Occurrence, solution structure and stability of DNA hairpins stabilized by a GA/CG helix unit

The occurrence and NMR solution structure of a class of blloop hairpins containing the sequence 5-CGXYAG are presented. These hairpins, which are variations on a sequence found in the reverse transcript of the human T-cell leukemia virus 2 (HLV2), show elevated melting points and high chemical stability toward denaturation by urea. Hairpins with the 5-CGXYAG configuration have melting points 18-20 ° higher than hairpins with 5-CAXYGG or 5-GGXYAC configur-ations. The Identities of the looping bases, X and Y above, play a negligible role in determining the stability of this DNA hairpin stability. This is very different from G-A based loops in RNA, where the third base must be a purine for high stability [the GNRA loops; V.P. Antao, S.Y. Lai and I. TInoco, Jr (1991) Nucleic Acids Res., 19, 5901-5905]. We show that these properties are asso-ciated with a four base helix unit that contains both a sheared GA base pair and a Watson-Crick CG base pair upon which it is stacked. As an understanding of the significance of AG base pairs has become increas-ingly important in the structural biology of nucleic acids, we compute an 0.7-0.9 A precision ensemble of NMR solution structures using iterative relaxation matrix methods. Calculations performed on NMR-de-rived structures indicate that neither base-base elec-trostatic interactions, nor base-solvent dispersive interactions, are significant factors in determining the observed differences in hairpin stability. Thus the stability of the 5-CGXYAG configuration would appear to derive from favorable base-base London/van der Waals interactions