Yu Kay Law - Sequence-dependent thymine dimer formation and photoreversal rates in double-stranded DNA

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      Publication Details (including relevant citation   information): Law, Yu Kay, Forties, Robert A., Liu, Xin,   Poirier, Michael G., Kohler, Bern, Photochem. Photobiol.   Sci., 2013, 12 (8), pp 1431-1439

      Abstract: The kinetics of thymine-thymine   cyclobutane pyrimidine dimer (TT-CPD) formation was studied at 23   thymine-thymine base steps in two 247-base pair DNA sequences   irradiated at 254 nm. Damage was assayed site-specifically and   simultaneously on both the forward and reverse strands by   detecting emission from distinguishable fluorescent labels at the   5[prime or minute]-termini of fragments cleaved at CPD sites by   T4 pyrimidine dimer glycosylase and separated by gel   electrophoresis. The total DNA strand length of nearly 1000 bases   made it possible to monitor damage at all 9 tetrads of the type   XTTY, where X and Y are non-thymine bases. TT-CPD yields for   different tetrads were found to vary by as much as an order of   magnitude, but similar yields were observed at all instances of a   given tetrad. Kinetic analysis of CPD formation at 23 distinct   sites reveals that both the formation and reversal photoreactions   depend sensitively on the identity of the nearest-neighbour bases   on the 5[prime or minute] and the 3[prime or minute] side of a   photoreactive TT base step. The lowest formation and reversal   rates occur when two purine bases flank a TT step, while the   highest formation and reversal rates are observed for tetrads   with at least one flanking C. Overall, the results show that the   probabilities of CPD formation and photoreversal depend   principally on interactions with nearest-neighbour bases.

      Address (URL): http://dx.doi.org/10.1039/C3PP50078K