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.
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.
Viruses whose hosts are bacterial cells.
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.
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.
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 2.7.7.7.
Viruses whose host is Escherichia coli.
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 2.7.7.7.
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 2.7.7.7.
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.
A DNA repair enzyme that catalyzes DNA synthesis during base excision DNA repair. EC 2.7.7.7.
Deoxyribonucleic acid that makes up the genetic material of viruses.
Bacteriophage in the genus T7-like phages, of the family PODOVIRIDAE, which is very closely related to BACTERIOPHAGE T7.
Proteins found in any species of virus.
The process by which a DNA molecule is duplicated.
A temperate inducible phage and type species of the genus lambda-like viruses, in the family SIPHOVIRIDAE. Its natural host is E. coli K12. Its VIRION contains linear double-stranded DNA with single-stranded 12-base 5' sticky ends. The DNA circularizes on infection.
Viruses whose nucleic acid is DNA.
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.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
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.
The phenomenon by which a temperate phage incorporates itself into the DNA of a bacterial host, establishing a kind of symbiotic relation between PROPHAGE and bacterium which results in the perpetuation of the prophage in all the descendants of the bacterium. Upon induction (VIRUS ACTIVATION) by various agents, such as ultraviolet radiation, the phage is released, which then becomes virulent and lyses the bacterium.
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.
A single-stranded DNA-dependent RNA polymerase that functions to initiate, or prime, DNA synthesis by synthesizing oligoribonucleotide primers. EC 2.7.7.-.
The functional hereditary units of VIRUSES.
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).
A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.
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.
Enzymes that catalyze the release of mononucleotides by the hydrolysis of the terminal bond of deoxyribonucleotide or ribonucleotide chains.
Phosphate esters of THYMIDINE in N-glycosidic linkage with ribose or deoxyribose, as occurs in nucleic acids. (From Dorland, 28th ed, p1154)
An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements. EC 2.7.7.49.
Enzymes that catalyze the template-directed incorporation of ribonucleotides into an RNA chain. EC 2.7.7.-.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
A temperate coliphage, in the genus Mu-like viruses, family MYOVIRIDAE, composed of a linear, double-stranded molecule of DNA, which is able to insert itself randomly at any point on the host chromosome. It frequently causes a mutation by interrupting the continuity of the bacterial OPERON at the site of insertion.
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).
A purine or pyrimidine base bonded to a DEOXYRIBOSE containing a bond to a phosphate group.
The rate dynamics in chemical or physical systems.
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.
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.
Enzymes that catalyze the incorporation of deoxyribonucleotides into a chain of DNA. EC 2.7.7.-.
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.
Virulent bacteriophage and sole member of the genus Cystovirus that infects Pseudomonas species. The virion has a segmented genome consisting of three pieces of doubled-stranded DNA and also a unique lipid-containing envelope.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6.
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.
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.
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.
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)
Proteins found in the tail sections of DNA and RNA viruses. It is believed that these proteins play a role in directing chain folding and assembly of polypeptide chains.
Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.
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.
Viruses whose host is Bacillus. Frequently encountered Bacillus phages include bacteriophage phi 29 and bacteriophage phi 105.
A subdiscipline of genetics which deals with the genetic mechanisms and processes of microorganisms.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
Guanine nucleotides which contain deoxyribose as the sugar moiety.
A family of BACTERIOPHAGES and ARCHAEAL VIRUSES which are characterized by long, non-contractile tails.
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.
A species of temperate bacteriophage in the genus P2-like viruses, family MYOVIRIDAE, which infects E. coli. It consists of linear double-stranded DNA with 19-base sticky ends.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
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.
Cytosine nucleotides which contain deoxyribose as the sugar moiety.
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.
Catalyze the joining of preformed ribonucleotides or deoxyribonucleotides in phosphodiester linkage during genetic processes. EC 6.5.1.
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)
Rupture of bacterial cells due to mechanical force, chemical action, or the lytic growth of BACTERIOPHAGES.
The sum of the weight of all the atoms in a molecule.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Ribonucleic acid that makes up the genetic material of viruses.
A species of temperate bacteriophage in the genus P1-like viruses, family MYOVIRIDAE, which infects E. coli. It is the largest of the COLIPHAGES and consists of double-stranded DNA, terminally redundant, and circularly permuted.
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.
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.
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.
A technique of bacterial typing which differentiates between bacteria or strains of bacteria by their susceptibility to one or more bacteriophages.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
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.
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.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
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.
An antiviral antibiotic produced by Cephalosporium aphidicola and other fungi. It inhibits the growth of eukaryotic cells and certain animal viruses by selectively inhibiting the cellular replication of DNA polymerase II or the viral-induced DNA polymerases. The drug may be useful for controlling excessive cell proliferation in patients with cancer, psoriasis or other dermatitis with little or no adverse effect upon non-multiplying cells.
The folding of an organism's DNA molecule into a compact, orderly structure that fits within the limited space of a CELL or VIRUS PARTICLE.
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.
Viruses whose host is Salmonella. A frequently encountered Salmonella phage is BACTERIOPHAGE P22.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.
Adenine nucleotides which contain deoxyribose as the sugar moiety.
An antibiotic first isolated from cultures of Streptomyces venequelae in 1947 but now produced synthetically. It has a relatively simple structure and was the first broad-spectrum antibiotic to be discovered. It acts by interfering with bacterial protein synthesis and is mainly bacteriostatic. (From Martindale, The Extra Pharmacopoeia, 29th ed, p106)
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.-.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
Proteins found in any species of bacterium.
A family of bacteriophages which are characterized by short, non-contractile tails.
Bacteriophages whose genetic material is RNA, which is single-stranded in all except the Pseudomonas phage phi 6 (BACTERIOPHAGE PHI 6). All RNA phages infect their host bacteria via the host's surface pili. Some frequently encountered RNA phages are: BF23, F2, R17, fr, PhiCb5, PhiCb12r, PhiCb8r, PhiCb23r, 7s, PP7, Q beta phage, MS2 phage, and BACTERIOPHAGE PHI 6.
Nuclear antigen with a role in DNA synthesis, DNA repair, and cell cycle progression. PCNA is required for the coordinated synthesis of both leading and lagging strands at the replication fork during DNA replication. PCNA expression correlates with the proliferation activity of several malignant and non-malignant cell types.
The adhesion of gases, liquids, or dissolved solids onto a surface. It includes adsorptive phenomena of bacteria and viruses onto surfaces as well. ABSORPTION into the substance may follow but not necessarily.
Proteins obtained from ESCHERICHIA COLI.
Viruses whose host is Pseudomonas. A frequently encountered Pseudomonas phage is BACTERIOPHAGE PHI 6.
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.
Bacteriophage and type species in the genus Tectivirus, family TECTIVIRIDAE. They are specific for Gram-negative bacteria.
The outer protein protective shell of a virus, which protects the viral nucleic acid.
Viruses whose host is Staphylococcus.
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.
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)
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.
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.
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)
A fractionated cell extract that maintains a biological function. A subcellular fraction isolated by ultracentrifugation or other separation techniques must first be isolated so that a process can be studied free from all of the complex side reactions that occur in a cell. The cell-free system is therefore widely used in cell biology. (From Alberts et al., Molecular Biology of the Cell, 2d ed, p166)
A heat stable DNA-DIRECTED DNA POLYMERASE from the bacteria Thermus aquaticus. It is widely used for the amplification of genes through the process of POLYMERASE CHAIN REACTION. EC 2.7.7.-.
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.
Any method used for determining the location of and relative distances between genes on a chromosome.
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.
Electrophoresis in which agar or agarose gel is used as the diffusion medium.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
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.
Viruses whose host is Streptococcus.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
The effects of ionizing and nonionizing radiation upon living organisms, organs and tissues, and their constituents, and upon physiologic processes. It includes the effect of irradiation on food, drugs, and chemicals.
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).
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Method for measuring viral infectivity and multiplication in CULTURED CELLS. Clear lysed areas or plaques develop as the VIRAL PARTICLES are released from the infected cells during incubation. With some VIRUSES, the cells are killed by a cytopathic effect; with others, the infected cells are not killed but can be detected by their hemadsorptive ability. Sometimes the plaque cells contain VIRAL ANTIGENS which can be measured by IMMUNOFLUORESCENCE.
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)
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.-.
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.
Poly(deoxyribonucleotide):poly(deoxyribonucleotide)ligases. Enzymes that catalyze the joining of preformed deoxyribonucleotides in phosphodiester linkage during genetic processes during repair of a single-stranded break in duplex DNA. The class includes both EC 6.5.1.1 (ATP) and EC 6.5.1.2 (NAD).
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.
Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.
Topical antiseptic used mainly in wound dressings.
The functional hereditary units of BACTERIA.
A basic enzyme that is present in saliva, tears, egg white, and many animal fluids. It functions as an antibacterial agent. The enzyme catalyzes the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrin. EC 3.2.1.17.
A purine that is an isomer of ADENINE (6-aminopurine).
An enzyme that catalyzes the conversion of linear RNA to a circular form by the transfer of the 5'-phosphate to the 3'-hydroxyl terminus. It also catalyzes the covalent joining of two polyribonucleotides in phosphodiester linkage. EC 6.5.1.3.
Viral proteins that are components of the mature assembled VIRUS PARTICLES. They may include nucleocapsid core proteins (gag proteins), enzymes packaged within the virus particle (pol proteins), and membrane components (env proteins). These do not include the proteins encoded in the VIRAL GENOME that are produced in infected cells but which are not packaged in the mature virus particle,i.e. the so called non-structural proteins (VIRAL NONSTRUCTURAL PROTEINS).
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.
Proteins prepared by recombinant DNA technology.
A simple organophosphorus compound that inhibits DNA polymerase, especially in viruses and is used as an antiviral agent.
Nucleotides in which the purine or pyrimidine base is combined with ribose. (Dorland, 28th ed)
A bacteriophage genus of the family LEVIVIRIDAE, whose viruses contain the short version of the genome and have a separate gene for cell lysis.
Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.
Mutation process that restores the wild-type PHENOTYPE in an organism possessing a mutationally altered GENOTYPE. The second "suppressor" mutation may be on a different gene, on the same gene but located at a distance from the site of the primary mutation, or in extrachromosomal genes (EXTRACHROMOSOMAL INHERITANCE).
A species of gram-positive bacteria that is a common soil and water saprophyte.
Proteins that form the CAPSID of VIRUSES.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. The enzyme functions in the nucleolar structure and transcribes DNA into RNA. It has different requirements for cations and salts than RNA polymerase II and III and is not inhibited by alpha-amanitin. EC 2.7.7.6.
Deoxycytidine (dihydrogen phosphate). A deoxycytosine nucleotide containing one phosphate group esterified to the deoxyribose moiety in the 2'-,3'- or 5- positions.
A pyrimidine base that is a fundamental unit of nucleic acids.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure where it transcribes DNA into RNA. It has specific requirements for cations and salt and has shown an intermediate sensitivity to alpha-amanitin in comparison to RNA polymerase I and II. EC 2.7.7.6.
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)
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
Dimers found in DNA chains damaged by ULTRAVIOLET RAYS. They consist of two adjacent PYRIMIDINE NUCLEOTIDES, usually THYMINE nucleotides, in which the pyrimidine residues are covalently joined by a cyclobutane ring. These dimers block DNA REPLICATION.
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.
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.
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).
A species of ALPHARETROVIRUS causing anemia in fowl.
The meaning ascribed to the BASE SEQUENCE with respect to how it is translated into AMINO ACID SEQUENCE. The start, stop, and order of amino acids of a protein is specified by consecutive triplets of nucleotides called codons (CODON).
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
The transfer of bacterial DNA by phages from an infected bacterium to another bacterium. This also refers to the transfer of genes into eukaryotic cells by viruses. This naturally occurring process is routinely employed as a GENE TRANSFER TECHNIQUE.
In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.
An enzyme responsible for producing a species-characteristic methylation pattern on adenine residues in a specific short base sequence in the host cell DNA. The enzyme catalyzes the methylation of DNA adenine in the presence of S-adenosyl-L-methionine to form DNA containing 6-methylaminopurine and S-adenosyl-L-homocysteine. EC 2.1.1.72.
An enzyme that catalyzes the transfer of a phosphate group to the 5'-terminal hydroxyl groups of DNA and RNA. EC 2.7.1.78.
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.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
A trace element with atomic symbol Mn, atomic number 25, and atomic weight 54.94. It is concentrated in cell mitochondria, mostly in the pituitary gland, liver, pancreas, kidney, and bone, influences the synthesis of mucopolysaccharides, stimulates hepatic synthesis of cholesterol and fatty acids, and is a cofactor in many enzymes, including arginase and alkaline phosphatase in the liver. (From AMA Drug Evaluations Annual 1992, p2035)
Unstable isotopes of phosphorus that decay or disintegrate emitting radiation. P atoms with atomic weights 28-34 except 31 are radioactive phosphorus isotopes.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Established cell cultures that have the potential to propagate indefinitely.
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.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
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.
Genomes of temperate BACTERIOPHAGES integrated into the DNA of their bacterial host cell. The prophages can be duplicated for many cell generations until some stimulus induces its activation and virulence.
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).
Presence of warmth or heat or a temperature notably higher than an accustomed norm.
The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.
A semisynthetic antibiotic produced from Streptomyces mediterranei. It has a broad antibacterial spectrum, including activity against several forms of Mycobacterium. In susceptible organisms it inhibits DNA-dependent RNA polymerase activity by forming a stable complex with the enzyme. It thus suppresses the initiation of RNA synthesis. Rifampin is bactericidal, and acts on both intracellular and extracellular organisms. (From Gilman et al., Goodman and Gilman's The Pharmacological Basis of Therapeutics, 9th ed, p1160)
A ribonuclease that specifically cleaves the RNA moiety of RNA:DNA hybrids. It has been isolated from a wide variety of prokaryotic and eukaryotic organisms as well as RETROVIRUSES.
Hydrogen-donating proteins that participates in a variety of biochemical reactions including ribonucleotide reduction and reduction of PEROXIREDOXINS. Thioredoxin is oxidized from a dithiol to a disulfide when acting as a reducing cofactor. The disulfide form is then reduced by NADPH in a reaction catalyzed by THIOREDOXIN REDUCTASE.
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.
Twenty-carbon compounds derived from MEVALONIC ACID or deoxyxylulose phosphate.
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.
A genus of filamentous bacteriophages of the family INOVIRIDAE. Organisms of this genus infect enterobacteria, PSEUDOMONAS; VIBRIO; and XANTHOMONAS.
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.
A class of enzymes that transfers nucleotidyl residues. EC 2.7.7.
Centrifugation using a rotating chamber of large capacity in which to separate cell organelles by density-gradient centrifugation. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
The process of cleaving a chemical compound by the addition of a molecule of water.
