STRUCTURAL POLYMORPHISM OF HOMOPURINE HOMOPYRIMIDINE SEQUENCES AT NEUTRAL PH

Under superhelical strain and mildly acidic pH, polyd(GA) · polyd(CT) sequences are known to adopt an H-y3 conformer of H-DNA. We studied the effects of the sequence length, metal ions, and pH on the structures formed by polyd(GA) · polyd(CT) sequences in supercoiled plasmid DNA at bacterial superhelicity. The results from experiments that distinguish multiple structures forming in a given plasmid DNA population strongly suggest that polyd(GA) · polyd(CT) sequences of 33 base-pairs or more can adopt both H-y3 and H-y5 isomeric forms of H-DNA at neutral pH either with or without magnesium ions. At pH 5 in the presence of zinc ions, H-DNA is formed. However, at pH 7 in the presence of zinc ions, polyd(GA) · polyd(CT) sequences form an intramolecular d(GA) · d(GA) · d(CT) triplex similar to a dG · dG · dC triplex, which is stabilized with magnesium ions for poly(dG) · poly(dC) sequences. Zinc ions also stabilize the dG · dG · dC triplex for relatively long poly(dG) · poly(dC) sequences (more than 24 base-pairs at pH 7). © 1993 Academic Press Limited.