Paper Citing NAMD - Abstract
Pan, Zhengzheng; McCullagh, Martin; Schatz, George C.; Lewis, Frederick D.
Conformational Control of Thymine Photodimerization in Purine-Containing Trinucleotides
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:1432-1438, JUN 16 2011
The effects of a flanking purine base on the thymine-thymine photodimerization efficiencies and product distributions have been determined for the trinucleotides 5'-ATT, TTA, GTT, and TTG and the results compared to those for the dinucleotide TT. The highest quantum yield and selectivity for formation of the major cis-syn (2 + 2) dimer was observed for ATT. The relative yields of (2 + 2) and (6 4) adduct formation from the four trinucleotides are well-correlated with ground-state conformational populations using the single-parameter model developed in our previous studies of TT dimerization. The effect of the flanking purine base is determined mainly by its influence on the extent of TT ground-state stacking, which is more extensive for A versus G. The low probability of stacking of all three nucleotides and the fast decay times of the nucleotide excited states can account for the apparent absence of electronic interactions between thymines and the flanking purine base.
