38, 1415-1430 (2010). Squires, J. E. et al. Widespread occurrence of 5-methylcytosine in human coding and ...

https://horizondiscovery.com/ja/custom-synthesis/custom-rna-synthesis

Nucleic Acid Conformation, Protein Binding, Protein Conformation, Recombinant Proteins chemistry, Recombinant Proteins ... Nucleic acids research. [Nucleic Acids Res] 2019 Jul 26; Vol. 47 (13), pp. 7118-7129. ... Amino Acid Motifs genetics, Amino Acid Sequence, Bacteriophage P22 genetics, Bacteriophage P22 metabolism, Crystallography, X- ... Ray, Models, Molecular, Podoviridae genetics, Protein Conformation, Sequence Homology, Amino Acid, Viral Tail Proteins genetics ...

https://searchworks.stanford.edu/articles?q=%22Bacteriophage+P22+metabolism%22&search_field=descriptor

This reaction is sterically prohibited for the B form DNA conformation. If, however, the nucleic acid structure is deformed, ... It was not possible to uniquely identify the preferred transition-state complex with respect to nucleic acid structure or ... In one, I was located "outside" the nucleic acid structure; in the other geometry, I was intercalated between adjacent base ... Terms: DNA or Deoxyribonucleic acid OR DNA or Deoxyribonucleic acid 574 - 574 of 583 Bibliographic entries ...

http://www2a.cdc.gov/nioshtic-2/BuildQyr.asp?s1=DNA+or+Deoxyribonucleic+acid&f1=TI&Startyear=&t1=1&s2=DNA+or+Deoxyribonucleic+acid&terms=3&Adv=1&ct=&B1=Search&f2=KW&Limit=500&Sort=DP+DESC&D1=10&EndYear=&PageNo=58&RecNo=574&View=f&

En: Nucleic Acids Research. 1989. Vol. 17. N m. 16. Pag. 6669-6680 Fern ndez Bola os Vazquez, Jose Manuel, Iglesias Guerra, ... Conformations in Crystals and Solutions of D(Cacgtg), D(Ccgcgg) and D(Ggcgcc) Studied by Vibrational Spectroscopy. ... Serinol-Based Benzoic Acid Esters as New Scaffolds for the Development of Adenovirus Infection Inhibitors: Design, Synthesis, ... Preparation of Crayfish Chitin by in Situ Lactic Acid Production. En: Process Biochemistry. 2001. Vol. 37. N m. 3. Pag. 229-234 ...

https://investigacion.us.es/sisius/sis_showpub.php?idpers=837

CADB: Conformation Angles DataBase of Proteins. ," Nucleic Acids Res.. 0305-1048, 31 ... Protofold: A Successive Kinetostatic Compliance Method for Protein Conformation Prediction J. Mech. Des (July,2005) ... between the resultant conformation and the PDB data is minimized to yield the best values for the bond length and bond angles ...

https://asmedigitalcollection.asme.org/mechanicaldesign/article-abstract/129/11/1130/447537/Improved-Molecular-Model-of-a-Peptide-Unit-for?redirectedFrom=PDF

... and decreased electronegativity of the thio-group leads to cytotoxicity by altering the hydrogen bonds between nucleic acid ... duplexes, resulting in the disruption the conformation of the DNA thus inhibiting replication and transcription. Through NMR ... THREE CEREAL GRAIN PROTEINS,TAABF, TAWD40, AND AFN1, HAVE PUTATIVE ROLES IN THE ABSCISIC ACID-MEDIATED GENE EXPRESSION PATHWAY ... The amino acid sequence is left unchanged when the mutation is synonymous and it is affected when the mutation is non- ...

https://www.colby.edu/sturesearch/ressymposium/RS2003/Abstracts.html

A C-C mismatch usually confers substantial destabilization to nucleic-acid structure, and disrupts helices and tertiary ... Translation-competent conformations of the tRNA, mRNA, and decoding center demonstrate how the ribosomal P site helps to ... arranging the cytosine-cytosine pair into a nearly planar conformation, resembling a Watson-Crick base pair formed by ...

https://www.umassmed.edu/korostelev-lab/research/non-canonical/

Nucleic Acid Conformation G2.111.570.790.486 G2.111.570.820.486 Nucleotide Motifs G2.111.570.790.486.662 G2.111.570.820.486.662 ... Nucleic Acid L1.700.508.300.188.400.300.500 L1.313.500.750.300.188.400.300.500 L1.700.508.300.188.400.325.630 L1.313.500.750. ... Arachidonic Acid D10.251.355.96.100 Arachidonic Acids D10.251.355.96 Arachis hypogaea J2.500.850.500.77 (Replaced for 2015 by ... Fusidic Acid D10.570.938.515 Fuzzy Logic L1.224.65.250 L1.224.50.375.250 G-Quadruplexes G2.111.570.790.486.550 G2.111.570.820. ...

