Polynucleotide base-pair orientation in solution: linear dichroism and molecular mechanical studies of poly[d(A)]-poly[d(T)

Model helices for poly[d(A)]-poly[d(T)] in solution were constructed based on the base orientations determined by linear dichroism [LD; S. P. Edmondson & W. C. Johnson, Jr. (1985) Biopolymers 24 , 824–841] and refined by molecular mechanical energy minimization. The results demonstrate that poly[d(A)]-poly[d(T)] can form energetically stable conformations with the base orientations measured by LD. Further, only one of the four possible base-pair orientations that are consistent with the LD results is feasible. Models with negative base tilts had large potential energies, indicating that the LD results do not reflect base motions. The LD models of poly[d(A)]-poly[d(T)] are stabilized mainly by intrastrand base-stacking interactions, particularly for the adenine strand.