A Novel Conformational Equivalence between the Heminucleotide Blocks of the Nucleotide Repeat. Its Implications in Conformation Analysis of Nucleic Acids

Abstract

A conformational equivalence between the heminucleotides in the repeating nucleotide backbone exists which permits to regard the sugar-phosphate-sugar backbone chain of nucleic acids to be comprised of these minimum energy compact blocks themselves as the repeating moieties, at least in the first approximation, instead of the conventional variable nucleotide unit spanning the successive phosphorous atoms. The heminucleotide scheme brings forth naturally the known variability in the sugar residue and phosphodiester conformations and the near neighbour longrange correlations that exist between them. These correlations which refer to the alignment of adjacent bases for optimal stacking and hydrogen bonding interactions in nucleic acid helices have been examined in terms of the torsions around the virtual bonds which span the successive heminucleotides. The relevance of these in describing the dynamical conformational movements and even local helical parameter variations in DNA helices is indicated. The constant and independent nature of the heminucleotides to the rotations which most often govern nucleic acid chain folding affords a common principle for description and hence comparison of different nucleic acid conformations. This has enabled us to obtain distance diagonal plots for different DNA helices as well as yeast tRNAphe. Analyses of these bring out visualisation of several features characteristic to each of them. Foremost among them concerns possible interpretation in terms of chain folding patterns into distinct domains which may provide an understanding of the apparent conservation of L shape structure for tRNAs lacking D stem.The diagonal plot also seems to suggest a correlation between the tRNA structure and the exon pattern of its gene.KeywordsMinor GrooveMajor GrooveNucleotide RepeatRadial ProjectionDistance PlotThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.