EFFECTS OF GA MISMATCHES ON THE STRUCTURE AND THERMODYNAMICS OF RNA INTERNAL LOOPS

UV melting, CD and NMR studies indicate rGCGAGCG and rGCAGGCG from unusually stable duplexes of type a and b. The observed ΔG°37’s in 1 M NaCl are −6.7 and −6.3 kcal/mol, respectively. For the related duplex, c, ΔG°37 is −4.2 kcal/mol. The predicted ΔG°37 from nearest-neighbor parameters [formula-omitted] for all three duplexes is −4.7 kcal/mol (Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T., & Turner, D. H. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 9373-9377). The results suggest a special interaction in the duplexes containing GA mismatches. Presumably, this is hydrogen bonding between G and A. While the thermodynamics for (rGCGAGCG)2 and (rGCAGGCG)2 are similar, CD and the imino region of the proton NMR spectra indicate their structures are different. In particular, (rGCAGGCG)2 exhibits a CD spectrum typical of A-form geometry with a weak negative band at 280 nm. In contrast, the CD spectrum for (rGCGAGCG)2 has an intense positive band at 285 nm. The NMR spectrum of (rGCAGGCG)2 has a resonance corresponding to a hydrogen-bonded GA mismatch, while for (rGCGAGCG)2 no hydrogen-bonded imino proton is observed for the mismatch. The glycosidic torsion angles of the bases in the GA mismatches of (rGCAGGCG)2 and (rCGCAGGCG)2 are anti. Duplexes of type d, where X is A, G, or U, are more stable than e, and the stability differences are similar to those [formula-omitted] observed for f versus g. Thus, 3′-dangling ends in this system make contributions to duplex stability that are similar to contributions observed with fully paired duplexes. © 1990, American Chemical Society. All rights reserved.