Cyclic adduct formation at structural perturbations in supercoiled DNA molecules

Supercoiled DNA can stabilize the existence of micropolymorphic structures, which may be sequence dependent. A good example is cruciform formation from inverted repeat sequences. DNA sequences exhibiting a high degree of two-fold symmetry, for instance, the 13-bp inverted repeat of ColE1, can adopt cruciform geometry when supercoiled, as judged by sensitivity to single-strand-specific nucleases and to resolvase and by topological changes revealed by gel electrophoresis. The present report shows that these structures are also excellent substrates for the local formation of cyclic adducts by bromoacetaldehyde, glyoxal or osmium tetroxide. Individual reagents may show pronounced differences in sequence selectivity, although all appear to react strongly at the ColE1 sequence. The reactions initially occur at the centre of the inverted repeats; this is followed by a conformational change such that the modification propagates outwards from the centre. These compounds constitute a valuable addition to the list of probes available for the investigation of local perturbations in DNA structure.