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Home >> Dictionary of Bioinformatics, Biochemistry, Biotechnology >> DNA Helicase DNA Polymerase Alpha DNA Polalpha
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DNA Helicase
An enzyme that catalyses the unwiding of the complementary strands of a DNA duplex. Helicases catalyses the separation of double stranded DNA to single stranded DNA using the energy derived from ATP hydrolysis.
These enzymes unwind the DNA duplex just ahead of the replication fork at a rate of 1000 bp/s. Two DNA Helicase are involved in unwiding DNA at a replication fork, one on the leading strand template and the other on the laging strand template.
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These enzymes move in opposite directions because of the opposite polarities of the DNA template. Helicase functions together with Topoisomerase to relieve torsional strain. In addition to replication, Helicases are required for homologous recombination, nucleotide excision repair, transcription termination and conjugation.
DNA hybridisation
Complementary base pairing between two DNA molecules, usually from different sources. It is used to detect the presence of a specific nucleotide sequence in a DNA sample.
DNA library
A collection of clones, each containing a DNA segment from a source organism ligated to a cloning vector.
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DNA ligase
An enzyme that catalyses a reaction that joins two DNA molecules via the formation of a phospho-diester bond between the 3’ hydrolysed and 5’ phosphate of adjacent nucleotides. The enzyme plays an important role in DNA repair and replication. It is one of the essential tools of recombinant DNA technology that enables the incorporation of foreign DNA into cloning vectors. The ligase from phage T4 commonly used in gene cloning experiments requires ATP as a cofactor. T4 is used in vitro to join the vector and insert DNAs.
DNA linkers
Short sequences of nucleotides that contain a restriction enzyme cleavage site. These can be ligated to the ends of a nucleotide or gene sequence to facilitate cloning into a vector.
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DNA looping
The interaction of proteins bound to different sites on DNA that brings the intervening region between these sites into juxtaposition in the form of a loop.
DNA methylation
Addition of methyl groups to DNA. Methylation of cytosine bases in CG sequences keeps genes in an inactive sate in eukaryotes.
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DNA mutants
Temperature sensitive mutants of bacteria that synthesis DNA at 37°C but not at 42°C.DNA only transposon A transposon that exists as DNA throughout its life cycle.
DNA PK DNA dependent protein kinase involved in double stranded break repair. Both Ku and DNA PK bind to free DNA ends, approximate the two strands and unwind them. This is followed by gap filling and ligation.
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DNA photolyase
An enzyme that catalyses repair of pyrimidines dimmers formed by ultraviolet radiation.
DNA microarray
A small glass surface to which an array of DNA fragments has been fixed in a defined position. A typical DNA chip contains 10 000 discretes spots fragment. When a sample of fluorescently labelled DNA fragments is hybridised to the chip, the spots which hybridise with the DNA fragments in the sample are visible as fluorescence. If the spots on the chip are genes (expressed sequence tags), hybridisation with cDNA from a particular tissue displays which genes are expressed in that tissues. The advantages of DNA chips is the ease of automation of genotyping, that enables large numbers of plants or animals to be genotyped for a number of loci.
DNA polymerase I (DNA pol I)
A bacterial enzyme isolated in 1955 by Arthur Kornberg. It is also known as the Kornberg enzyme or Kornberg polymerase. The enzyme is a single polypeptide of 1000 amino acid residues encoded by the poIA gene. It is a metalloenzyme containing 1 or 2 atoms of Zn at the active site, nonessential –SH group and an intrachain S-S group. The enzyme has 5’→3’ polymerase and both 5’→3’ and 3’→5’ exonuclease activities. Pol I has a low rate of chain elongation and processivity. It is not the primary enzyme for replication. It function in gap filling and exonuclease activity during replication, repair and recombination. It is also used in vitro in the preparation of labelled DNA probes and for DNA sequencing by the dideoxy method.
DNA polymerase II (DNA pol II)
a minor component of the cell during normal bacterial growth induced by the SOS response. The enzyme has 3’→5’ exonuclease activity, lacks 5’→3’ exonuclease activity, has more stringent requirements for both template and primer and is effective activity, has more stringent requirements for both template and primer, and is effective only on duplex DNA with gaps or single stranded ends of < 10 nucleotides. It cannot replicate long single strands with short, complementary primers unlike pol I. It is inhibited by –SH blocking agents. Pol II is involved in proofreading and DNA repair.
DNA polymerase III (DNA pol III)
An E. coil polymerase that has the highest rate of chain enlogation and processivity. It polymerases 0.5 mb of DNA during one cycle on the leading strand. It is the most active of the three polymerases; 15 times more than pol I and 300 times more than pol II. It is inhibited by –SH blocking agents and has both exonuclease activities. It has the same template primer dependence as polymerase II and high km for dNTP substrates. It is a product of the dnaE gene. The enzyme functions in the form of a large complex called DNA polymerase III holoenzyme, which has 10 types of subunits.
DNA polymerase a (DNA pol a)
A eukaryotic enzyme that functions in the synthesis of short primers that are subsequently extended by pol d. It is present as a multisubunit polymerase activity but lacks 3’→5’ proofreading function. Pol a provides the template for an accessory factor called replication factor C (RFC), which loads polymerase and controls the processivity of replication on the lagging strand similar to the E.coli g complex. The enzyme is inhibited by –SH blocking agents and can be phosporylated by cAMP – dependent protein kinase. Phosphorylation activity.
DNA polymerase b (DNA pol b)
The smallest of the eukaryotic polymerases. It has lowest fidelity and processivity. It is a single polypeptide not inhibited by –SH group blocking agents, exists as a monomer in cytoplasm and dimer in the nucleus. The active form is a dimer. Pol b catalyses DNA repair.
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