PubMed · 4687708
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J C Catlin, F Cramer. 1973-01-26. Deoxy oligonucleotide synthesis via the triester method.. https://doi.org/10.1021/jo00942a011
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Double-helix formation of self-complementary deoxyribooctanucleotides, d(TCTATAGA) and d(TAGATCTA), with identical nearest neighbor base pairs has been studied by means of UV melting and temperature-jump techniques. The self-complementary duplexes of both octanucleotides with identical nearest neighbors had similar stabilities: The stabilization energies of the octanucleotides at 25 degrees C were 5.8 kcal mol-1 for d(TCTATAGA) and 6.7 kcal mol-1 for d(TAGATCTA). On the kinetic curve the melting reactions finished within 20 ms for d(TCTATAGA) and 40 ms for d(TAGATCTA) at 20 degrees C. For both octanucleotides the rate constants of dissociation increased and the rate constants of association decreased with increasing temperature.
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.