Specific loci on both the bacterial DNA (attB) and the phage DNA (attP) which delineate the sites where recombination takes place between them, as the phage DNA becomes integrated (inserted) into the BACTERIAL DNA during LYSOGENY.
Electron microscopy involving rapid freezing of the samples. The imaging of frozen-hydrated molecules and organelles permits the best possible resolution closest to the living state, free of chemical fixatives or stains.
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.
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)
Gram-negative aerobic rods found in warm water (40-79 degrees C) such as hot springs, hot water tanks, and thermally polluted rivers.
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.
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
A DNA-binding protein that consists of 5 polypeptides and plays an essential role in DNA REPLICATION in eukaryotes. It binds DNA PRIMER-template junctions and recruits PROLIFERATING CELL NUCLEAR ANTIGEN and DNA POLYMERASES to the site of DNA synthesis.
In T7 bacteriophages myricetin competitively inhibited DNA template binding to RNA polymerase. Myricetin has been seen to ... cellular DNA polymerase, and cellular RNA polymerase. Inhibition of cellular DNA polymerases could have dangerous effects on ... Inhibition of cellular RNA polymerase could have deleterious effects on the cell's capacity to transcribe and translate DNA and ... The resulting hydroxy radicals are often linked to DNA degradation, however, there are doubts as to whether or not this damage ...
Bonocora RP, Shub DA (December 2004). "A self-splicing group I intron in DNA polymerase genes of T7-like bacteriophages". J. ... T-even and T7-like bacteriophages. Both intron-early and intron-late theories have found evidences in explaining the origin of ... Two-metal-ion mechanism seen in protein polymerases and phosphatases was proposed to be used by group I and group II introns to ... Lee CN, Lin JW, Weng SF, Tseng YH (December 2009). "Genomic characterization of the intron-containing T7-like phage phiL7 of ...
Tabor, S.; Richardson, C. C. (July 1, 1987). "DNA sequence analysis with a modified bacteriophage T7 DNA polymerase". ... coli DNA polymerase III in 1975, T4 polynucleotide kinase in 1981, T7 DNA primase in the late 1980s and early 1990s, and T7 DNA ... Tabor, S.; Richardson, C. C. (July 1, 1987). "DNA sequence analysis with a modified bacteriophage T7 DNA polymerase". ... Richardson complexed the T7 bacteriophage DNA polymerase with a primer-template and a nucleoside triphosphate in the polymerase ...
Upon infection with the bacteriophage T7, E. coli thioredoxin forms a complex with T7 DNA polymerase, which results in enhanced ... T7 DNA replication, a crucial step for successful T7 infection. Thioredoxin binds to a loop in T7 DNA polymerase to bind more ... The anti-oxidant function of thioredoxin is fully autonomous and fully independent of T7 DNA replication, in which the protein ... DNA rearrangement, or post-translational processing. It is also different from multifunctionality of the protein, in which the ...
... it is more closely related to RNA polymerases of bacteriophage (including T7 RNA polymerase), mitochondrial polymerases of ... DNA-directed RNA polymerase, mitochondrial is an enzyme that in humans is encoded by the POLRMT gene. This gene encodes a ... "Entrez Gene: POLRMT polymerase (RNA) mitochondrial (DNA directed)". Hillen, HS; Morozov, YI; Sarfallah, A; Temiakov, D; Cramer ... Overview of all the structural information available in the PDB for UniProt: O00411 (Human DNA-directed RNA polymerase, ...
... is typically studied in the T3 and T7 RNA polymerases in bacteriophages and in E. coli. Abortive initiation ... RNA polymerase binds to promoter DNA to form an RNA polymerase-promoter closed complex RNA polymerase then unwinds one turn of ... RNA polymerase re-winds and ejects the upstream portion of the unwound DNA, breaking RNA polymerase-promoter interactions, ... thereby transcribing the DNA without moving. This causes the unwound DNA to accumulate within the enzyme, hence the name DNA " ...
... is an enzyme used during the DNA replication of the T7 bacteriophage. During this process, the DNA polymerase ... It is a member of the Family A DNA polymerases, which include E. coli DNA polymerase I and Taq DNA polymerase. This polymerase ... Nucleotidyl transfer by DNA polymerase. T7 DNA polymerase catalyzes the phosphoryl transfer during DNA replication of the T7 ... Instead, the T7 DNA polymerase complex requires only three proteins for processive DNA polymerization: T7 polymerase (gp5), ...
... to DNA polymerases and reverse transcriptases. Perhaps the most widely studied such single-subunit RNAP is bacteriophage T7 RNA ... DNAi - DNA Interactive, including information and Flash clips on RNA Polymerase. RNA+Polymerase at the US National Library of ... RNA polymerase then starts to synthesize the initial DNA-RNA heteroduplex, with ribonucleotides base-paired to the template DNA ... One lineage led to the modern DNA polymerases and reverse transcriptases, as well as to a few single-subunit RNA polymerases ( ...
... is an RNA polymerase from the T7 bacteriophage that catalyzes the formation of RNA from DNA in the 5'→ 3' ... T7 polymerase is extremely promoter-specific and transcribes only DNA downstream of a T7 promoter. The T7 polymerase also ... Similar to other viral nucleic acid polymerases, including T7 DNA polymerase from the same phage, the conserved C-terminal of ... T7 polymerase has been crystallised in several forms and the structures placed in the PDB. These explain how T7 polymerase ...
It is also a primase, making short stretches of RNA that initiates DNA synthesis. It forms a complex with T7 DNA polymerase. ... "DNA-induced switch from independent to sequential dTTP hydrolysis in the bacteriophage T7 DNA helicase". Mol. Cell. 21 (2): 165 ... T7 DNA helicase (gp4) is a hexameric motor protein encoded by T7 phages that uses energy from dTTP hydrolysis to process ... Helicase Lee SJ, Richardson CC (October 2011). "Choreography of bacteriophage T7 DNA replication". Current Opinion in Chemical ...
T7 DNA polymerase, assisted by E. coli thioredoxin, performs both leading and lagging-strand DNA synthesis. In phage T7, DNA ... Dunn, J. J.; Studier, F. W. (1983). "Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic ... Gp5 (encoded by gene gp5) is T7 phage's DNA polymerase. T7 polymerase uses E. coli's endogenous thioredoxin, a REDOX protein, ... Bacteriophage T7 (or the T7 phage) is a bacteriophage, a virus that infects bacteria. It infects most strains of Escherichia ...
"The thioredoxin binding domain of bacteriophage T7 DNA polymerase confers processivity on Escherichia coli DNA polymerase I". ... Tabor, S; Richardson, C. C. (1987). "DNA sequence analysis with a modified bacteriophage T7 DNA polymerase". Proceedings of the ... When associated with a DNA clamp, DNA polymerase is dramatically more processive; without the clamp most polymerases have a ... "DNA polymerase switching: I. Replication factor C displaces DNA polymerase α prior to PCNA loading". Journal of Molecular ...
T7 or T3. These promoters are recognized by DNA dependent RNA polymerases originally characterized from bacteriophages. The ... Uncomplemented DNA or RNA is cleaved off by nucleases. When the probe is a DNA molecule, S1 nuclease is used; when the probe is ... Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nature Rev. Genet. 8, 424-436 (2007) v t e. ... The extracted RNA is first mixed with antisense RNA or DNA probes that are complementary to the sequence or sequences of ...
Then the DNA polymerase forms a protein complex with two primase subunits to form the alpha DNA Polymerase primase complex. ... between different bacteria and viruses where the primase covalently link to helicase in viruses such as the T7 bacteriophage. ... new DNA strands by the herpes simplex virus-1 primase-helicase complex and either herpes DNA polymerase or human DNA polymerase ... DNA primase is an enzyme involved in the replication of DNA and is a type of RNA polymerase. Primase catalyzes the synthesis of ...
The bacteriophage T4 DNA polymerase (family A) was also initially used in PCR. It has a higher fidelity of replication than the ... T7 DNA polymerase (family B) has similar properties and purposes. It has been applied to site-directed mutagenesis and Sanger ... chimeras of Thermus aquaticus DNA polymerase, Escherichia coli DNA polymerase I and Thermotoga neapolitana DNA polymerase". ... "DNA sequencing with Thermus aquaticus DNA polymerase and direct sequencing of polymerase chain reaction-amplified DNA". Proc. ...
... it was the first known T7-like phage which encoded a single-subunit RNA polymerase gene downstream its DNA metabolism genes ... 2003). "The genome of bacteriophage φKMV, a T7-like virus infecting Pseudomonas aeruginosa". Virology. 312 (1): 49-59. doi: ... DNA-templated transcription is the method of transcription. The virus exits the host cell by lysis, and holin/endolysin/spanin ... There are currently 16 species in this genus including the type species Pseudomonas virus phiKMV.Bacteriophage phiKMV and its ...
... is an RNA polymerase from the T7 bacteriophage that catalyzes the formation of RNA from DNA in the 5'→ 3' ... T7 polymerase is extremely promoter-specific and transcribes only DNA downstream of a T7 promoter (TAATACGACTCACTATAG, ... T7 polymerase has been crystallised in several forms and the structures placed in the PDB. These explain how T7 polymerase ... In biotechnology applications, T7 RNA polymerase is commonly used to transcribe DNA that has been cloned into vectors that have ...
Since the 1990s, the term "T7 supergroup" has been coined for the expanding group of bacteriophages related to coliphage T7, as ... DNA templated transcription is the method of transcription. The virus exits the host cell by lysis, and holin/endolysin/spanin ... RNA polymerase, a common characteristic among its members. Viruses in Autographiviridae are non-enveloped, with icosahedral and ... "Genomic analysis of bacteriophages SP6 and K1-5, an estranged subgroup of the T7 supergroup". Journal of Molecular Biology. 335 ...
"Nucleotide sequence of an RNA polymerase binding site from the DNA of Bacteriophage fd". PNAS. 72 (2): 737-741. Bibcode: ... "Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter". PNAS. 72 (3): 784-788. Bibcode:1975PNAS...72.. ... it is recognized and bound by a subunit of RNA polymerase during initiation of transcription. This region of the DNA is also ... Feklistov, Andrey; Darst, Seth (2011). "Structural Basis for Promoter −10 Element Recognition by the Bacterial RNA Polymerase σ ...
T7 phage T12 phage Viruses portal Virophage, viruses that infect other viruses Bacterivore CrAssphage DNA viruses Phage ecology ... Proteins modify the bacterial RNA polymerase so it preferentially transcribes viral mRNA. The host's normal synthesis of ... coli bacteria Phage.org general information on bacteriophages bacteriophages illustrations and genomics Bacteriophages get a ... The largest bacteriophage genomes reach a size of 735 kb. Bacteriophage genomes can be highly mosaic, i.e. the genome of many ...
This article is called, "Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates." They found that ... Johansson, H. E. (1998). "A thermodynamic analysis of the sequence-specific binding of RNA by bacteriophage MS2 coat protein". ... most notably the enzymatic synthesis of RNAs from synthetic DNA templates using T7 RNA polymerase. Olke was a founding member ... "Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates". Nucleic Acids Research. 15 (21): 8783-98. ...
In contrast, eukaryotic RNA polymerase I and II as well as single-subunit RNA polymerases of bacteriophage T7 and SP6 are ... The third theory suggests that TGT forms predominantly a binary RNAP-TGT complex and inhibits RNAP translocation along the DNA ... Chloroplast RNA polymerase belongs to ubiquitous family of multisubunit RNA polymerases (RNAP) and is most closely related to ... Klyuyev, Sergiy; Vassylyev, Dmitry G. (2012). "The binding site and mechanism of the RNA polymerase inhibitor tagetitoxin: An ...
"Discrimination between bacteriophage T3 and T7 promoters by the T3 and T7 RNA polymerases depends primarily upon a three base- ... Jorgensen, Ellen; Zhao, Hong; Traganos, Frank; Albino, Anthony; Darzynkiewicz, Zbigniew (2010-06-01). "DNA damage response ... "Specific labelling of the active site of T7 RNA polymerase". Nucleic Acids Research. 15: 8773-81. doi:10.1093/nar/15.21.8773. ... Zhao, Hong; Albino, Anthony; Jorgensen, Ellen; Traganos, Frank; Darzynkiewicz, Zbigniew (2009-10-01). "DNA Damage Response ...
"Incorporation of multiple sequential pseudothymidines by DNA polymerases and their impact on DNA duplex structure". Nucleosides ... The GRO exhibited increased resistance to T7 bacteriophage, thus showing that alternative genetic codes do reduce genetic ... 2013). "A synthetic substrate of DNA polymerase deviating from the bases, sugar, and leaving group of canonical deoxynucleoside ... Extended bases using a natural DNA backbone could, likewise, be transliterated into natural DNA, although to a more limited ...
For example, T7 phages have two operons. The first operon codes for various products, including a special T7 RNA polymerase ... "Displacements of prohead protease genes in the late operons of double-stranded-DNA bacteriophages". Journal of Bacteriology. ... Close to the promoter lies a section of DNA called an operator. All the structural genes of an operon are turned ON or OFF ... When an inducer is bound by the activator protein, it undergoes a change in conformation so that it can bind to the DNA and ...
Gabashvili, I.; Khan, S.; Hayes, S.; Serwer, P. (1997). "Polymorphism of bacteriophage T7". Journal of Molecular Biology. 273 ( ... Of the viral families with DNA genomes, only two have single-stranded genomes. Eight of the viral families with DNA genomes ... Proteins modify the bacterial RNA polymerase so it preferentially transcribes viral mRNA. The host's normal synthesis of ... Bacteriophages are among the most common and diverse entities in the biosphere.[1] Bacteriophages are ubiquitous viruses, found ...
DNA polymerase (DNA-directed DNA polymerase, DdDP) Family A: DNA polymerase I; Pol γ, θ, ν Family B: DNA polymerase II; Pol α, ... RNA polymerase I, RNA polymerase II, RNA polymerase III Single-subunit (ssDdRP): T7 RNA polymerase, POLRMT Primase, PrimPol RNA ... Right hand structure of Bacteriophage RB69, a family B DdRP. Central dogma of molecular biology Exonuclease Ligase Nuclease PCR ... DNA polymerase and RNA polymerase are used to assemble DNA and RNA molecules, respectively, by copying a DNA template strand ...
... capping enzyme with a mutant DNA-dependent RNA polymerase from the K1E bacteriophage. Such C3P3 enzyme produces mRNA capping ... "Cytoplasmic expression system based on constitutive synthesis of bacteriophage T7 RNA polymerase in mammalian cells". ... The chimeric cytoplasmic capping-prone phage polymerase (also named C3P3 system) is an artificial eukaryotic expression system ... The specific DNA templates are therefore transcribed by the C3P3 enzyme and generate the mRNA of interest in the cytoplasm of ...
