Structural features and properties of an extraordinarily stable hairpin-turn structure of d(GCGAAGC)

The extraordinarily stable hairpin-like structure formed by a short DNA fragment, d(GCGAAGC), has been studied by NMR spectroscopy and UV melting behaviour. The fragment is folded back between A4 and A5, and forms two terminal G-C base pairs and a non-Watson-Crick G-A base pair. All the nucleotides adopt C2'-endo sugar puckers. Both G1C2G3A4 and A5G6C7 moieties have characteristics of B-form geometry and within each moiety all the bases are involved in extensive base-base interactions. Distortion from B-form occurs in only the three torsion angles between A4 and A5 residues, which causes a sharp turn in the structure. There is no clear distinction between a stem and a loop region, as observed in usual hairpin structures, so that we classify it as a turn (hairpin-turn) structure. In addition to the thermal stability, this fragment is more stable towards the attack of some nucleases than other single-stranded as well as usual hairpin DNA fragments.