https://decs.bvs.br/P/mnchg2016.txt

Diekmann, S.; Zarling, D. A.: Unique poly(dA).poly(dT) B-conformation in cellular and synthetic DNAs. Nucleic Acids Research ... In: Nucleic acids and molecular biology, Vol. 1, pp. 1138 - 156 (Ed. Eckstein, F.). Springer, Berlin (1987) ...

https://www.mpinat.mpg.de/publication-search/642977?person=%2Fpersons%2Fresource%2Fpersons240509

Chymotrypsin -- A protease that catalyses the hydrolysis (the breakdown) of proteins into peptides or amino acids in the small intestine. (nih.gov)
Cysteine -- A sulfur-containing nonessential amino acid produced by the enzymatic or acid hydrolysis of proteins. (nih.gov)
Glutamic acid -- A nonessential amino acid occurring in proteins. (nih.gov)
Genetic Code Expansion (GCE) technology - the engineering of cellular translation to express proteins containing non-canonical amino acids - provides unprecedented ways to probe and manipulate macromolecular structure and function, analyze protein malfunctions in disease, engineer bioanalytical tools, and create precision biotherapeutics. (nih.gov)
Raman microscopy is a suitable technique for the studies of cells, tissues, biomolecules such as proteins and nucleic acids, as well as pharmacological formulations and microplastics. (photonics.com)
All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. (embl.de)
Ubiquitous in all life forms and central to any research or development program involving biomolecules, the interactions between proteins, nucleic acids, peptides and other biomacromolecules lie at the heart of biology, physiology, and medicine. (wyatt.com)

Amino acid residues from the polymerase active site region, including amino acid residues of the conserved Tyr-Met-Asp-Asp (YMDD) motif and the "primer grip," interact with 3'-terminal nucleotides of the primer strand and are involved in positioning the primer terminal nucleotide and its 3'-OH group at the polymerase active site. (nih.gov)
Amino acid residues of the "template grip" have close contacts with the template strand and aid in positioning the template strand near the polymerase active site. (nih.gov)
Amino acid residues of beta 1', alpha A', alpha B', and the loop containing His539 of the RNase H domain interact with the primer strand of the dsDNA. (nih.gov)
Proteome-wide identification of amino acid substitutions deleterious for protein function. (washington.edu)
The fourth domain of A561L is a 242 amino acid C-terminal domain, named A561LD4, with cell wall degrading activity. (weizmann.ac.il)
Interaction of Charged Amino-Acid Side Chains with Ions: An Optimization Strategy for Classical Force Fields. (mpg.de)
Through this process, Anfinsen could analyze the fragments of the three-dimensional amino acid chain. (nih.gov)
Our previous studies using gene-targeted mouse models of chronic wasting disease (CWD) demonstrated that Norway and North America cervids are infected with distinct prion strains that respond differently to naturally occurring amino acid variation at residue 226 of the prion protein. (cdc.gov)
Acetyl CoA transfer acetyl group to lysine amino acid with the presence of acetyltransferases enzymes. (avensonline.org)

Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions, and the adoption of ChIP techniques to 3C-based protocols makes it possible to identify long-range interactions. (biomedcentral.com)

A G-quadruplex (GQ) is a type of noncanonical nucleic acid structure that can form in regions of nucleic acids rich in guanine nucleotides. (vt.edu)

The conformation of the DNA and the interactions of the nucleic acid with the protein in a complex of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) and 19-mer/18-mer double-stranded DNA template-primer (dsDNA) are described. (nih.gov)
The interactions between the dsDNA and protein primarily involve the sugar-phosphate backbone of the nucleic acid and structural elements of the palm, thumb, and RNase H of p66, and are not sequence specific. (nih.gov)
The COMD/NMR Center develops advanced methods in NMR spectroscopy for studying conformation and dynamics of protein and nucleic acid during biological processes and makes these sophisticated methods accessible to a wider research community to facilitate applications to biomedical questions. (nih.gov)
Much of our work focuses on the viral nucleocapsid protein (NC), a nucleic acid chaperone that remodels nucleic acid structures so that the most thermodynamically stable conformations are formed-an activity that is critical for highly efficient and specific viral DNA synthesis. (nih.gov)
Selection of fully processed HIV-1 nucleocapsid protein is required for optimal nucleic acid chaperone activity in reverse transcription. (nih.gov)
Aberrant bcl-2 GQ conformations result in increased production of the BCL2 protein, which is an apoptosis inhibitor. (vt.edu)
Shortly after SARS-CoV emerged at the turn of the 21st century, the spike (S) protein (particularly in its native conformation) was identified as the immunodominant antigen of the virus3. (who.int)

