DNA, Single-Stranded: A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.DNA Replication: The process by which a DNA molecule is duplicated.DNA Helicases: Proteins that catalyze the unwinding of duplex DNA during replication by binding cooperatively to single-stranded regions of DNA or to short regions of duplex DNA that are undergoing transient opening. In addition DNA helicases are DNA-dependent ATPases that harness the free energy of ATP hydrolysis to translocate DNA strands.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Rec A Recombinases: A family of recombinases initially identified in BACTERIA. They catalyze the ATP-driven exchange of DNA strands in GENETIC RECOMBINATION. The product of the reaction consists of a duplex and a displaced single-stranded loop, which has the shape of the letter D and is therefore called a D-loop structure.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Replication Protein A: A single-stranded DNA-binding protein that is found in EUKARYOTIC CELLS. It is required for DNA REPLICATION; DNA REPAIR; and GENETIC RECOMBINATION.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Nucleic Acid Denaturation: Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)DNA, Circular: Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)Bacteriophage phi X 174: The type species of the genus MICROVIRUS. A prototype of the small virulent DNA coliphages, it is composed of a single strand of supercoiled circular DNA, which on infection, is converted to a double-stranded replicative form by a host enzyme.Viral Proteins: Proteins found in any species of virus.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Templates, Genetic: Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Coliphages: Viruses whose host is Escherichia coli.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.DNA Primase: A single-stranded DNA-dependent RNA polymerase that functions to initiate, or prime, DNA synthesis by synthesizing oligoribonucleotide primers. EC 2.7.7.-.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Kinetics: The rate dynamics in chemical or physical systems.Exonucleases: Enzymes that catalyze the release of mononucleotides by the hydrolysis of the terminal bond of deoxyribonucleotide or ribonucleotide chains.Deoxyribonucleases: Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.Poly T: A group of thymine nucleotides in which the phosphate residues of each thymine nucleotide act as bridges in forming diester linkages between the deoxyribose moieties.DNA-Directed DNA Polymerase: DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.Exodeoxyribonucleases: A family of enzymes that catalyze the exonucleolytic cleavage of DNA. It includes members of the class EC 3.1.11 that produce 5'-phosphomonoesters as cleavage products.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.RNA Nucleotidyltransferases: Enzymes that catalyze the template-directed incorporation of ribonucleotides into an RNA chain. EC 2.7.7.-.Bacteriophage M13: Temperate bacteriophage of the genus INOVIRUS which infects enterobacteria, especially E. coli. It is a filamentous phage consisting of single-stranded DNA and is circularly permuted.Adenosine Triphosphatases: A group of enzymes which catalyze the hydrolysis of ATP. The hydrolysis reaction is usually coupled with another function such as transporting Ca(2+) across a membrane. These enzymes may be dependent on Ca(2+), Mg(2+), anions, H+, or DNA.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Nucleic Acid Renaturation: The reformation of all, or part of, the native conformation of a nucleic acid molecule after the molecule has undergone denaturation.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.DNA Repair: The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Endonucleases: Enzymes that catalyze the hydrolysis of the internal bonds and thereby the formation of polynucleotides or oligonucleotides from ribo- or deoxyribonucleotide chains. EC 3.1.-.RNA, Double-Stranded: RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms.Polydeoxyribonucleotides: A group of 13 or more deoxyribonucleotides in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.DNA Viruses: Viruses whose nucleic acid is DNA.Bacteriophage T7: Virulent bacteriophage and type species of the genus T7-like phages, in the family PODOVIRIDAE, that infects E. coli. It consists of linear double-stranded DNA, terminally redundant, and non-permuted.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Bacterial Proteins: Proteins found in any species of bacterium.Bacteriophage T4: Virulent bacteriophage and type species of the genus T4-like phages, in the family MYOVIRIDAE. It infects E. coli and is the best known of the T-even phages. Its virion contains linear double-stranded DNA, terminally redundant and circularly permuted.Nucleic Acid Heteroduplexes: Double-stranded nucleic acid molecules (DNA-DNA or DNA-RNA) which contain regions of nucleotide mismatches (non-complementary). In vivo, these heteroduplexes can result from mutation or genetic recombination; in vitro, they are formed by nucleic acid hybridization. Electron microscopic analysis of the resulting heteroduplexes facilitates the mapping of regions of base sequence homology of nucleic acids.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.DNA Breaks, Single-Stranded: Interruptions in one of the strands of the sugar-phosphate backbone of double-stranded DNA.Telomere: A terminal section of a chromosome which has a specialized structure and which is involved in chromosomal replication and stability. Its length is believed to be a few hundred base pairs.Exodeoxyribonuclease V: An ATP-dependent exodeoxyribonuclease that cleaves in either the 5'- to 3'- or the 3'- to 5'-direction to yield 5'-phosphooligonucleotides. It is primarily found in BACTERIA.T-Phages: A series of 7 virulent phages which infect E. coli. The T-even phages T2, T4; (BACTERIOPHAGE T4), and T6, and the phage T5 are called "autonomously virulent" because they cause cessation of all bacterial metabolism on infection. Phages T1, T3; (BACTERIOPHAGE T3), and T7; (BACTERIOPHAGE T7) are called "dependent virulent" because they depend on continued bacterial metabolism during the lytic cycle. The T-even phages contain 5-hydroxymethylcytosine in place of ordinary cytosine in their DNA.RNA Viruses: Viruses whose genetic material is RNA.PolynucleotidesDNA, Superhelical: Circular duplex DNA isolated from viruses, bacteria and mitochondria in supercoiled or supertwisted form. This superhelical DNA is endowed with free energy. During transcription, the magnitude of RNA initiation is proportional to the DNA superhelicity.Polymorphism, Single-Stranded Conformational: Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.Telomere-Binding Proteins: Proteins that specifically bind to TELOMERES. Proteins in this class include those that perform functions such as telomere capping, telomere maintenance and telomere stabilization.Virus Replication: The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.Molecular Weight: The sum of the weight of all the atoms in a molecule.Endodeoxyribonucleases: A group of enzymes catalyzing the endonucleolytic cleavage of DNA. They include members of EC 3.1.21.-, EC 3.1.22.-, EC 3.1.23.- (DNA RESTRICTION ENZYMES), EC 3.1.24.- (DNA RESTRICTION ENZYMES), and EC 3.1.25.-.Bacteriophages: Viruses whose hosts are bacterial cells.DNA Polymerase III: A DNA-dependent DNA polymerase characterized in E. coli and other lower organisms but may be present in higher organisms. Use also for a more complex form of DNA polymerase III designated as DNA polymerase III* or pol III* which is 15 times more active biologically than DNA polymerase I in the synthesis of DNA. This polymerase has both 3'-5' and 5'-3' exonuclease activities, is inhibited by sulfhydryl reagents, and has the same template-primer dependence as pol II. EC, Density Gradient: Separation of particles according to density by employing a gradient of varying densities. At equilibrium each particle settles in the gradient at a point equal to its density. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Rad51 Recombinase: A Rec A recombinase found in eukaryotes. Rad51 is involved in DNA REPAIR of double-strand breaks.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Adenosine Triphosphate: An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter.Single-Strand Specific DNA and RNA Endonucleases: Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Nucleic Acids: High molecular weight polymers containing a mixture of purine and pyrimidine nucleotides chained together by ribose or deoxyribose linkages.Hydrolysis: The process of cleaving a chemical compound by the addition of a molecule of water.DNA Damage: Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. These deviations may be caused by physical or chemical agents and occur by natural or unnatural, introduced circumstances. They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR). If the damage is extensive, it can induce APOPTOSIS.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Microscopy, Electron: Microscopy using an electron beam, instead of light, to visualize the sample, thereby allowing much greater magnification. The interactions of ELECTRONS with specimens are used to provide information about the fine structure of that specimen. In TRANSMISSION ELECTRON MICROSCOPY the reactions of the electrons that are transmitted through the specimen are imaged. In SCANNING ELECTRON MICROSCOPY an electron beam falls at a non-normal angle on the specimen and the image is derived from the reactions occurring above the plane of the specimen.Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Oligoribonucleotides: A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Ultraviolet Rays: That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.Parvoviridae: A family of very small DNA viruses containing a single molecule of single-stranded DNA and consisting of two subfamilies: PARVOVIRINAE and DENSOVIRINAE. They infect both vertebrates and invertebrates.DNA Polymerase I: A DNA-dependent DNA polymerase characterized in prokaryotes and may be present in higher organisms. It has both 3'-5' and 5'-3' exonuclease activity, but cannot use native double-stranded DNA as template-primer. It is not inhibited by sulfhydryl reagents and is active in both DNA synthesis and repair. EC Proteins conjugated with deoxyribonucleic acids (DNA) or specific DNA.Rad52 DNA Repair and Recombination Protein: A DNA-binding protein that mediates DNA REPAIR of double strand breaks, and HOMOLOGOUS RECOMBINATION.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Replication Origin: A unique DNA sequence of a replicon at which DNA REPLICATION is initiated and proceeds bidirectionally or unidirectionally. It contains the sites where the first separation of the complementary strands occurs, a primer RNA is synthesized, and the switch from primer RNA to DNA synthesis takes place. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Recombinant Proteins: Proteins prepared by recombinant DNA technology.Electrophoresis, Agar Gel: Electrophoresis in which agar or agarose gel is used as the diffusion medium.Geminiviridae: A family of plant viruses where the VIRION possesses an unusual morphology consisting of a pair of isometric particles. Transmission occurs via leafhoppers or whitefly. Some viruses cause economically important diseases in cultivated plants. There are four genera: Mastrevirus, Curtovirus, Topocuvirus, and BEGOMOVIRUS.Polyribonucleotides: A group of 13 or more ribonucleotides in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Magnesium Chloride: Magnesium chloride. An inorganic compound consisting of one magnesium and two chloride ions. The compound is used in medicine as a source of magnesium ions, which are essential for many cellular activities. It has also been used as a cathartic and in alloys.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.Deinococcus: A genus of gram-positive aerobic cocci found in the soil, that is highly resistant to radiation, especially ionizing radiation (RADIATION, IONIZING). Deinococcus radiodurans is the type species.GuanineNucleotides: 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)DNA Topoisomerases, Type I: DNA TOPOISOMERASES that catalyze ATP-independent breakage of one of the two strands of DNA, passage of the unbroken strand through the break, and rejoining of the broken strand. DNA Topoisomerases, Type I enzymes reduce the topological stress in the DNA structure by relaxing the superhelical turns and knotted rings in the DNA helix.Ribonucleases: Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.Magnesium: A metallic element that has the atomic symbol Mg, atomic number 12, and atomic weight 24.31. It is important for the activity of many enzymes, especially those involved in OXIDATIVE PHOSPHORYLATION.Deamination: The removal of an amino group (NH2) from a chemical compound.DNA Polymerase II: A DNA-dependent DNA polymerase characterized in E. coli and other lower organisms. It may be present in higher organisms and has an intrinsic molecular activity only 5% of that of DNA Polymerase I. This polymerase has 3'-5' exonuclease activity, is effective only on duplex DNA with gaps or single-strand ends of less than 100 nucleotides as template, and is inhibited by sulfhydryl reagents. EC Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).Genes, Viral: The functional hereditary units of VIRUSES.Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.DNA-Directed RNA Polymerases: Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).SOS Response (Genetics): An error-prone mechanism or set of functions for repairing damaged microbial DNA. SOS functions (a concept reputedly derived from the SOS of the international distress signal) are involved in DNA repair and mutagenesis, in cell division inhibition, in recovery of normal physiological conditions after DNA repair, and possibly in cell death when DNA damage is extensive.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.DNA Nucleotidyltransferases: Enzymes that catalyze the incorporation of deoxyribonucleotides into a chain of DNA. EC 2.7.7.-.Dependovirus: A genus of the family PARVOVIRIDAE, subfamily PARVOVIRINAE, which are dependent on a coinfection with helper adenoviruses or herpesviruses for their efficient replication. The type species is Adeno-associated virus 2.G-Quadruplexes: Higher-order DNA and RNA structures formed from guanine-rich sequences. They are formed around a core of at least 2 stacked tetrads of hydrogen-bonded GUANINE bases. They can be formed from one two or four separate strands of DNA (or RNA) and can display a wide variety of topologies, which are a consequence of various combinations of strand direction, length, and sequence. (From Nucleic Acids Res. 2006;34(19):5402-15)Cytosine: A pyrimidine base that is a fundamental unit of nucleic acids.DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.DnaB Helicases: A family of DNA helicases that participate in DNA REPLICATION. They assemble into hexameric rings with a central channel and unwind DNA processively in the 5' to 3' direction. DnaB helicases are considered the primary replicative helicases for most prokaryotic organisms.Binding, Competitive: The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.RecQ Helicases: A family of structurally-related DNA helicases that play an essential role in the maintenance of genome integrity. RecQ helicases were originally discovered in E COLI and are highly conserved across both prokaryotic and eukaryotic organisms. Genetic mutations that result in loss of RecQ helicase activity gives rise to disorders that are associated with CANCER predisposition and premature aging.RNA Helicases: A family of proteins that promote unwinding of RNA during splicing and translation.Macromolecular Substances: Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Plant Viruses: Viruses parasitic on plants higher than bacteria.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Endoribonucleases: A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.Ribonucleoproteins: Complexes of RNA-binding proteins with ribonucleic acids (RNA).Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.Nanopores: Small holes of nanometer dimensions in a membrane, that can be used as single molecule detectors. The pores can be biological or synthetic.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).UracilChromatography, Affinity: A chromatographic technique that utilizes the ability of biological molecules to bind to certain ligands specifically and reversibly. It is used in protein biochemistry. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Poly U: A group of uridine ribonucleotides in which the phosphate residues of each uridine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Poly C: A group of cytosine ribonucleotides in which the phosphate residues of each cytosine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Thermodynamics: A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)Poly G: A group of guanine ribonucleotides in which the phosphate residues of each guanine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Heterogeneous-Nuclear Ribonucleoproteins: A family of ribonucleoproteins that were originally found as proteins bound to nascent RNA transcripts in the form of ribonucleoprotein particles. Although considered ribonucleoproteins they are primarily classified by their protein component. They are involved in a variety of processes such as packaging of RNA and RNA TRANSPORT within the nucleus. A subset of heterogeneous-nuclear ribonucleoproteins are involved in additional functions such as nucleocytoplasmic transport (ACTIVE TRANSPORT, CELL NUCLEUS) of RNA and mRNA stability in the CYTOPLASM.Spectrometry, Fluorescence: Measurement of the intensity and quality of fluorescence.Heterogeneous-Nuclear Ribonucleoprotein Group A-B: A class of closely related heterogeneous-nuclear ribonucleoproteins of approximately 34-40 kDa in size. Although they are generally found in the nucleoplasm, they also shuttle between the nucleus and the cytoplasm. Members of this class have been found to have a role in mRNA transport, telomere biogenesis and RNA SPLICING.Phosphorus Isotopes: Stable phosphorus atoms that have the same atomic number as the element phosphorus, but differ in atomic weight. P-31 is a stable phosphorus isotope.Salts: Substances produced from the reaction between acids and bases; compounds consisting of a metal (positive) and nonmetal (negative) radical. (Grant & Hackh's Chemical Dictionary, 5th ed)Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Aptamers, Nucleotide: Nucleotide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.Levivirus: A bacteriophage genus of the family LEVIVIRIDAE, whose viruses contain the short version of the genome and have a separate gene for cell lysis.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Simian virus 40: A species of POLYOMAVIRUS originally isolated from Rhesus monkey kidney tissue. It produces malignancy in human and newborn hamster kidney cell cultures.SELEX Aptamer Technique: A method of generating a large library of randomized nucleotides and selecting NUCLEOTIDE APTAMERS by iterative rounds of in vitro selection. A modified procedure substitutes AMINO ACIDS in place of NUCLEOTIDES to make PEPTIDE APTAMERS.DNA Breaks, Double-Stranded: Interruptions in the sugar-phosphate backbone of DNA, across both strands adjacently.Cross-Linking Reagents: Reagents with two reactive groups, usually at opposite ends of the molecule, that are capable of reacting with and thereby forming bridges between side chains of amino acids in proteins; the locations of naturally reactive areas within proteins can thereby be identified; may also be used for other macromolecules, like glycoproteins, nucleic acids, or other.Cations, Divalent: Positively charged atoms, radicals or groups of atoms with a valence of plus 2, which travel to the cathode or negative pole during electrolysis.ThymineCytidine Deaminase: An enzyme that catalyzes the deamination of cytidine, forming uridine. EC Nucleotides: Adenine nucleotides which contain deoxyribose as the sugar moiety.Sodium Chloride: A ubiquitous sodium salt that is commonly used to season food.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Bacillus subtilis: A species of gram-positive bacteria that is a common soil and water saprophyte.Poly dA-dT: Polydeoxyribonucleotides made up of deoxyadenine nucleotides and thymine nucleotides. Present in DNA preparations isolated from crab species. Synthetic preparations have been used extensively in the study of DNA.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Nanovirus: A genus in the family NANOVIRIDAE containing multiple circular single-stranded DNA molecules. The type species is Subterranean clover stunt virus.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Nucleoside-Triphosphatase: An enzyme which catalyzes the hydrolysis of nucleoside triphosphates to nucleoside diphosphates. It may also catalyze the hydrolysis of nucleotide triphosphates, diphosphates, thiamine diphosphates and FAD. The nucleoside triphosphate phosphohydrolases I and II are subtypes of the enzyme which are found mostly in viruses.TritiumMutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Pseudomonas Phages: Viruses whose host is Pseudomonas. A frequently encountered Pseudomonas phage is BACTERIOPHAGE PHI 6.Hydroxyapatites: A group of compounds with the general formula M10(PO4)6(OH)2, where M is barium, strontium, or calcium. The compounds are the principal mineral in phosphorite deposits, biological tissue, human bones, and teeth. They are also used as an anticaking agent and polymer catalysts. (Grant & Hackh's Chemical Dictionary, 5th ed)Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Base Pair Mismatch: The presence of an uncomplimentary base in double-stranded DNA caused by spontaneous deamination of cytosine or adenine, mismatching during homologous recombination, or errors in DNA replication. Multiple, sequential base pair mismatches lead to formation of heteroduplex DNA; (NUCLEIC ACID HETERODUPLEXES).Capsid: The outer protein protective shell of a virus, which protects the viral nucleic acid.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Minute virus of mice: The type species of PARVOVIRUS prevalent in mouse colonies and found as a contaminant of many transplanted tumors or leukemias.Uracil-DNA Glycosidase: An enzyme that catalyzes the HYDROLYSIS of the N-glycosidic bond between sugar phosphate backbone and URACIL residue during DNA synthesis.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Chromatography: Techniques used to separate mixtures of substances based on differences in the relative affinities of the substances for mobile and stationary phases. A mobile phase (fluid or gas) passes through a column containing a stationary phase of porous solid or liquid coated on a solid support. Usage is both analytical for small amounts and preparative for bulk amounts.Thymine Nucleotides: Phosphate esters of THYMIDINE in N-glycosidic linkage with ribose or deoxyribose, as occurs in nucleic acids. (From Dorland, 28th ed, p1154)Oligonucleotide Probes: Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.Chromatography, DEAE-Cellulose: A type of ion exchange chromatography using diethylaminoethyl cellulose (DEAE-CELLULOSE) as a positively charged resin. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)RNA Replicase: An enzyme that catalyses RNA-template-directed extension of the 3'- end of an RNA strand by one nucleotide at a time, and can initiate a chain de novo. (Enzyme Nomenclature, 1992, p293)Deoxyribonucleotides: A purine or pyrimidine base bonded to a DEOXYRIBOSE containing a bond to a phosphate group.Toll-Like Receptor 7: A pattern recognition receptor that binds several forms of imidazo-quinoline including the antiviral compound Imiquimod.Transformation, Genetic: Change brought about to an organisms genetic composition by unidirectional transfer (TRANSFECTION; TRANSDUCTION, GENETIC; CONJUGATION, GENETIC, etc.) and incorporation of foreign DNA into prokaryotic or eukaryotic cells by recombination of part or all of that DNA into the cell's genome.Oxytricha: A genus of ciliate protozoa having a unique cursorial type of locomotion.Microviridae: A large family of lytic bacteriophages infecting enterobacteria; SPIROPLASMA; BDELLOVIBRIO; and CHLAMYDIA. It contains four genera: MICROVIRUS; Spiromicrovirus; Bdellomicrovirus; and Chlamydiamicrovirus.Ribonucleotides: Nucleotides in which the purine or pyrimidine base is combined with ribose. (Dorland, 28th ed)Chromatography, Gel: Chromatography on non-ionic gels without regard to the mechanism of solute discrimination.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Hot Temperature: Presence of warmth or heat or a temperature notably higher than an accustomed norm.Toll-Like Receptor 8: A pattern recognition receptor that recognizes GUANOSINE and URIDINE-rich single-stranded RNA.Electrophoretic Mobility Shift Assay: An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.Genetic Vectors: DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.DNA Glycosylases: A family of DNA repair enzymes that recognize damaged nucleotide bases and remove them by hydrolyzing the N-glycosidic bond that attaches them to the sugar backbone of the DNA molecule. The process called BASE EXCISION REPAIR can be completed by a DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE which excises the remaining RIBOSE sugar from the DNA.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Nucleoproteins: Proteins conjugated with nucleic acids.

