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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

Typical configurations of HET60DS (left panel),HET60SS within nearest-neighbor approximation (middle panel)andHET60SS for full physics-based model (right panel).
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fig6: Typical configurations of HET60DS (left panel),HET60SS within nearest-neighbor approximation (middle panel)andHET60SS for full physics-based model (right panel).

Mentions: Persistence lengthsof both HETSS and HETDS were computed from 0.1μs canonicalsimulations at 300 K with 145 mM salt concentration for both fullPB and simplified NN model. The results are presented in Table 9. For both chains PB model produces smaller persistencelengths than NN model, although the relative difference is much biggerfor ssDNA. This behavior is expected, because switching off some ofthe intrastrand base–base interactions should decrease bendingof the chain, especially for ssDNA, in which bases are exposed tosolvent and can easily form intrastrand hairpins with complementarybases. Figure 6 presents typical configurationsof HET60SS and HET60DS molecules taken from T = 300 K canonical simulation. The conformation of ssDNAtaken from full PB model simulation differs significantly from theone taken from NN approximation. The ssDNA obtained from full PB modelbends and forms hairpins, which can act as kinetic traps in the foldingprocess of dsDNA.


DNA Duplex Formation with a Coarse-Grained Model.

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

Typical configurations of HET60DS (left panel),HET60SS within nearest-neighbor approximation (middle panel)andHET60SS for full physics-based model (right panel).
© Copyright Policy
Related In: Results  -  Collection

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

fig6: Typical configurations of HET60DS (left panel),HET60SS within nearest-neighbor approximation (middle panel)andHET60SS for full physics-based model (right panel).
Mentions: Persistence lengthsof both HETSS and HETDS were computed from 0.1μs canonicalsimulations at 300 K with 145 mM salt concentration for both fullPB and simplified NN model. The results are presented in Table 9. For both chains PB model produces smaller persistencelengths than NN model, although the relative difference is much biggerfor ssDNA. This behavior is expected, because switching off some ofthe intrastrand base–base interactions should decrease bendingof the chain, especially for ssDNA, in which bases are exposed tosolvent and can easily form intrastrand hairpins with complementarybases. Figure 6 presents typical configurationsof HET60SS and HET60DS molecules taken from T = 300 K canonical simulation. The conformation of ssDNAtaken from full PB model simulation differs significantly from theone taken from NN approximation. The ssDNA obtained from full PB modelbends and forms hairpins, which can act as kinetic traps in the foldingprocess of dsDNA.

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