... and Vent exo-DNA polymerase for DNA amplification, and T7 RNA polymerase for RNA amplification. Since Phi29 DNA polymerase has ... Rolling circle DNA replication is initiated by an initiator protein encoded by the plasmid or bacteriophage DNA, which nicks ... A DNA polymerase A suitable buffer that is compatible with the polymerase. A short DNA or RNA primer A circular DNA template ... DNA to make another double-stranded circle. DNA polymerase I removes the primer, replacing it with DNA, and DNA ligase joins ...
BacteriophageEdit. There are a number of bacteriophages that infect Pseudomonas, e.g. ... differing lengths of chromosomal DNA are isolated from samples containing bacterial species, and digested into fragments.[37] ... are visualized and their lengths compared to each other by Southern blotting or by the much faster method of polymerase chain ... "Genomic Analysis of Pseudomonas aeruginosa Phages LKD16 and LKA1: Establishment of the KMV Subgroup within the T7 Supergroup" ...
The ε subunit is one of three core proteins in the DNA polymerase complex. It functions as a 3'→5' DNA directed proofreading ... Studies with T4 bacteriophage and E. coli with defective dnaQ genes give evidence that the mutA tRNA may not have any effect on ... "The proofreading exonuclease subunit epsilon of Escherichia coli DNA polymerase III is tethered to the polymerase subunit alpha ... dnaQ is the gene encoding the ε subunit of DNA polymerase III in Escherichia coli.[1] ...
T7 RNA polymerase (blue) producing an mRNA (green) from a DNA template (orange)[93] ... bacteriophages) is to avoid the restriction enzymes present in bacteria. This enzyme system acts at least in part as a ... DNA exists in many possible conformations that include A-DNA, B-DNA, and Z-DNA forms, although, only B-DNA and Z-DNA have been ... In DNA replication, DNA-dependent DNA polymerases make copies of DNA polynucleotide chains. To preserve biological information ...
The first DNA polymerase, DNA polymerase I, was discovered by Arthur Kornberg and his colleagues in 1956,[8] reviewed in.[9] In ... Tyrosine Y701 functions similarly to tyrosine Y567 in the RB69 bacteriophage orthologue as the sugar steric gate that prevents ... DNA damage response, detection of DNA damage. • nucleotide-excision repair, DNA incision, 5'-to lesion. • DNA ligation. • DNA ... delta DNA polymerase complex. • cytosol. Biological process. • nucleotide-excision repair, DNA gap filling. • DNA synthesis ...
... the desired protease cut site is used to link a T7 RNA polymerase and a T7 lysozyme. The T7 lysozyme prevents the T7 polymerase ... C in genomic DNA without DNA cleavage". Nature. 551: 464-471. doi:10.1038/nature24644. PMC 5726555. Wang, T.; Badran, A.H.; ... It relies on relating the desired activity of a target protein with the fitness of an infectious bacteriophage which carries ... The T7 polymerase can only function when the N-terminus portion can bind to the rest of the polymerase. Since APOBEC1 must be ...
Step 3: Gap formation T7 exonuclease is added which uses the nicks in the DNA molecules to expand the gaps in a 5'-3' direction ... Selection of an appropriate DNA polymerase is critical to the efficiency of the base addition step and must meet several ... "Bacteriophage strain typing by rapid single molecule analysis". Nucleic Acids Research. 43 (18): e117. doi:10.1093/nar/gkv563. ... Step 1: DNA barcoding Cells are lysed to release genomic DNA. These DNA molecules are untangled, placed onto optical mapping ...
... for DNA synthesis by bacterial DNA polymerase III (Pol III). DnaG is important in bacterial DNA replication because DNA ... bacteriophage, prokaryotic and eukaryotic DNA primases. The primase zinc-binding domain is part of the subfamily of zinc- ... "Interaction of ribonucleoside triphosphates with the gene 4 primase of bacteriphage T7". Journal of Biological Chemistry. 274 ( ... further facilitating DNA binding. Based on previous studies of DNA binding by DNA Primases, it is thought that DNA binds to the ...
Entire Two T7 DNA polymerase/Trx complexes interacting with primase doma.... Entire. Name: Two T7 DNA polymerase/Trx complexes ... Component #1: protein, Two T7 DNA polymerase/Trx complexes interacting with pri.... Protein. Name: Two T7 DNA polymerase/Trx ... Name: gene product 5 DNA polymerase / Recombinant expression: No. Source. Species: Enterobacteria phage T7 (bacteriophage). ... Structure of two bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A )/Trx interacting with primase domains, one Pol with ...
A portion (approximately 45%) of the molecule displays extensive structural homology to the polymerase domain of Klenow ... The crystal structure of T7 RNA polymerase reveals a molecule organized around a cleft that can accommodate a double-stranded ... crystal structure of T7 RNA polymerase reveals a molecule organized around a cleft that can accommodate a double-stranded DNA ... Crystal structure of bacteriophage T7 RNA polymerase at 3.3 A resolution Nature. 1993 Aug 12;364(6438):593-9. doi: 10.1038/ ...
Bacteriophage T7 DNA polymerase: an an emzyme composed of phage- and host-specific subunits., Polymerase: T7 ... T7 Bacteriophage T7 deoxyribonucleic acid replication invitro. Bacteriophage T7 DNA polymerase: an an emzyme composed of phage ... T7 Bacteriophage T7 deoxyribonucleic acid replication invitro. Bacteriophage T7 DNA polymerase: an an emzyme composed of phage ... T7 Bacteriophage T7 deoxyribonucleic acid replication invitro. Bacteriophage T7 DNA polymerase: an an emzyme composed of phage ...
The thioredoxin binding domain of bacteriophage T7 DNA polymerase confers processivity on Escherichia coli DNA polymerase I., ... T7 The thioredoxin binding domain of bacteriophage T7 DNA polymerase confers processivity on Escherichia coli DNA polymerase I. ... The thioredoxin binding domain of bacteriophage T7 DNA polymerase confers processivity on Escherichia coli DNA polymerase I., ... Polymerase: T7, Property: Processivity Welcome to the results summary page. This page presents all the results for a polymerase ...
Bacteriophage T7 / genetics* * Bacteriophages / classification * Bacteriophages / genetics* * DNA-Directed RNA Polymerases / ... We found the podovirus contained 15 of 26 core T7-like genes and the two myoviruses contained 43 and 42 of 75 core T4-like ... Thus, these marine cyanophages appear to be variations of two well-known phages-T7 and T4-but contain genes that, if functional ... The morphology, overall genome features, and gene content of these phages suggest that they are quite similar to T7-like (P- ...
T7 DNA polymerase is an enzyme used during the DNA replication of the T7 bacteriophage. During this process, the DNA polymerase ... It is a member of the Family A DNA polymerases, which include E. coli DNA polymerase I and Taq DNA polymerase. This polymerase ... Nucleotidyl transfer by DNA polymerase. T7 DNA polymerase catalyzes the phosphoryl transfer during DNA replication of the T7 ... Instead, the T7 DNA polymerase complex requires only three proteins for processive DNA polymerization: T7 polymerase (gp5), ...
1975) Bacteriophage T7 deoxyribonucleic acid replication in vitro. Bacteriophage T7 DNA polymerase: An enzyme composed of phage ... 1976) Escherichia coli thioredoxin: A subunit of bacteriophage T7 DNA polymerase. Proc Natl Acad Sci USA 73(3):780-784. ... and transcribed with T7 RNA Polymerase (mMessage-mMachine T7 kit; Ambion) using an input of 2 μg of BAC DNA per 20-μL reaction ... Polymerase processivity factors have been identified for DNA viruses such as the gp45 protein of bacteriophage T4 (64), the ...
Tabor, S. et al., "DNA sequence analysis with a modified bacteriophage T7 DNA polymerase" Proc. Natl. Acad. Sci. USA 84:4767-71 ... "DNA sequencing with Thermus aquaticus DNA polymerase and direct sequencing of polymerase chain reaction-simplified DNA" Proc ... USA, 85: 9436 (1988)) or specially modified T7 DNA polymerase ("SEQUENASE") (see, S. Tabor and C. C. Richardson, Proc. Natl. ... The sequencing reactions are either performed in solution with the use of different DNA polymerases, such as the thermophilic ...
DNA coding for bacteriophage T7 RNA polymerase was ligated to a vaccinia virus transcriptional promoter and integrated within ... Eukaryotic transient-expression system based on recombinant vaccinia virus that synthesizes bacteriophage T7 RNA polymerase. T ... Eukaryotic transient-expression system based on recombinant vaccinia virus that synthesizes bacteriophage T7 RNA polymerase ... Eukaryotic transient-expression system based on recombinant vaccinia virus that synthesizes bacteriophage T7 RNA polymerase ...
Insights into the structural dynamics of the bacteriophage T7 DNA polymerase and its complexes. ... Pf16 and phiPMW: Expanding the realm of Pseudomonas putida bacteriophages.. Magill DJ, Krylov VN, Shaburova OV, McGrath JW, ... Mismatched Prenatal and Postnatal Maternal Depressive Symptoms and Child Behaviours: A Sex-Dependent Role for NR3C1 DNA ...
DNA sequence analysis with a modified bacteriophage T7 DNA polymerase.Proc. Natl. Acad. Sci. USA84198747674771. ... perfringens RNA polymerase and extracts from sporulating cells strongly indicated that linear DNA does not function efficiently ... Plasmid constructs and DNA manipulations.The plasmids used in this study are listed in Table 2. Nested deletions of the NCTC ... DNA sequences upstream of P1 were similar to consensus SigK-dependent promoters, while P2 and P3 were similar to consensus SigE ...
1976) Escherichia coli thioredoxin: a subunit of bacteriophage T7 DNA polymerase. Proc. Natl. Acad. Sci. USA 73:780-784. ... Radioimmunological and enzymatic determinations in wild type cells and mutants defective in phage T7 DNA replication. J. Biol. ... The DNA upstream of the promoter fragment inserted into pWH262 was cloned by inverse PCR. Chromosomal DNA from B. subtilis was ... 1991) Simultaneous and rapid isolation of bacterial and eucaryotic DNA and RNA-a new approach for isolation DNA. BioTechniques ...
In T7 bacteriophages myricetin competitively inhibited DNA template binding to RNA polymerase. Myricetin has been seen to ... cellular DNA polymerase, and cellular RNA polymerase. Inhibition of cellular DNA polymerases could have dangerous effects on ... Inhibition of cellular RNA polymerase could have deleterious effects on the cells capacity to transcribe and translate DNA and ... The resulting hydroxy radicals are often linked to DNA degradation, however, there are doubts as to whether or not this damage ...
Thioredoxin, the processivity factor, sequesters an exposed cysteine in the thumb domain of bacteriophage T7 DNA polymerase. ... Hydrophobic Residue in Escherichia coli Thioredoxin Critical for the Processivity of T7 DNA Polymerase. ... Helicase-DNA polymerase interaction is critical to initiate leading-strand DNA synthesis. ... Characterization of a nucleotide kinase encoded by bacteriophage T7.. Tran NQ, Tabor S, Amarasiriwardena CJ, Kulczyk AW, ...
Tabor, S. and Richardson, C. C.: DNA sequence analysis with a modified bacteriophage T7 DNA polymerase.Proc Natl Acad Sci USA ... Gyllensten, U. B. and Erlich, H. A.: Generation of single-stranded DNA by the polymerase chain reaction and its application to ...
DNA transport in Streptococcus pneumoniaewas studied using donor molecules labelled either at the 3′ or at the 5′ end, on one ... Tabor S, Richardson CC (1987) DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Proc Natl Acad Sci USA 84: ... Characterization of strand displacement synthesis catalyzed by bacteriophage T7 DNA polymerase. J Biol Chem 258:11174-11184 ... DNA transport in Streptococcus pneumoniae was studied using donor molecules labelled either at the 3′ or at the 5′ end, on one ...
The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at ... A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic ... See Huber et al., "Escherichia coli Thioredoxin Stabilizes Complexes of Bacteriophage T7 DNA Polymerase and Primed Templates," ... coli DNA polymerase, the Klenow fragment of E. coli DNA polymerase, T4 DNA polymerase, T7 DNA polymerase, and others. Examples ...
Expression and purification of histidine-tagged bacteriophage T7 DNA polymerase. Protein Expr. Purif. 39:247-253. ... The expression of T7-ISG15P-PLpro(C1)-His6 and T7-ISG15P-PLpro(C2)-His6 wild-type (wt) proteins (lanes 1, 3, 5, and 7) and ... Expression and purification of SARS-CoV PLpro from E. coli.The plasmids encoding T7-ISG15P-PLpro(C1)-His6, T7-ISG15P-PLpro(C2)- ... was mutated to an alanine in the plasmids encoding T7-ISG15P-PLpro(C1)-His6, T7-ISG15P-PLpro(C2)-His6, and PLpro(C3)-GFP using ...
DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Tabor, S; Richardson, CC ... Using miniprep plasmid DNA for sequencing double stranded templates with sequenase. Kraft, R; Tardiff, J; Krauter, KS; Leinwand ... Restriction enzyme analysis and cloning of high molecular weight genomic DNA isolated from Chlorella sorokiniana (Chlorophyta) ... Analysis of the genes encoding the largest subunit of RNA polymerase II in Arabidopsis and soybean ...
Tabor S. and Richardson C. (1987). DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Proc. Natl Acad. Sci ... These blunt-end DNA fragments were ligated and pMJ441, which encoded gus RU-AE01 promoter lacZ, RP4 oriT tet and the broad ... 6) Finally, pMJ441 was digested with Bgl II, to excise the RU-AE01 promoter fragment, and the DNA backbone re-circularized to ... We were able to introduce DNA fragments up to 1 kb between the genes for the reporter enzymes. We also successfully applied the ...
DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Proc. Natl. Acad. Sci. USA 84 1987 4767 4771 ... 2 μl of a template DNA sample, and 2 U of Taq DNA polymerase (Boehringer Mannheim). The reactions were performed on a DNA ... For gyrA and gyrB, sequence reactions were performed on both DNA strands with the T7 sequencing kit (Pharmacia Biotech) by the ... PCR amplification and DNA sequencing.For DNA extraction, 2 ml of an 18-h culture in brain heart infusion broth was centrifuged ...
DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Proc. Natl. Acad. Sci. USA 84 1987 4767 4771 ... An EcoRI digest of bacteriophage SPP1 (Geneworks) was used as size markers. Plasmid DNA for sequencing was purified using the ... DNA sequencing and analysis.The DNA sequence of at least one strand of fragments of Tn1403 cloned in plasmid vectors was ... DNA isolation and restriction mapping.Plasmid DNA for restriction analysis and cloning was isolated using an alkaline lysis ...
