DNA exonuclease See deoxyribonuclease exonuclease

DNA probes

DNA gyrase A topoisomerase type II present in bacteria which introduces negative superhelical twists into relaxed closed circular DNA molecules. Several DNA phages require the action of this enzyme during replication of their DNA.

Denhardt DT (1979) Nature 280, 196

DNA helicase A DNA unwinding enzyme - a single-stranded DNA-dependent nucleoside 5'-triphosphatase involved in DNA replication. Has ATPase activity and hydrolyzes two molecules of ATP per DNA base pair broken.

Kuhn B et al (1978) Cold Spring Harbor Symp 43, 63

DNA insert A DNA sequence inserted into a cloning vector.

DNA ligase An enzyme involved in DNA synthesis, and in repair of single-stranded breaks (nicks) in native double-stranded DNA, as well as circularization of DNA. Catalyzes the formation of a phosphodi-ester bond between the 5'-phosphate end of one nucleotide and the 3'-OH group of another. Requires ATP or NAD as a cofac-tor. Ligases are present in both animal and plant cells, including bacteria. Cf. DNA polymerase and see semi-conservative replication.

Lehman IR (1974) Science 186, 790

DNA methylase An enzyme that catalyzes specific methylation of DNA bases. Occurs in most organisms, and involves the enzymatic transfer of the methyl group of the S-adenosyl-methionine to specific bases in DNA. Functions after incorporation of the base into the polynu-cleotide strand. In eukaryotic cells, the most common methylated base is 5-methyl-cytosine.

DNA polymerase One of a number of enzymes involved in DNA replication which catalyze the addition of deoxyri-bonucleotide units to a DNA chain by forming a phosphodiester bond between the 3'-OH group on the growing end of the DNA molecule (known as the primer strand) and the 5'-phosphate on the incoming deoxyribonucleotide. The reaction requires a template (DNA or sometimes RNA), all four deoxyribonucleoside triphosphates and a primer with a free 3'-hydroxyl group. The primer can be an uncompleted DNA strand, but is more usually a short RNA strand. Synthesis of at least one strand is discontinuous and yields a series of Okazaki fragments. Three types of DNA polymerase have been described in prokaryotes. DNA polymerase I (Kornberg enzyme) has a 5'-3' exonucle-ase activity as well as polymerase activity and is mainly involved in repair synthesis of DNA. DNA polymerase II has a 3'-5' nuclease activity but lacks the 5'-3' nucle-ase activity. DNA polymerase III has both 5'-3' and 3'-5' exonuclease activities and appears to be the true DNA replicating enzyme in Escherichia coli; the role of DNA polymerase II is uncertain. In eukaryotic cells, four distinct species of DNA poly-merase have been described. (1) DNA polymerase alpha has a high molecular weight and contains associated DNA primase activity; it is the major enzyme involved in DNA replication. (2) DNA polymerase beta is a low molecular weight enzyme, present in cell nuclei, the function of which is unknown. (3) DNA polymerase gamma is only found in mitochondria and functions in the replication of mitochondrial DNA. (4) DNA poly-merase delta has a high molecular weight and contains associated 3'-exonuclease activity. Many viruses induce new DNA polymerase activity upon infection (e.g. adeno- or herpesviruses) whilst others, notably parvoviruses, use existing host cell enzymes. Retroviridae contain a different type of DNA polymerase which is RNA template-dependent (See reverse transcriptase).

Wickner SH (1978) Annu Rev Biochem 47, 1163

DNA primase An RNA polymerase activity which synthesizes the RNA primers that are extended by DNA polymerases to form Okazaki fragments. Associated with DNA polymerase alpha activity in eukaryotic cells.

Scherzinger E et al (1977) Nucl Acids Res 4, 4151

DNA probes Molecules of DNA whose sequence is specific for a particular virus nucleic acid and can be used, e.g. by hybridization, to detect the presence of the virus nucleic acid in a sample, e.g. a PCR product.

DNA provirus

DNA provirus A duplex DNA copy of a virus nucleic acid (usually a retrovirus) that is integrated into the host cell genome and is transmitted from one cell generation to another without causing lysis of the host.

DNA relaxing enzyme A topoisomerase that catalyzes the conversion of superhe-lical DNA to a non-superhelical covalently closed form.

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