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. 1995 Jan 25;23(2):302–306. doi: 10.1093/nar/23.2.302

Purine-purine mismatches in RNA helices: evidence for protonated G.A pairs and next-nearest neighbor effects.

S E Morse 1, D E Draper 1
PMCID: PMC306669  PMID: 7532297

Abstract

Thermodynamic parameters are presented for 12 different RNA duplexes containing A.A, A.G, G.A and G.G mismatches flanked by C-G base pairs. UV melting studies were conducted under three different buffer conditions in order to evaluate the effects of salt concentration and pH on the stability of each mismatch-containing duplex. The main findings are: (i) the mismatches have a wide range of effects on duplex stability, decreasing delta G degrees 37 of denaturation by approximately 0-7 kcal/mol; (ii) the nearest-neighbor assumption commonly used to calculate helix stability breaks down for G.A mismatches; and (iii) G.A mismatches separated by 2 bp form a protonated structure.

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Selected References

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