THERMODYNAMIC PARAMETERS TO PREDICT STABILITY OF RNA DNA HYBRID DUPLEXES/

The thermodynamic parameters (Delta H degrees, Delta S degrees, and De lta G degrees(37)) for 16 nearest-neighbor sets and one initiation fac tor are presented here in order to predict stability of RNA/DNA hybrid duplexes. To determine the nearest-neighbor parameters, thermodynamic s for 68 different hybrid sequences (136 single-stranded oligonucleoti des) with 5-13 nucleotide length including several duplexes with ident ical nearest-neighbors were measured by UV melting procedure. These se quences were selected to have many different combinations of nearest-n eighbor pairs, and so that the number of the 16 nearest-neighbor seque nces in the oligomers were as equal as possible. The structures of the hybrids were also investigated by measuring circular dichroism spectr a. Comparing Delta G degrees(37) values of the hybrids with DNA/DNA an d RNA/RNA parameters reported previously (Breslauer, K. J., Frank, R., Blocker, H., & Marky, L. A. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 3746-3750; Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Ca ruthers, M. H., Neilson, T., & Turner, D. H. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 9373-9377), RNA/RNA double helix is the most stable of the three kinds of helixes with the same nearest-neighbor sequences. Which is more stable between DNA/DNA and RNA/DNA hybrid duplexes depen ds on its sequence. Calculated thermodynamic values of hybrid formatio n with the present parameters reproduce the experimental values within reasonable errors.