Molecular orbital calculations on the conformation of nucleic acids and their constituents

Saran, Anil; Pérahia, David; Pullman, Bernard

doi:10.1007/bf00527633

Cited by 84 publications

(39 citation statements)

References 39 publications

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“…However, in thymidine itself (Young, Tollin & Wilson, 1969), the sugar ring pucker, P = 187 °, is markedly different although the value of 2~ is similar, -139 °. The present conformation is close to the theoretical minimum obtained from conformational energy calculations (Saran, Perahia & Pullman, 1973).…”

Section: _1 • •supporting

confidence: 85%

Structure of 5-(trifluoromethyl)-2'-deoxyuridine

Low¹,

Tollin²,

Howie³

1989

Acta Crystallogr C

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Section: _1 • •supporting

confidence: 85%

Structure of 5-(trifluoromethyl)-2'-deoxyuridine

Low¹,

Tollin²,

Howie³

1989

Acta Crystallogr C

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“…PCILO calculations have shown that N % S interconversions pass via P = 90" and not via 270", since the energy barrier is lower at 90" [39]. We have seen above that for C(3), a negative P angle occurs only if both ammine .…”

Section: Coupling Constantsmentioning

confidence: 72%

A d(GpG)‐platinated decanucleotide duplex is kinked

Herman

Kozelka

Stoven

et al. 1990

European Journal of Biochemistry

108

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A conformational study of the double‐stranded decanucleotide d(GCCG*G*ATCGC) · d(GCGATCCGGC), with the G* guanines chelating a cis‐Pt(NH3)2 moiety, has been accomplished using 1H and 31P NMR, and molecular mechanics. Correlation of the NMR data with molecular models has disclosed an equilibrium between several kinked conformations and has ruled out an unkinked structure. The deformation is localized at the CG*G*· CCG trinucleotide where the helix is kinked by approximately 60° towards the major groove and unwound by 12–19°. The models revealed an unexpected mobility of the cytosine complementary to the 5′‐G*. This cytosine can stack on either branch of the kinked complementary strand. The energy barrier between the two positions has been calculated to be ≤ 12 kJ/mol. The NMR data are in support of rapid flip‐flopping of this cytosine. An explanation for the strong downfield shift observed in the 31P resonance of the G*pG* phosphate is given.

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“…Subsequently, numerous QM calculations were performed with this and related models from which more quantitative evaluations of the impact of the local energetics of the peptide backbone on conformational properties of proteins were obtained 54–56. With nucleic acids early work was also initiated using hard-sphere models 57 58 59 as well as force field 60 61 62,63 and semiempirical methods64 65–67. These studies yielded a range of insights into the conformational properties of nucleic acids, including oligonucleotides.…”

Section: Resultsmentioning

confidence: 99%

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

MacKerell

2009

J. Phys. Chem. B

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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 primarly samples folded conformations thereby possibly lowering the entropic barrier to the formation of duplex DNA.

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Molecular orbital calculations on the conformation of nucleic acids and their constituents

Cited by 84 publications

References 39 publications

Structure of 5-(trifluoromethyl)-2'-deoxyuridine

Structure of 5-(trifluoromethyl)-2'-deoxyuridine

A d(GpG)‐platinated decanucleotide duplex is kinked

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

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Molecular orbital calculations on the conformation of nucleic acids and their constituents

Cited by 84 publications

References 39 publications

Structure of 5-(trifluoromethyl)-2'-deoxyuridine

Structure of 5-(trifluoromethyl)-2'-deoxyuridine

A d(GpG)‐platinated decanucleotide duplex is kinked

Contribution of the Intrinsic Mechanical Energy of the Phosphodiester Linkage to the Relative Stability of the A, BI, and BII Forms of Duplex DNA

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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