The effect of zinc on the secondary structure of d(GA·TC)n DNA sequences of different length: A model for the formation H-DNA

Abstract

Alternating d(GA·TC)n DNA sequences are known to undergo transition to *H-DNA in the presence of zinc. Here, the effect of zinc on the secondary DNA structure of d(GA·TC)n sequences of different length (n = 5, 8, 10 and 19) was determined. Short d(GA·TC)n sequences form *H-DNA with a higher difficulty than longer ones. At bacterial negative superhelical density (- σ = 0.05), zinc still induces transition to the *H-DNA conformation at a d(GA·TC)10 sequence but shorter sequences do not form * H-DN A. Transition to * H-DN A at a d(GA·TC)8 sequence is observed under conditions which destabilize the DNA double helix such as high negative supercoiling or low ionic strength. Our results Indicate that a first step in the transition to *H-DNA is the formation of a denaturation bubble at the centre of the repeated DNA sequence, suggesting that the primary role of zinc is to induce a local denaturation of the DNA double helix. Subsequently, zinc might also participate in the stabilization of the altered DNA conformation through its direct interaction with the bases. Based on these results a model for the formation of *H-DN A is proposed. © 1993 Oxford University Press.