Purine-purine mismatches in RNA helices: evidence for protonated G.A pairs and next-nearest neighbor effects.
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.
Morse
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Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218.
Draper
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D000225:Adenine / Q000737:chemistry*; D001482:Base Composition; D001483:Base Sequence; D006147:Guanine / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011522:Protons; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
D011522:Protons; D006147:Guanine; D012313:RNA; D000225:Adenine