Molecular Modeling of Nucleic Acid Structure: Energy and Sampling

Cheatham, Thomas E.; Brooks, Bernard R.; Kollman, Peter A.

doi:10.1002/0471142700.nc0708s04

Cited by 4 publications

(1 citation statement)

References 125 publications

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“…The structure and properties of DNA have been widely studied over the past decades, due to its central role in biology. In this regard, semi-and empirical methods and molecular mechanics (MM) approaches have been widely used to study the molecular interactions between nucleic acids and other molecules [3,4].…”

Section: Introductionmentioning

confidence: 99%

Residue Interactions Affecting The Deprotonation of Internal Guanine Moieties In Oligodeoxyribonucleotides, Calculated By FMO Methods

Zamorano-Carrillo

Arreola-Jardón

Pless

et al. 2021

Preprint

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The effect of vicinal molecular groups on the intrinsic acidity of a central guanine residue in short single-stranded DNA models, and the potentials exerted by the backbone and the nucleobases on the leaving proton were determined by the Fragment Molecular Orbital (FMO) method, in terms of quantum descriptors (QD) and pair interaction interfragment decomposition analysis (PIEDA). The acidity of the central guanine moiety decreased with increasing oligonucleotide length, in response to changes by less than1 eV in the ionization potential, global softness, electrophilicity index and electronegativity descriptors. The differences in these descriptors were majorly interpreted in terms of the electrostatic influence of the negative charges residing on the backbone of the molecule. Additionally, this electric-field effect was determined explicitly for the displacement of the test hydronium ion to a distance of 250 Å from its original position, resulting in good agreement with calculations of the variation in Gibbs free energies, obtained from physical experiments conducted on the identical oligonucleotide sequences. The reported results are useful for biophysical applications of deoxyriboligonucleotides containing guanine residues in order to induce local negative charges at specific positions in the DNA chain.

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Section: Introductionmentioning

confidence: 99%

Residue Interactions Affecting The Deprotonation of Internal Guanine Moieties In Oligodeoxyribonucleotides, Calculated By FMO Methods

Zamorano-Carrillo

Arreola-Jardón

Pless

et al. 2021

Preprint

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Residue interactions affecting the deprotonation of internal guanine moieties in oligodeoxyribonucleotides, calculated by FMO methods

et al. 2022

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The effect of vicinal molecular groups on the intrinsic acidity of a central guanine residue in short singlestranded DNA models, and the potentials exerted by the backbone and the nucleobases on the leaving proton were determined by the Fragment Molecular Orbital (FMO) method, in terms of quantum descriptors (QD) and pair interaction interfragment decomposition analysis (PIEDA). The acidity of the central guanine moiety decreased with increasing oligonucleotide length, in response to changes by less than1 eV in the ionization potential, global softness, electrophilicity index and electronegativity descriptors. The differences in these descriptors were majorly interpreted in terms of the electrostatic influence of the negative charges residing on the backbone of the molecule. Additionally, this electric-field effect was determined explicitly for the displacement of the test hydronium ion to a distance of 250 Å from its original position, resulting in good agreement with calculations of the variation in Gibbs free energies, obtained from physical experiments conducted on the identical oligonucleotide sequences. The reported results are useful for biophysical applications of deoxyriboligonucleotides containing guanine residues in order to induce local negative charges at specific positions in the DNA chain.

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The ABCs of molecular dynamics simulations on B-DNA, circa 2012

2012

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This article provides a retrospective on the ABC initiative in the area of all-atom molecular dynamics (MD) simulations including explicit solvent on all tetranucleotide steps of duplex B-form DNA duplex, ca. 2012. The ABC consortium has completed two phases of simulations, the most current being a set of 50–100 trajectories based on the AMBER ff99 force field together with the parmbsc0 modification. Some general perspectives on the field of MD on DNA and sequence effects on DNA structure are provided, followed by an overview our MD results, including a detailed comparison of the ff99/parmbsc0 results with crystal and NMR structures available for d(CGCGAATTCGCG). Some projects inspired by or related to the ABC initiative and database are also reviewed, including methods for the trajectory analyses, informatics of dealing with the large database of results, compressions of trajectories for efficacy of distribution, DNA solvation by water and ions, parameterization of coarse-grained models with applications and gene finding and genome annotation

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Molecular Modeling of Nucleic Acid Structure: Energy and Sampling

Cited by 4 publications

References 125 publications

Residue Interactions Affecting The Deprotonation of Internal Guanine Moieties In Oligodeoxyribonucleotides, Calculated By FMO Methods

Residue Interactions Affecting The Deprotonation of Internal Guanine Moieties In Oligodeoxyribonucleotides, Calculated By FMO Methods

Residue interactions affecting the deprotonation of internal guanine moieties in oligodeoxyribonucleotides, calculated by FMO methods

The ABCs of molecular dynamics simulations on B-DNA, circa 2012

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