The A and B conformations of DNA and RNA subunits. Potential energy calculations for dGpdC

Abstract

AbstractIn order to obtain a molecular picture of the A and B forms of a DNA subunit, potential energy calculations have been made for dGpdC with C(3′)‐endo and C(2′)‐endo [or C(3′)‐exo] sugar puckerings. These are compared with results for GpC. The global minima for dGpdC and GpC are almost identical. They are like A‐form duplex DNA and RNA, respectively, with bases anti, the ω′, ω angle pair near 300°, 280°, and sugar pucker C(3′)‐endo. For dGpdC, a B‐form helical conformer, with sugar pucker C(2′)‐endo and ω′ = 257°, ω = 298°, is found only 0.4 kcal/mol above the global minimum. A second low‐energy conformation (2.3 kcal/mol) has ω′ = 263°, ω = 158° and ψ near 180°. This has dihedral angles like the original Watson–Crick model of the double helix. In contrast, for GpC, the C(2′)‐endo B form is 6.9 kcal/mol above the global minimum. These theoretical results are consistent with experimental studies on DNA and RNA fibers. DNA fibers exist in both A and B forms, while RNA fibers generally assume only the A form. A low‐energy conformation unlike the A or B forms was found for both dGpdC and GpC when the sugars were C(3′)‐endo. This conformation—ω′,ω near 20°,80°—was not observed for C(2′)‐endo dGpdC. Energy surface maps in the ω′,ω plane showed that C(2′)‐endo dGpdC has one low‐energy valley. It is in the B‐form helical region (ω′ ∼ 260°, ω ∼ 300). When the sugar pucker is C(3′)‐endo, dGpdC has two low‐energy regions: the A‐form helical region and the region with the minimum at ω′ = 16°, ω = 85°.