Limits...
DNA Duplex Formation with a Coarse-Grained Model.

Maciejczyk M, Spasic A, Liwo A, Scheraga HA - J Chem Theory Comput (2014)

Bottom Line: Chem. 2010, 31, 1644].Interactions with the solvent and an ionic cloud are approximated by a multipole-multipole Debye-Hückel model.It is the first coarse-grained model, in which both bonded and nonbonded interactions were parametrized ab initio and which folds stable double helices from separated complementary strands, with the final conformation close to the geometry of experimentally determined structures.

View Article: PubMed Central - PubMed

Affiliation: Baker Laboratory of Chemistry, Cornell University , Ithaca, New York 14850, United States ; Department of Physics and Biophysics, Faculty of Food Sciences, University of Warmia and Mazury , 11-041 Olsztyn, Poland.

ABSTRACT
A middle-resolution coarse-grained model of DNA is proposed. The DNA chain is built of spherical and planar rigid bodies connected by elastic virtual bonds. The bonded part of the potential energy function is fit to potentials of mean force of model systems. The rigid bodies are sets of neutral, charged, and dipolar beads. Electrostatic and van der Waals interactions are parametrized by our recently developed procedure [Maciejczyk, M.; Spasic, A.; Liwo, A.; Scheraga, H.A. J. Comp. Chem. 2010, 31, 1644]. Interactions with the solvent and an ionic cloud are approximated by a multipole-multipole Debye-Hückel model. A very efficient R-RATTLE algorithm, for integrating the movement of rigid bodies, is implemented. It is the first coarse-grained model, in which both bonded and nonbonded interactions were parametrized ab initio and which folds stable double helices from separated complementary strands, with the final conformation close to the geometry of experimentally determined structures.

No MeSH data available.


Related in: MedlinePlus

Examples of slitheringpathways of DNA hybridization of (a) 3BSE and (b) 2JYK molecules.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4230386&req=5

fig13: Examples of slitheringpathways of DNA hybridization of (a) 3BSE and (b) 2JYK molecules.

Mentions: As can be expected, the zippering mechanism was also observedforlonger molecules, 3BSE and 2JYK.Nevertheless, some trajectories with a slithering folding mechanismwere also recorded. At first, this observation is surprising because,as opposed to the 1BNA molecule, the initial mis-alignment of the two strands creates anumber of mismatched base–base pairs. Therefore, the fact thatthe simulated folding of 3BSE and 2JYK proceeded almost as frequently by the zippering and by the slitheringmechanism probably resulted from low base–base pairing specificityof the model. The snapshot from helix initiation process for 3BSE molecule is shownin Figure 13a). The 3′-end of a complementarystrand made contacts with 3′-end of the leading strand. Besidesthree nonative Watson–Crick contacts (two A/T and one G/C)and two mismatched contacts (G/T and T/T) were established. ThreeWatson–Crick pairs and two mismatched pairs form initial structurefrom which monomers start slithering with respect to each other untilfinal proper double-helix is formed. The helix nucleation occurredbetween nucleotides of 3′-ends but also the mechanisms where3′-end (or 5′-end) of one chain made a contact withmidsection of the other chain were observed.


DNA Duplex Formation with a Coarse-Grained Model.

Maciejczyk M, Spasic A, Liwo A, Scheraga HA - J Chem Theory Comput (2014)

Examples of slitheringpathways of DNA hybridization of (a) 3BSE and (b) 2JYK molecules.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230386&req=5

fig13: Examples of slitheringpathways of DNA hybridization of (a) 3BSE and (b) 2JYK molecules.
Mentions: As can be expected, the zippering mechanism was also observedforlonger molecules, 3BSE and 2JYK.Nevertheless, some trajectories with a slithering folding mechanismwere also recorded. At first, this observation is surprising because,as opposed to the 1BNA molecule, the initial mis-alignment of the two strands creates anumber of mismatched base–base pairs. Therefore, the fact thatthe simulated folding of 3BSE and 2JYK proceeded almost as frequently by the zippering and by the slitheringmechanism probably resulted from low base–base pairing specificityof the model. The snapshot from helix initiation process for 3BSE molecule is shownin Figure 13a). The 3′-end of a complementarystrand made contacts with 3′-end of the leading strand. Besidesthree nonative Watson–Crick contacts (two A/T and one G/C)and two mismatched contacts (G/T and T/T) were established. ThreeWatson–Crick pairs and two mismatched pairs form initial structurefrom which monomers start slithering with respect to each other untilfinal proper double-helix is formed. The helix nucleation occurredbetween nucleotides of 3′-ends but also the mechanisms where3′-end (or 5′-end) of one chain made a contact withmidsection of the other chain were observed.

Bottom Line: Chem. 2010, 31, 1644].Interactions with the solvent and an ionic cloud are approximated by a multipole-multipole Debye-Hückel model.It is the first coarse-grained model, in which both bonded and nonbonded interactions were parametrized ab initio and which folds stable double helices from separated complementary strands, with the final conformation close to the geometry of experimentally determined structures.

View Article: PubMed Central - PubMed

Affiliation: Baker Laboratory of Chemistry, Cornell University , Ithaca, New York 14850, United States ; Department of Physics and Biophysics, Faculty of Food Sciences, University of Warmia and Mazury , 11-041 Olsztyn, Poland.

ABSTRACT
A middle-resolution coarse-grained model of DNA is proposed. The DNA chain is built of spherical and planar rigid bodies connected by elastic virtual bonds. The bonded part of the potential energy function is fit to potentials of mean force of model systems. The rigid bodies are sets of neutral, charged, and dipolar beads. Electrostatic and van der Waals interactions are parametrized by our recently developed procedure [Maciejczyk, M.; Spasic, A.; Liwo, A.; Scheraga, H.A. J. Comp. Chem. 2010, 31, 1644]. Interactions with the solvent and an ionic cloud are approximated by a multipole-multipole Debye-Hückel model. A very efficient R-RATTLE algorithm, for integrating the movement of rigid bodies, is implemented. It is the first coarse-grained model, in which both bonded and nonbonded interactions were parametrized ab initio and which folds stable double helices from separated complementary strands, with the final conformation close to the geometry of experimentally determined structures.

No MeSH data available.


Related in: MedlinePlus