Conformational properties and thermodynamics of the RNA duplex r(CGCAAAUUUGCG)2: Comparison with the DNA analogue d(CGCAAATTTGCG)2

Abstract

The thermodynamic stability of nine dodecamers (four DNA and five RNA) of the same base composition has been compared by UV-melting. The ΔG of stabilisation were in the order: r(GACUGAUCAGUC)2 > r(CGCAAATTTGCG)2 ≃ r(CGCAUAUAUGCG)2 > d(CGCAAATTTGCG)2 ≃ r(CGCAAAUUUGCG)2 > d(CGCATATATGCG)2 ≃ d(GACTGATCAGTC)2 > r(CGCUUUAAAGCG)2 ≃ d(CGCTTTAAAGCG)2. Compared with the mixed sequences, both r(AAAUUU) and r(UUUAAA) are greatly destablising in RNA, whereas in DNA, d(TTTAAA) is destabilising but d(AAATTT) is stabilising, which has been attributed to the formation of a special B' structure involving large propeller twists of the A-T base pairs. The solution structure of the RNA dodecamer r(CGCAAAUUUGCG)2 has been determined using NMR and restrained molecular dynamics calculations to assess the conformational reasons for its stability in comparison with d(CGCAAATTTGCG)2. The structures refined to a mean pairwise r.m.s.d. of 0.89 ± 0.29 Å. The nucleotide conformations are typical of the A family of structures. However, although the helix axis displacement is ≃ 4.6 Å into the major groove, the rise (3.0 Å) and base inclination (≃ 6°) are different from standard A form RNA. The extensive base-stacking found in the AAATTT tract of the DNA homologue that is largely responsible for the higher thermodynamic stability of the DNA duplex is reduced in the RNA structure, which may account for its low relative stability.