Molecular structure of free canonical 2′-deoxyribonucleosides: a density functional study

Шишкин, Олег В.; Pelmenschikov, Alexander; Hovorun, Dmytro М.; Leszczyński, Jerzy

doi:10.1016/s0022-2860(00)00497-x

Cited by 76 publications

(94 citation statements)

References 37 publications

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“…6–31+G(d) or larger) and the explicit treatment of electron correlation with either MP2 or density functional methods. Notably these studies have shown that the low energy regions of dihedral energy surfaces for the model compounds correspond to regions sampled with high probabilities in surveys of the crystallographic structures 35,71 72 73 74 33,75–77 78. Analysis of these results yielded insights into the Analysis conformational properties of oligonucleotides as well as serving as part of the target data for the optimization of the CHARMM27 force field for nucleic acids 43,44.…”

Section: Resultsmentioning

confidence: 94%

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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Section: Resultsmentioning

confidence: 94%

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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“…However, recently it has become possible to analyze these conformational properties using highlevel ab initio QM methods. 55,[75][76][77][78][79][80][81][82][83][84][85] In this paper, we attempt to gain insight into the complexity, modeling, and conformational flexibility of the DNA backbone. This is achieved by calculations on two model systems mimicking the basic building block of the DNA phosphodiester backbone.…”

Section: Introductionmentioning

confidence: 99%

Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids

Svozil¹,

Šponer²,

Marchán³

et al. 2008

J. Phys. Chem. B

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The anionic sugar-phosphate backbone of nucleic acids substantially contributes to their structural flexibility. To model nucleic acid structure and dynamics correctly, the potentially sampled substates of the sugar-phosphate backbone must be properly described. However, because of the complexity of the electronic distribution in the nucleic acid backbone, its representation by classical force fields is very challenging. In this work, the three-dimensional potential energy surfaces with two independent variables corresponding to rotations around the R and γ backbone torsions are studied by means of high-level ab initio methods (B3LYP/ 6-31+G*, MP2/6-31+G*, and MP2 complete basis set limit levels). [3817][3818][3819][3820][3821][3822][3823][3824][3825][3826][3827][3828][3829] force fields to describe the various R/γ conformations of the DNA backbone accurately is assessed by comparing the results with those of ab initio quantum chemical calculations. Two model systems differing in structural complexity were used to describe the R/γ energetics. The simpler one, SPM, consisting of a sugar and methyl group linked through a phosphodiester bond was used to determine higher-order correlation effects covered by the CCSD(T) method. The second, more complex model system, SPSOM, includes two deoxyribose residues (without the bases) connected via a phosphodiester bond. It has been shown by means of a natural bond orbital analysis that the SPSOM model provides a more realistic representation of the hyperconjugation network along the C5′-O5′-P-O3′-C3′ linkage. However, we have also shown that quantum mechanical investigations of this model system are nontrivial because of the complexity of the SPSOM conformational space. A comparison of the ab initio data with the ff99 potential energy surface clearly reveals an incorrect ff99 force-field description in the regions where the γ torsion is in the trans conformation. An explanation is proposed for why the R/γ flips are eliminated so successfully when the parmbsc0 force-field modification is used.

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“…The structural components of DNA -nucleosides and their derivatives -are important objects of investigation for the modern science of life [1][2][3][4][5][6][7][8][9][10][11]. The main experimental methods of investigation of nucleosides are NMR spectroscopy and crystallography [1].…”

mentioning

confidence: 99%

“…In the present research, FTIR spectra of dT in Ar matrices were obtained by using an enhanced experimental setup. The new spectral data suggest the existence of more types of isomers with intramolecular H-bonds in the isolated pyrimidine nucleosides than had been considered before [7][8][9][10][11].…”

mentioning

confidence: 99%

Molecular structures of thymidine isomers isolated in low-temperature inert matrices

Ivanov

Sheina

Krasnokutski

2003

Low Temperature Physics

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The Fourier transform infrared spectra of 2'-deoxyribonucleoside -thymidine (dT) in low-temperature Ar matrices are obtained in the range 4000-1300 ñm -1 . It is determined that anti-conformers of thymidine are dominant. The ribose rings of the main anti-conformers dT_a0, dT_a1 are in the Ñ2'-endo conformation, but the ribose rings of minor anti-conformers dT_a2, dT_a3 have the Ñ3'-endo conformation, stabilized by intramolecular hydrogen bonds O3'H…O5' and O5'H…O3', respectively. The main syn-conformer dT_s2 is stabilized by the intramolecular hydrogen bond O5'H…O2 and has Ñ2'-endo conformation of the ribose ring.PACS: 33.15.-e, 67.80.Cx

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Molecular structure of free canonical 2′-deoxyribonucleosides: a density functional study

Cited by 76 publications

References 37 publications

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

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

Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids

Molecular structures of thymidine isomers isolated in low-temperature inert matrices

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Molecular structure of free canonical 2′-deoxyribonucleosides: a density functional study

Cited by 76 publications

References 37 publications

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

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

Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids

Molecular structures of thymidine isomers isolated in low-temperature inert matrices

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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

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