A model for base overlap in RNA

Duplexed RNA in the solid state conforms to the A-family of structures with 3′-endo sugars and bases arranged outside the helix axis in a spiral staircase arrangement^1-4. Recent experiments^5-11 suggest that parameters of RNA and DNA helices depend on the sequence of bases in the chain. Furthermore, the average conformation of these flexible molecules may differ between the solution and solid states. The NMR chemical shifts of the base protons in ten oligo-RNA duplexes^5,12-18 have been determined. We have now adjusted the helix winding angle, W, between adjacent base pairs (see Fig. 1a) to fit these data. There is extensive overlap of the hydrophobic surfaces of the bases at the proposed angles. These overlaps depend on the arrangement of purines and pyrimidines along the chain and offer a mechanism for recognition of specific sequences by enzymes.