Classical potential energy calculations for ApA, CpC, GpG, and UpU. The influence of the bases on RNA subunit conformations

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Abstract
Classical potential energy calculations have been made for the ribodinucleoside monophosphates ApA, CpC, GpG, and UpU. Van der Waal's, electrostatic, and torsional contributions to the energy were calculated, and the energy was minimized with the seven backbone conformational angles as simultaneously variable parameters. At the global minimum, ApA and CpC have conformations like double helical RNA: the angles ω′ and ω are g−g−, the sugar pucker is C3′‐endo, and the bases are anti. GpG and UpU, on the other hand, have the ω′,ω angle pair g−t at the global minimum, and for GpG the bases are syn. Energy contour maps for ω′ and ω show two broad, low energy regions for ApA, CpC, and UpU: one is g−g−, and the second encompasses g−t and g+g+ within a single lowenergy contour. The two regions are connected by a path at 10–13 kcal./mole. For GpG, with bases syn, however, only a small low‐energy region at g−t is found. The helical ‘A’ RNA conformation is 8.5 kcal/mole higher for this molecule. Thus, the base composition is shown to influence the conformations adopted by dinucleoside phosphates. Comparison of calculations with experimetal data, where available, show good agreement.