Stabilization of the purine•purine•pyrimidine dna base triplets by divalent metal cations

Journal of Biomolecular Structure and Dynamics

Volumn 16, Issue 1, 1998, Pages 139-143

  Šponer, Jiři ^a,b   Sabat, Michal ^c   Burda, Jaroslav V ^d   Doody, Anne M ^e   Leszczynski, Jerzy ^f   Hobza, Pavel ^a  

^a J HEYROVSKÝ INSTITUTE OF PHYSICAL CHEMISTRY   (Czech Republic)

^b INSTITUTE OF BIOPHYSICS   (Czech Republic)

^c UNIVERSITY OF VIRGINIA   (United States)

^d CHARLES UNIVERSITY   (Czech Republic)

^e Department of Population Medicine and Diagnostic Sciences   (United States)

^f JACKSON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIVALENT CATION; DNA; MAGNESIUM; PURINE; PURINE DERIVATIVE; PYRIMIDINE; PYRIMIDINE DERIVATIVE; ZINC; ADENINE; CYTOSINE; GUANINE; HYDROGEN; METAL ION; THYMINE;

ARTICLE; BASE PAIRING; ENERGY; GENE EXPRESSION; GENETIC STABILITY; HYDROGEN BOND; NOTE; PRIORITY JOURNAL;

BASE PAIRING; CATIONS, DIVALENT; DNA; MAGNESIUM; PURINES; PYRIMIDINES; ZINC;

EID: 0031593720     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1998.10508235     Document Type: Article

References (18)

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10. 11 as in our previous studies (12). The interaction energies were evaluated for the HF-optimized geometries by using the full second-order Moeller-Plesset perturbational method (MP2). The main task of the present study was to estimate the influence of the solvated metal cation on the stability of the purine-purine base pairs. Therefore, the remote pyrimidine base was neglected in the calculation of interaction energies, as this base does not have any significant effect on the purine-purine interaction. The cation with its hydration sphere was considered as one subsystem. Thus, the energy calculations were performed for the purine-purine-hydrated cation “trimer”. The energy of interactions within the trimer was decomposed into the individual pair wise contributions and a three-body term. (9c, 12b, c). The interaction energies were corrected for the basis set superposition error (13) in the trimer-centered basis set. All of the calculations were done by using the Gaussian 94 suite of programs (14)
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13. 2+ system without inclusion of the BSSE corrections. The uncorrected value of the interaction energy is −147.4 kcal/mol, ca.18 kcal/mol lower than the BSSE-corrected value in Table I. Thus, in contrast to the popular belief that BSSE is quite negligible for ionic systems, the correction is quite significant and we recommend correcting all data for larger systems by applying the countepoise procedure
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