Abstract
Double‐helical polynucleotide conformations, poly(dA)·poly(dT), poly(d(A‐T))·poly(d(T‐A))·poly(dG)·poly(dC), and poly(d(G‐C))·poly(d(C‐G)) are analyzed by the atom–atom potential method. The energy optimization is carried out in the space of eight independent geometric parameters using analytical procedures for the constraints, taking into account the flexibility of the β‐D‐deoxyribose rings. At the first stage, the full screening of atomic partial charges was assumed. The structures of the calculated B and the A forms of DNA are characterized by low energy and absence of short contacts; the dihedral angles are near the average values in the monomers. With the typical energy difference of 3–5 kcal/mol nucleotide pairs in all cases, the B form is more preferable as compared to the A form. At the final step the effect of the Coulomb term is evaluated for poly(dA)·poly(dT) using various values of the effective dielectric constant (ϵ = 28, 24, 20, 18, 14, 12, 10, 8, 6, 4, and 1). If ϵ ⩽24, the energy optimization leads A to B. We discuss the stereochemical details of the intermediate conformations on the A–B path and hypothesize the nature of stability of the A and the B forms and the mechanism of the A–B transition.