The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at ... A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic ... See Huber et al., "Escherichia coli Thioredoxin Stabilizes Complexes of Bacteriophage T7 DNA Polymerase and Primed Templates," ... coli DNA polymerase, the Klenow fragment of E. coli DNA polymerase, T4 DNA polymerase, T7 DNA polymerase, and others. Examples ...
... displaced by the lagging strand DNA polymerase, are processed. 3′-extensions generated during degradation of duplex DNA by the ... Flap endonuclease of bacteriophage T7: Possible roles in RNA primer removal, recombination and host DNA breakdown. ... "Flap endonuclease of bacteriophage T7: Possible roles in RNA primer removal, recombination and host DNA breakdown." ... Gene 6 protein of bacteriophage T7 has 5′-3′-exonuclease activity specific for duplex DNA. We have found that gene 6 protein ...
Bacteriophage T7 RNA polymerase is a DNA-dependent RNA polymerase that is encoded in the T7 bacteriophage genome. The enzyme ... Genetic Analysis of T7 RNA Polymerase:. The genome of bacteriophage T7 was sequenced by Dunn et. al. 1983 and Moffatt et. al., ... The coding region of T7 RNA polymerase is located between nucleotides 3170 and 5819. Thus T7 RNA polymerase consists of 883 ... Figure 1. Schematic representation summarizing the most important features of bacteriophage T7 RNA polymerase. [Constructed ...
Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7. Nat.Struct.Mol. ... TERNARY 5 COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/TEMPLATE CONTAINING A CIS-SYN THYMINE DIMER ON THE TEMPLATE AND AN ... DNA POLYMERASE (E.C.2.7.7.7)/THIOREDOXIN 1/DNA Complex. Deposited:. 2004-03-05 Released:. 2004-07-06 Structural Keywords:. A ...
1987). DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Proc. Nat. Acad. Sci. USA 84, 4767-4771. ... 1977). Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J. Mol. ... 1982). A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene 19, 269-276. ... 1977). DNA sequencing with chain-terminating inhibitors. Proc. Nat. Acad. Sci. USA 74, 5463-5467. ...
Transcription of DNA containing the 5-guanidino-4-nitroimidazole lesion by human RNA polymerase II and bacteriophage T7 RNA ... bacteriophage T7 RNA polymerase. Known as: T7 RNA polymerase, bacteriophage T7 induced RNA polymerase, polymerase rna t7 ... To make messenger RNA transcripts, bacteriophage T7 RNA polymerase (T7 RNAP) undergoes a transition from an initiation phase… ( ... Bacteriophage T7 RNA polymerase-based expression in Pichia pastoris.. *Birgit Hobl, Bjoern Hock, Sandra Schneck, Reinhard ...
Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Nature 391 : 251-258. ... DNA polymerase assays.The standard DNA polymerase reaction mixture contained 25 mM Tris HCl (pH 7.5), 5 mM dithiothreitol, 0.1 ... Classical DNA polymerases (Pols) replicate DNA with a high fidelity and are unable to replicate through DNA-distorting lesions ... Members of the Y family of DNA polymerases replicate DNA with a low fidelity, and unlike the classical polymerases, they are ...
The 99 KD enzyme catalyzes in vitro RNA synthesis from a cloned DNA sequence under the T7 promoters. ... Bacteriophage T7 RNA Polymerase is a DNA-dependent RNA polymerase that is highly specific for the T7 phage promoters. ... Bacteriophage T7 RNA Polymerase is a DNA-dependent RNA polymerase that is highly specific for the T7 phage promoters. The 99 KD ... T7 RNA Polymerase GMP-grade reagent also available. Learn more. T7 RNA Polymerase is used for in vitro mRNA synthesis and is ...
  • Bacteriophage T7 DNA polymerase: an an emzyme composed of phage- and host-specific subunits. (neb.com)
  • T7 DNA polymerase catalyzes the phosphoryl transfer during DNA replication of the T7 phage. (wikipedia.org)
  • While phage T7 mediates DNA replication in very similar manner to higher organisms, T7 system is generally simpler compared to other replication systems. (wikipedia.org)
  • Barany F (1982) Transformation of Streptococcus pneumoniae by single-stranded plasmid-phage hybrid DNA. (springer.com)
  • T7 RNA Polymerase is used for in vitro mRNA synthesis and is highly specific for the T7 phage promoter. (neb.com)
  • Bacteriophage T7 RNA Polymerase is a DNA-dependent RNA polymerase that is highly specific for the T7 phage promoters. (neb.com)
  • Zhu B, Wang L, Mitsunobu H, Lu X, Hernandez AJ, Yoshida-Takashima Y, Nunoura T, Tabor S, Richardson CC. Deep-sea vent phage DNA polymerase specifically initiates DNA synthesis in the absence of primers. (harvard.edu)
  • We determined the nucleotide sequence of gene 1 of Klebsiella phage K11, which is a member of the T7 group of phages. (springer.com)
  • Dietz A, Kössel H, Hausmann R (1985) On the evolution of the terminal redundancies of Klebsiella phage No. 11 and of coliphages T3 and T7. (springer.com)
  • Korsten KH, Tomkiewicz C, Hausmann R (1979) The strategy of infection as a criterion for phylogenetic relationships of noncoliphages morphologically similar to phage T7. (springer.com)
  • Here we introduce a new approach for the screening of DNA binding proteins, using a phage library based on a phage display technique. (ejbiotechnology.info)
  • In principal, a complementary DNA (cDNA) library based on the recombinant bacteriophage T7 expressing target proteins on its capsid (phage display) is constructed. (ejbiotechnology.info)
  • These phage particles are hybridized with a biotinylated target DNA fragment which is immobilized on the surface of streptavidin paramagnetic particle (SA-PMP). (ejbiotechnology.info)
  • The phage particles are released from the target DNA fragment by a nuclease treatment and the recovered phages are used to the next round of hybridization. (ejbiotechnology.info)
  • We could validate that our new application of phage display is a superior method for isolation of DNA binding proteins with a broad range of potential applications. (ejbiotechnology.info)
  • The bacteriophage T4 encodes 10 proteins, known collectively as the replisome, that are responsible for the replication of the phage genome. (pubmedcentralcanada.ca)
  • The core of T4 gp32 and two proteins from the T4 related phage RB69, the gp43 polymerase and the gp45 clamp are also solved. (pubmedcentralcanada.ca)
  • Promoters of T7 bacteriophage are recognized by the two forms of RNA-polymerase - the major form of RNA-polymerase (Es70) of Escherichia coli serves the early genes, while RNA-polymerase of the phage itself takes care of the late genes. (jbsdonline.com)
  • the only essential phage gene is gene 1, coding for the T7 RNA polymerase, which transcribes the class II genes, mainly involved in phage DNA metabolism, and the class III genes, whose functions are predominantly morphogenetic. (jbsdonline.com)
  • It was shown that during the phage infection pH becomes higher and that T7 RNAP has higher pH optimum then that of E.coli. (jbsdonline.com)
  • GTE7 phage DNA was isolated and sequenced as described previously ( 15 ). (asm.org)
  • At the DNA level, only 6% of the sequence shares similarity with that of the phage ReqiDocB7 genome ( 20 ), and the remainder (94%) shares no sequence similarity to any other DNA sequence in GenBank. (asm.org)
  • Replication of RNA by the DNA-dependent RNA polymerase of phage T7. (naver.com)
  • Visualization in atomic detail of the replisome that performs concerted leading- and lagging-DNA strand synthesis at a replication fork has not been reported. (pdbj.org)
  • Results for Reference: Bacteriophage T7 deoxyribonucleic acid replication invitro. (neb.com)
  • T7 DNA polymerase is an enzyme used during the DNA replication of the T7 bacteriophage. (wikipedia.org)
  • The helicase domain unwinds double-stranded DNA to provide template for replication. (wikipedia.org)
  • In Escherichia coli , thioredoxin is necessary for the assembly of filamentous phages ( 45 ) and the replication of T7 ( 31 ) but is not essential for DNA synthesis and growth ( 21 , 34 ). (asm.org)
  • Major advantages of this method are that the ligation step can be manipulated to obtain allelic discrimination, the DNA replication step is isothermal, and signals are strictly quantitative because the amplification reaction is linear and is catalyzed by a highly processive enzyme. (patents.com)
  • Bacterial primase DnaG is an essential nucleic acid polymerase that generates primers for replication of chromosomal DNA. (rcsb.org)
  • This plasmid-mediated function is inducible with arabinose and leads to a decrease in a proofreading function that normally operates during DNA replication. (evmedreview.com)
  • We describe a method for observing real time replication of individual DNA molecules mediated by proteins of the bacteriophage replication system. (jove.com)
  • Length differences between single- and double-stranded DNA are utilized to obtain real-time information on the activity of the replication proteins at the fork. (jove.com)
  • DNA for the reaction is a linearized λ DNA modified by annealing of oligonucleotides to form a replication fork. (jove.com)
  • Finally, anneal the oligonucleotide D to the DNA replication template by adding 100-fold excess of oligonucleotide D with respect to l DNA in T4 DNA ligase buffer. (jove.com)
  • The final DNA replication template is now ready for use. (jove.com)
  • They can be then attached to the DNA replication template 2 . (jove.com)
  • To ensure accurate DNA replication, a replisome must effectively overcome numerous obstacles on its DNA substrate. (nature.com)
  • Using single-molecule and ensemble methods, we find that T7 helicase interacts strongly with a non-replicating T7 DNA polymerase (DNAP) at a replication fork. (nature.com)
  • These observations exhibit T7 helicase's novel role in replication re-initiation. (nature.com)
  • In addition, as replication and transcription proceed simultaneously on the same template DNA, the two must inevitably collide. (nature.com)
  • A prerequisite for a replisome to resume replication after the lesion is the acquisition of a primer, which allows DNA polymerase (DNAP) to re-initiate DNA synthesis. (nature.com)
  • Here, we investigate this replication re-initiation pathway using the bacteriophage T7 replisome. (nature.com)
  • In this report, we address the questions of whether and how a non-replicating T7 DNAP in the presence of helicase could use a nascent RNA transcript from an RNAP polymerase (RNAP) as a primer to re-initiate DNA replication. (nature.com)
  • The lack of a cell culture system for human pathogens has necessitated a recombinant DNA-based approach for the classification of circulating strains, the generation of diagnostic tests, and the elucidation of a proposed virus replication strategy. (asm.org)
  • In this review, we provide an overview of the various force- and fluorescence-based single-molecule methods with applications both in vitro and in vivo, highlighting these advances by describing their applications in studies on cytoskeletal motors and DNA replication. (rupress.org)
  • To guide our review of the main technological developments and the biological breakthroughs they have allowed, in the context of what seems like an overwhelming amount of examples and applications, we focus on studies of the molecular motors that carry cellular cargo and the multiprotein complex involved in DNA replication, the replisome. (rupress.org)
  • To investigate how G‐quadruplex structures are resolved during DNA replication, we developed a model system using ssDNA templates and Xenopus egg extracts that recapitulates eukaryotic G4 replication. (embopress.org)
  • Here, we show that G‐quadruplex structures form a barrier for DNA replication. (embopress.org)
  • G quadruplex (G4)‐forming DNA motifs are prone to replication‐associated genomic instability. (embopress.org)
  • A cell‐free model system recapitulating replication of G4 DNA shows that G4 motifs form a transient replication barrier, which is unwound and overcome through the help of the FANCJ/BRIP1 helicase. (embopress.org)
  • One of the cellular processes that can be a source of genome instability is DNA replication. (embopress.org)
  • A model is proposed in which the sci1 promoter is regulated by iron availability, adenine methylation, and DNA replication. (prolekare.cz)
  • The T4 provides a model system for DNA replication. (pubmedcentralcanada.ca)
  • To better understand the functionality of T4 DNA replication, in depth structural analysis will require complexes between proteins and DNA substrates. (pubmedcentralcanada.ca)
  • The semi-conservative, semi-discontinuous process of DNA replication is conserved in all life forms. (pubmedcentralcanada.ca)
  • In order to examine the effect of adenine N 6 adducts of styrene oxide (SO) on DNA replication, 33-mer templates were constructed bearing site-specific and stereospecific SO modifications. (elsevier.com)
  • Replication of the damaged templates was analyzed under conditions defining single and/or multiple encounters between the polymerase and the substrate. (elsevier.com)
  • Significantly, the degree of adduct-directed termination and translesion synthesis during replication was also dependent on the choice of polymerase. (elsevier.com)
  • Thus, the activities of these enzymes on the SO-modified substrates produced replication profiles, or "fingerprints", that were unique to each polymerase. (elsevier.com)
  • When both DNA and RNA templates were present, transcription and replication competed, but T7 RNA polymerase preferred DNA as a template. (naver.com)
  • Such enzymes are of particular importance, because DNA damage can block progression of replication forks. (embopress.org)
  • Enzymes that could efficiently bypass AP sites encountered during DNA replication could be valuable in promoting cellular survival and minimizing chromosomal breakage. (embopress.org)
  • The most extensively studied A‐family polymerase, Escherichia coli pol I, is a high‐fidelity enzyme that assists in maturation of Okazaki fragments during DNA replication and also participates in gap‐filling during base excision repair, nucleotide excision repair, and repair of DNA interstrand crosslinks. (embopress.org)
  • The Keystone Symposia "DNA Replication and Recombination" meeting, the longest standing meeting of this multi-decade series continues to meld investigators representing a range of disciplines who otherwise would not have a format for sharing novel approaches and groundbreaking discoveries. (keystonesymposia.org)
  • Major pivotal questions include (1) the role of condensins in DNA pairing and replication fork movement, (2) mechanisms by which stalled replication forks are recognized and replication is restarted, (3) the role of recombinational mechanisms in the maintenance of telomeres in the absence of telomerase, (4) the architecture of forks and replication origins, and (5) the mechanisms by which fork initiation is timed with the cell cycle. (keystonesymposia.org)
  • EvolvR's on-target mutagenesis rate was 2.5 x 10 -6 mutations per nucleotide per generation vs. 10 x 10 -10 mutations per nucleotide per generation of wild-type E. coli , while only increasing the standard mutation rate seen during DNA replication by 120-fold over background. (addgene.org)
  • Interestingly, even though HR was stimulated by the presence of a viral origin of DNA replication, virally stimulated HR could proceed in the presence of the DNA synthesis inhibitor aphidicolin. (labome.org)