Altogether, this suggests that tC works well as a cytosine analogue, i.e. it is situated in the base stack, forming hydrogen bonds with G in the complementary strand, without distorting the DNA backbone conformation. (chalmers.se)

G-quadruplexes (G4s) are four-stranded nucleic acid structures abundant at gene promoters. (nature.com)
Later, as they improved their understanding of the structures and the conformations ind the bases in the nucleic acids, they had more exact models machined from metal. (forextrading-madeeasy.com)
Using a dihedral angle metric and an affinity propagation technique, we have clustered the conformations of each CDR and unique loop length of antibody structures in the PDB, at this time, a total of 115 unique clusters [3] . (fccc.edu)
Dr. Duckett earned his PhD degree in Biochemistry from the University of Dundee under the mentorship of Professor David M. J. Lilley, a Member of Royal Society and the Director of the Cancer Research UK Nucleic Acid Structure Research Group, where Derek had a remarkable string of studies that defined the structures for DNA and RNA four-way helical junctions, and how these interact with resolving enzymes (Duckett, et al. (moffitt.org)

A C-C mismatch usually confers substantial destabilization to nucleic-acid structure, and disrupts helices and tertiary interactions. (umassmed.edu)

Unique poly(dA).poly(dT) B'-conformation in cellular and synthetic DNAs. (mpg.de)
DNA, or deoxyribonucleic acid -- The primary genetic material of all cellular organisms and the DNA viruses. (nih.gov)

The replicative properties of prions stem from the capacity of PrP Sc to template its conformation on PrP C in a cyclical process resulting in exponential accumulation of prion infectivity ( 8 - 11 ). (cdc.gov)
Although they lack nucleic acids, prions exhibit heritable strain properties that influence disease outcomes, including the time between infection and disease onset (incubation period), clinical signs, patterns of neuronal degeneration and PrP Sc deposition in the central nervous system (CNS), and the ability to replicate in non-CNS tissues such as the lymphoreticular system and musculature ( 12 ). (cdc.gov)

Incorporation of locked nucleic acid bases increases sequence melting temperature. (idtdna.com)
When locked nucleic acid modified bases are incorporated into a DNA sequence (such as a qPCR probe), its duplex melting characteristics are changed, resulting in increased T m . (idtdna.com)
As with locked nucleic acid qPCR probes, hybridization T m can be manipulated by the number of locked nucleic acid bases incorporated. (idtdna.com)
Remarkably, the ribosome stabilizes the mismatched codon-anticodon helix, arranging the cytosine-cytosine pair into a nearly planar conformation, resembling a Watson-Crick base pair formed by complementary bases (e.g. (umassmed.edu)
The guanine bases form a square planar conformation via Hoogsteen hydrogen bonding. (vt.edu)

Molecular genetic tests for detecting drug-resistance are, in general, just a variation of nucleic acid amplification (NAA) tests and can reliably provide information on the presence of mutations associated with drug resistance in 1 to 2 days. (cdc.gov)
During examination at the HIV clinic, specimens were obtained from the pharynx, rectum, and urine for culture and a nucleic acid amplification test (NAAT). (cdc.gov)

It provides information about their chemical composition, the spatial distribution of the individual compounds, the conformation of the molecules, their crystallinity, and details of other properties. (photonics.com)

Gel electrophoresis is a standard laboratory procedure that is indispensable for nucleic acid visualization and purification. (integra-biosciences.com)

Nucleic acids research, 38, D105-110. (uib.no)

Through an optimization process, the structural error (root mean square deviation of all atoms) between the resultant conformation and the PDB data is minimized to yield the best values for the bond length and bond angles in the calibrated peptide unit. (asme.org)
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape. (bvsalud.org)

Structural determinants of human APOBEC3A enzymatic and nucleic acid binding properties. (nih.gov)

When incorporated into an oligonucleotide probe, locked nucleic acid monomers impart heightened structural stability, resulting in increased hybridization melting temperature (T m ), both in vitro and in vivo (Figure 2). (idtdna.com)

Heritable strain information appears to be enciphered by distinct PrP Sc conformations that are faithfully propagated during prion replication ( 14 , 15 ). (cdc.gov)

The NMR structure determination of the self-complementary sequence 5'-CTC(tC)ACGTGGAG shows a DNA conformation consistent with B-form for the whole duplex. (chalmers.se)
Locked nucleic acid oligonucleotides are useful in template switching oligo designs and for strengthening target oligo binding in challenges sequence regions, such as AT-rich areas. (idtdna.com)
Cistron -- A basic unit of hereditary material, it is the smallest genetic unit that must be intact to function as a transmitter of genetic information, i.e., to determine the sequence of amino acids of one polypeptide chain. (nih.gov)

