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• W2084367556 endingPage "3244" @default.
• W2084367556 startingPage "3235" @default.
• W2084367556 abstract "Canonical forms of duplex DNA are known to sample well-defined regions of the α, β, γ, ε, and ζ dihedral angles that define the conformation of the phosphodiester linkage in the backbone of oligonucleotides. While extensive studies of base composition and base sequence dependent effects on the sampling of the A, BI, and BII canonical forms of duplex DNA have been presented, our understanding of the intrinsic contribution of the five dihedral degrees of freedom associated with the phosphodiester linkage to the conformational properties of duplex DNA is still limited. To better understand this contribution, ab initio quantum mechanical (QM) calculations were performed on a model compound representative of the phosphodiester backbone to systematically sample the energetics about the α, β, γ, ε, and ζ dihedral angles relevant to the conformational properties of duplex DNA. Low-energy regions of dihedral potential energy surfaces are shown to correlate with the regions of dihedral space sampled in experimental crystal structures of the canonical forms of DNA, validating the utility of the model compound and emphasizing the contribution of the intrinsic mechanical properties of the phosphodiester backbone to the conformational properties of duplex DNA. Those contributions include the relative stability of the A, BI, and BII conformations of duplex DNA, where the gas-phase energetics favor the BI form over the A and BII forms. In addition, subtle features of the potential energy surfaces mimic changes in the probability distributions of α, β, γ, ε, and ζ dihedral angles in A, BI, and BII forms of DNA as well as with conformations sampled in single-stranded DNA. These results show that the intrinsic mechanical properties of the phosphodiester backbone make a significant contribution to conformational properties of duplex DNA observed in the condensed phase and allow for the prediction that single-stranded DNA primarily samples folded conformations thereby possibly lowering the entropic barrier to the formation of duplex DNA." @default.
• W2084367556 created "2016-06-24" @default.
• W2084367556 creator A5056944006 @default.
• W2084367556 date "2009-02-16" @default.
• W2084367556 modified "2023-10-18" @default.
• W2084367556 title "Contribution of the Intrinsic Mechanical Energy of the Phosphodiester Linkage to the Relative Stability of the A, B_I, and B_II Forms of Duplex DNA" @default.
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• W2084367556 doi "https://doi.org/10.1021/jp8102782" @default.
• W2084367556 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2784611" @default.

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