  • These results indicate that SSRP1 is a novel cellular protein involved in LANA-dependent DNA replication. (labome.org)
  • Duggan L, Hill T, Wu S, Garrison K, Zhang X, Gottlieb P. Using modified nucleotides to map the DNA determinants of the Tus-TerB complex, the protein-DNA interaction associated with termination of replication in Escherichia coli. (labome.org)
  • Krings G, Bastia D. Molecular architecture of a eukaryotic DNA replication terminus-terminator protein complex. (labome.org)
  • This model helps explain how origin-independent initiation of DNA replication is restricted to repaired replication forks, preventing overreplication of the genome. (labome.org)
  • 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. (curehunter.com)
  • Replication of the DNA genome is performed by a replisome complex composed of numerous proteins. (sciencemag.org)
  • The replisome functions at a Y junction, or replication fork, and is a complex task because DNA Pols can only extend DNA in a 3′-to-5′ direction. (sciencemag.org)
  • Using bacteriophage T7 as a model system, we determined cryo-electron microscopy structures up to 3.2-angstroms resolution of helicase translocating along DNA and of helicase-polymerase-primase complexes engaging in synthesis of both DNA strands. (pdbj.org)
  • Two lagging-strand polymerases are attached to the primase, ready for Okazaki fragment synthesis in tandem. (pdbj.org)
  • Lechner RL, Eugler MJ, Richardson CC (1983) Characterization of strand displacement synthesis catalyzed by bacteriophage T7 DNA polymerase. (springer.com)
  • Special attention will be paid to those structural motifs that are responsible for DNA promoter recognition and RNA synthesis. (cuny.edu)
  • DNA synthesis by Polη, a low-fidelity polymerase able to replicate through DNA lesions, however, is inhibited in the presence of such an analog, suggesting a dependence of this polymerase upon W-C hydrogen bonding. (asm.org)
  • From the ternary crystal structure of Polι, with a templating A and an incoming dTTP, it has been determined that unlike all other DNA polymerases, which impose Watson-Crick base pairing in their active site, Polι uses Hoogsteen base pairing for DNA synthesis ( 25 ). (asm.org)
  • The 99 KD enzyme catalyzes in vitro RNA synthesis from a cloned DNA sequence under the T7 promoters. (neb.com)
  • One structure, obtained with ds DNA, reveals interactions with DnaG as it slides on ds DNA and suggests how DnaG binds template for primer synthesis. (rcsb.org)
  • Zhang H, Lee SJ, Zhu B, Tran NQ, Tabor S, Richardson CC. Helicase-DNA polymerase interaction is critical to initiate leading-strand DNA synthesis. (harvard.edu)
  • Transcription, or the synthesis of RNA from DNA, is one of the most important processes in the cell. (plos.org)
  • DNA polymerases are enzymes that catalyze the template-directed synthesis of DNA. (frontiersin.org)
  • It catalyzes the 5'→3' synthesis of RNA on either single-stranded DNA or double-stranded DNA downstream from it promoter. (thermofisher.com)
  • After encountering an obstacle, a progressing replisome often aborts DNA synthesis but continues to unwind. (nature.com)
  • However, little is known about how DNA synthesis is resumed downstream of an obstacle. (nature.com)
  • Such a direct lesion bypass event occurred in only about 28% of the T7 replisomes, while the remaining population continued helicase unwinding without DNA synthesis beyond the lesion. (nature.com)
  • DNA primases catalyze the synthesis of the oligoribonucleotides required for the initiation of lagging strand DNA synthesis. (harvard.edu)
  • We present a model in which conformational changes induced during primer synthesis facilitate contact between the zinc-binding domain and the polymerase domain. (harvard.edu)
  • 5') nuclease activity that acts on both single and double stranded DNA and appears to be responsible for the high fidelity of this enzyme and prevents strand displacement synthesis (3,4,5) . (mclab.com)
  • Thermally Induced DNA.RNA Hybrid to G-Quadruplex Transitions: Possible Implications for Telomere Synthesis byTelomerase", Biochemistry vol. 35, pp. 16110-16115 (1996). (patentgenius.com)
  • G‐quadruplex structures transiently block DNA synthesis on ssDNA templates in Xenopus egg extracts. (embopress.org)
  • The proposed approach for the synthesis of short oligoribonucleotides is based on the in vitro transcription with bacteriophage T7 DNA-dependent RNA polymerase. (mybiosource.com)
  • Synthesis of a mRNA begins before the entire region of DNA coding for that mRNA has entered the cell and entry of ~97 percent of T7 DNA is driven by transcribing RNA polymerase. (jbsdonline.com)
  • Numerous studies of the impact of accessory proteins upon the fidelity of DNA synthesis have provided a complex and sometimes discordant picture. (genetics.org)
  • The contributions of polymerase accessory proteins to the accuracy of DNA synthesis have also been explored, both in vivo and in vitro . (genetics.org)
  • Because unassisted DNA polymerases often suffice in vitro in a simple gap-closing mutation-reporter assay such as lacZ α ( B ebenek and K unkel 1995 ), it is possible to probe the specific contributions of accessory proteins to the accuracy of DNA synthesis. (genetics.org)
  • Although SO adducts directed termination either opposite the lesion or 1 base 3' to the damage using all five polymerases, templates that were poor substrates for bypass synthesis with one enzyme were often read-through much more efficiently when a different polymerase was used. (elsevier.com)
  • Synthesis of small RNAs using T7 RNA polymerase. (naver.com)
  • T7 RNA polymerase is also used in a system for selective, high-level synthesis of RNAs and proteins in suitable host cells. (osti.gov)
  • 3' synthesis of RNA on either single-stranded or double-stranded DNA under control of the T7 promoter. (biogen.cz)
  • 3' synthesis of RNA on either single-stranded DNA or double-stranded DNA downstream from it promoter. (biogen.cz)
  • In addition to T7 DNA polymerase (also known as gp5), T7 replisome requires only four accessory proteins for proper function: host thioredoxin, gp4, gp2.5, and gp1.7. (wikipedia.org)
  • In conjunction with the recent cryo-EM structure of the bacteriophage T7 replisome, this study yields a model for primer elongation and hand-off to DNA polymerase. (rcsb.org)
  • Here, we examine the consequences of a non-replicating replisome collision with a co-directional RNA polymerase (RNAP). (nature.com)
  • A functional replisome requires, at a minimum, a helicase to unwind the DNA duplex, two DNA polymerases (Pols) to replicate the two DNA strands, and a primase to form RNA primers that DNA Pols extend. (sciencemag.org)
  • 1 ) report the cryo-electron microscopy (cryo-EM) structure of the T7 bacteriophage replisome at a high atomic detail. (sciencemag.org)
  • The study not only advances our understanding of the helicase mechanism but also reveals an unexpected arrangement of the two DNA Pols in the replisome. (sciencemag.org)
  • Several studies suggest that the electrostatic interaction between these positively charged basic residues with the negatively charged phosphate backbone of DNA and other accessory proteins is responsible for increased processivity in gp5/thioredoxin complex. (wikipedia.org)
  • ROS can damage lipids, DNA, and proteins. (wikipedia.org)
  • We find that TraI, the central regulator of conjugative DNA processing, interacts physically, and functionally with the plasmid partitioning proteins ParM and ParR. (frontiersin.org)
  • Moreover, the conjugative pilus and underlying secretion machinery assembled in the absence of Par proteins mediate poor biofilm formation and are completely dysfunctional for pilus specific R17 bacteriophage uptake. (frontiersin.org)
  • Research in the Ellenberger laboratory focuses on the molecular structures and cellular functions of proteins that replicate DNA, repair chemical damage, and regulate chromatin structure. (wustl.edu)
  • Immunoprecipitation and Western blot analysis of proteins produced in virus-infected cells demonstrated efficient cleavage of the proteinase-polymerase precursor. (asm.org)
  • Construction and characterization of a quadruplex DNA selective single-chain autoantibody from a viable motheaten mouse hybridoma with homology to telomeric DNa binding proteins," Biochemistry, vol. 37, No. 46, Mar. 1998, pp.16338-16348. (patentgenius.com)
  • The exciting discoveries that two core components exhibit remarkable structure conservation with two bacteriophage structural proteins reshaped this field [7] . (prolekare.cz)
  • Two T6SS proteins released in the environmental milieu, Hcp and VgrG, are structurally related to the tail tube and the cell-puncturing device of bacteriophage T4, gp19 and the gp27-gp5 complex respectively [8] - [11] . (prolekare.cz)
  • DNA plasmids encoding foreign proteins may be used as immunogens by direct intramuscular injection alone, or with various adjuvants and excipients, or by delivery of DNA-coated gold particles to the epidermis through biolistic immunization. (who.int)
  • Antibody, helper T lymphocyte, and cytotoxic T lymphocyte (CTL) responses have been induced in laboratory and domesticated animals by the direct inoculation of DNA plasmids encoding foreign proteins, either intramuscularly or by delivery of DNA-coated gold particles to the epidermis through biolistic immunization. (who.int)
  • Administration of plasmid DNA has proven to be an effective means of generating humoral immune responses against various foreign proteins in laboratory and domesticated animals and in some nonhuman primates. (who.int)
  • In the last decades, crystallography has been highly successful in delivering structural information about proteins, DNA, and RNA, the substrates of life on earth. (mybiosource.com)
  • the replicase, responsible for duplicating DNA, the primosomal proteins, responsible for unwinding and Okazaki fragment initiation, and the Okazaki repair proteins. (pubmedcentralcanada.ca)
  • The structures of T4 gp41 helicase, gp61 primase, and T4 DNA ligase are unknown, structures from bacteriophage T7 proteins are discussed instead. (pubmedcentralcanada.ca)
  • We previously described such an analysis conducted in vitro using various bacteriophage RB69 gp43 mutator DNA polymerases with or without the accessory proteins gp32 (which binds single-stranded DNA) plus gp45/44/62 (processivity clamp and its loaders). (genetics.org)
  • The crystal structure of T7 RNA polymerase reveals a molecule organized around a cleft that can accommodate a double-stranded DNA template. (nih.gov)
  • Our results together with those of previous studies are consistent with a model for entry in which double-stranded donor DNA is nicked on binding at the cell surface. (springer.com)
  • Transcription is the fundamental process by which RNA is synthesized by RNA polymerases on double-stranded DNA templates. (cuny.edu)
  • Thermo Scientific Bacteriophage T7 RNA polymerase is a DNA-dependent RNA polymerase with strict specificity for its respective double-stranded promoters. (thermofisher.com)
  • Inhibition of TOP2 activity could activate cell cycle checkpoints, including the DNA damage checkpoint, because of double-stranded breaks mediated by TOP2 ( Nitiss, 2009 ). (rupress.org)
  • The human immunodeficiency virus (HIV) polymerase, reverse transcriptase (RT), uses a single-stranded RNA template to create double-stranded DNA during the course of the viral life cycle. (umd.edu)
  • Terminal deoxynucleotidyl transferase (TdT) is a template-independent DNA polymerase that catalyzes the addition of deoxynucleotides to the 3' hydroxyl terminus of single or double stranded DNA molecules. (mclab.com)
  • After denaturation and bisulfite modification, double-stranded DNA is obtained by primer extension and the fragment of interest is amplified by PCR . (protocol-online.org)
  • First, the polymerase is able to transcribe in vitro from both supercoiled and linear DNA templates and is highly effective with double- and single-stranded synthetic templates containing a double-stranded T7 promoter. (mybiosource.com)
  • The T7 DNA polymerase requires a host factor, E. coli thioredoxin, in order to carry out its function. (wikipedia.org)
  • It is a member of the Family A DNA polymerases, which include E. coli DNA polymerase I and Taq DNA polymerase. (wikipedia.org)
  • The E. coli strains DH5α and RR1 were used for DNA manipulations. (asm.org)
  • Hydrophobic Residue in Escherichia coli Thioredoxin Critical for the Processivity of T7 DNA Polymerase. (nih.gov)
  • 3. The composition of claim 2 , wherein the polymerase is selected from the group of Taq DNA polymerase, T7 DNA polymerase, SEQUENASE (DNA polymerase), and the Klenow fragment from E. coli DNA polymerase. (google.com)
  • 4 To facilitate easy propagation and extraction of plasmid DNA in high concentrations in E. coli DH5 α , pMJ445 carries the F1 ori as well as genes conferring resistance to ampicillin ( E. coli DH5 α ) and tetracycline (broad host range). (scielo.org.za)
  • Isolated from E.coli carrying a plasmid which contains the T7 RNA Polymerase gene. (neb.com)
  • Burgers, P. and Eckstein, F., "A study of the mechanism of DNA polymerase I from escherichia coli with diastereomeric phosphorothioate analogs of deoxyadenosine triphosphate", J. of Biological Chemistry 1979, 254(15), 6889-6893. (patents.com)
  • Burgers, P. and Eckstein, F., "Absolute configuration of the diastereomers of adenosine 5'-O-(1-thiotriphosphate): Consequences for the stereochemistry of polymerization by DNA-dependent RNA polymerase from Escherichia coli", Proc. (patents.com)
  • Brody, R. and Frey, P., "Unambiguous determination of the sterochemistry of nucleotidyl transfer catalyzed by DNA polymerase I from escherichia coli", Biochemistry 1981, 20, 1245-1252. (patents.com)
  • Akabayov B, Akabayov SR, Lee SJ, Tabor S, Kulczyk AW, Richardson CC. Conformational dynamics of bacteriophage T7 DNA polymerase and its processivity factor, Escherichia coli thioredoxin. (harvard.edu)
  • Nevertheless, a molecular understanding of the details of E. coli transcription and its regulation, and therefore its full exploitation as a model system, has been hampered by the absence of high-resolution structural information on E. coli RNA polymerase (RNAP). (plos.org)
  • We report a steady-state kinetic characterization of the rate with which the Klenow fragment of E. coli DNA polymerase I synthesizes the d NaM -d TPT3 UBP and its mispairs in a variety of sequence contexts. (scripps.edu)
  • It consists of T7 DNAP (gp5 protein), T7 helicase-primase (gp4), processivity factor Escherichia coli thioredoxin (trx), and the single strand binding protein (gene 2.5 protein). (nature.com)
  • T7 DNA Polymerase is a two subunit protein that consists of a polymerase domain (gene 5 from the T7 bacteriophage) and a processivity factor ( E. coli trxA gene thioredoxin) (1, 2) . (mclab.com)
  • A recombinant E. coli strain carrying the bacteriophage T7 gene 5. (mclab.com)
  • 5' exo-, is the large fragment of E.coli DNA polymerase I with a molecular weight of 68kDa. (mclab.com)
  • Characterization of a temperature-sensitive DNA ligase from Escherichia coli. (semanticscholar.org)
  • During the first few minutes after infection of E. coli by the bacteriophage T7, transcription is dependent on the host's RNA polymerase and is confined to the "early" operon at the "left" end of the genome. (jbsdonline.com)
