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Published February 27, 2001 | Supplemental Material
Journal Article Open

Thermodynamics of RNA Internal Loops with a Guanosine-Guanosine Pair Adjacent to Another Noncanonical Pair

Abstract

Thermodynamic parameters measured by optical melting are reported for formation of RNA duplexes containing tandem noncanonical pairs with at least one guanosine-guanosine (GG) pair. For selected sequences, imino proton NMR provides evidence that the desired duplex forms and that the structure of a GG pair adjacent to a noncanonical pair depends on context. A GG pair next to a different noncanonical pair is more stable than expected from measurements of adjacent GG pairs. This is likely due to an unfavorable stacking interaction between adjacent GG pairs, where areas of high negative charge probably overlap. The results suggest a model where tandem noncanonical pairs closed by two GC pairs are assigned the following free energy increments at 37 °C:  0.8 kcal/mol for adjacent GG pairs, 1.0 kcal/mol for GG next to UU, and −0.3 kcal/mol for all others. These values are adjusted by 0.65 kcal/mol for each closing AU pair.

Additional Information

© 2001 American Chemical Society. Received 30 May 2000. Published online 1 February 2001. Published in print 1 February 2001. We thank an anonymous reviewer for bringing to our attention water-inserted CU pairs. This work was supported by NIH Grant GM 22939. M.E.B. is a trainee in the Medical Scientist Training Program funded by NIH Grant T32 GM07356.

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