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Hydrogen bonding within base pairs is one of the decisive factors that determine structure and stability of nucleic acids. It is well-known, especially from RNA structures, that in addition to Watson-Crick base pairs noncanonical pairs can be formed. All of them have at least two direct standard hydrogen bonds (H-bonds). 1 Recently, however, base pairs with only one or even no direct standard H-bond have been found. In these cases NH ‚‚‚F, 2, 3 CH ‚‚‚O, 4 CH ‚‚‚N5 contacts, and water-mediated H-bonds6, 7 play a role. Thus far, it is not clear, whether the geometry of these complexes is a consequence of their intrinsic properties or enforced by backbone or stacking restraints exerted by the nucleic acid environment. Moreover, their stability remains to be assessed. Quantum-chemical ab initio calculations with the inclusion of correlation energy have provided a relatively consistent picture of Watson-Crick and noncanonical base pairs. 8 Therefore, these studies can be extended to the unusual complexes. Until now water-mediated base pairs have only been detected in two RNA structures. 6, 7 We have performed ab initio calculations on a water-mediated uracil-cytosine base pair (WUC). Our results indicate that the WUC complex is a structurally autonomous building block of RNA structure with a high degree of cooperativity.

In 1991 Holbrook et al. found that in the RNA duplex (r-GGACUUCGGUCC) 2 the central GU and UC mismatches do not form an internal loop, but rather a highly regular helix. 6 In the UC base pair H4 of cytosine is hydrogen-bonded to O4 of uracil, and H3 of uracil and N3 of cytosine are linked by H-bonds to a tightly associated …