DNA Damage Repair Applications

DNA Damage Repair Applications

Many DNA damage/repair studies are focused on the potential mutational or genotoxic consequences that could arise from specific single types of DNA lesions. However, more recently, attention has begun to be paid on the potential deleterious effects of clusters of lesions, located on either the same or complementary strands. Lesion cluster formation is particularly relevant when the damaging agent is ionizing radiation, and the relative repairability of such clusters compared with single-base lesions is an active research topic (7). Another recent area of interest is the relationship between DNA sequence context (for example, single vs. runs of Gs) and both the location and number of lesions caused by DNA damaging agents, oxidizers in particular (8).

A variety of modified nucleotide phosphoramidites, suitable for use in investigational studies of DNA damage/repair mechanisms, are commercially available that can be incorporated into oligonucleotides during solid-phase synthesis. In addition, Gene Link’s extensive experience in synthesizing oligos with unusual, or challenging combinations of, modifications makes us an attractive choice for supplying modified oligos for use in (a) DNA damage and repair studies, (b) the development of assays for detecting specific types of DNA damage, or monitoring specific DNA repair processes, (c) the development of assays that utilize DNA damage and repair processes to detect mutagenic or genotoxic substances in the environment. See the relevant tech sheet for a particular modification for details.

References

(1) Lodish, H., Berk, A., Matsudaira, P., Kaiser, C.A., Krieger, M., Scott, M.P., Zipursky, S.L., Darnell, J. (2004). In Molecular Biology of the Cell 5th ed., WH Freeman, New York, NY, 963.
(2) Lindahl, T. (1993) “Instability and decay of the primary structure of DNA”, Nature 362: 709-715.
(3) Nilsen, H., Krokan, H.E. (2001) “Base excision repair in a network of defence and tolerance”, Carcinogenesis 22: 987-998.
(4) de Laat, W.L, Jaspers, N.G.J., Hoeijmakers, J.H.J. (1999) “Molecular mechanism of nucleotide excision repair”, Genes & Development 13: 768-785.
(5) Iyer R., Pluciennik A., Burdett V., Modrich P. (2006). "DNA mismatch repair: functions and mechanisms". Chem Rev 106: 302–23.
(6) Sancar A. (2003). “Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors”, Chem Rev 103:2203–37.
(7) Shikazono, N., Pearson, C., O’Neill, P., Thacker, J. (2006) “The roles of specific glycosylases in determining the mutagenic consequences of clustered DNA”, Nucleic Acids Res. 34: 3722-3730.
(8) Margolin, Y., Shafirovich, V., Geacintov, N.E., DeMott, M.S., Dedon, P.C. (2008) “DNA Sequence Context as a Determinant of the Quantity and Chemistry of Guanine Oxidation Produced by Hydroxyl Radicals and One-Electron Oxidants”, J. Biol. Chem. 283: 35569-35578.
(9) Reardon, J.T., Sancar, A. Recognition and repair of the cyclobutane thymine dimer, a major cause of skin cancers, by the human excision nuclease. Genes Dev (2003), 17: 2359-2551.
(10) Prakash, S., Prakash, L. Nucleotide excision repair in yeast. Mutat. Res. (2000), 451: 13-24.
(11) Asagoshi, K., Tano, K., Chastain, P.D., et al. FEN1 Functions in Long Patch Base Excision Repair Under Conditions of Oxidative Stress in Vertebrate Cells. Mol Cancer Res (2010), 8: 204-215.
(12) Sundaresakumar, P. Use of novel assays to measure in vivo base excision DNA repair. M.S. Thesis, San Jose State Univ, 2009, 105 pages, Pub # 1470953. (13) Tornaletti, S., Pfeifer G.P. Ligation-Mediated PCR for Analysis of UV damage. In: Pfeifer, G.P., ed., Technologies for detection of DNA damage and mutations. New York: Plenum Press, 1996, pp. 199-209.
(14) Rochette, P.J., Brash, D.E. Human Telomeres Are Hypersensitive to UV-Induced DNA Damage and Refractory to Repair. PLoS Genetics (2010), 6(4): e1000926.