*  Single-Stranded DNA Uptake during Gonococcal Transformation

ComE binds to both double-stranded and single-stranded DNA (27). Single-stranded DNA enters the cytoplasm through a channel ... Double-stranded DUS supports uptake of otherwise single-stranded DNA. We set out to compare the DNA uptake efficiency of single ... Gonococcal Nuc can degrade double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) of various origins (8). Methylation of ... Here, we addressed the question whether this machine imports single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) at ...


Roles of functional loops and the C-terminal segment of a single-stranded DNA binding protein elucidated by X-Ray structure ... SINGLE STRANDED DNA BINDING PROTEIN A, B, C, D 178 Escherichia coli Gene Name(s): ssb exrB lexC b4059 JW4020 ... SINGLE STRANDED DNA BINDING PROTEIN AND SSDNA COMPLEX. *DOI: 10.2210/pdb1eqq/pdb ...

*  Sequence Similarity - 1GVP: GENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN) Sequence Similarity Report Page

1GVP: Analyses of the stability and function of three surface mutants (R82C, K69H, and L32R) of the gene V protein from Ff phage by X-ray crystallography.

*  DNA single-strand breaks - Humpath.com - Human pathology

DNA single strand damage, DNA single strand breaks, SSBs ... DNA single-strand breaks. DNA single-strand breaks. Tuesday 7 ... These include bulky, helix distorting damage, such as thymine dimerization caused by UV light as well as single-strand breaks. ... When only one of the two strands of a chromosome has a defect, the other strand can be used as a template to guide the ... In order to repair damage to one of the two helical domains of DNA, there are numerous mechanisms by which DNA repair can take ...


