15-mer DNA duplexes containing an abasic site are thermodynamically more stable with adjacent purines than with pyrimidines

Abasic site (AP)-containing duplexes, with flanking adenine (A) or cytosine (C) bases, were shown to be more stable with flanking A than with C bases [Sagi, J., Hang, B., and Singer, B. (1999) Chem. Res. Toxicol. 12, 917-923] . We investigated whether the lower-magnitude destabilization by an AP site , with A neighbors, is a general effect of the purine versus the pyrimidine neighbors. Duplex stability, as compared to that of the corresponding cont rol duplexes, was markedly decreased by the incorporation of the AP site (x ) opposite any of the four bases. However, for the duplexes containing T, A , or C opposite the AP site, replacement of the symmetric doublet flanking pyrimidine bases with purines resulted in a smaller destabilization effect. The average stabilizing effect of the symmetric doublet purine neighbors o f an AP site opposite T, A, or C bases was 3.2 degreesC (DeltaT(m)) and 1.3 kcal/mol (Delta DeltaG degrees (37)) compared to those of pyrimidine neigh bors. In contrast, a G.AP pair reduced or eliminated the differential effec t of the neighbors. Using unrestrained molecular dynamics, it was shown tha t for the duplexes containing T opposite the AP site, with doublet pyrimidi ne neighbors, there was a larger magnitude of curvature around the lesion s ite than for the duplexes with the purines flanking the AP site. Purines fl anking the AP site tend to shift toward each other, creating overlap, in co ntrast to the flanking pyrimidines. This indicates the possibility of stack ing between purine bases at the AP site and can be the reason for the obser ved smaller thermodynamic destabilization of the duplexes with the AAxAA an d GGxGG central sequences, as compared to those with TTxTT and CCxCC sequen ces. This work showed that for an AP site the GC content is not the only de terminant of duplex stability, but rather is influenced more by whether pur ines or pyrimidines flank the AP site.