Structures of apurinic and apyrimidinic sites in duplex DNAs

Natural and exogenous processes can give rise to abasic sites with either a purine or pyrimidine as the base on the opposing strand. The solution state structures of the apyrimidinic DNA duplex, with D(6) indicating an abasic site, d(C(1) G(2) C(3) G(4) A(5) D(6) R(7) C(8) G(9) C(10)C(11)) d( G(22)C(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 abasic site in CD is predominantly a beta hemiacetal, whereas in AD the alpha 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. Comparison 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 duplex DNA containing an abasic site in the middle of a curved DNA sequence offers some insight into the common and distinct structural features of damaged DNA sites.