Ability of empirical potentials (AMBER, CHARMM, CVFF, OPLS, Poltev) and semi-empirical quantum chemical methods (AM1, MNDO/M, PM3) to describe H-bonding in DNA base pairs; comparison with ab initio results

Hobza, Pavel; Hubálek, F.; Kabeláč, Martin; Mejzlík, Petr; Šponer, Jiřı́; Vondrášek, Jiřı́

doi:10.1016/0009-2614(96)00537-4

Cited by 102 publications

(115 citation statements)

References 16 publications

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“…The gas phase (D(r) ) 1) base pair energies (Table 1) are in line with the values reported in the literature, 28,38,40,49 indicating the correctness of the application of the force fields from the published data. The differences between the present set and the literature values are attributable to the differences in the geometry of the base pairs and also to the presence of a methyl group in place of a H on the N9 or N1 of purine or pyrimidine, respectively.…”

Section: Resultssupporting

confidence: 86%

Energetics of Base Pairs in B-DNA in Solution: An Appraisal of Potential Functions and Dielectric Treatments

Arora

Jayaram

1998

J. Phys. Chem. B

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The energetics of base pairs in B-DNA in solution has been estimated via recently reported versions of some empirical potential energy functions, namely, AMBER, CHARMM, GROMOS, and OPLS used commonly in biomolecular simulations. The electrostatic component of the interaction energy between bases involved in Watson-Crick pairing in B-DNA in aqueous environment, evaluated via the finite difference PoissonBoltzmann methodology with all the above force fields, is in the range of -2 to -3 kcal/mol per H-bond. An examination of different dielectric functions used in conjunction with the above force fields suggests that a sigmoidal function, with an estimate of -2 kcal/mol per H-bond, comes closest to mimicking the electrostatics of AT and GC base pairs under aqueous conditions.

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Section: Resultssupporting

confidence: 86%

Energetics of Base Pairs in B-DNA in Solution: An Appraisal of Potential Functions and Dielectric Treatments

Arora

Jayaram

1998

J. Phys. Chem. B

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“…The energy for G · C is significantly greater than that of any of the other pairs [18]. Ab initio calculations have provided both binding energies and structures of guanine-cytidine pair in the absence of solvent [24][25][26]. However, the more rigorous calculations only include the nucleobase pairs and no phosphate and deoxyribose moieties.…”

mentioning

confidence: 99%

Dissociation energies of deoxyribose nucleotide dimer anions measured using blackbody infrared radiative dissociation

