title: Stereochemical effects of non-ionic methylphosphonates on nucleotide conformations.
abstract: The preferred conformations of deoxyribo and ribonucleoside 3'-methylphosphonates are analysed by minimizing the conformational energy as a function of all the major parameters including the sugar ring for both the S- and R-isomers. The results show that neither the substitution nor the nature of the diastereomer affects significantly the preferred conformations compared to the naturally occurring nucleoside 3'-phosphates. The preferred range of C3'-O3' bond torsions or the phase angles of pseudorotation (P) of the sugar are unaffected. The chiral substitution on the phosphate always adopts a conformation distal to the secondary C3' carbon atom in the minimum energy conformational state. Further, it introduces certain restrictions on the preferred range of P-O3' torsions depending on the methylphosphonate configuration. Methylphosphonate, especially the S-isomer, renders the normal gauche- range of P-O3' bond torsions responsible for the stacked helical duplexes to be energetically unfavourable besides introducing a high energy barrier between trans and gauche conformations. Therefore it is suggested that duplexes with S-methylphosphonate may favour extended phosphodiester conformations. These factors explain the observed lower melting temperature as well as the downfield shifts in the 31P signals in duplexes containing the S-isomer.
authors.affiliation: Department of Crystallography and Biophysics, University of Madras, India.
authors.forename: Y S
authors.initials: YS
authors.lastname: Latha
authors.forename: N
authors.initials: N
authors.lastname: Yathindra
mesh_terms: D003854:Deoxyribonucleotides / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008968:Molecular Conformation; D009943:Organophosphorus Compounds / Q000737:chemistry*; D012265:Ribonucleotides / Q000737:chemistry*; D013237:Stereoisomerism
chemical_list: D003854:Deoxyribonucleotides; D009943:Organophosphorus Compounds; D012265:Ribonucleotides; C032627:methylphosphonic acid