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Backbone conformations in nucleic acids: The occurrence of g + g + internucleotide phosphodiester conformation
Author(s) -
Jayaraman S.,
Yathindra N.,
Sundaralingam M.
Publication year - 1982
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360210614
Subject(s) - phosphodiester bond , chemistry , polynucleotide , stereochemistry , van der waals force , nucleic acid , crystallography , deoxyribose , alkane stereochemistry , nucleotide , crystal structure , molecule , biochemistry , rna , organic chemistry , gene
Semiempirical conformational energy calculations have been performed on dinucleoside triphosphate models with and without base interactions to investigate the conformational requirement for the stereochemical and energetic feasibility of ( gauche + , gauche + ) phosphodiester conformation in a polynucleotide chain. Results show that the trans conformation of the C4′C5′ bond on the 5′‐sugar (either C3′‐ endo or C2′‐ endo ) of a dinucleoside triphosphate renders the g + g + phosphodiester energetically favorable. The degree of energetic preference shows a dependence on the C3′O3′ bond torsions (ϕ′); higher g + g + conformation populations are correlated with higher values of ϕ′ ≃ 270° due to increased van der Waals interactions between adjacent sugar residues. For similar reasons, the g + g + phosphodiester displays an energetic dependence on the nature and sequence of bases and their orientations. Other conformational combinations that also stereochemically permit the g + g + phosphodiester are discussed along with base effects.