Efficiency of coaxial stacking depends on the DNA duplex structure |
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Authors: | Pyshnyi Dmitrii V Goldberg Eugenii L Ivanova Eugenia M |
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Institution: | Institute of Biological Chemistry and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090, Novosibirsk, Prospect Akad, Lavrentyeva 8. pyshnyi@niboch.nsc.ru |
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Abstract: | Thermodynamic parameters of coaxial stacking at complementary helix-helix interfaces GX*pYG/CZVC (X,Y=A,C,T,G;*-nick) created by contiguous oligonucleotide hybridization were determined. The data obtained were compared to the thermodynamic parameters of coaxial stacking at the interfaces CX*pYC/GZVG. Multiple linear regression analysis has revealed that the free-energy increments of interaction for the contacts GX*pYG/CZVC and CX*pYC/GZVG can be described by a set of uniform Delta G degrees(X*pY/ZV) values. The difference in the observed free-energy of the coaxial stacking between the two sets is defined by the contribution from the factors reflecting structural differences between compared DNA duplexes. |
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