Efficiency of coaxial stacking depends on the DNA duplex structure.
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.
Pyshnyi
Dmitrii V
DV
Institute of Biological Chemistry and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090, Novosibirsk, Prospect Akad, Lavrentyeva 8. pyshnyi@niboch.nsc.ru
Goldberg
Eugenii L
EL
Ivanova
Eugenia M
EM
D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D016014:Linear Models; D008956:Models, Chemical; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D009711:Nucleotides; D009841:Oligonucleotides / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
D009711:Nucleotides; D009841:Oligonucleotides; D004247:DNA