Issue June 2001

category image Volume 18
No. 6 (p 783-1032)
June 2001
ISSN 0739-1102

The Occurrence of the syn-C3? Endo Conformation and the Distorted Backbone Conformations for C4?-C5? and P-O5? in Oligo and Polynucleotides (p. 824-831)

The nucleoside constituents of nucleic acids prefer the anti conformation (1). When the sugar pucker is taken into account the nucleosides prefer the C2`endo-anti conformation. Of the nearly 300 nucleosides known, about 250 are in the anti conformation and 50 are in the syn-conformation, i.e., anti to syn conformation is 5:1. The nucleotide building blocks of nucleic acids show the same trend as nucleosides. Both the deoxy-guanosine and ribo-guanosine residues in nucleosides and nucleotides prefer the syn-C2?endo conformation with an intra-molecular hydrogen bond (for nucleosides) between the O5`- H and the N3 of the base and, a few syn-C3?endo conformations are also observed. Evidence is presented for the occurrence of the C3`endo-syn conformation for guanines in mis-paired double helical right-handed structures with the distorted sugar phosphate C4?-C5? and P-O5? bonds respectively, from g+ (gg) and g- to trans. Evidence is also provided for guanosine nucleotides in left-handed double-helical (Z-DNA) oligo and polynucleotides which has the same syn-C3?endo conformation and the distorted backbone sugar-phosphate bonds (C4?-C5? and P-O5?) as in the earlier right-handed case.

Sanjay S. Vasudevan
Muttaiya Sundaralingam*

The Biological Macromolecular Structure Center
Departments of Chemistry and Biochemistry
The Ohio State Biochemistry Program
Ohio State University
1060 Carmack Road
012 Rightmire Hall
Columbus, Ohio 43210
*sundaral@chemistry.ohiostate.edu

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