Cooperative Non-enzymatic Base Recognition and the Stability of the G-U Wobble Pair

INVESTIGATIONS of paired complementary polynucleotides containing occasional mismatched bases have indicated that these bases are looped out of the double helical regions thereby making the helix unstable. But in a system containing mismatched G and U bases, no such definite conclusion could be drawn^1–4—stoichiometry and T_m values of such complexes can be interpreted in terms of the formation of a G-U wobble pair⁴. Recently the complexes formed by self-complementary block oligomers interrupted by mismatched bases, for example, A_nXU_n (X=G, C and U), have been studied in detail⁵·⁶. It seems that stacking interactions play a much more dominant role in the stabilization of double helices than was previously thought. Thus the extent of looping out and of non-Watson-Crick base pairing can hardly be assessed independently.