  • Class I genes are transcribed by E.coli RNAP which recognizes three promoters (A1-A3, B and C) positioned near the leading end of T7 DNA. (jbsdonline.com)
  • Kamzolova S.G., Sorokin A.A., Dzhelyadin T.D., Beskaravainy P.M., Osypov A.A., Electrostatic potentials of E.coli genome DNA. (jbsdonline.com)
  • Reference: A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy- and dideoxyribonucleotides. (neb.com)
  • 2000-fold, while replacing the phenylalanine at the homologous position in E. coli DNA polymerase I (position 762) or T. aquaticus DNA polymerase (position 667) with tyrosine decreases discrimination against the four dideoxynucleotides 250- to 8000-fold. (neb.com)
  • A procedure for the rapid, large-scall purification of Escherichia coli DNA-dependent RNA polymerase involving Polymin P precipitation and DNA-cellulose chromatography. (naver.com)
  • 6S RNA Regulates E. coli RNA Polymerase Activity (2000) Wassarman Karen Montzka et al. (naver.com)
  • ompT encodes the Escherichia coli outer membrane protease that cleaves T7 RNA polymerase during purification. (naver.com)
  • Expression of an error prone polymerase I (PolI3M) is capable of mutagenesis in E. Coli , but this approach requires special bacterial growth conditions in order to maximize the mutation rate. (addgene.org)
  • E. coli cells with a cloned gene encoding T7 RNA polymerase. (biogen.cz)
  • DNA templates containing 5-hydroxymethyluracil or 5-hydroxymethylcytosine were used in an in vitro transcription assay with RNA polymerase from Escherichia coli. (usda.gov)
  • The Escherichia coli cAMP receptor protein (CRP) utilizes the helix-turn-helix motif for DNA binding. (usda.gov)
  • In addition, in vitro transcription assays were performed with the cpe promoter region as the DNA template for extracts made from sporulating cells. (asm.org)
  • Transcription of DNA containing the 5-guanidino-4-nitroimidazole lesion by human RNA polymerase II and bacteriophage T7 RNA polymerase. (semanticscholar.org)
  • Transcription reinitiation properties of bacteriophage T7 RNA polymerase. (semanticscholar.org)
  • Effect of 8-oxoguanine on transcription elongation by T7 RNA polymerase and mammalian RNA polymerase II. (semanticscholar.org)
  • Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. (semanticscholar.org)
  • The central enzyme of transcription is the DNA-dependent RNA polymerase (RNAP), a large, macromolecular assembly consisting of at least five subunits. (plos.org)
  • We report the in vivo transcription of DNA containing d NaM and d TPT3 into mRNAs with two different unnatural codons and tRNAs with cognate unnatural anticodons, and their efficient decoding at the ribosome to direct the site-specific incorporation of natural or non-canonical amino acids into superfolder green fluorescent protein. (scripps.edu)
  • Using thermocycling and a novel DNA template, we demonstrate a polymerase chain transcription (PCT) reaction that results in the exponential production of orders of magnitude more RNA or modified RNA than is available by conventional transcription. (scripps.edu)
  • The 2006 Nobel Prize in Chemistry was awarded to [[Roger Kornberg]] for creating detailed molecular images of RNA polymerase during various stages of the transcription process. (wikidoc.org)
  • Homologous recombination of a particular DNA sequence is strongly stimulated by transcription, a phenomenon observed from bacteria to mammals, which we refer to as transcription-associated recombination (TAR). (genetics.org)
  • In this study we tested the possibility that transcription induces recombination by making DNA more susceptible to recombinogenic DNA damage. (genetics.org)
  • 4-NQO and MMS stimulated recombination of a transcriptionally active DNA sequence up to 12,800- and 130-fold above the spontaneous levels observed in the absence of transcription, whereas 4-NQO and MMS alone increased recombination 193- and 4.5-fold, respectively. (genetics.org)
  • Our results provide evidence that TAR is due, at least in part, to the ability of transcription to enhance the accessibility of DNA to exogenous chemicals and internal metabolites responsible for recombinogenic lesions. (genetics.org)
  • TRANSCRIPTION of a DNA sequence increases its level of instability. (genetics.org)
  • It is possible that DNA becomes more susceptible to chemical reactions yielding DNA breaks during proper transcription elongation. (genetics.org)
  • O rphanides and R einberg 2000 ) associated with transcription might increase the probability of occurrence of single-strand DNA (ssDNA) regions that are more susceptible to recombinogenic damage. (genetics.org)
  • In this study we directly tested the possibility that transcription induced recombination by making DNA more accessible to damaging agents. (genetics.org)
  • Transcription of the circular mammalian mtDNA depends on a single mitochondrial RNA polymerase (POLRMT). (sciencemag.org)
  • Determining the consequences of platinum-DNA adduct formation at the nucleosome level is an important step in understanding the details of cellular recognition of platinum drugs and of transcription stalling. (aacrjournals.org)
  • This requirement may be avoided by use of a bacteriophage T7 promoter system, where expression of the T7 RNA polymerase can drive expression of antigen controlled by the T7 promoter without need for host cell transcription machinery. (who.int)
  • Second, a T7 polymerase can prematurely terminate transcription in the presence of an incomplete set of NTPs. (mybiosource.com)
  • These factors generally recognize and bind to unique 10-15 bp DNA sequences in or near the promoter regions and these bindings cause a change in DNA conformation to enhance the transcription by RNA polymerase complex. (ejbiotechnology.info)
  • Yeast one hybrid system is one of the most widely used systems in many studies to isolate and characterize transcription factors which can directly bind to target DNA sequences, but there are several disadvantages in this system. (ejbiotechnology.info)
  • First of all, this system is only fit for a 10-15 bp short DNA sequences, but completely not for a comprehensive screening of the transcription factors using a whole part of the target promoter region. (ejbiotechnology.info)
  • Promoter recognition and open complex formation are central events in the initiation of transcription by RNA-polymerase and are shown to be affected by electrostatic properties of promoter DNA. (jbsdonline.com)
  • The target protein is encoded on a plasmid in which the gene has been cloned so that transcription will be driven by the T7 RNA polymerase. (biomedcentral.com)
  • Digestion of plasmid constructs with Pst I followed by incubation with T4 DNA polymerase resulted in templates for transcription that initiate with the 5′ guanosine and terminate with the 3′ cytosine of the S4 gene. (bioz.com)
  • A strong enhancement of transcription was observed from DNA containing the Pveg promoter whereas a decrease was observed from DNA containing the rrnB P1 promoter, suggesting that they may act as epigenetic marks. (usda.gov)
  • At the end of protein-coding genes, RNA polymerase (Pol) II undergoes a concerted transition that involves 3′-processing of the pre-mRNA and transcription termination. (usda.gov)
  • Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular model for basal Pol I initiation. (usda.gov)
  • Discrete interactions between bacteriophage T7 primase-helicase and DNA polymerase drive the formation of a priming complex containing two copies of DNA polymerase. (wustl.edu)
  • However, the physical interactions of the primase with the DNA template to explain the basis of specificity have not been demonstrated. (harvard.edu)
  • Using a combination of surface plasmon resonance and biochemical assays, we show that T7 DNA primase has only a slightly higher affinity for DNA containing the primase recognition sequence (5′-TGGTC-3′) than for DNA lacking the recognition site. (harvard.edu)
  • Alterations in subdomains of the primase result in loss of selective DNA binding. (harvard.edu)
  • Tabor, S. and Richardson, C. C.: DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. (springer.com)
  • The whole DNA sequence consists of 399,336 base pairs. (cuny.edu)
  • The amino acid sequence of T7 RNA polymerase (GenBank accession number ( M38308 ). (cuny.edu)
  • DNA sequence analysis reveals this protein to be a human homologue of HP1, a heterochromatin protein of Drosophila melanogaster. (biologists.org)
  • 2. A DNA molecule encoding a human Tumor Necrosis Factor Stimulated Gene 6 (TSG-6), protein having the amino acid sequence SEO ID NO:2, substantially free of other human nucleotide sequences. (google.com)
  • 5. A DNA molecule according to claim 2 having the nucleotide sequence SEQ ID NO:1. (google.com)
  • used PACE to evolve bacteriophage T7 RNA polymerases with new DNA sequence (i.e., promoter) specificities and other characteristics. (evmedreview.com)
  • In many cases, an analysis of past evolution of these polymerases (as inferred by examining multiple sequence alignments) can help explain some of the mutations delivered by directed evolution. (frontiersin.org)
  • The deduced amino acid sequence of this polypeptide shows 71% homology to the T7 RNA polymerase (the product of T7 gene 1 ), 72% homology to the T3 RNA polymerase and 27% homology to the SP6 RNA polymerase. (springer.com)
  • Dunn JJ, Studier FW (1983) The complete nucleotide sequence of bacteriophage T7 dNA and the locations of T7 genetic elements. (springer.com)
  • Kotani H, Ishizaki Y, Hiraoka N, Obayashi A (1987) Nucleotide sequence and expression of the cloned gene of bacteriophage SP6 RNA polymerase. (springer.com)
  • Moffatt BA, Dunn JJ, Studier FW (1984) Nucleotide sequence of the gene for bacteriophage T7 RNA polymerase. (springer.com)
  • This suggests a shared sequence preference that might be present in all Family A DNA polymerases, derived from a common ancestor. (umd.edu)
  • Tso I is a thermostable Type IIC enzyme that recognises the DNA sequence TARCCA (R = A or G) and cleaves downstream at N11/N9. (springer.com)
  • The use is concerned with the incorporation of dNTPs into DNA templates in order to determine the concentration and / or sequence of said templates. (google.com)
  • Recently, CRISPR/Cas technology was used for creating antimicrobials with a programmable spectrum of activities.This strategy exploits the fact that CRISPR/Cas system can be designed to break a specific DNA sequence. (openwetware.org)
  • With the use of DNA probes containing site-specific cisplatin lesions, hydroxyl radical footprinting experiments revealed that a cisplatin 1,2-d(GpG) or a 1,3-d(GpTpG) intrastrand crosslink overrides the rotational setting predefined in a nucleosome positioning sequence. (aacrjournals.org)
  • This structure can form in DNA sequences that contain four stretches of three or more guanines (Gs) interspaced by at least one random nucleotide (Fig 1 A, hereafter referred to as G4 sequence). (embopress.org)
  • Buffer gradient gels and a 35 -S label as an aid to rapid DNA sequence determination. (microbiologyresearch.org)
  • Therefore, a DNA template can be easily prepared by annealing two chemically synthesized DNA oligonucleotides, which reconstitutes the T7 promoter, followed by the target RNA sequence. (mybiosource.com)
  • These mutations allow the engineering of new DNA polymerases with enhanced properties for use in DNA sequence analysis. (neb.com)
  • DNA Sequence and Genetic Content of the HindIII /Region in the Short Unique Component of the Herpes Simplex Virus Type 2 Genome: Identification of the Gene Encoding Glycoprotein G, and Evolutionary Comparisons" J. Gen. Virol. (freepatentsonline.com)
  • T7 RNA polymerase transcribes DNA very efficiently and is highly selective for a relatively long promoter sequence. (osti.gov)
  • DNA polymerases are divided into families denoted A, B, X, and Y based on amino‐acid sequence relationships. (embopress.org)
  • Making changes to a DNA sequence can help scientists identify and/or facilitate the evolution of new phenotypes, and forward genetics harnesses this at a large scale by screening diverse libraries of genetic variants. (addgene.org)
  • While diversity was low, however, our results demonstrate that the short-term evolutionary rate in this natural population of MRSA resulted in the accumulation of measurable DNA sequence variation within two decades, which we could exploit to reconstruct its recent demographic history and the spatiotemporal dynamics of spread. (pubmedcentralcanada.ca)
  • Demographic analysis based on DNA sequence variation indicated a sharp increase of bacterial population size from 2001 to 2004, which is concordant with the reported prevalence of this strain in several European countries. (pubmedcentralcanada.ca)
  • By comparing 118 kilobases of DNA from MRSA isolates that had been collected at different points in time, we demonstrate that this strain has accumulated measurable DNA sequence variation within two decades. (pubmedcentralcanada.ca)
  • Target genes were constructed by inserting DNA segments that code for beta-galactosidase or chloramphenicol acetyltransferase into a plasmid with bacteriophage T7 promoter and terminator regions. (pnas.org)
  • 7. A DNA molecule according to claim 6, wherein said vehicle is a plasmid. (google.com)
  • These interactions stimulate TraI catalyzed relaxation of plasmid DNA in vivo and in vitro and increase ParM ATPase activity. (frontiersin.org)
  • We demonstrated that decreases in protein overproduction levels are not due to significant plasmid loss nor to mutations arising on the plasmid, but instead largely are attributable to chromosomal mutations that diminish the level of functional T7 RNA polymerase, resulting in decreased expression from the plasmid. (biomedcentral.com)
  • Isolation of plasmid DNA from non-expressing strains and reintroduction of the plasmid into a T7 RNA polymerase-producing strain such as BL21(λDE3) reproducibly restored high level protein production. (biomedcentral.com)
  • Thus, expression of the T7 RNA polymerase gene is controlled by addition of IPTG to the growth media, and in turn, production of the polymerase controls expression of the plasmid-borne target gene. (biomedcentral.com)
  • Active T7 RNA polymerase is produced from the cloned gene, and a plasmid has been constructed that can produce the active enzyme in large amounts. (osti.gov)
  • The RNA polymerase gene of bacteriophage T7 has been cloned into the plasmid pBR322 below the inducible management of the lambda PL promoter. (cellsociety.org)
  • Enzyme activity is assayed in the following mixture: 40 mM Tris-HCl (pH 8.0), 6 mM MgCl 2 , 10 mM DTT, 2 mM spermidine, 0.5 mM of each NTP, 0.6 MBq/mL [3H]-ATP, 20 µg/mL plasmid DNA containing the appropriate promoter sequences. (biogen.cz)
  • For T7 DNA polymerase, the fingers, palm and thumb (Figure 1) position the primer-template so that the 3'-end of the primer strand is positioned next to the nucleotide-binding site (located at the intersection of the fingers and thumb). (wikipedia.org)
  • The rate-limiting step in the catalytic cycle occurs after the nucleoside triphosphate binds and before it is incorporated into the DNA (corresponding to the closure of the fingers subdomain around the DNA and nucleotide). (wikipedia.org)