Single Stranded DNA Binding * DNA Replication * Rolling Circle Single Stranded Viral DNA Replication ...



*  How single mutations in genes can be repaired with single-strand DNA fragments - InfoBarrel

Sequence-specific strings of (less than fifty) nucleotides can serve as primers for the polymerase chain reaction and DNA ... Short, single-strand nucleotides have emerged as a group of extremely useful and versatile molecules that can direct an array ... How single mutations in genes can be repaired with single-strand DNA fragments. By ScienceOfSimplicity Jun 19, 2010 ... Gene repair is initiated by the introduction of short single strands of naked DNA molecules that are designed to anneal with a ...

*  APOBEC3A deaminates transiently exposed single-strand DNA during LINE-1 retrotransposition | eLife

... that the cytidine deaminase APOBEC3A can inhibit LINE-1 retrotransposition by deaminating transiently exposed single-strand DNA ... mediated deamination events occur on single-strand DNA during TPRT rather than on L1 mRNA or single-strand episomal plasmid DNA ... recreate the copying of LINE-1 RNA back into DNA in a test tube-and reveal that APOBEC3A can mutate single-strand LINE-1 DNA. ... As expected rA3A had cytidine deaminase activity on single-strand (Figure 2B), but not on double-stranded DNA (Figure 2-figure ...

*  European Commission : CORDIS : Publications : DNA double strand breaks from two single strand breaks and cell cycle radiation...

DNA double strand breaks from two single strand breaks and cell cycle radiation sensitivity. Funded under: FP2-RADPROT 7C ... DNA double strand breaks from two single strand breaks and cell cycle radiation sensitivity ...

*  Study on the electrical control of graphene with single-stranded DNA | (2015) | Kim | Publications | Spie

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Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule. ... NONCOVALENT COMPLEX OF E.COLI DNA TOPOISOMERASE III WITH AN 8-BASE SINGLE-STRANDED DNA OLIGONUCLEOTIDE. ...


... similarity to other proteins binding to single-stranded nucleic acids. ... Solution structure of the single-stranded DNA binding protein of the filamentous Pseudomonas phage Pf3: ... SOLUTION NMR STRUCTURE OF THE SINGLE-STRANDED DNA BINDING PROTEIN OF THE FILAMENTOUS PSEUDOMONAS PHAGE PF3, MINIMIZED AVERAGE ...

*  Federal Circuit holds that claims directed to single-stranded DNA primers and screening methods using those DNA primers were...

The CAFC held that claims directed to single-stranded DNA primers and screening methods using those DNA primers were directed ... The CAFC explained that the single-strand DNA primers were structurally identical to DNA strands found in nature. Citing the ... Federal Circuit holds that claims directed to single-stranded DNA primers and screening methods using those DNA primers were ... The CAFC held that claims directed to single-stranded DNA primers and screening methods using those DNA primers were directed ...

*  Chimerx: Taq Single-stranded DNA Binding Protein - DNA/RNA Modifying Enzymes

Thermostable single-stranded specific DNA binding protein suitable for high temperature DNA manipulations ... Prevents inhibition of PCR by template DNA contaminants (2). *Improves the efficiency of DNA amplification by Taq DNA ...

*  FARA - LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures

The anti-gene strategy is based on sequence-specific recognition of double-strand DNA by triplex forming (TFOs) or DNA strand ... LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures Details Written by Jen Farmer ... LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures ... We found that LNA-containing single strand TFOs are conformationally pre-organized for major groove binding. Reduced content of ...

*  Chimerx: Single-stranded DNA Binding Protein, E. coli - DNA/RNA Modifying Enzymes

Prevents inhibition of PCR by template DNA contaminants (2). *Improves efficiency of DNA amplification by Taq DNA Polymerase (3 ... Prevents degradation of single stranded DNA by nucleases. * ... DNA/RNA Modifying Enzymes / * Single-stranded DNA Binding ... Enhances fidelity of modified T4 DNA Polymerase (8). Storage Buffer. 20 mM Tris-HCl (pH 7.8 at 22°C). 300 mM NaCl. 5 mM β- ... Improves efficiency of DNA synthesis by T4 DNA Polymerase (8). * ... Single-stranded DNA Binding Protein, E. coli. Catalog No. 4200 ...

*  Chimerx: RecA Protein - Single-Stranded DNA Binding Proteins - DNA/RNA Modifying Enzymes

Bacterial recombination protein that enhances interaction and exchange of homologous DNA strands. ... Binds cooperatively and stechiometrically to single-stranded DNA.. *In presence of ATP-g-S, locates and pairs a single-stranded ... DNA sequence to its homologous double-stranded DNA.. *Cleaves large fragments of DNA (RARE-Rec A Assisted Restriction ... All preparations are assayed for endonuclease and nonspecific single- and double-stranded DNase activities. Typically ...

*  Decomposition of thymidine by low-energy electrons: Implications for the molecular mechanisms of single-strand breaks in DNA -...

Decomposition of thymidine by low-energy electrons: Implications for the molecular mechanisms of single-strand breaks in DNA ... Decomposition of thymidine by low-energy electrons: Implications for the molecular mechanisms of single-strand breaks in DNA.. ... anions; DNA damage; electron attachment; gas-phase reactions; nucleotides. Academic Unit/School:. Faculty of Science, ...

*  Reactome | DNA ligase I ligates single stranded nick in double stranded DNA

DNA ligase I ligates single stranded nick in double stranded DNA Stable Identifier ... DNA ligase I ligates single stranded nick in double stranded DNA (Drosophila melanogaster) ... DNA ligase I ligates single stranded nick in double stranded DNA (Drosophila melanogaster) ... DNA ligase I ligates single stranded nick in double stranded DNA (Homo sapiens) ...

*  Ultrafast redistribution of E. coli SSB along long single-stranded DNA via intersegment transfer - The Ha Lab

Ultrafast redistribution of E. coli SSB along long single-stranded DNA via intersegment transfer (K. S. Lee, A. B. Marciel, A. ... Ultrafast redistribution of E. coli SSB along long single-stranded DNA via intersegment transfer ... Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation ( September 17, 2015 ) ... along long single-stranded {D}{N}{A} via intersegment transfer}', Journal='J. Mol. Biol.', Year='2014', Volume='426', Number=' ...

*  Histone methyltransferase Dot1 and Rad9 inhibit single-stranded DNA accumulation at DSBs and uncapped telomeres - ePrints -...

Histone methyltransferase Dot1 and Rad9 inhibit single-stranded DNA accumulation at DSBs and uncapped telomeres. *Lookup NU ...

*  Vol 14: Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria Desulfotalea psychrophila,...

This article is from BMC Microbiology, volume 14.AbstractBackground: Single-stranded DNA-binding proteins (SSBs) play es. ... Vol 14: Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria Desulfotalea psychrophila, ... Single-stranded DNA-binding proteins (SSBs) play essential roles in DNA replication, recombination and repair in Bacteria, ... Download or read this book online for free in PDF: Vol 14: Characterization of single-stranded DNA-binding proteins from the ...

*  Chimeras between single-stranded DNA-binding proteins from Escherichia coli and Mycobacterium tuberculosis reveal that their C...

Chimeras between single-stranded DNA-binding proteins from Escherichia coli and Mycobacterium tuberculosis reveal that their C- ... Priya, Handa and Narottam, Acharya and Umesh, Varshney (2001) Chimeras between single-stranded DNA-binding proteins from ... We recently reported that the Escherichia coli single-stranded DNA binding protein (SSB) facilitated uracil excision from ... Chimeras_between_single-stranded.pdf Restricted to Registered users only Download (482Kb) , Request a copy ...

*  EMD-2339 -- Variable internal flexibility characterizes the helical capsid formed by agrobacterium VirE2 protein on single...

