Conformational studies of nucleic acids: III. Empirical multiple correlation functions for nucleic acid torsion angles.
There are seven significantly variable torsion angles in each monomer unit of a polynucleotide. Because of this, it is computationally infeasible to consider the energetics of all conformations available to a nucleic acid without the use of simplifications. In this paper, we develop functions suggested by and regression fit to crystallographic data which allow three of these torsion angles, alpha (O3'-P-O5'-C5'), delta (C5'-C4'-C3'-O3') and epsilon (C4'-C3'-O3'-P), to be calculated as dependent variables of those remaining. Using these functions, the seven independent torsions are reduced to four, a reduction in complexity sufficient to allow an examination of the global conformational energetics of a nucleic acid for the remaining independent torsion angles. These functions are the first to quantitatively relate a dependent nucleic acid torsion angle to several different independent angles. In all three cases the data are fit reasonably well, and in one case, alpha, the fit is exceptionally good, lending support for the suitability of the functions in conformational searches. In addition, an examination of the most significant terms in each of the correlation functions allows insight into the physical basis for the correlations.
Pearlman
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Department of Chemistry, Lawrence berkeley Laboratory, University of California, Berkeley 94720.
Kim
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D001483:Base Sequence; D004278:DNA, Superhelical; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D012343:RNA, Transfer; D012984:Software
D004278:DNA, Superhelical; D012343:RNA, Transfer