  • The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. (google.com)
  • 4. The composition of claim 3 , wherein the polymerase comprises Taq DNA Polymerase having a label attached to an amino acid of the Taq DNA polymerase that is less than 60 Å from a nucleotide that would be incorporated by said polymerase. (google.com)
  • Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7. (rutgers.edu)
  • The efficiency and fidelity of nucleotide incorporation by high-fidelity replicative DNA polymerases (Pols) are governed by the geometric constraints imposed upon the nascent base pair by the active site. (asm.org)
  • rather, it is apparently the geometric fit within the active site of the incoming nucleoside triphosphate with the templating nucleotide that governs polymerase efficiency and accuracy ( 3 , 5 , 13 , 15 ). (asm.org)
  • In contrast to the specificity of Rev1 and Polι for nucleotide incorporation opposite template bases, all other known DNA polymerases, including the high-fidelity replicative/repair DNA polymerases, as well as the two other members of the Y family, Polη and Polκ ( 10 , 12 , 41 ), form the four possible correct base pairs with nearly equivalent catalytic efficiencies. (asm.org)
  • In another structure, DNA in the active site of DnaG mimics the primer, providing insight into mechanisms for the nucleotide transfer and DNA translocation. (rcsb.org)
  • Tran NQ, Tabor S, Amarasiriwardena CJ, Kulczyk AW, Richardson CC. Characterization of a nucleotide kinase encoded by bacteriophage T7. (harvard.edu)
  • Tran NQ, Lee SJ, Richardson CC, Tabor S. A novel nucleotide kinase encoded by gene 1.7 of bacteriophage T7. (harvard.edu)
  • This review focuses primarily on polymerase variants that accept nucleic acids having additional nucleotide "letters" that form additional nucleobase pairs. (frontiersin.org)
  • A β hairpin from the leading-strand polymerase separates two parental DNA strands into a T-shaped fork, thus enabling the closely coupled helicase to advance perpendicular to the downstream DNA duplex. (pdbj.org)
  • Thus, as the helicase unwinds the antiparallel DNA strands, the DNA Pol on one strand (the leading strand) can go in the same direction as the helicase and replicate DNA continuously, but the DNA Pol on the antiparallel strand (the lagging strand) is generated in the opposite direction. (sciencemag.org)
  • The procedure is to mutagenize a large population of worms with trimethylpsoralen and UV irradiation, set up 1152 subpopulations, screen DNA made from this library for deletions in specific genes by nested PCR , and then to recover single worms carrying the deletions through a sib-selection process. (protocol-online.org)
  • Three classes of T7 genes have been recognized according to their expression time. (jbsdonline.com)
  • S inha and G oodman 1983 ), these studies reported small mutator effects from mutations in genes 32 , 44 , 45 , and 62 , whereas mutations in gene 43 (which encodes gp43, the DNA polymerase/proofreading exonuclease itself) could produce huge mutator factors. (genetics.org)
  • The high activity and stringent promoter specificity of T7 RNA polymerase are exploited in technologies for expressing heterologous genes in vivo, and for synthesizing RNAs in vitro. (uthscsa.edu)
  • A bacteriophage T7 RNA polymerase/promoter system for managed unique expression of particular genes. (cellsociety.org)
  • Transcriptional luxAB fusions to the DNA regions 5′ of the hpmB and hpmA genes confirmed that hpmB σ 70 promoter activity increased in swarm cells, and that there was no independent hpmA promoter. (microbiologyresearch.org)
  • T7 DNA Polymerase is a mesophilic, highly processive, and replicative DNA polymerase from bacteriophage T7. (mclab.com)
  • A portion (approximately 45%) of the molecule displays extensive structural homology to the polymerase domain of Klenow fragment and more limited homology to the human immunodeficiency virus HIV-1 reverse transcriptase. (nih.gov)
  • I will compare important structural motifs that are present in the Klenow fragment, HIV-1 RT, and T7 RNA polymerase. (cuny.edu)
  • DNA polymerase I (Klenow), to selectively and tightly bind primer-template complexes. (umd.edu)
  • pol and Klenow tightly bind to sequences containing regions that match the initiation and melting domains of promoters for the structurally similar bacteriophage T7-like RNA polymerases. (umd.edu)
  • The resulting eight templates were replicated in primer extension assays using the Klenow fragment, Sequenase 2.0, T4 polymerase holoenzyme, polymerase α, and polymerase β. (elsevier.com)
  • RNA in all cellular organisms is synthesized by a complex molecular machine, the DNA-dependent RNA polymerase (RNAP). (plos.org)
  • The molecular basis for this difference has been determined by constructing active site hybrids of these polymerases. (neb.com)
  • Mutagenesis is a tool that both evolution and molecular biologists use to tinker with DNA. (addgene.org)
  • This polymerase has various applications in site-directed mutagenesis as well as a high-fidelity enzyme suitable for PCR. (wikipedia.org)
  • It has also served as the precursor to Sequenase, an engineered-enzyme optimized for DNA sequencing. (wikipedia.org)
  • 2. The composition of claim 1 , wherein the polymerizing enzyme is a polymerase or reverse transcriptase. (google.com)
  • Portions of the enzyme were made transparent so as to make the path of RNA and DNA more clear. (wikidoc.org)
  • The enzyme exhibits extensive top-strand nicking of the supercoiled single-site DNA substrate. (springer.com)
  • This enzyme has the highest processivity and strand displacement activity among known DNA polymerases - more than 70 kb long DNA stretches can be synthesized. (mclab.com)
  • An initial physical and biochemical characterization of the enzyme reveals that it exists as a monomer and can ligate nicked, cohesive, and blunt-ended DNA fragments. (semanticscholar.org)
  • A large variety of different RNA species that are replicated by DNA-dependent RNA polymerase from bacteriophage T7 have been generated by incubating high concentrations of this enzyme with substrate for extended time periods. (naver.com)
  • DNA polymerase θ is a newly identified enzyme encoded by the human POLQ gene. (embopress.org)
  • One insert of ∼22 residues into the tip of the polymerase thumb subdomain is predicted to confer considerable flexibility and additional DNA contacts to affect enzyme fidelity. (embopress.org)
  • We recently identified the DNA polymerase activity of an A‐family enzyme found in mammalian cells, POLQ ( Seki et al , 2003 ). (embopress.org)
  • To examine the immunological relatedness of this enzyme with other retroviral DNA polymerases, remaining Sm-MTV DNA polymerase activity was measured after treatment of this enzyme with various antisera prepared against each of the reverse transcriptases of Mason-Pfizer monkey virus (MPMV), murine mammary tumor virus (MuMTV), simian sarcoma virus-simian sarcoma associated virus (SSV/SSAV), and Rauscher murine leukemia virus (RLV). (curehunter.com)
  • The coding region of T7 RNA polymerase is located between nucleotides 3170 and 5819. (cuny.edu)
  • Here we examine whether human Polκ, which differs from Polη in having a higher fidelity and which, unlike Polη, is inhibited at inserting nucleotides opposite DNA lesions, shows less of a dependence upon W-C hydrogen bonding than does Polη. (asm.org)
  • This review focuses on experiments that, by directed evolution, have created variants of DNA polymerases that are better able to accept unnatural nucleotides. (frontiersin.org)
  • Polymerases are also used to incorporate modified nucleotides, including those that tag, report, or signal the presence of product DNA molecules. (frontiersin.org)
  • Major advances in "next generation" sequencing, which requires the use of modified nucleotides and DNA polymerases, are considered in a separate review in this series ( Chen, 2014 ). (frontiersin.org)
  • Related work included the evolution of polymerases to accept the UBPs, which more recently has transitioned to application of the mutant polymerases for SELEX to evolve stable aptamers made up of modified or unnatural nucleotides. (scripps.edu)
  • We report that the polymerase mutant SFM4-3 can efficiently synthesize polymers composed of nucleotides with 2′-azido, 2′-chloro, 2′-amino, or arabinose sugars, and that SFM4-3 can PCR amplify these modified oligonucleotides. (scripps.edu)
  • Zhang X, Lee I, Berdis A. The use of nonnatural nucleotides to probe the contributions of shape complementarity and pi-electron surface area during DNA polymerization. (labome.org)
  • The DNA sequences analysed were capable of activating expression of the reporter enzymes, β - glucuronidase and β -galactosidase, present on pMJ445, indicating the presence of divergent promoters in the sequences selected. (scielo.org.za)
  • RNA polymerase enzymes are essential to life and are found in all organisms and many [[virus]]es. (wikidoc.org)
  • Polymerases are enzymes used by all cellular and viral organisms to replicate their genomes. (umd.edu)
  • SAC could be used as an alternative to SAM, SAH, and SIN to modify the frequency of DNA cleavage of the enzymes of this kind. (springer.com)
  • The T7 RNA polymerase is structurally similar to DNA polymerases, reverse transcriptases, and RNA-directed RNA polymerases, and these structural similarities define a polymerase superfamily that includes the majority of nucleic acid-synthesizing enzymes. (uthscsa.edu)
  • Each domain of the spiral-shaped hexameric helicase translocates sequentially hand-over-hand along a single-stranded DNA coil, akin to the way AAA+ ATPases (adenosine triphosphatases) unfold peptides. (pdbj.org)
  • The C-terminal tail of helicase domain contains several negatively charged acidic residues which make contact with the exposed basic residue of T7 polymerase/thioredoxin. (wikipedia.org)
  • one DNA Pol is on top of the helicase, and one DNA Pol is below (see the figure). (sciencemag.org)
  • This architecture is unlike textbook illustrations of both DNA Pols trailing behind the helicase. (sciencemag.org)
  • And lastly, I will consider the factors that are involved in the unique specificity found in some polymerases. (cuny.edu)
  • A quantitative assay reveals ligand specificity of the DNA scaffold repair protein XRCC1 and efficient disassembly of complexes of XRCC1 and the poly(ADP-ribose) polymerase 1 by poly(ADP-ribose) glycohydrolase. (wustl.edu)
  • The T7 bacteriophage encodes a single-subunit RNA polymerase of 99. (uthscsa.edu)
  • The flap endonuclease activity provides a mechanism by which RNA-terminated Okazaki fragments, displaced by the lagging strand DNA polymerase, are processed. (harvard.edu)
  • DNA coding for bacteriophage T7 RNA polymerase was ligated to a vaccinia virus transcriptional promoter and integrated within the vaccinia virus genome. (pnas.org)
  • The goal to elucidate the entire human genome has created an interest in technologies for rapid DNA sequencing, both for small and large scale applications. (google.es)
  • Bacteriophage T7 RNA polymerase is a DNA-dependent RNA polymerase that is encoded in the T7 bacteriophage genome. (cuny.edu)
  • 2017 ). Therefore, genome fragmentation methods are still being improved and new DNA fragmentation tools are being created, which include our previous work concerning Type IIS REases from the Thermus -family (Skowron et al. (springer.com)
  • Our genome contains many G‐rich sequences, which have the propensity to fold into stable secondary DNA structures called G4 or G‐quadruplex structures. (embopress.org)
  • Genome stability is ensured by a large variety of specialized DNA surveillance and repair pathways. (embopress.org)
  • Progeny cells therefore inherit one parental strand and one newly synthesized strand comprising a new duplex DNA genome. (pubmedcentralcanada.ca)
  • Electrostatic Potential Map of the Whole Genome DNA of T7 Bacteriophage. (jbsdonline.com)
  • Here we calculated the electrostatic potential profile of the whole genome DNA of bacteriophage T7 and draw electrostatic potential map of the whole genome and its promoter regions. (jbsdonline.com)
  • A full-length DNA clone encoding the genome of odontoglossum ringspot tobamovirus (ORSV) was synthesized and placed adjacent to a bacteriophage T7 RNA polymerase promoter. (nus.edu.sg)
  • The resulting hydroxy radicals are often linked to DNA degradation, however, there are doubts as to whether or not this damage would be significant when analyzed in vivo since in vitro studies with both bovine and human serum albumin exhibited extensive protection against it. (wikipedia.org)
  • Interestingly, we find that in vivo SARs differ from those collected in vitro, and most importantly, we identify four UBPs whose retention in the DNA of the SSO is higher than that of d NaM -d TPT3 . (scripps.edu)
  • In vitro transcribed single guide RNA (sgRNA) is generated enzymatically using a DNA template, ribonucleoside triphosphates and a bacteriophage RNA polymerase, most commonly T7. (horizondiscovery.com)
  • Significant specific IFN-γ T-cell responses were induced in all patients tested by DCs electroporated with patients' autologous polymerase chain reaction (PCR)-amplified and in vitro-transcribed proviral and plasma viral mRNA encoding either Gag or Env. (bloodjournal.org)
  • In in vitro experiments, the human norovirus 3CL Pro recognized five cleavage sites within ORF1 with various efficiencies to release six mature cleavage products with the gene order Nterm-NTPase-p20/p22-VPg-Pro-polymerase (Pol) ( 4 , 5 , 15 , 25 , 26 , 39 ). (asm.org)
  • On a more biochemical level, it was shown that topical application of myricetin to mice inhibited the binding of benzo(a)pyrenes to DNA and protein native to epidermal skin cells. (wikipedia.org)
  • Gene 6 protein of bacteriophage T7 has 5′-3′-exonuclease activity specific for duplex DNA. (harvard.edu)
  • 3′-extensions generated during degradation of duplex DNA by the exonuclease activity of gene 6 protein are inhibitory to further degradation of the 5′-terminus by the exonuclease activity of gene 6 protein. (harvard.edu)
  • The single-stranded DNA binding protein of T7 overcomes this inhibition. (harvard.edu)
  • Bacterial conjugation is a form of type IV secretion used to transport protein and DNA directly to recipient bacteria. (frontiersin.org)
  • Marintcheva B, Qimron U, Yu Y, Tabor S, Richardson CC, Richardson C. Mutations in the gene 5 DNA polymerase of bacteriophage T7 suppress the dominant lethal phenotype of gene 2.5 ssDNA binding protein lacking the C-terminal phenylalanine. (harvard.edu)
  • Finally, RNA must be purified from unincorporated triphosphates, protein and DNA. (horizondiscovery.com)
  • The interaction between polynucleotide kinase phosphatase and the DNA repair protein XRCC1 is critical for repair of DNA alkylation damage and stable association at DNA damage sites. (wustl.edu)
  • The yeast telomere-binding protein RAP1 binds to and promotes the formation of DNA quadruplexes in telomeric DNA", The EMBO J., vol. 13, pp. 2411-2420 (1994). (patentgenius.com)
  • Two obtained candidates, RING zinc finger protein and AtHB6, showed DNA binding activity to the AtGST11 promoter region. (ejbiotechnology.info)
