The removal of damaged segments, e.g. pyrimidine dimers, from one strand of double-stranded DNA and its correct resynthesis.
(= DNA fingerprinting (DNA profiling))
(= exonuclease footprinting (DNase footprinting))
double-stranded DNA. (see also double helix (Watson-Crick model))
A method for identification of a protein-binding region in a double-stranded DNA fragment. One 5'-end of the DNA fragment is labelled with 32P and the DNA-fragment-protein complex is treated with a 3'-exonuclease to digest from the 3'-end until it meets the region protected by the DNA-binding protein. The labelled strand is characterized subsequently by its size to indicate the distance of the site of the binding protein from the 5'-end of the fragment. The technique is suitable for localization of a binding site to a specific region of a large DNA fragment, whereas footprinting gives the exact sequence of the binding site of a smaller fragment. (see also footprinting)Revzin, A. (ed.) (1993) footprinting of Nucleic Acid-Protein Complexes, Academic Press, San Diego
Automated DNA sequencing using single-lane sequencing; adaptable to automated data collection.
see quadruplex DNA
Genomic DNA refers to the genetic material that in eukaryotes is found organized into multiple chromosomes within a nucleus, while in prokaryotes is organized as circular DNA residing within the cytoplasm. In eukaryotic cells, genomic DNA includes protein-coding (exons) and non-coding sequences (introns); in contrast, prokaryotes’ genomic DNA only contains exon sequences. Different molecular biology applications (e.g., Sanger, Next-generation sequencing) require the isolation of genomic DNA from whole blood or tissues. Isolation of genomic DNA from whole blood may be achieved through different methods (e.g., solution-based or solid-phase DNA extraction) involving several basic steps such as cell lysis, nucleoprotein denaturation, enzyme inactivation, contaminant removal (i.e., RNA, lipids, and proteins), and lastly DNA precipitation.
A form of triplex DNA characterized by Hoogstein base pairing.Yagil, G. (1991) Crit. Rev. Biochem. Mol. Biol. 26, 475-559; Frank-Kamenetskii, M.D. and Mirkin, S.M. (1995) Annu. Rev. Biochem. 64, 65-95; Vasquez, K.M. and Wilson, J.H. (1998) Trends Biochem. Sci. 23, 4-9
A branched double-stranded DNA structure, a chi-form in which each of four polynucleotide chains is complementary to and base-paired with the 3'-end of one polynucleotide and the 5'-end of another; unlike in a recombination intermediate, the junction cannot migrate (i.e. slide its branch point along the duplex) without breaking many more Watson-Crick base-pair hydrogen bonds as it advances than can re-form behind it. (see also Holliday model)
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