STRUCTURES OF APURINIC AND APYRIMIDINIC SITES IN DUPLEX DNAS

Natural and exogenous processes can give rise to abasic sites with eit her a purine or pyrimidine as the base on the opposing strand. The sol ution state structures of the apyrimidinic DNA duplex, with D-6 indica ting an abasic site, d(C-1 G(2) C-3 G(4) A(5) D-6 R-7 C-8 G(9) C10C11) d( (21)G(20)C(19)T(18)A(17)T(16)G(15)C(14)G(13)G(12)) referred to as AD, and the apurinic DNA duplex with a dC(17), referred to as CD, have been determined, A particularly striking difference is that the abasi c site in CD is predominantly a beta hemiacetal, whereas in AD the alp ha and beta forms are equally present. Hydrogen bonding with water by the abasic site and the base on the opposite strand appears to play a large role in determining the structure near the damaged site. Compari son of these structures with that of a duplex DNA containing a thymine glycol at the same position as the abasic site and with that of a dup lex DNA containing an abasic site in the middle of a curved DNA sequen ce offers some insight into the common and distinct structural feature s of damaged DNA sites.