It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. ... Variable internal flexibility characterizes the helical capsid formed by agrobacterium VirE2 protein on single-stranded DNA ... Variable internal flexibility characterizes the helical capsid formed by Agrobacterium VirE2 protein on single-stranded DNA.. ... Variable internal flexibility characterizes the helical capsid formed by agrobacterium VirE2 protein on single-stranded DNA. ...

*  DSpace at KIST: Optimal conditions of single cell gel electrophoresis(comet) assay to detect DNA single strand breaks in mouse...

Optimal conditions of single cell gel electrophoresis(comet) assay to detect DNA single strand breaks in mouse lymphoma L5178Y ... Optimal conditions of single cell gel electrophoresis(comet) assay to detect DNA single strand breaks in mouse lymphoma L5178Y ... single cell gel electrophoresis; Comet; Tail Moment; Mouse lymphoma L5178 cell; DNA single strand breakage; Methyl ... Recently, single cell gel electrophoresis, also known as comet assay, is widely used for the detection and measurement of DNA ...

Sticky and blunt ends: DNA end or sticky end refers to the properties of the end of a molecule of DNA or a recombinant DNA molecule. The concept is important in molecular biology, especially in cloning or when subcloning inserts DNA into vector DNA.Nucleic acid structure: Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar.Symmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.DNA re-replication: DNA re-replication (or simply rereplication) is an undesirable and possibly fatal occurrence in eukaryotic cells in which the genome is replicated more than once per cell cycle. Rereplication is believed to lead to genomic instability and has been implicated in the pathologies of a variety of human cancers.DNA-binding proteinColes PhillipsDNA condensation: DNA condensation refers to the process of compacting DNA molecules in vitro or in vivo. Mechanistic details of DNA packing are essential for its functioning in the process of gene regulation in living systems.List of strains of Escherichia coli: Escherichia coli is a well studied bacterium that was first identified by Theodor Escherich, after whom it was later named.Hyperchromicity: Hyperchromicity is the increase of absorbance (optical density) of a material. The most famous example is the hyperchromicity of DNA that occurs when the DNA duplex is denatured.Abscription: During normal transcription, RNA polymerase transcribes a number of short nonproductive oligonucleotides, and this process is called abortive transcription. The trapped RNAPs have been named abscriptases and the synthesis of specific length oligonucleotides called abscription.CccDNA: cccDNA (covalently closed circular DNA) is a special DNA structure that arises during the propagation of some viruses in the cell nucleus and may remain permanently there. It is a double-stranded DNA that originates in a linear form that is ligated by means of DNA ligase to a covalently closed ring.Microviridae: Microviridae is a family of bacteriophages with a single-stranded DNA genome. The name of this family is derived from the Greek micro, meaning small.Proximity ligation assay: Proximity ligation assay (in situ PLA) is a technology that extends the capabilities of traditional immunoassays to include direct detection of proteins, protein interactions and modifications with high specificity and sensitivity. Protein targets can be readily detected and localized with single molecule resolution and objectively quantified in unmodified cells and tissues.YjdF RNA motifEnterobacteria phage G4: Enterobacteria phage G4 is a bacteriophage capable of infecting susceptible bacterial cells. The phage was originally isolated from samples of raw sewage and infects E.CpG OligodeoxynucleotidePrimase: DNA primase, also called as DNA primerase, is an enzyme involved in the replication of DNA. DNA primase is a type of RNA polymerase which creates an RNA primer (later this RNA piece is removed by a 5' to 3' exonuclease); next, DNA polymerase uses the RNA primer to replicate ssDNA.Triparental mating: Triparental mating is a form of Bacterial conjugation where a conjugative plasmid present in one bacterial strain assists the transfer of a mobilizable plasmid present in a second bacterial strain into a third bacterial strain. Plasmids are introduced into bacteria for such purposes as transformation, cloning, or transposon mutagenesis.Burst kinetics: Burst kinetics is a form of enzyme kinetics that refers to an initial high velocity of enzymatic turnover when adding enzyme to substrate. This initial period of high velocity product formation is referred to as the "Burst Phase".Exonuclease: Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain. A hydrolyzing reaction that breaks phosphodiester bonds at either the 3’ or the 5’ end occurs.DeoxyribonucleaseT7 DNA polymerase: T7 DNA polymerase is an enzyme used during the DNA replication of the T7 bacteriophage. During this process, the DNA polymerase “reads” existing DNA strands and creates two new strands that match the existing ones.Specificity constant: In the field of biochemistry, the specificity constant (also called kinetic efficiency or k_{cat}/K_{M}), is a measure of how efficiently an enzyme converts substrates into products. A comparison of specificity constants can also be used as a measure of the preference of an enzyme for different substrates (i.Recombination (cosmology): In cosmology, recombination refers to the epoch at which charged electrons and protons first became bound to form electrically neutral hydrogen atoms.Note that the term recombination is a misnomer, considering that it represents the first time that electrically neutral hydrogen formed.AAA proteins: For other uses see AAA (disambiguation)DNA binding site: DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites are distinct from other binding sites in that (1) they are part of a DNA sequence (e.Protein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.Base excision repair: frame|right|Basic steps of base excision repair|Basic steps of base excision repairSilent mutation: Silent mutations are mutations in DNA that do not significantly alter the phenotype of the organism in which they occur. Silent mutations can occur in non-coding regions (outside of genes or within introns), or they may occur within exons.Excision repair cross-complementing: Excision repair cross-complementing (ERCC) is a set of proteins which are involved in DNA repair.RNA interference: RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecules. Historically, it was known by other names, including co-suppression, post-transcriptional gene silencing (PTGS), and quelling.Nudivirus: A nudivirus (family Nudiviridae) is a large, rod-shaped virus with a circular, double stranded DNA genome of 96–231 kb. The genome encodes 98 to 154 open reading frames.Reaction coordinateFerric uptake regulator family: In molecular biology, the ferric uptake regulator (FUR) family of proteins includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria.Escherichia coli (molecular biology): Escherichia coli (; commonly abbreviated E. coli) is a gammaproteobacterium commonly found in the lower intestine of warm-blooded organisms (endotherms).Telomere: A telomere is a region of repetitive nucleotide sequences at each end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes. Its name is derived from the Greek nouns telos (τέλος) 'end' and merοs (μέρος, root: μερ-) 'part.Chi site: A Chi site or Chi sequence is a short stretch of DNA in the genome of a bacterium near which homologous recombination is more likely than expected to occur. Chi sites serve as stimulators of DNA double-strand break repair in bacteria, which can arise from radiation or chemical treatments, or result from replication fork breakage during DNA replication.Mycovirus: Mycoviruses (ancient Greek μύκης mykes: fungus and Latin virus) are viruses that infect fungi. The majority of mycoviruses have double-stranded RNA (dsRNA) genomes and isometric particles, but approximately 30% have positive sense, single-stranded RNA (+ssRNA) genomes.Polynucleotide: A polynucleotide molecule is a biopolymer composed of 13 or more nucleotide monomers covalently bonded in a chain. DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are examples of polynucleotides with distinct biological function.Single-strand conformation polymorphism: Single-strand conformation polymorphism (SSCP), or single-strand chain polymorphism, is defined as conformational difference of single-stranded nucleotide sequences of identical length as induced by differences in the sequences under certain experimental conditions. This property allows sequences to be distinguished by means of gel electrophoresis, which separates fragments according to their different conformations.Telomere-binding protein: Telomere-binding proteins are proteins that mediate telomere function by binding to them. There are two types of telomere-binding proteins: single-strand DNA telomere binding proteins and double-strand DNA telomere binding proteins.Molar mass distribution: In linear polymers the individual polymer chains rarely have exactly the same degree of polymerization and molar mass, and there is always a distribution around an average value. The molar mass distribution (or molecular weight distribution) in a polymer describes the relationship between the number of moles of each polymer species (Ni) and the molar mass (Mi) of that species.Excinuclease: Excision endonuclease, also known as excinuclease or UV-Specific Endonuclease, is a nuclease (enzyme) which excises a fragment of nucleotides during DNA repair. The excinuclease cuts out a fragment by hydrolyzing two phosphodiester bonds, one on either side of the lesion in the DNA.CTXφ Bacteriophage: The CTXφ bacteriophage is a filamentous bacteriophage that contains the genetic material needed by the Vibrio cholerae bacterium for the production of cholera toxin, or CT. CTXφ is a positive virus with single-stranded DNA (ssDNA).HolE: In E. coli and other bacteria, holE is a gene that encodes the theta subunit of DNA polymerase III.Buoyant density ultracentrifugation: Buoyant density centrifugation uses the concept of buoyancy to separate molecules in solution. Usually a caesium chloride (CsCl) solution is used, but in the general case it's usually approximately the same density as the molecules that are to be centrifuged.Ligation-independent cloning: Ligation-independent cloning (LIC) is a form of molecular cloning that is able to be performed without the use of restriction endonucleases or DNA ligase. This allows genes that have restriction sites to be cloned without worry of chopping up the insert.Inhibitor protein: The inhibitor protein (IP) is situated in the mitochondrial matrix and protects the cell against rapid ATP hydrolysis during momentary ischaemia. In oxygen absence, the pH of the matrix drops.Margaret Jope: Margaret Jope (1913–2004) was a Scottish biochemist, born as Henrietta Margaret Halliday in Peterhead, Scotland.Nucleic acid secondary structure: The secondary structure of a nucleic acid molecule refers to the basepairing interactions within a single molecule or set of interacting molecules, and can be represented as a list of bases which are paired in a nucleic acid molecule.G2-M DNA damage checkpoint: The G2-M DNA damage checkpoint is an important cell cycle checkpoint in eukaryotic organisms ranging from yeast to mammals. This checkpoint ensures that cells don't initiate mitosis before they have a chance to repair damaged DNA after replication.Zuotin: Z-DNA binding protein 1, also known as Zuotin, is a Saccharomyces cerevisiae yeast gene.FERM domain: In molecular biology, the FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane.Low-voltage electron microscope: Low-voltage electron microscope (LVEM) is an electron microscope which operates at accelerating voltages of a few kiloelectronvolts or less. While the low voltage electron microscopy technique will never replace conventional high voltage electron microscopes, it is quickly becoming appreciated for many different disciplines.Permissive temperature: The permissive temperature is the temperature at which a temperature sensitive mutant gene product takes on a normal, functional phenotype.http://www.UVB-induced apoptosis: UVB-induced apoptosis is the programmed cell death of cells that become damaged by ultraviolet rays. This is notable in skin cells, to prevent melanoma.Bovine parvovirus: Bovine parvovirus (BPV), also known as Haemadsorbing Enteric Virus, is a member of the parvivirus group, with three significant sub-species: BPV1, 2 and 3. BPV most commonly causes diarrhoea in neonatal calves and respiratory and reproductive disease in adult cattle.Klenow fragmentRestriction fragment: A restriction fragment is a DNA fragment resulting from the cutting of a DNA strand by a restriction enzyme (restriction endonucleases), a process called restriction. Each restriction enzyme is highly specific, recognising a particular short DNA sequence, or restriction site, and cutting both DNA strands at specific points within this site.Origin of replication: The origin of replication (also called the replication origin) is a particular sequence in a genome at which replication is initiated.Technical Glossary Edward K.Eukaryotic transcription: Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells.RNA-binding protein database: The RNA-binding Proteins Database (RBPDB) is a biological database of RNA-binding protein specificities that includes experimental observations of RNA-binding sites. The experimental results included are both in vitro and in vivo from primary literature.Base pair: Base pairs (unit: bp), which form between specific nucleobases (also termed nitrogenous bases), are the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs (guanine-cytosine and adenine-thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence.

