CRYSTAL AND MOLECULAR-STRUCTURE OF R(CGCGAAUUAGCG) - AN RNA DUPLEX CONTAINING 2 G(ANTI)CENTER-DOT-A(ANTI) BASE-PAIRS

Background: Non-Watson-Crick base pair associations contribute signifi cantly to the stabilization of RNA tertiary structure. The conformatio n adopted by such pairs appears to be a function of both the sequence and the secondary structure of the RNA molecule. G.A mispairs adopt G( anti).A(anti) configurations in some circumstances, such as the ends o f helical regions of rRNAs, but in other circumstances probably adopt an unusual configuration in which the inter-base hydrogen bonds involv e functional groups from other bases. We investigated the structure of G.A pairs in a synthetic RNA dodecamer, r(CGCGAAUUUAGCG), which forms a duplex containing two such mismatches. Results: The structure of th e RNA duplex was determined by single crystal X-ray diffraction techni ques to a resolution in the range 7.0-1.8 Angstrom, and found to be an A-type helical structure with 10 Watson-Crick pairs and two G.A mispa irs. The mispairs adopt the G(anti).A(anti) conformation, held togethe r by two obvious hydrogen bonds. Unlike analogous base pairs seen in a DNA duplex, they do not exhibit a high propeller twist and may theref ore be further stabilized by weak, reverse, three-center hydrogen bond s. Conclusions: G(anti).A(anti) mispairs are held together by two hydr ogen bonds between the O6 and N1 of guanine and the N6 and N1 of adeni ne. if the mispairs do not exhibit high propeller twist they may be fu rther stabilized by inter-base reverse three-centre hydrogen bonds. Th ese interactions, and other hydrogen bonds seen in our study, may be i mportant in modelling the structure of RNA molecules and their interac tions with other molecules.