ALTERNATING D(GA)(N) DNA-SEQUENCES FORM ANTIPARALLEL STRANDED HOMODUPLEXES STABILIZED BY THE FORMATION OF G.A BASE-PAIRS

Alternating d(GA)n DNA sequences form antiparallel stranded homoduplex es which are stabilized by the formation of G.A pairs. Three base pair ings are known to occur between adenine and guanine: AH+ (anti).G(syn) , A(anti).G(anti) and A(syn).G(anti). Protonation of the adenine resid ues is not involved in the stabilization of this structure, since it i s observed at any pH value from 8.3 to 4.5; at pH less-than-or-equal-t o 4.0 antiparallel stranded d(GA.GA) DNA is destabilized. The results reported in this paper strongly suggest that antiparallel stranded d(G A.GA) homoduplexes are stabilized by the formation of alternating A(an ti).G(anti) and G(anti).A(syn) pairs. In this structure, all guanine r esidues are in the anti conformation with their N7 position freely acc essible to DMS methylation. On the other hand, adenines in one strand adopt the anti conformation, with their N7 position also free for reac tion, while those of the opposite strand are in the syn conformation, with their N7 position hydrogen bonded to the guanine N1 group of the opposite strand. A regular right-handed helix can be generated using a lternating G(anti).A(syn) and A(anti).G(anti) pairs.