A molecular orbital study on the incorporation of nucleotides into RNA

Abstract

Stacking and hydrogen bond energies between bases are calculated by means of a molecular orbital method assuming the A form of DNA, and the results are compared with the values for the DNA B form. Based on the results of calculation that the stacking energies vary depending upon the base sequence, it is attempted to explain the experimental fact that incorporation of nucleotides into RNA by RNA polymerase depends on the base sequence of the template assuming two nucleotide binding sites in RNA polymerase. The incorporation process was assumed to be composed of two processes, the polymerization process and the translocation one. In the polymerization process, the stronger the stacking interaction of the substrate base with the base at the product terminus site and with the base(s) in the template and the hydrogen-bonding interaction with the complementary base are, the substrate seems to be more easily incorporated. While, in the systems involving the translocation process, when the difference in the stacking energies is relatively small and that in the hydrogen bond energies is large, the smaller the hydrogen bond energies are, the more the substrates seem to be incorporated. This result was consistently explained by assuming that the translocation process participates in determining the easiness of incorporation of the substrates in such a way that the less hydrogen bond energies are rather preferable. Good correlations between the calculated values of stacking and hydrogen bond energies and experimentally observed incorporation of nucleotides into RNA are obtained when the DNA B-like conformation was assumed at the incorporation region.