SURVEY AND SUMMARY Unusual DNA duplex and hairpin motifs

Single-stranded DNA or double-stranded DNA has the potential to adopt a wide variety of unusual duplex and hairpin motifs in the presence (trans) or absence (cis) of ligands. Several principles for the formation of those unusual structures have been established through the observation of a number of recurring structural motifs associated with different sequences. These include: (i) internal loops of con-secutive mismatches can occur in a B-DNA duplex when sheared base pairs are adjacent to each other to confer extensive cross- and intra-strand base stacking; (ii) interdigitated (zipper-like) duplex struc-tures form instead when sheared G´A base pairs are separated by one or two pairs of purine´purine mis-matches; (iii) stacking is not restricted to base, deoxyribose also exhibits the potential to do so; (iv) canonical G´C or A´T base pairs are ¯exible enough to exhibit considerable changes from the regular H-bonded conformation. The paired bases become stacked when bracketed by sheared G´A base pairs, or become extruded out and perpendicular to their neighboring bases in the presence of interacting drugs; (v) the purine-rich and pyrimidine-rich loop structures are notably different in nature. The purine-rich loops form compact triloop structures closed by a sheared G´A, A´A, A´C or sheared-like Ganti´Csyn base pair that is stacked by a single residue. On the other hand, the pyrimidine-rich loops with a thymi-dine in the ®rst position exhibit no base pairing but are characterized by the folding of the thymidine residue into the minor groove to form a compact loop structure. Identi®cation of such diverse duplex or hairpin motifs greatly enlarges the repertoire for unusual DNA structural formation