(1/5092) Impaired translesion synthesis in xeroderma pigmentosum variant extracts.

Xeroderma pigmentosum variant (XPV) cells are characterized by a cellular defect in the ability to synthesize intact daughter DNA strands on damaged templates. Molecular mechanisms that facilitate replication fork progression on damaged DNA in normal cells are not well defined. In this study, we used single-stranded plasmid molecules containing a single N-2-acetylaminofluorene (AAF) adduct to analyze translesion synthesis (TLS) catalyzed by extracts of either normal or XPV primary skin fibroblasts. In one of the substrates, the single AAF adduct was located at the 3' end of a run of three guanines that was previously shown to induce deletion of one G by a slippage mechanism. Primer extension reactions performed by normal cellular extracts from four different individuals produced the same distinct pattern of TLS, with over 80% of the products resulting from the elongation of a slipped intermediate and the remaining 20% resulting from a nonslipped intermediate. In contrast, with cellular extracts from five different XPV patients, the TLS reaction was strongly reduced, yielding only low amounts of TLS via the nonslipped intermediate. With our second substrate, in which the AAF adduct was located at the first G in the run, thus preventing slippage from occurring, we confirmed that normal extracts were able to perform TLS 10-fold more efficiently than XPV extracts. These data demonstrate unequivocally that the defect in XPV cells resides in translesion synthesis independently of the slippage process.  (+info)

(2/5092) The DNA binding activity of Translin is mediated by a basic region in the ring-shaped structure conserved in evolution.

DNA binding proteins, for the most part, function as dimers or tetramers which recognize their target sequences. Here we show that Translin, a novel single-stranded DNA end binding protein, forms a ring-shaped structure conserved throughout evolution and that this structure is responsible for its DNA binding activity. Point mutations at Leu184 and Leu191 in the leucine zipper motif of human Translin resulted in loss of the multimeric structure and abrogation of DNA binding. Point mutations at R86, H88, H90 to T86, N88, N90 in one of the basic regions, however, completely inhibited the DNA binding activity without affecting the multimeric structure. These results support the view that the DNA binding domain of Translin is formed in the ring-shaped structure in combination with its basic region (amino acids 86-97) polypeptides.  (+info)

(3/5092) Mutations and allelic deletions of the MEN1 gene are associated with a subset of sporadic endocrine pancreatic and neuroendocrine tumors and not restricted to foregut neoplasms.

Endocrine pancreatic tumors (EPT) and neuroendocrine tumors (NET) occur sporadically and rarely in association with multiple endocrine neoplasia type 1 (MEN1). We analyzed the frequency of allelic deletions and mutations of the recently identified MEN1 gene in 53 sporadic tumors including 30 EPT and 23 NET (carcinoids) of different locations and types. Allelic deletion of the MEN1 locus was identified in 18/49 (36.7%) tumors (13/30, 43.3% in EPT and 5/19, 26.3% in NET) and mutations of the MEN1 gene were present in 8/52 (15.3%) tumors (4/30 (13.3%) EPT and 4/22 (18.1%) NET). The somatic mutations were clustered in the 5' region of the coding sequence and most frequently encompassed missense mutations. All tumors with mutations exhibited a loss of the other allele and a wild-type sequence of the MEN1 gene in nontumorous DNA. In one additional patient with a NET of the lung and no clinical signs or history of MEN1, a 5178-9G-->A splice donor site mutation in intron 4 was identified in both the tumor and blood DNA, indicating the presence of a thus far unknown MEN1 syndrome. In most tumor groups the frequency of allelic deletions at 11q13 was 2 to 3 times higher than the frequency of identified MEN1 gene mutations. Some tumor types, including rare forms of EPT and NET of the duodenum and small intestine, exhibited mutations more frequently than other types. Furthermore, somatic mutations were not restricted to foregut tumors but were also detectable in a midgut tumor (15.2% versus 16.6%). Our data indicate that somatic MEN1 gene mutations contribute to a subset of sporadic EPT and NET, including midgut tumors. Because the frequency of mutations varies significantly among the investigated tumor subgroups and allelic deletions are 2 to 3 times more frequently observed, factors other than MEN1 gene inactivation, including other tumor-suppressor genes on 11q13, may also be involved in the tumorigenesis of these neoplasms.  (+info)

(4/5092) An allosteric synthetic DNA.

