2000
DOI: 10.1021/ja9936060
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Global Minimum of the Adenine···Thymine Base Pair Corresponds Neither to Watson−Crick Nor to Hoogsteen Structures. Molecular Dynamic/Quenching/AMBER and ab Initio beyond Hartree−Fock Studies

Abstract: Computational analysis of complete gas-phase potential energy and free energy surfaces of the adenine···thymine base pair has been carried out. The study utilizes a combination of molecular dynamics simulations performed with Cornell et al. empirical force field and quenching technique. Twenty seven energy minima have been located at the potential energy surface of the adenine···thymine base pair:  nine of them are H-bonded structures, eight are T-shaped dimers, and the remaining nine correspond to various sta… Show more

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Cited by 78 publications
(74 citation statements)
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“…[ [18][19][20]23] The critical parameters in the UFF potential are the partial atomic charges, and the values derived by charge equilibration [21] were not accurate enough. New values were obtained by using restrained fit to the electrostatic potential (RESP) [14] at the B3LYP/cc-pVTZ level, as is used with the current AMBER force field (ff03).…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…[ [18][19][20]23] The critical parameters in the UFF potential are the partial atomic charges, and the values derived by charge equilibration [21] were not accurate enough. New values were obtained by using restrained fit to the electrostatic potential (RESP) [14] at the B3LYP/cc-pVTZ level, as is used with the current AMBER force field (ff03).…”
Section: Methodsmentioning
confidence: 99%
“…The combination of MD simulations with the quenching (Q) technique is an efficient tool for studying the PESs of molecular clusters, and we used this technique previously to determine the PESs of various DNA base pairs. [18][19][20]23] The quality of the theoretical predictions depends on the quality of the empirical potential used, and this point was critical in the present study, since the parameters of the boron atom are not included in most of the empirical potentials. After description of the PESs of the studied complexes it is necessary to reinvestigate the global and the deepest local minima with accurate methods of quantum chemistry, and only these predictions are reliable enough.…”
Section: Strategy Of Calculationmentioning
confidence: 99%
“…First, individual base pairs were studied (uracil dimer 143 , the adenine...2,4-difluorotoluene pair 144 , methyluracil dimers 145 , the adenine...thymine pair 146 and the methyladenine...methylthymine pair 147 ), and, later, all the DNA base pairs and methylated DNA base pairs were also considered 148 .…”
Section: Nucleic Acid Base Pairsmentioning
confidence: 99%
“…The complexity of the problem will be demonstrated on the case of the adenine...thymine (non-methylated) base pairs 146 . MD/Q calculations revealed twenty-seven energy minima, of which nine were H-bonded, eight T-shaped and ten stacked (cf.…”
Section: Nucleic Acid Base Pairsmentioning
confidence: 99%
“…According to ab initio calculations [21], the Watson-Crick (W-C) uracil/adenine pair is more stable than the Hoogsteen (HG) pair in vacuum (see Fig. 3 for schematic structures of both W-C and HG pairs).…”
Section: Estimation Of H-bond Energies In the Mixed Crystalmentioning
confidence: 99%