Improper GQ conformations can lead to improper regulation of gene expression, potentially resulting in genetic diseases or cancer. (vt.edu)
In most cases, addition of acetyl groups to histone tails causes gene activation by inducing and recruiting a euchromatin conformation and bromodomain containing transcription factors respectively for genes in close closeness to the acetylated histone [ 7,8 ]. (avensonline.org)

This first example of an artificial, highly fluorescent DNA base that does not perturb the DNA conformation could have valuable applications for the study of the structure and dynamics of nucleic acid systems. (chalmers.se)
If, however, the nucleic acid structure is deformed, such that the distance between two adjacent base pairs (one containing guanine and cytosine) is maximized, sterically allowed transition-state geometries can be identified. (cdc.gov)
It was not possible to uniquely identify the preferred transition-state complex with respect to nucleic acid structure or isomer of I. However, two types of general transition-state geometries were observed. (cdc.gov)

G-C). Translation-competent conformations of the tRNA, mRNA, and decoding center demonstrate how the ribosomal P site helps to establish and maintain the open reading frame. (umassmed.edu)

The enzyme crystallizes in two different conformations (open and closed). (embl.de)

Because of the afforded increase in T m , locked nucleic acid qPCR probes can be designed with shorter lengths than standard probes. (idtdna.com)

16 this range (primarily cytochrome P-450 mediated oxidation to fatty acids and alcohols) is slow, while the aromatics are metabolized faster (oxidation of alkyl site and/or ring, sometimes with formation of reactive intermediates, and conjugation with glutathione, glucuronic acid, or glycine) (ATSDR 1999). (cdc.gov)

This reaction is sterically prohibited for the B form DNA conformation. (cdc.gov)

This induces migration towards the anode due to the negative charge of the nucleic acids, separating the individual components by size and/or conformation. (integra-biosciences.com)

Pioneering biocontainment systems used metabolic auxotrophy in which target cells could only grow in the presence of an exogenously supplied metabolite 7,8 , and the recent creation of an E. coli strain with an altered genetic code enabled production of synthetic auxotrophy strains in which an exogenous supply of non-natural amino acids is required for cell survival 9,10 . (justia.com)

Anatomy4

Organisms8

Chemicals and Drugs106

Analytical, Diagnostic and Therapeutic Techniques and Equipment51

Phenomena and Processes89

Disciplines and Occupations10

Technology, Industry, Agriculture4

Information Science10

Health Care3

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

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

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)

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

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)

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

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

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

Nucleic Acid Conformation

Protein Conformation

Peptide Nucleic Acids

Molecular Conformation

Nucleic Acid Probes

DNA

Molecular Sequence Data

Nucleic Acid Amplification Techniques

Nucleic Acid Denaturation

Amino Acid Sequence

Nucleic Acid Hybridization

Crystallography, X-Ray

RNA

Binding Sites

Circular Dichroism

Protein Structure, Secondary

Protein Binding

Magnetic Resonance Spectroscopy

Thermodynamics

Protein Structure, Tertiary

Kinetics

Hydrogen Bonding

Oligonucleotides

Solutions

Structure-Activity Relationship

Protein Folding

Nuclear Magnetic Resonance, Biomolecular

Escherichia coli

Mutation

Base Sequence

Temperature

Spectrometry, Fluorescence

Models, Chemical

Molecular Structure

Ligands

Peptides

Polymerase Chain Reaction

Molecular Dynamics Simulation

Polymorphism, Single-Stranded Conformational

Oligodeoxyribonucleotides

Proteins

RNA, Viral

Hydrogen-Ion Concentration

Base Pairing

Spectrophotometry, Ultraviolet

Self-Sustained Sequence Replication

DNA, Single-Stranded

Polydeoxyribonucleotides

Protein Structure, Quaternary

Computer Simulation

X-Ray Diffraction

DNA, Viral

Dimerization

Carbohydrate Conformation

Recombinant Proteins

Nucleotides

Protein Denaturation

Catalytic Domain

Nucleic Acid Heteroduplexes

Mutagenesis, Site-Directed

Static Electricity

Aptamers, Nucleotide

RNA, Bacterial

Fluorescent Dyes

Crystallography

Substrate Specificity

G-Quadruplexes

Bacterial Proteins

Water

Guanine

Sensitivity and Specificity

DNA, Bacterial

DNA Probes

Cell Line

Amino Acid Substitution

Sequence Homology, Amino Acid

Peptide Fragments

Catalysis

Sequence Alignment

Spectrum Analysis, Raman