Conformational Transmission in Nucleotides Containing Trigonal Bipyramidal Phosphorus as the Internucleoside Linkage

Article abstract of DOI:10.1021/jo00257a012

A set of nucleotide analogues containing a stable trigonal bipyramidal phosphorus (P^V TBP) moiety (5-11) has been developed, and their conformational properties were studied with 300- and 500-MHz 1H NMR.In the solvent acetone-d₆, it is found that the conformation of the model compounds is determined by a hydrogen bond between the backbone atom O5', and the base proton H6 (pyrimidine base) or H8 (purine base), resulting in a preference for the standard gauche(+) conformation around the C4'-C5' bond.In the hydrogen bond disrupting solvent DMSO-d₆, the P^V TBP nucleotides 5-8 clearly show conformational transmission, i.e., a preference for the unusual gauche(-) (g^-) rotamer around the C4'-C5' bond is found.This structural distortion opposes stacking of the bases, as is confirmed by the observation that the preference for g^- is strongest for 7 and 8, in which stacking is eliminated.The present results provide support to our earlier proposition that formation of P^V TBP locations in DNA can lead to a marked change of the secondary structure (Buck, H.M.Recl.Trav.Chim.Pays-Bas 1980, 99, 181).