G.A and U.U mismatches can stabilize RNA internal loops of three nucleotides

Biochemistry
S SchroederD H Turner

Abstract

Optical melting experiments on oligoribonucleotides containing internal loops of three nucleotides (two nucleotides opposing one nucleotide) flanked by CG pairs show that the free energy of internal loop formation depends on the sequence of nucleotides within the loop. Internal loops with the potential for A.G and U.U mismatch pairing generally have more favorable free energies of formation than internal loops with potential AA, CC, AC, or UC pairings. In most cases, potential A.G and U.U pairings leaving a single unpaired nucleotide 5' to a flanking CG pair are most stable; those leaving a single nucleotide 3' to a flanking CG pair have intermediate stability. Internal loops of three nucleotides without potential A.G or U.U pairs are the least stable. The results provide an improved model for predicting the folding stabilities of internal loops of three nucleotides.

References

Jan 1, 1988·Annual Review of Biophysics and Biophysical Chemistry·D H TurnerS M Freier
Jul 15, 1974·Journal of Molecular Biology·P N BorerO C Uhlenbeck
Aug 5, 1973·Journal of Molecular Biology·J Gralla, D M Crothers

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Citations

Jan 1, 1997·Biopolymers·J SantaLucia, D H Turner
Apr 11, 2001·Biopolymers·S J SchroederD H Turner
Jun 14, 2000·Current Opinion in Structural Biology·M Zuker
Jun 23, 2012·Biochemistry·Nina Z Hausmann, Brent M Znosko
Nov 29, 2011·Nature·Brian Houck-LoomisVictoria M D'Souza
Aug 22, 2003·Nucleic Acids Research·Geneviève GirardHerman P Spaink
Oct 14, 2010·RNA·Mirela AndronescuKevin P Murphy
Jul 28, 2010·RNA·Evgenia N Nikolova, Hashim M Al-Hashimi
May 5, 2004·Proceedings of the National Academy of Sciences of the United States of America·David H MathewsDouglas H Turner
Sep 20, 2005·The Journal of Biological Chemistry·Serena BernacchiPhilippe Dumas
Oct 5, 2018·The Journal of Physical Chemistry. B·Yen-Lin ChenLois Pollack

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