Characterization of the zinc-induced structural transition to *H-DNA at a d(GA.CT)22 sequence

Zinc induces transition of a d(GA.CT)22 sequence to a novel DNA conformation, called *H-DNA. In this paper, the structural characteristics of this altered DNA conformation are determined. Formation of *H-DNA is induced at zinc concentrations higher than 70 microM (Zn/P = 2) and it is favoured by negative supercoiling and low ionic strength. Two different structural conformations of the d(GA.CT)22 sequence are observed upon increasing the zinc concentration. At low zinc concentration (Zn/P < 15), half of the purine strand falls back upon itself giving rise to the formation of an RRY intramolecular triplex (H*-triplex). At higher zinc concentration, the complete pyrimidine strand is single-stranded and an RR hairpin is formed (*H-hairpin). Protection towards dimethylsulphate modification suggests that zinc binds to the N-7 group of guanine residues in the *H-hairpin with a higher affinity than in B-DNA. The dissociation constant of the *H-zinc complex is estimated to be in the range of 10(-3) M to 10(-4) M.