Strittmatter

Schnier

Klassen

et al. 1999

J. Am. Soc. Mass Spectrom.

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The dissociation kinetics of deprotonated deoxyribose nucleotide dimers were measured using blackbody infrared radiative dissociation. Experiments were performed with noncovalently bound dimers of phosphate, adenosine (dAMP), cytosine (dCMP), guanosine (dGMP), thymidine (dTMP), and the mixed dimers dAMP · dTMP and dGMP · dCMP. The nucleotide dimers fragment through two parallel pathways, resulting in formation of the individual nucleotide or nucleotide + HPO 3 ion. Master equation modeling of this kinetic data was used to determine threshold dissociation energies. The dissociation energy of (dGMP · dCMP − H) − is much higher than that for the other nucleotide dimers. This indicates that there is a strong interaction between the nucleobases in this dimer, consistent with the existence of Watson-Crick hydrogen bonding between the base pairs. Molecular mechanics simulations indicate that Watson-Crick hydrogen bonding occurs in the lowest energy structures of (dGMP · dCMP − H) − , but not in (dAMP · dTMP − H) − . The trend in gas phase dissociation energies is similar to the trend in binding energies measured in nonaqueous solutions within experimental error. Finally, the acidity ordering of the nucleotides is determined to be dTMP < GMP < CMP < AMP, where dAMP has the highest acidity (largest ΔG acid ).Electrospray ionization (ESI) mass spectrometry (MS) is a powerful technique for obtaining molecular weights and structural information from biopolymers [1][2][3][4][5]. The application of mass spectrometry methods to the analysis of oligonucleotides has recently been reviewed [4,5]. The base composition of DNA strands can be obtained from accurate mass measurements of double stranded DNA [6]. Sequence information can be obtained from both single and double stranded DNA using tandem mass spectrometry (MS n ) [4,5,[7][8][9]. Using several dissociation methods, McLafferty and co-workers obtained complete sequence information for a 50-mer nucleotide and nearly complete sequence information for a 100-mer [7]. Sequence construction algorithms have been used to determine the primary structure of oligonucleotides up to 20-mers from low energy collisional activation spectra [9]. In combination with solution-phase techniques, such as the Sanger method, MS and MS n have been used to verify sequences of DNA [4]. Mass spectrometry techniques have also been applied to the identification of antisense [10], labeled [11], and posttranscriptionally modified [12] oligonucleotides where other methods are often unsuitable.In ESI, gas-phase ions are formed directly from solution. This makes possible the direct coupling of mass spectrometry to solution-based separation and amplification techniques, such as HPLC or PCR. For example, Muddiman et al. demonstrated that sequence information can be obtained from oligonucleotides after amplification using PCR [13]. Noncovalent complexes are often observed in ESI mass spectra if source conditions are adjusted to minimize collisional activation in the electrospray interface. Many studies o...

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“…The different nature of stabilization forces in these two types of dimers cause different approaches to their theoretical investigation. The electrostatic origin of the hydrogen bonds allows to study H-bonded complexes of bases with a wide range of quantum chemical and force field methods [4][5][6][7], and , therefore, these calculations were easily extended from base pairs to trimers, tetramers, etc. [8], studying effects of cooperativity of interactions, different ways of hydrogen bonding, non-planarity of base pairs, etc.…”

Section: Introductionmentioning

confidence: 99%

“…Empirical force field methods are widely used for the simulation of the structure and dynamics of large fragments of DNA and it has been demonstrated recently, that several force fields describe hydrogen bonding and stacking interactions between bases very accurately [7]. However, force fields do not cover the polarization of DNA bases due to interaction with each other.…”

Section: Introductionmentioning

confidence: 99%

Structure of Stacked Dimers of N-Methylated Watson–Crick Adenine–Thymine Base Pairs

Шишкин

Elstner

Frauenheim

et al. 2003

IJMS

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Abstract:The structure of two isomeric stacked dimers of Watson-Crick 9-methyladenine-1-methylthymine pairs was fully optimized using an approximate density functional theory (DFT) method augmented with an empirical dispersion interaction. The results of the calculations reveal that head-to-tail (AT-TA) and head-to-head (AT-AT) dimers possess a significantly different geometry. The structure of both complexes is stabilized by vertical C-H…O and C-H…N hydrogen bonds with the participation of the hydrogen atoms of the methyl groups. The energy of hydrogen bonding and stacking interactions was additionally calculated using the MP2/6-31G*(0.25) method. Differences in the mutual arrangement of the base pairs in two isomeric dimers lead to significant changes of intra and interstrand stacking interaction energies.

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Ability of empirical potentials (AMBER, CHARMM, CVFF, OPLS, Poltev) and semi-empirical quantum chemical methods (AM1, MNDO/M, PM3) to describe H-bonding in DNA base pairs; comparison with ab initio results

Cited by 102 publications

References 16 publications

Energetics of Base Pairs in B-DNA in Solution: An Appraisal of Potential Functions and Dielectric Treatments

Energetics of Base Pairs in B-DNA in Solution: An Appraisal of Potential Functions and Dielectric Treatments

Dissociation energies of deoxyribose nucleotide dimer anions measured using blackbody infrared radiative dissociation

Structure of Stacked Dimers of N-Methylated Watson–Crick Adenine–Thymine Base Pairs

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