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Polynucleotide base‐pair orientation in solution: Linear dichroism and molecular mechanical studies of poly[d(A)]‐poly[d(T)]
Author(s) -
Edmondson Stephen P.
Publication year - 1987
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360261108
Subject(s) - polynucleotide , chemistry , base (topology) , stacking , base pair , circular dichroism , linear dichroism , crystallography , stereochemistry , dna , organic chemistry , biochemistry , mathematical analysis , mathematics
Abstract 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.