Thermodynamics of RNA internal loops with a guanosine-guanosine pair adjacent to another noncanonical pair

Biochemistry
M E BurkardD H Turner

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 degrees 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.

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Citations

Jan 6, 2011·Bulletin of Mathematical Biology·Valerie Hower, Christine E Heitsch
Jun 11, 2009·Nucleic Acids Research·Martha E Christiansen, Brent M Znosko
May 21, 2011·Nucleic Acids Research·Agnieszka KiliszekWojciech Rypniewski
Oct 14, 2010·RNA·Mirela AndronescuKevin P Murphy
May 5, 2004·Proceedings of the National Academy of Sciences of the United States of America·David H MathewsDouglas H Turner
Mar 22, 2006·Biochemistry·Gang Chen, Douglas H Turner
Apr 25, 2015·Biochemistry·Jonathan L ChenDouglas H Turner
Jan 30, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Tim BožičPrimož Šket

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