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DNA repairany of the processes in the CELL in which damaged DNA is recognized and repaired. The process may involve precise reversal of the damage, or removal of the damage followed by replacement with normal DNA. See, for example, DARK REPAIR, EXCISION REPAIR, MISMATCH REPAIR.
DNA binding proteins
are of two general types, histone proteins which are part of the unit structure of chromosomes called nucleosomes and nonhistone proteins which are present in small amounts and include regulatory proteins.
a DNA molecule that is a closed-ring structure, found in mitochondria, prokaryote chromosomes, plasmids, and certain viruses.
closed DNA complexes
the first of two kinetically distinct steps required for RNA polymerase to initiate transcription in which the RNA polymerase holoenzyme binds electrostatically to the promoter DNA.
a DNA molecule which has been inserted into a cloning vector.
a DNA copy of mRNA which contains only regulatory and coding sequences, i.e. introns have been removed. mRNA is copied into double-stranded DNA using reverse transcriptase; the cDNA can then be cloned and amplified and introduced into an expression vector (plasmid or phage) and its protein product produced in either bacterial, yeast, insect or mammalian cells. Called also cDNA.
DNA double helix
see double helix.
end labeling DNA
methods for labeling DNA with radioisotopes or other detectable marker molecules at the ends using the terminal transferase 3′-labeling or polynucleotide kinase for 5′-labeling.
that present in a cell as extra chromosomal; exemplified by plasmids of prokaryotic cells. See plasmid.
the DNA that has been introduced into a host by cloning.
enzymes involved in the excision-repair mechanisms for DNA.
duplex DNA with each strand from a different origin.
a collection of cloned DNA molecules from a genome.
an enzyme that seals nicks in the DNA helix, joins Okazaki fragments together during DNA replication and is essential in recombinant DNA technology for DNA cloning.
an ordered set of thousands of different oligonucleotides immobilized on a microscope slide or other solid surface used for the detection of cognate nucleotide sequences such as the pattern of gene expression in a particular cell population by hybridization with fluorescently labeled cDNA prepared from total mRNA isolated from the cells.
a sequence present in the variable locations on the chromosome. Called also jumping genes. See also retrotransposon and transposable genetic elements.
open DNA complex
a local opening of about 10 base pairs formed at the transcription initiation site following the electrostatic binding of RNA polymerase holoenzyme to the promoter region.
of Escherichia coli; has three distinct enzymatic activities: (a) a 5′ to 3′ polymerase activity which, under the direction of a template DNA, catalyzes the addition of mononucleotide units, produced from deoxynucleoside 5′-triphosphates, to the 3′-hydroxyl terminus of a primer chain; (b) a 5′ to 3′ exonuclease active only on duplex DNA; (c) a 3′ to 5′ exonuclease primarily active on single-stranded DNA which can selectively remove mismatched terminal nucleotides, thus carrying out a proofreading function. Additionally it catalyzes both the pyrophosphorolysis of DNA, a reaction which is the reverse of polymerization, and pyrophosphate exchange which represents a repetitive sequence of nucleotide addition and pyrophosphorolysis.
see probe (2).
a series of enzymatic mechanisms whereby errors or damage to one of the two DNA strands are removed by excision and replaced by correct nucleotides using the undamaged strand as template. The mechanisms include removal of lesions of depurination and DNA glycosylases which recognize altered bases.
repeat DNA, repetitive DNA
includes (a) satellite DNA and so-called (b) interspersed repeated DNA sequences. The latter are interspread throughout the chromosomes in hundreds of thousands of individual copies, each about 300 nucleotides long; they are, unlike satellite DNA, transcribed.
serially repeated DNA sequences of one or a few nucleotides with a repeat length of up to 250 nucleotides that are not transcribed and commonly located in the heterochromatin associated with the centrometric regions of chromosomes.
a mobile DNA element that appears to have no function except to replicate itself. Part of junk DNA.
determining the order of nucleotides in DNA from which amino acid in a polypeptide chain can be predicted.
the fraction of DNA that contains most of the protein-coding genes and reassociates most slowly.
produced when double-stranded DNA is denatured or found naturally in some viruses.
single-copy DNA sequences which do not encode proteins or functional RNA molecules.
the double helix is itself twisted.
a twisted structure formed by circular DNA molecules. See also supercoiled DNA (above).
DNA sequences that occur only once in the haploid genome.
contain a single molecule of DNA that is either double or single stranded. Parvoviruses and circoviruses are single stranded, hepadnaviruses are partially double stranded and all others are double stranded. DNA virus families are: Poxviridae, Asfarviridae,Herpesviridae, Adenoviridae, Papovaviridae, Parvoviridae, Circoviridae, and Hepadnaviridae.
an alternative structural form of DNA which differs from the more commonly occurring B- and related A-form in that the helix is left handed compared with the right hand helixes of B- and A-forms. Z is for zig-zag. The functional significance of Z-DNA is unknown.