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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

Snapshots of trajectory of a zippering mechanism of thefoldingprocess of the Drew–Dickerson dodecamer.
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fig11: Snapshots of trajectory of a zippering mechanism of thefoldingprocess of the Drew–Dickerson dodecamer.

Mentions: The representative of the first most common mechanism(93 of 158trajectories) is shown in Figure 11. Two separatedchains (0 ns) were heated to 600 K and evolved into random chains(0.11 ns, T = 550 K). At 0.56 ns (T = 350 K) the 5′-GCGC-end established native contacts withthe complementary 3′-CGCG-end, and since then, more nativecontacts were formed, and the dsDNA molecule was zipped. At 0.68 ns,all native Watson–Crick hydrogen bonds were formed. This typeof folding mechanism is referred to as zippering.31


DNA Duplex Formation with a Coarse-Grained Model.

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

Snapshots of trajectory of a zippering mechanism of thefoldingprocess of the Drew–Dickerson dodecamer.
© Copyright Policy
Related In: Results  -  Collection

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

fig11: Snapshots of trajectory of a zippering mechanism of thefoldingprocess of the Drew–Dickerson dodecamer.
Mentions: The representative of the first most common mechanism(93 of 158trajectories) is shown in Figure 11. Two separatedchains (0 ns) were heated to 600 K and evolved into random chains(0.11 ns, T = 550 K). At 0.56 ns (T = 350 K) the 5′-GCGC-end established native contacts withthe complementary 3′-CGCG-end, and since then, more nativecontacts were formed, and the dsDNA molecule was zipped. At 0.68 ns,all native Watson–Crick hydrogen bonds were formed. This typeof folding mechanism is referred to as zippering.31

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