Conformational studies of nucleic acids. V. Sequence specificities in the conformational energetics of oligonucleotides: the homo-tetramers.

Abstract

AbstractThe conformational energetics of the tetranucleoside triphosphates d(ApApApA), d(GpGpGpG), d(CpCpCpC), d(TpTpTpT), ApApApA, GpGpGpG, CpCpCpC, and UpUpUpU are thoroughly examined using a classical potential energy function. The sugar modeling method and multiple correlation functions derived in previous papers of this series are utilized in these examinations. The data are analyzed and compared in terms of the energy profiles for rotation about the conformation‐determining torsion angles in the tetramers. Overall, the predictions are in reasonable qualitative agreement with the existing experimental data. It is found that the base type does not greatly affect the locations of the important minima in these profiles, but rather exerts a large influence on the relative depths of the minima and the barriers to conversion between them. Conformational sequence dependence is manifest to a greater extent by the DNA tetramers than the RNA tetramers. Of the DNA tetramers, d(CpCpCpC) appears, from the results presented herein, to have the greatest potential for polymorphism. This and other findings are analyzed in terms of the preferences of particular DNA sequences for either the A‐, B‐, or Z‐conformation.