  • The replicase includes the gp43 DNA polymerase, the gp45 processivity clamp, the gp44/62 clamp loader complex, and the gp32 single-stranded DNA binding protein. (pubmedcentralcanada.ca)
  • A DNA primer template bound by gp43 polymerase, a fork DNA substrate bound by RNase H, gp43 polymerase bound to gp32 protein, and RNase H bound to gp32 have been crystallographically determined. (pubmedcentralcanada.ca)
  • RNA can be viewed as the evolutionary center of this juxtaposition of DNA and protein. (pubmedcentralcanada.ca)
  • Protein expression vectors that utilize the bacteriophage T7 polymerase/promoter system are capable of very high levels of protein production. (biomedcentral.com)
  • Consistent with this hypothesis, we found that optimal protein overproduction was obtained reproducibly from T7 promoters using freshly transformed cells that had not been subjected to outgrowth during which mutations could accumulate. (biomedcentral.com)
  • The recombinant vaccinia virus retained infectivity and stably expressed T7 RNA polymerase in mammalian cells. (pnas.org)
  • Binding of thioredoxin exposes a large number of basic amino acid residues in the thumb region of T7 polymerase. (wikipedia.org)
  • Mitsunobu H, Zhu B, Lee SJ, Tabor S, Richardson CC. Flap endonuclease activity of gene 6 exonuclease of bacteriophage T7. (harvard.edu)
  • The RNaseH, a 5' to 3' exonuclease and T4 DNA ligase comprise the activities necessary for Okazaki repair. (pubmedcentralcanada.ca)
  • They also possess exonuclease activity and therefore function in DNA repair. (curehunter.com)
  • Same efficiency of the extension of DNA and RNA primers on hetero-homopolymeric hybrid and heteropolymeric DNA templates by the p180ΔN-core. (bioz.com)
  • A comparison of the structures and sequences of these polymerases identifies structural elements that may be responsible for discriminating between ribonucleotide and deoxyribonucleotide substrates, and RNA and DNA templates. (nih.gov)
  • DNA sequences upstream of P1 were similar to consensus SigK-dependent promoters, while P2 and P3 were similar to consensus SigE-dependent promoters. (asm.org)
  • DNA polymerases have been classified into evolutionary families based on an analysis of their amino acid sequences. (frontiersin.org)
  • Britten RJ, Kohne DE (1968) Repeated sequences in DNA. (springer.com)
  • Most recognise specific DNA sequences 4-8 bp long, with very few exceptions cleaving DNA more frequently. (springer.com)
  • The T7 and Sp6 sequences encode promoters from bacteriophages T7 and sp6, respectively. (bioz.com)
  • By applying Bayesian coalescent methods on DNA sequences serially sampled through time, we estimated that ST225 had diverged since approximately 1990 (1987 to 1994), and that expansion of the European clade began in 1995 (1991 to 1999), several years before the new clone was recognized. (pubmedcentralcanada.ca)
  • The mechanisms of quinolone resistance described in P. aeruginosa are mutations in the DNA gyrase gyrA gene ( 15 , 32 , 34 ) and, recently, in the topoisomerase IV parC gene ( 19 ), decreased permeability of the cell wall, and multidrug efflux systems ( 17 ). (asm.org)
  • Lee SJ, Chowdhury K, Tabor S, Richardson CC. Rescue of bacteriophage T7 DNA polymerase of low processivity by suppressor mutations affecting gene 3 endonuclease. (harvard.edu)
  • Mutations of Asp540 and the domain-connecting residues synergistically enhance Pyrococcus furiosus DNA ligase activity. (semanticscholar.org)
  • Similar to mutagenesis with error prone PCR, EvolvR uses an error prone polymerase to introduce mutations. (addgene.org)
  • Because regions of DNA in front of RNAP are unwound, there is compensatory positive supercoils. (wikidoc.org)
  • The major DNA adducts formed by cisplatin are cis -{Pt(NH 3 ) 2 } 2+ 1,2-d(GpG) and -d(ApG) intrastrand crosslinks, and minor adducts include 1,3-d(GpNpG) intrastrand crosslinks and 5′-d(GpC)/5′-d(GpC) interstrand crosslinks (ICL). (aacrjournals.org)
  • Fasullo M, Sun M, Egner P. Stimulation of sister chromatid exchanges and mutation by aflatoxin B1-DNA adducts in Saccharomyces cerevisiae requires MEC1 (ATR), RAD53, and DUN1. (labome.org)
  • As shown in Figure 2, the 3' hydroxyl group of a primer acts as a nucleophile and attacks the phosphodiester bond of nucleoside 5'-triphosphate (dTMP-PP). This reaction adds a nucleoside monophosphate into DNA and releases a pyrophosphate (PPi). (wikipedia.org)
  • The hydrophobic interaction between thioredoxin and T7 polymerase helps to stabilize the binding of T7 polymerase to primer-template. (wikipedia.org)
  • This reaction is similar to that catalyzed by conventional 5′-3′ polymerases, except that the attacking oxygen nucleophile is the GTP 3′ OH moiety instead of the 3′ OH group of the elongating primer strand ( Fig. 2 ). (pnas.org)
  • A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. (google.com)
  • 2014. "Flap endonuclease of bacteriophage T7: Possible roles in RNA primer removal, recombination and host DNA breakdown. (harvard.edu)
  • In multiplex assays, the primer oligonucleotide used for the DNA polymerase reaction can be the same for all probes. (patents.com)
  • Mitsunobu H, Zhu B, Lee SJ, Tabor S, Richardson CC. Flap endonuclease of bacteriophage T7: Possible roles in RNA primer removal, recombination and host DNA breakdown. (harvard.edu)
  • Stereochemical coruse of nucleotidyl catalyzed by bacteriophage T7 induced DNA polymerase", Biochemistry 1982, 21, 2570-2572. (patents.com)
  • Selection of zinc fingers that bind single-stranded telomeric DNA in the G-quadruplex conformation," Biochemistry, vol. 40, No. 3, Jan. 23, 2001, pp. 830-836. (patentgenius.com)
  • Isolation and characterization of a monoclonal anti-quadruplex DNA antibody from autoimmune "viable motheaten" mice," Biochemistry, vol. 37, No. 46, Mar. 1998, pp. 16325-16337. (patentgenius.com)
  • DNA polymerases have evolved for billions of years to accept natural nucleoside triphosphate substrates with high fidelity and to exclude closely related structures, such as the analogous ribonucleoside triphosphates. (frontiersin.org)
  • The precise mechanism for how the thioredoxin-T7 polymerase complex is able to achieve such increase in processivity is still unknown. (wikipedia.org)
  • Structure of a transcribing T7 RNA polymerase initiation complex. (semanticscholar.org)
  • After binding to the DNA, the RNA polymerase switches from a closed complex to an open complex. (wikidoc.org)
  • By using Xenopus laevis egg extract, we found that SUMOylation of DNA topoisomerase IIα (TOP2A) CTD regulates the localization of the histone H3 kinase Haspin and phosphorylation of histone H3 at threonine 3 at the centromere, two steps known to be involved in the recruitment of the chromosomal passenger complex (CPC) to kinetochores in mitosis. (rupress.org)
  • The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA", Cell, vol. 85, 1996, p. 125-136. (patentgenius.com)
  • Nonhomologous end joining of complex DNA double-strand breaks with proximal thymine glycol and interplay with base excision repair. (semanticscholar.org)
  • A gRNA is used to direct the PolI3M-nCas9 complex to a DNA site of interest, which nCas9 nicks and then dissociates from. (addgene.org)
  • The results reveal that Sap1-DNA affinity alone is insufficient to account for fork arrest and suggest that Sap1 binding-induced structural changes may result in formation of a competent fork-blocking complex. (labome.org)
  • In addition, comparative genomics indicated complex bacteriophage dynamics. (pubmedcentralcanada.ca)
  • Upon infection of the host, T7 polymerase binds to host thioredoxin in 1:1 ratio. (wikipedia.org)
  • Cisplatin binds both free and nucleosomal DNA ( 9 ). (aacrjournals.org)
  • PolI3M then binds the nicked DNA, and extends it from the 3' end, while its native endonuclease activity degrades the displaced strand. (addgene.org)
  • Gyllensten, U. B. and Erlich, H. A.: Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus. (springer.com)
  • Currently, many DNA polymerases are used in polymerase chain reaction (PCR) and other procedures that involve the copying of nucleic acids. (frontiersin.org)
  • The bacteriophage T7 DNA ligase gene was amplified using polymerase chain reaction-based methods and cloned into a T7 promoter-based expression vector. (semanticscholar.org)
  • 4. A DNA molecule according to claim 2 which is genomic DNA. (google.com)
  • DNA topoisomerase II (TOP2) plays a pivotal role in faithful chromosome separation through its strand-passaging activity that resolves tangled genomic DNA during mitosis. (rupress.org)
  • In a prokaryotic cell without efficient DNA repair, such genomic cleavage often results in cell death. (openwetware.org)
  • By delivering the designed CRISPR/Cas system to a microbial population one could selectively knockdown a subpopulation whose genomic DNA is targeted. (openwetware.org)
  • Protection of the integrity of genomic DNA is vital to the survival of all organisms. (pubmedcentralcanada.ca)
  • Consequently, these polymerases can efficiently and accurately replicate through the template bases which are isosteric to natural DNA bases but which lack the ability to engage in Watson-Crick (W-C) hydrogen bonding. (asm.org)
  • Classical DNA polymerases (Pols) replicate DNA with a high fidelity and are unable to replicate through DNA-distorting lesions. (asm.org)
  • Members of the Y family of DNA polymerases replicate DNA with a low fidelity, and unlike the classical polymerases, they are able to replicate through DNA lesions ( 28 , 29 ). (asm.org)
  • Template-free generation of RNA species that replicate with bacteriophage T7 RNA polymerase. (naver.com)
  • These remarkable findings open new vistas in tRNA enzymology and the evolution of nucleic acid polymerases. (pnas.org)
  • Finally, I will briefly go over the evidences that support a common ancestor for the nucleic acid polymerases. (cuny.edu)
  • Lacks SA, Greenberg B (1976) Single-strand breakage on binding of DNA to cells in the genetic transformation of Diplococcus pneumoniae . (springer.com)
  • Of these, Rev1 is a highly specialized polymerase which predominantly incorporates a C opposite template G and also opposite an abasic site ( 8 , 26 ), and genetic studies of Saccharomyces cerevisiae have suggested that a major role of Rev1 is to act as an assembly factor in Polζ-dependent lesion bypass ( 28 ). (asm.org)
  • Tran NQ, Tabor S, Richardson CC. Genetic requirements for sensitivity of bacteriophage t7 to dideoxythymidine. (harvard.edu)
  • TAR might be an accidental feature of DNA chemistry with important consequences for genetic stability. (genetics.org)
  • This 3′-5′ polymerase activity also functions in vivo in yeast, but only if the tRNA His substrate is mutated to contain C73 ( 14 ). (pnas.org)
  • A method comprises magnetically holding a bead carrying biological material (e.g., nucleic acid, which may be in the form of DNA fragments or amplified DNA) in a specific location of a substrate, and applying an electric field local to the bead to isolate the biological material or products or byproducts of reactions of the biological material. (freepatentsonline.com)
  • The second DNA strand of such substrate is specifically cleaved only in the presence of duplex oligonucleotides containing a cognate site. (springer.com)
  • The structures show that the catalytic domain of Thg1 shares both a common architecture and a two-metal ion-dependent mechanism with canonical 5′-3′ DNA polymerases. (pnas.org)
  • Here we report the first crystal structures of noncovalent DnaG-DNA complexes, obtained with the RNA polymerase domain of Mycobacterium tuberculosis DnaG and various DNA ligands. (rcsb.org)
  • Although the intrinsic error rate of this process is extremely low, its fidelity is continuously threatened, including by stable secondary structures in the DNA (Aguilera & Garcia‐Muse, 2013 ). (embopress.org)
  • Evidence for de novo production of self-replicating and environmentally adapted RNA structures by bacteriophage Qbeta replicase. (naver.com)
  • RNA Polymerase binding involves the α subunit recognizing the upstream element (-40 to -70) in DNA, as well as the σ factor recognizing the -10 to -35 region. (wikidoc.org)
  • 3 ) therefore provides a remarkable dénouement by showing that Nature accomplishes 3′-5′ nucleic acid polymerization using a structural fold homologous to the palm domain of canonical 5′-3′ DNA polymerases ( 15 ). (pnas.org)
  • Barany F, Kahn ME, Hamilton HO (1983) Directional transport and integration of donor DNA in Haemophilus influenzae . (springer.com)
  • 1983 ). A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. (biologists.org)
  • Studier FW, Dunn JJ (1983) Organization and expression of bacteriophage T7 DNA. (springer.com)
  • However, polymerases that can accept unnatural nucleoside triphosphates are desired for many applications in biotechnology. (frontiersin.org)
  • I will then examine the catalytic mechanism of the T7 RNA polymerase with an emphasis of the different stages. (cuny.edu)
  • The mechanism of autocatalytic amplification of RNA by T7 RNA polymerase proved to be analogous to that observed with viral RNA-dependent RNA polymerases (replicases): only single-stranded templates are accepted and complementary replica strands are synthesized. (naver.com)
  • Our results suggest that a major contributing factor to decreased expression levels in T7 based systems is chromosomal mutation resulting in loss of functional T7 RNA polymerase. (biomedcentral.com)
  • Lacks SA (1977) Binding and entry of DNA in bacterial transformation. (springer.com)
  • DNA transfer via conjugation plays a major role in the dissemination of antibiotic resistance among medically significant bacterial species. (openwetware.org)
  • can be applied to other T7-like phages to obtain clones that produce RNA polymerases having different promoter specificities, different bacterial hosts, or other desirable properties. (osti.gov)
  • This field drives DNA sequencing technology, the design of myriad anti-viral and anti-bacterial drugs, and the development of novel strategies for gene targeting and generation of transgenic animals. (keystonesymposia.org)
  • We show that the evolved Stoffel fragment mutant, SFM4-3, efficiently transcribes RNA or 2′-F-modified RNA and that it also efficiently PCR amplifies oligonucleotides of mixed RNA and DNA composition. (scripps.edu)
  • These mechanisms efficiently deal with DNA damage from exogenous sources as well as damage generated intracellularly. (embopress.org)
  • Anneal oligonucleotides A, B, and C to the λ DNA in one step by adding a 10-fold excess of oligonucleotides A and B, and a 100-fold excess of oligonucleotide C in T4 DNA ligase buffer. (jove.com)
  • Add T4 DNA ligase to the mixture and incubate at room temperature for 2 hours. (jove.com)
  • T4 DNA Ligase will catalyze the correct joining of oligonucleotides A and B, and λ DNA. (jove.com)
  • Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining. (wustl.edu)
  • Human DNA ligase III recognizes DNA ends by dynamic switching between two DNA-bound states. (wustl.edu)
  • Fidelity of RNA templated end-joining by chlorella virus DNA ligase and a novel iLock assay with improved direct RNA detection accuracy. (bireme.br)
  • Bacteriophage T7 DNA ligase. (semanticscholar.org)
  • article{Doherty1996BacteriophageTD, title={Bacteriophage T7 DNA ligase. (semanticscholar.org)