Conformational characteristics of the dinucleoside triphosphate pCpGp from energy-minimization studies

Abstract

The influence of the 3'- and 5'- terminal phosphates on the conformational characteristics of the dinucleoside monophosphate CpG is described in this paper. The computed potential energy of the system is minimized with respect to the relevant 10 dihedral angles permitting the two sugar rings to adopt the alternative puckering states, 2E and 3E. Of the 84 conformations considered, 22 become energetically accessible. The familiar A-, B-, Z- and Watson-Crick-type backbone states of DNA subunits become low-energy forms for this RNA unit pCpGp also. The Watson-Crick-type backbone is invariably preferred in all the four sugar pucker sequences, indicating its importance in the dynamics of sugar pucker fluctuations and in the DNA-RNA association. The interphosphate geometries and the possible hydrogen-bonded states are discussed in relation to the varied folded/extended polynucleotide structures.