Correlation of Tm,sequence, and ΔH of complementary RNA helices and comparison with DNA helices |
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Authors: | Rick L Ornstein Jacques R Fresco |
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Abstract: | Tm values of 16 fully complementary RNA duplexes with repeating base sequence have been employed as the empirical basis for developing a reliable and practical method for computing apparent enthalpies (ΔH calc) for their helix → coil transitions. The approach taken is the same as in the accompanying investigation of DNA duplexes, although some of the computational variables of the “best-fit” function are necessarily different due to the distinguishing structural properties of the RNA-type helix. An excellent linear correlation was thus obtained between experimental Tm and ΔH calc values. An equally good fit was obtained between Tm and ΔH calc for five unrelated (to the 16 RNAs) decaribonucleotide duplexes. The differences in computational variables between the best-fit methods for RNA and DNA duplexes are shown to be a reflection of differences in cation binding and the effective local dielectric. The greater Tm dependence on G·C content of RNA helices than of DNA helices is shown to be due to a greater latitude of stacking stabilities of complementary dinucleotide fragments containing A·T than A·U base pairs. |
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