DIVALENT ZINC CATIONS INDUCE THE FORMATION OF 2 DISTINCT HOMODUPLEXESOF A D(GA)(20) DNA-SEQUENCE

Homopurine DNA sequences are highly structurally polymorphic. In parti cular, d(GA)(n) DNA sequences are known to be capable of forming intra molecular foldbacks, bimolecular homoduplexes, and tetrastranded compl exes. Counterions play a determinant role on the equilibria between th e different structural conformers of d(GA)(n) sequences. In this paper , the effect of divalent zinc cations on the structure of a d(GA)(20) oligonucleotide has been analyzed by CD spectroscopy and polyacrylamid e gel electrophoresis. Depending on the precise experimental condition s at which zinc is added, two distinct conformations of the d(GA)(20) oligonucleotide are stabilized. At neutral pH in the absence of zinc, d(GA)(20) is partially organized into intramolecular foldbacks and bim olecular homoduplexes [Casasnovas et al. (1993) J. Mel. Biol. 233, 671 -681]. Under these conditions, addition of zinc results in the stabili zation of the bimolecular homoduplex which is nonspecific for zinc sin ce it is also stabilized by divalent magnesium cations, increasing ion ic strength, or decreasing pH. Its CD spectrum is identical to that re ported earlier for parallel-stranded d(GA)(n) homoduplexes [Rippe et a l. (1992) EMBO J. 11, 3777-3786]. On the other hand, if zinc is added under conditions where the d(GA)(20) oligonucleotide is exclusively si ngle-stranded, a different bimolecular homoduplex appears which is onl y observed in the presence of zinc. The zinc-specific duplex melts coo peratively, and, in contrast to the nonspecific duplex, its thermostab ility is high. Transition from the nonspecific to the zinc-specific du plex is observed at high zinc concentrations or at high temperatures. The transition is cooperative. These results are discussed in the cont ext of the specification effects on the formation of intramolecular R . R . Y triplexes at d(GA . TC)(n) DNA sequences.