Allosteric DNA oligonucleotides are potentially useful diagnostic reagents. Here we develop a model system for the study of allosteric interactions in DNAs. A DNA that binds either Cibacron blue or cholic acid was isolated and partially characterized. Isolation was performed using a multi-stage SELEX. First, short oligos that bind either Cibacron blue or cholic acid were enriched from random oligonucleotide pools. Then, members of the two pools were fused to form longer oligos, which were then selected for theability to bind Cibacron blue columns and elute with cholic acid. One resulting isolate (A22) was studied. Dye- and cholate-binding functions can be separated on sequences from the 5'- and 3'-regions, respectively. Ligand-column affinity assays indicate that each domain binds only its respective ligand. However, the full-length A22 will bind either dye or cholate columns and elute with the other ligand, as if binding by the ligands is mutually exclusive. Furthermore, S1 nuclease protection assays show that Cibacron blue causes a structural change in A22 and that cholic acid inhibits this change. This system will be useful for elucidating mechanisms of allosteric interactions in synthetic DNAs.  (+info)

(5/5092) The binding affinity of Ff gene 5 protein depends on the nearest-neighbor composition of the ssDNA substrate.

The Ff gene 5 protein (g5p) is considered to be a nonspecific single-stranded DNA binding protein, because it binds cooperatively to and saturates the Ff bacteriophage single-stranded DNA genome and other single-stranded polynucleotides. However, the binding affinity Komega (the intrinsic binding constant times a cooperativity factor) differs by over an order of magnitude for binding to single-stranded polynucleotides such as poly[d(A)] and poly[d(C)]. A polynucleotide that is more stacked, like poly[d(A)], binds more weakly than one that is less stacked, like poly[d(C)]. To test the hypothesis that DNA base stacking, a nearest-neighbor property, is involved in the binding affinity of the Ff g5p for different DNA sequences, Komega values were determined as a function of NaCl concentration for binding to six synthetic sequences 48 nucleotides in length: dA48, dC48, d(AAC)16, d(ACC)16, d(AACC)12, and d(AAACC)9A3. The binding affinities of the protein for these sequences were indeed found to be related to the nearest-neighbor compositions of the sequences, rather than to simple base compositions. That is, the g5p binding site, which is spanned by four nucleotides, discriminates among these sequences on the basis of the relative numbers of nearest neighbors (AA, CC, and AC plus CA) in the sequence. The results support the hypothesis that the extent of base stacking/unstacking of the free, nonbound ssDNA plays an important role in the binding affinity of the Ff gene 5 protein.  (+info)

(6/5092) Identification of RNase T as a high-copy suppressor of the UV sensitivity associated with single-strand DNA exonuclease deficiency in Escherichia coli.

There are three known single-strand DNA-specific exonucleases in Escherichia coli: RecJ, exonuclease I (ExoI), and exonuclease VII (ExoVII). E. coli that are deficient in all three exonucleases are abnormally sensitive to UV irradiation, most likely because of their inability to repair lesions that block replication. We have performed an iterative screen to uncover genes capable of ameliorating the UV repair defect of xonA (ExoI-) xseA (ExoVII-) recJ triple mutants. In this screen, exonuclease-deficient cells were transformed with a high-copy E. coli genomic library and then irradiated; plasmids harvested from surviving cells were used to seed subsequent rounds of transformation and selection. After several rounds of selection, multiple plasmids containing the rnt gene, which encodes RNase T, were found. An rnt plasmid increased the UV resistance of a xonA xseA recJ mutant and uvrA and uvrC mutants; however, it did not alter the survival of xseA recJ or recA mutants. RNase T also has amino acid sequence similarity to other 3' DNA exonucleases, including ExoI. These results suggest that RNase T may possess a 3' DNase activity capable of substituting for ExoI in the recombinational repair of UV-induced lesions.  (+info)

(7/5092) Nuclear foci of mammalian recombination proteins are located at single-stranded DNA regions formed after DNA damage.

A sensitive and rapid in situ method was developed to visualize sites of single-stranded (ss) DNA in cultured cells and in experimental test animals. Anti-bromodeoxyuridine antibody recognizes the halogenated base analog incorporated into chromosomal DNA only when substituted DNA is in the single strand form. After treatment of cells with DNA-damaging agents or gamma irradiation, ssDNA molecules form nuclear foci in a dose-dependent manner within 60 min. The mammalian recombination protein Rad51 and the replication protein A then accumulate at sites of ssDNA and form foci, suggesting that these are sites of recombinational DNA repair.  (+info)

(8/5092) Structure of DNA-dependent protein kinase: implications for its regulation by DNA.

DNA double-strand breaks are created by ionizing radiation or during V(D)J recombination, the process that generates immunological diversity. Breaks are repaired by an end-joining reaction that requires DNA-PKCS, the catalytic subunit of DNA-dependent protein kinase. DNA-PKCS is a 460 kDa serine-threonine kinase that is activated by direct interaction with DNA. Here we report its structure at 22 A resolution, as determined by electron crystallography. The structure contains an open channel, similar to those seen in other double-stranded DNA-binding proteins, and an enclosed cavity with three openings large enough to accommodate single-stranded DNA, with one opening adjacent to the open channel. Based on these structural features, we performed biochemical experiments to examine the interactions of DNA-PKCS with different DNA molecules. Efficient kinase activation required DNA longer than 12 bp, the minimal length of the open channel. Competition experiments demonstrated that DNA-PKCS binds to double- and single-stranded DNA via separate but interacting sites. Addition of unpaired single strands to a double-stranded DNA fragment stimulated kinase activation. These results suggest that activation of the kinase involves interactions with both double- and single-stranded DNA, as suggested by the structure. A model for how the kinase is regulated by DNA is described.  (+info)


  • Uracil, a promutagenic base in DNA can arise by spontaneous deamination of cytosine or incorporation of dUMP by DNA polymerase. (iisc.ernet.in)
  • Incoming partly double stranded hepatitis B virus (HBV) DNA genomes are completed by the viral polymerase generating relaxed circular DNA (rcDNA). (biomedcentral.com)
  • The copy of gp5 (the DNA polymerase) acting on the lagging strand can be washed away, allowing observation of the processivity of leading-strand replication in isolation. (biomedcentral.com)
  • Restoring the second polymerase and adding the T7 single-strand binding protein makes the looping out of lagging strand DNA itself observable as transient changes in the length of the tethered DNA. (biomedcentral.com)
  • In prokaryotes, the leading strand replication apparatus consists of a DNA polymerase (pol III core), a sliding clamp (beta), and a clamp loader (gamma delta complex). (genome.jp)
  • DNA primase forms a permanent complex with DNA polymerase alpha. (genome.jp)

binding protein

  • We recently reported that the Escherichia coli single-stranded DNA binding protein (SSB) facilitated uracil excision from certain structured substrates by E. coli UDG (EcoUDG) and suggested the existence of interaction between SSB and UDG. (iisc.ernet.in)


  • By using hydroxyurea to introduce similar DNA replication defects, we found that single-stranded DNA breaks frequently lead to double-stranded DNA breaks that are not rapidly repaired in rad52 mutants. (genetics.org)
  • Taken together, these data suggest that the RAD52 recombinational repair pathway is required to prevent or repair double-stranded DNA breaks caused by defective DNA replication in mec1-srf mutants. (genetics.org)
  • Measurements of processivity are possible because the passage of the replication fork on the tethered DNA causes long double-stranded (ds) DNA to be transformed into more compact single-stranded (ss) DNA. (biomedcentral.com)


