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, Piotr; Czyżnikowska, Żaneta

doi:10.1002/jhet.5570440403

Cited by 9 publications

(2 citation statements)

References 26 publications

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“…On the other hand, single-point calculations and scans with rigid planar monomers in carefully selected geometries are preferred for investigation of the stacking patterns seen in nucleic acids as well as for force-field parameterisation and verification. 17,23,24,[63][64][65][66][67][68][69][70][71] Table 1 shows that the stacked mGmC dimer is more stable than the horizontal mAmT H base pair having two H-bonds. The theoretical level used is very high (and thus should provide reliable results) but its performance can only be proven by comparison with experimental data.…”

Section: Resultsmentioning

confidence: 99%

Nature and magnitude of aromatic stacking of nucleic acid bases

Šponer

Riley

Hobza

2008

Phys. Chem. Chem. Phys.

322

342

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This review summarises recent advances in quantum chemical calculations of base-stacking forces in nucleic acids. We explain in detail the very complex relationship between the gas-phase base-stacking energies, as revealed by quantum chemical (QM) calculations, and the highly variable roles of these interactions in nucleic acids. This issue is rarely discussed in quantum chemical and physical chemistry literature. We further extensively discuss methods that are available for base-stacking studies, complexity of comparison of stacking calculations with gas phase experiments, balance of forces in stacked complexes of nucleic acid bases, and the relation between QM and force field descriptions. We also review all recent calculations on base-stacking systems, including details analysis of the B-DNA stacking. Specific attention is paid to the highest accuracy QM calculations, to the decomposition of the interactions, and development of dispersion-balanced DFT methods. Future prospects of computational studies of base stacking are discussed.

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Section: Resultsmentioning

confidence: 99%

Nature and magnitude of aromatic stacking of nucleic acid bases

Šponer

Riley

Hobza

2008

Phys. Chem. Chem. Phys.

322

342

View full text Add to dashboard Cite

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“…Due to their importance, there numerous studies have been performed on the stacking interactions, both experimental [22,23] and theoretical [24,25]. The computational studies range from analyzing canonical base stacking [26] to unusual base stacking [27]. Among natural products which are biologically active, indoles are the most plentiful heterocycles, pharmaceuticals, agrochemicals and also are pertinent substructures in functional materials (Fig.…”

Section: Introductionmentioning

confidence: 99%

An in-depth study on noncovalent stacking interactions between DNA bases and aromatic drug fragments using DFT method and AIM analysis: conformers, binding energies, and charge transfer

Toupkanloo

Rahmani

2018

Appl Biol Chem

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This work is aimed at providing physical insights about the p-p stacking interactions of some popular drug fragments (DF) including indole (I), benzothiophene (Bt), benzofuran (Bf) and guanine (G), adenine (A), A-thymine (AT), G-cytosine (GC) base pairs using density functional theory (DFT), the atoms in molecule (AIM) theory, and natural bond orbital (NBO) analysis. Several stable conformers of present molecules and complexes were optimized at the M062X/6-311??G(d,p) level of theory. The result shows that the IG1 (see the notation below) and IA6 have maximum interaction energy in all of the two G-based and A-based conformers; and order of the adsorption strength is IG1 [ BtG6 [ BfG1 for G-based complexes and IA6 [ BtA6 [ BfG6 for A-based complexes. For the base pair-drug fragment complexes, the order of interaction energy was found according to IAT4 [ BtAT3 [ BfAT4 and IGC3 [ BtGC2 [ BfGC2, for AT and GC base pairs, respectively. Furthermore, our results show that stacking interaction leads to an increase and decrease in hydrogen bond length that involved in the nucleic base-drug fragment interactions. DFT-calculated interaction energies for all present conformers were found to be in a good agreement with the bond critical points data from AIM analysis. In contrast, no reasonable linear correlation was observed between NBO analysis and stability of the all studied conformers. Finally, in order to verify the DFT and AIM results, docking calculations were performed using AutoDock software. According to the binding energy of drug-DNA from AutoDock calculations, the D2-Bt and D1-Bf are the most and the least stable structures, respectively.

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The post-SCF quantum chemistry characteristics of inter- and intra-strand stacking interactions in d(CpG) and d(GpC) steps found in B-DNA, A-DNA and Z-DNA crystals

Cysewski

2008

J Mol Model

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The energies of intra- and inter-strand stacking interactions in model d(GpC) and d(CpG) two-base-pair steps were estimated by MP2/aug-cc-pVDZ single point calculations corrected for basis superposition errors. The stacked two-nucleobase pairs were constructed using experimental values of base pair and base step parameters taken from Nucleic Acid Database (http://ndbserver.rutgers.edu/). Three distinct polymorphic forms were analysed, namely A-, B- and Z-DNA. The applied methodology enables statistical analysis of structural and energetic diversities. The structural relationships between polymorphic forms are quite complex and depend on the sequence of pairs. The variability of parameters such as shift and tilt is almost the same irrespective of the polymorphic form and sequence of steps analysed. In contrast, shift and twist distributions easily discriminate all three polymorphic forms of DNA. Interestingly, despite significant structural diversities, the energies of the most frequent energy ranges are comparable irrespective of the polymorphic form and base sequence. There was observed compensation of inter- and intra-strand interactions, especially for d(GpC) and d(CpG) steps found in A- and B-DNA. Thus, among many other roles, these pairs act as a kind of energetic buffer, balancing the double helix.

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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

Cited by 9 publications

References 26 publications

Nature and magnitude of aromatic stacking of nucleic acid bases

Nature and magnitude of aromatic stacking of nucleic acid bases

An in-depth study on noncovalent stacking interactions between DNA bases and aromatic drug fragments using DFT method and AIM analysis: conformers, binding energies, and charge transfer

The post-SCF quantum chemistry characteristics of inter- and intra-strand stacking interactions in d(CpG) and d(GpC) steps found in B-DNA, A-DNA and Z-DNA crystals

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