Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), andab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock results

Hobza, Pavel; Kabeláč, Martin; Šponer, Jiřı́; Mejzlík, Petr; Vondrášek, Jiřı́

doi:10.1002/(sici)1096-987x(19970715)18:9<1136::aid-jcc3>3.0.co;2-s

Cited by 258 publications

(154 citation statements)

References 42 publications

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“…The potential energy of the model is parameterized using a hybrid approach that combines the ClayFF (Cygan et al, 2004), a forcefield for the simulation of minerals such as LDHs, and the Amber parm99 forcefield (Wang et al, 2000) widely used to simulate DNA and RNA (Hobza et al, 1997;Young et al, 1997). In order to simulate PNA, we utilized the forcefield developed by Shields et al (1998) which was found to reproduce PNA structural properties with good accuracy.…”

Section: Potential Parameterizationmentioning

confidence: 99%

Stability of free and mineral-protected nucleic acids: Implications for the RNA world

Swadling¹,

Coveney²,

Greenwell³

2012

Geochimica et Cosmochimica Acta

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Using molecular dynamics simulations we study the structural stability of three different nucleic acids intercalated within a magnesium aluminium layered double hydroxide (LDH) mineral, at varying degrees of hydration, and free in aqueous solution. The nucleotides investigated are ribose nucleic acid (RNA), deoxyribose nucleic acid (DNA) and peptide nucleic acid (PNA), all in duplex form. Our simulations show that DNA has enhanced Watson-Crick hydrogen-bonding when intercalated within the LDH clay interlayers, compared with intercalated RNA and PNA, whilst the reverse trend is found for the nucleic acids in bulk water. The tendency for LDH to alter the stability of the three nucleic acids persists for higher temperature and pressure conditions. The uncharged protein backbone of PNA is found to have a detrimental effect on the overall stability of the duplex, as it experiences a greatly reduced electrostatic interaction with the charged LDH sheets compared to RNA and DNA. Assuming an RNA world, in which RNA preceded the DNA/protein world, at some point in time DNA must have taken over the role as the information storage molecule from RNA. These results suggest that a mineral based origin of life may have favoured DNA as the information-storage biomolecule over potentially competing RNA and PNA, providing a route to modern biology from the RNA world.

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Section: Potential Parameterizationmentioning

confidence: 99%

Stability of free and mineral-protected nucleic acids: Implications for the RNA world

Swadling¹,

Coveney²,

Greenwell³

2012

Geochimica et Cosmochimica Acta

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“…The structures of the chalcones were sketched and their energies were minimized using consistent valence force field (CVFF) available in Cerius 2 software. This force field is ideally suited for modeling small molecules and it is also called a universal force field (Hobza et al, 1997). Minimum energy conformations of several structures were determined and the conformation which had the lowest energy was selected.…”

Section: Qsar Developmentmentioning

confidence: 99%

Synthesis, antioxidant evaluation, and quantitative structure–activity relationship studies of chalcones

2010

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Synthesis, antioxidant activity, and quantitative structure-activity relationship (QSAR) of 25 of chalcone derivatives is reported here. They were synthesized by Claisen-Schmidt reaction and were characterized by FTIR, NMR, and mass spectroscopy. Antioxidant activity is evaluated through four different methods namely, superoxide radical-scavenging, hydrogen peroxide scavenging, reducing power, and DPPH radical-scavenging assays. Generally, compounds with -SCH 3 and -OCH 3 in the para position of the A-ring and -OH in the B-ring were more active than others. In few cases some of the compounds were more active than ascorbic acid or butylated hydroxytoluene. QSAR was developed correlating the antioxidant activity with the structural features of the compounds and the predictive capability of the models was estimated using internal and external validation methods. All the predictions were within the 99% confidence level. Spatial, structural, and lipophilic properties of the compounds determine their antioxidant properties.

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“…Note that semiempirical approaches should be used with care when considering DNA base assemblies as both the geometry and the energetics they predict are unreliable. [43][44][45][46] This approach that combines STM experimental images with a systematic theoretical analysis of all possible structures enables us to make a substantial step forward from "guessing" to "deriving" the observed molecular structures.…”

Section: Introductionmentioning

confidence: 99%

Understanding the disorder of the DNA base cytosine on the Au(111) surface

Kelly

Lukas

Kantorovich

et al. 2008

The Journal of Chemical Physics

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Using ultrahigh vacuum scanning tunneling microscopy ͑STM͒ and ab initio density functional theory, we have investigated in detail structures formed by cytosine on the Au͑111͒ surface in clean ultrahigh vacuum conditions. In spite of the fact that the ground state of this DNA base on the surface is shown to be an ordered arrangement of cytosine one-dimensional branches ͑filaments͒, this structure has never been observed in our STM experiments. Instead, disordered structures are observed, which can be explained by only a few elementary structural motifs: filaments, five-and sixfold rings, which randomly interconnect with each other forming bent chains, T junctions, and nanocages. The latter may have trapped smaller structures inside. The formation of such an unusual assembly is explained by simple kinetic arguments as a liquid-glass transition.

show abstract

Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), andab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock results

Cited by 258 publications

References 42 publications

Stability of free and mineral-protected nucleic acids: Implications for the RNA world

Stability of free and mineral-protected nucleic acids: Implications for the RNA world

Synthesis, antioxidant evaluation, and quantitative structure–activity relationship studies of chalcones

Understanding the disorder of the DNA base cytosine on the Au(111) surface

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