  • David Sherratt (University of Oxford, UK) presented the latest news on the death of the stationary 'replication factory' model of DNA replication in Escherichia coli , reporting the work of his colleague Rodrigo Reyes, who has fluorescently labeled many of the components of the DNA replication machinery to track the progress of the replication forks in vivo . (biomedcentral.com)

compensating for DNA replication

  • To examine the role of the RAD52 recombinational repair pathway in compensating for DNA replication defects in Saccharomyces cerevisiae , we performed a genetic screen to identify mutants that require Rad52p for viability. (genetics.org)

leading-strand replication

  • On the leading strand, replication occurs continuously in a 5 to 3 direction, whereas on the lagging strand, DNA replication occurs discontinuously by synthesis and joining of short Okazaki fragments. (genome.jp)


  • Proteins essential for homologous recombination play a pivotal role in the repair of DNA double strand breaks, DNA inter-strand crosslinks and replication fork stability. (washington.edu)
  • RAD51, an essential factor for homologous recombination and replication fork protection, accumulates and forms immunocytochemically detectable nuclear foci at sites of DNA damage. (washington.edu)
  • Interestingly, we found that knockout of Nek8 in murine embryonic fibroblasts leads to cellular sensitivity to the replication inhibitor, hydroxyurea (HU), but not to other DNA damaging agents. (washington.edu)
  • Loading of the essential DNA repair and replication fork protection factors, RAD51 and BRCA2, was decreased in NEK8 depleted and deficient cells lines. (washington.edu)
  • Thus, NEK8 plays a critical role in replication fork stability through its regulation of the DNA repair and replication fork protection protein RAD51. (washington.edu)
  • Thus, it appears to be the DNA replication defects in mec1-srf mutants that cause the requirement for Rad52p. (genetics.org)
  • Proper replication of the genome is also ensured by regulatory mechanisms that must coordinate the activity of DNA synthesis and DNA repair pathways. (genetics.org)
  • The replication of HBV involves the production of covalently closed circular DNA (cccDNA) from the HBV genome through the repair of virion relaxed circular DNA (rcDNA) in the virion. (biomedcentral.com)
  • this report describes just a few of the most striking innovations in technology and concepts presented at the meeting, with particular reference to bacterial DNA replication. (biomedcentral.com)
  • Antoine van Oijen (Harvard Medical School, Boston, USA) amusingly described the problem of ensemble averaging in DNA replication as an alien race concluding that humans must each have one testicle and one ovary. (biomedcentral.com)
  • Stephen Bell (University of Oxford, UK) described his laboratory's investigations into DNA replication in the archaeal genus Sulfolobus . (biomedcentral.com)
  • Ever since Watson and Crick first proposed their model of DNA replication, the topological problem of overwinding the helix during its duplication has been obvious. (biomedcentral.com)
  • The primary conclusions of these experiments is that at short time scales the replisome assembled at each replication fork moves separately along what is assumed to be the path of the compacted DNA. (biomedcentral.com)
  • These observations defy the possibility of a stationary replication factory from which the nascent DNA is extruded, at least in E. coli . (biomedcentral.com)
  • A complex network of interacting proteins and enzymes is required for DNA replication. (genome.jp)
  • Generally, DNA replication follows a multistep enzymatic pathway. (genome.jp)
  • At the DNA replication fork, a DNA helicase (DnaB or MCM complex) precedes the DNA synthetic machinery and unwinds the duplex parental DNA in cooperation with the SSB or RPA. (genome.jp)
  • Normally, during replication of the lagging-strand DNA template, an RNA primer is removed either by an RNase H or by the 5 to 3 exonuclease activity of DNA pol I, and the DNA ligase joins the Okazaki fragments. (genome.jp)
  • Smart machines at the DNA replication fork. (genome.jp)
  • The DNA replication fork in eukaryotic cells. (genome.jp)


  • THE activities of many different proteins must be coordinated to perform the different steps of DNA synthesis, and defects in these proteins can result in the requirement for compensatory mechanisms to complete DNA synthesis. (genetics.org)
  • These proteins are of interest as alteration in their expression results in defects in DNA segregation. (biomedcentral.com)


  • FEN 1 and RNase H1 remove the RNA from the Okazaki fragments and DNA ligase I joins the DNA. (genome.jp)


  • Using single-molecule DNA fiber analysis, we show that nascent DNA tracts are degraded in the absence of NEK8 following treatment with HU. (washington.edu)


  • Uracil is removed from DNA by uracil DNA glycosylase (UDG), the first enzyme in the uracil excision repair pathway. (iisc.ernet.in)
  • While the RAD52 recombinational repair pathway was originally identified as being important for the repair of DNA damage caused by ionizing radiation ( G ame and M ortimer 1974 ), it also appears to be important for compensating for defects in DNA synthesis. (genetics.org)


  • There is however, a potentially confounding issue in that PCR can generate larger targets from collections of small DNA fragments, a phenomenon known as PCR recombination. (biomedcentral.com)
  • The impact of PCR recombination towards the amplification of this cccDNA specific target was explored by mixing three marked, yet overlapping HBV DNA fragments. (biomedcentral.com)
  • Primers incorporated mutations (underlined) to distinguish PCR fragments from input HBVayw DNA. (biomedcentral.com)


  • Interestingly, despite the ample evidence suggesting that Rad52p is required to overcome the consequences of DNA synthesis defects, the mechanisms of this compensatory role for recombinational repair remain unclear. (genetics.org)


  • Here strand switching occurs by the second round of PCR and larger single stranded DNA molecules are built up extending from the outer primers until they overlap. (biomedcentral.com)
  • The DNA primase (DnaG) is needed to form RNA primers. (genome.jp)


  • We found that NEK8, a NIMA family kinase member, is required for efficient DNA damage-induced RAD51 focus formation. (washington.edu)



  • Velocity sedimentation in alkaline sucrose gradients revealed that mec1-srf mutants accumulate small single-stranded DNA synthesis intermediates, suggesting that Mec1p is required for the normal progression of DNA synthesis. (genetics.org)
  • sml1 suppressor mutations suppress both the accumulation of DNA synthesis intermediates and the requirement for Rad52p in mec1-srf mutants, but they do not suppress the checkpoint defect in mec1-srf mutants. (genetics.org)
  • When the cell does not properly compensate for defective DNA synthesis or a damaged DNA template, progression through the cell cycle results in broken chromosomes and an accumulation of mutations. (genetics.org)
  • Under conditions of genotoxic stress, the cell division cycle arrests at the G1 or G2/M checkpoint, DNA synthesis is slowed, and the transcription of damage response genes is stimulated. (genetics.org)


  • Uncovering the mechanisms of DNA maintenance in the third domain of life might also shed light on more complicated eukaryotic systems. (biomedcentral.com)


  • Following translocation to the nucleus, the gaps are repaired by the host repair system to generate covalently closed circular DNA (cccDNA), the template for the HBV pregenome and viral mRNAs. (biomedcentral.com)


  • To identify previously unknown kinases that may regulate RAD51 localization to sites of DNA damage, we performed a human kinome siRNA library screen, using DNA damage-induced RAD51 focus formation as readout. (washington.edu)


  • The EcoSSB or a chimera containing its C-terminal domain interacts with EcoUDG in a binary (SSB-UDG) or a ternary (DNA-SSB-UDG) complex. (iisc.ernet.in)


  • Marcelo Foiani (Fondazione Italiana per la Ricerca sul Cancro, Milan, Italy) described his group's chromatin immunoprecipitation-DNA microarray analysis of synchronized yeast cultures in early S phase. (biomedcentral.com)