Thermodynamic and structural features of ultrastable DNA and RNA hairpins

Abstract

Short RNA and DNA hairpins have been analysed in aqueous phase by means of UV absorption and vibrational spectroscopy in the following oligodeoxynucleotide and oligoribonucleotide sequences: 5′-d(GC- GAA-GC)-3′, 5′-r(CGC- GNRA-GCG)-3′ (where N=U, A, C, G and R=A, G) and 5′-r(GCG- UGAA-CGC)-3′. These hairpins contain GAA triloop, GNRA and UGAA tetraloops stabilised by two or three GC base pairs in their stems. The analysis of UV absorption melting profiles allowed us to confirm the high (to very high) thermodynamic stability of these hairpins through the estimation of their melting temperature ( T m). FT-IR spectra revealed the presence of N-type and/or S-type sugar puckers in the hairpins. Raman spectra at the temperatures below T m provided information on the conformations of certain nucleosides involved in the hairpins, as well as on the global conformation (A or B forms) of their stems. Raman spectra recorded as a function of temperature, are consistent with the hairpin-to-random coil conformational transitions through the breakdown of interbase H-bonds, and the loss of stacking between the bases. A discussion has been carried out on the agreement between vibrational data and those available from NMR on a few number of these hairpins.