Conformations of deoxydodecanucleotides with pyrimidine (6-4)-pyrimidone photoadducts.

Abstract

Abstract— We have carried out molecular mechanical simulations of dodecanucleotide d(CGCGAAXYCGCG).d(CGCGX'Y'TTCGCG) with XY being CC, TC, TT and CT and X'Y'being their corresponding base paired dinucleotides on the complementary strand. Simulations were also carried out with the corresponding pyrimidine (6‐4)‐pyrimidone photoadducts incorporated in these dodecanucleotides. As in the case of the cyclobutane dimer incorporated dodecanucleotide structures (Rao et al., 1984), those regions of the DNA modified by6–4 pyrimidine adducts are found to undergo little conformational changes except in the dimer region. The conformational characteristics of the6–4 pyrimidine adduct incorporated structures seem to be influenced by the nature of the base at the 3' end of the dimer. Specifically, favorable hydrogen bonding interactions between the 5' end base and its preceding phosphate group are present in structures which have cytosine at the 3' end of the photodimer. The energetics of these structures relative to those without incorporated dimers have been discussed and the results have been analysed in the light of the currently prevalent ideas on the role of the6–4 photoadducts in mutagenesis in various organisms.