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A method for the determination of furanose ring coordinates in its pseudorotation circuit for different amplitudes of
1Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison 53706.
Abstract:
Interconversion between energetically favored molecular conformations must proceed through less favored intermediate states. Thus, a knowledge of the nucleotide furanose ring conformations, other than the crystallographically well-determined ones, are of interest in investigating nucleotide conformational energies and dynamics. The sugar ring flexibility affects the conformation and dynamics of the monomer and determines the range of feasible nucleic acid secondary and tertiary structures. We have generated furanose geometries for varying amplitudes of pucker over its entire range of pseudorotation by making use of a ring closure procedure and the empirical dependence of endocyclic bond lengths and bond angles on sugar pucker. Atomic coordinates are tabulated here for the furanose ring at pseudorotation phase angle intervals of 9 degrees for the average amplitude (tau m) of pucker of 39 degrees as well as for decreased (20 degrees and 30 degrees) and increased (44 degrees) values of tau m. However, the coordinates for any values of P and tau m can be readily calculated.