REGIOSELECTIVE EFFECT OF ZWITTERIONIC DNA SUBSTITUTIONS ON DNA ALKYLATION - EVIDENCE FOR A STRONG SIDE-CHAIN ORIENTATIONAL PREFERENCE

The incorporation of zwitterionic residues (5-substituted omega-aminoa lkyl-2'-deoxypyrimidines) into DNA has been reported to bend DNA as me asured by aberrant gel mobility [Strauss et al. (1996) Proc. Natl. Aca d. Sci. U.S.A. 93, 9515-9520]. Herein we report that DNA methylation b y N-methyl-N-nitrosourea at N7-guanine is regioselectively inhibited b y point substitutions of the zwitterionic residues 5-(6-aminohexyl)-2' -deoxycytidine, 5-(6-aminohexyl)-2'-deoxyuridine, or 5-(3-aminopropyl) -2'-deoxyuridine. No inhibition is observed for DNA methylation by dim ethyl sulfate. On the basis of inhibition patterns for methylation wit h the different zwitterionic substitutions and the different length te thers, the omega-aminoalkyl side chains prefer to adopt a conformation that points them toward the 3'-base. Molecular modeling grid searches , coupled with energy minimizations, and simulated annealing molecular dynamics studies indicate that unfavorable steric interactions with t he 5'-base and backbone, as well as stabilizing electrostatic interact ions with electronegative atoms on the 3'-side, are responsible for th e observed conformational preference. No evidence for association of t he cationic side chain with the phosphate backbone is observed. The ob served bending of DNA induced by the tethered ammonium ions may simply arise from their localization in the major groove.