The MP2 quantum chemistry study on the local minima of guanine stacked with all four nucleic acid bases in conformations corresponding to mean B-DNA

Cysewski, Piotr; Czyżnikowska, Żaneta

doi:10.1016/j.theochem.2005.06.014

Cited by 32 publications

(27 citation statements)

References 42 publications

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“…Such geometries can be rather easily constructed for B-DNA. 23,[59][60][61][62] However, preparation of equivalent structures of A-RNA base pair steps is much less straightforward. To do so, one would need to set up and vary more conformational parameters than in B-DNA, considering, for example, sequence-dependent redistribution of base pair roll and variations of displacement of the base pairs from the helix axis.…”

Section: Methodsmentioning

confidence: 99%

“…The d-polarization functions are capable of filling the gap between the interacting monomers, which significantly improves the description of base stacking interactions compared with the standard 6-31G* basis set. The MP2/6-31G*(0.25) method has been the most widely used ab initio technique to study aromatic stacking in the past literature 31,35,50,51,60,85,100,101,[107][108][109][110][111][112][113][114][115][116][117][118][119][120] and has only recently been replaced by CBS(T). The MP2/6-31G*(0.25) method is entirely sufficient to capture the nature of base stacking, and therefore all conclusions reported with this method remain qualitatively valid.…”

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confidence: 99%

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Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

Svozil¹,

Hobza²,

Šponer³

2010

J. Phys. Chem. B

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High level ab initio methods have been used to study stacking interactions in ten unique base pair steps both in A-RNA and in B-DNA duplexes. The protocol for selection of geometries based on molecular dynamics (MD) simulations is proposed, and its suitability is demonstrated by comparison with stacking in steps at fiber diffraction geometries. It is shown that fiber diffraction geometries are not sufficiently accurate for interaction energy calculations. In addition, the protocol for selection of geometries based on MD simulations allows for the evaluation of the variability of the intrinsic stacking energies along the MD trajectories. The uncertainty in stacking energies (difference between the most and least stable geometry) due to the dynamical nature of systems can be, in some cases, as large as 3.0 kcal · mol, which is almost 50% of the actual sequence dependence of base stacking energies (the energy difference between the most and least stable sequences). Thus, assessing the relative magnitude of the gas phase stacking energy using a single geometry for each sequence is insufficient to obtain an unambiguous order of gas phase stacking energies in canonical double helices. Though the ordering of ten unique dinucleotide steps cannot be definitive, some general conclusions were drawn. The stacking energies of base pair steps in A-RNA are more evenly separated compared to B-DNA, and their ordering is less sensitive to the dynamics of the system compared to be B-DNA. The most stable step both in B-DNA and A-RNA is the CG/CG step that is well separated from the second most stable step GC/GC. Also the least stable step (the CC/GG step) is well separated from the rest of the structures. The calculations further show that B-DNA stacking is favorable only marginally (on average by 1.14 kcal · mol -1 per base pair step) over A-RNA stacking, and this difference vanishes after subtracting the stabilizing van der Waals effect of the thymine 5-methyl group that is absent in RNA. Basically, no correlation between the sequence dependence of gas phase stacking energies and the sequence dependence of ∆G°3 7 free energies used in nearest-neighbor models was found either for B-DNA or for A-RNA. This reflects the complexity of the balance of forces that are responsible for the sequence dependence of thermodynamics stability of nucleic acids, which masks the effect of the intrinsic interactions between the stacked base pairs.

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

Svozil¹,

Hobza²,

Šponer³

2010

J. Phys. Chem. B

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“…However, the stacking properties of 8-oxo-guanine in B-DNA context were not the subject of detailed studies up to date. Although in previous paper [10] the global minima of 8-oxo-guanine stacked with canonical bases were presented, no direct comparison to B-DNA conformations were provided till now. Recently, the method for PES scan [11] has been successfully applied for the regions corresponding to the mean B-DNA [12] conformations.…”

Section: Introductionmentioning

confidence: 99%

“…Although in previous paper [10] the global minima of 8-oxo-guanine stacked with canonical bases were presented, no direct comparison to B-DNA conformations were provided till now. Recently, the method for PES scan [11] has been successfully applied for the regions corresponding to the mean B-DNA [12] conformations. In this paper we intend to describe the local minima of stacked pairs of 8-oxoguanine with all four nucleic acid bases in conformations potentially present in B-DNA.…”

Section: Introductionmentioning

confidence: 99%

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A post‐SCF quantum chemistry study on local minima of 8‐oxo‐guanine stacked with all four nucleic acid bases in B‐DNA conformations

Cysewski

Czyżnikowska

2007

Journal of Heterocyclic Chem

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The post SCF MP2/6-31G*(d=0.25) method was applied to obtain potential energy surface of 8-oxoguanine stacked with all four canonical DNA bases. The spatial neighbourhood was scanned of stacked complexes found in the native B-DNA. The presented results suggest that the hydroxyl radical modification of guanine at C 8 position has significant impact on structural, energetic, orbital and electrostatic properties of stacked complexes with canonical DNA bases. The pair stabilization energy, including electron correlation terms, suggests that the 5'-A/GA-3' pair is the most stable among all of the studied complexes. The 8-oxo-guanine has been found as a source of significant changes in electroaccepting properties compared to stacked pairs formed by canonical guanine since both electron affinities and localization of HOMO orbital were altered. However, electro-donation abilities are not modified after replacement of guanine with 8-oxo-guanine irrespectively on the context of B-DNA bases.

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Quantum Mechanical Studies of Noncovalent DNA–Protein Interactions

Rutledge

Wetmore

2010

Quantum Biochemistry

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The MP2 quantum chemistry study on the local minima of guanine stacked with all four nucleic acid bases in conformations corresponding to mean B-DNA

Cited by 32 publications

References 42 publications

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

A post‐SCF quantum chemistry study on local minima of 8‐oxo‐guanine stacked with all four nucleic acid bases in B‐DNA conformations

Quantum Mechanical Studies of Noncovalent DNA–Protein Interactions

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