Slight changes in conditions influence the family of non-B-DNA conformations of the herpes simplex virus type 1 DR2 repeats.

The segment inversion site of herpes simplex virus type 1 contains a series of tandem repeats with a purine bias on one strand and high G + C content (DR2 repeats) capable of adopting a non-B-DNA structure under a variety of conditions. Plasmids carrying eight contiguous copies of DR2 sequences undergo a series of supercoil-driven conformational transitions resulting in different extents of relaxation at pH 5.0. These transitions depend on the presence of an appropriate concentration of divalent cations (Mg2+ and Ca2+) which seem to interact specifically with the alternate structure(s). The transitions occurred at approximately the same superhelical density for all lengths of inserts studied. However, the onset of the transition can be shifted to lower negative superhelical densities by increasing NaCl concentrations. This leads to a reduction of the cooperativity of the transition, which takes place over a range of linking isomers under these conditions. Extrapolating from these results, we established physiological conditions where the alternate DNA structure is found at negative superhelical densities as low as -0.035. The existence of non-B-DNA conformations and/or the structural transitions of these sequences located in this region of intense biological activity implies their involvement in the life cycle of the virus.