The occurence of the syn-C3' endo conformation and the distorted backbone conformations 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., 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 riboguanosine 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.
Vasudevan
S S
SS
Department of Chemistry, Ohio State University, Columbus 43210, USA.
Sundaralingam
M
M
D020029:Base Pairing; D004247:DNA / Q000737:chemistry; D006860:Hydrogen Bonding; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D009705:Nucleosides / Q000737:chemistry; D009711:Nucleotides / Q000737:chemistry; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011089:Polydeoxyribonucleotides / Q000737:chemistry*; D013873:Thionucleotides / Q000737:chemistry
D009705:Nucleosides; D009711:Nucleotides; D009838:Oligodeoxyribonucleotides; D011089:Polydeoxyribonucleotides; D013873:Thionucleotides; D004247:DNA