The occurrence of the syn-C3' endo conformation and the distorted backboneconformations for C4'-C5' and P-O5' in oligo and polynucleotides

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., ant i to syn conformation is 5.1. The nucleotide building blocks of nucleic aci ds show the same trend as nucleosides. Both the deoxy-guanosine and ribogua nosine residues in nucleosides and nucleotides prefer the syn-C2 ' endo con formation with an intra-molecular hydrogen bond (for nucleosides) between t he O5 '- H and the N3 of the base and, a few syn-C3 ' endo conformations ar e also observed. Evidence is presented for the occurrence of the C3 ' endo- syn conformation for guanines in mis-paired double helical right-handed str uctures with the distorted sugar phosphate C4 ' -C5 ' and P-O5 ' bonds resp ectively, from g+ (gg) and g- to trans. Evidence is also provided for guano sine nucleotides in left-handed double-helical (Z-DNA) oligo and polynucleo tides which has the same syn-C3 ' endo conformation and the distorted backb one sugar-phosphate bonds (C4 ' -C5 ' and PO5 ') as in the earlier right-ha nded case.