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

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

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

fig12: Snapshots of trajectory of a slithering mechanism of thefoldingprocess of the Drew–Dickerson dodecamer.

Mentions: A different and less common folding process (65 of 158 trajectories)is shown in Figure 12. It was started fromtwo separated ssDNA chains, which were heated to 600 K and, after0.3 ns (T = 500 K), evolved into a completely randomconformation. First, contacts between the bases of the 5′-endsof the chains were established after 0.49 ns. It should be noted thatthese are non-native Watson–Crick G/C contacts. After that,the chains started to slide with respect to each other along a Watson–Crickinterface. After 0.89 ns, two G/C contacts were estabilished but alsoA/C and A/G mismatched pairs were formed. A 1.4 ns snapshot showsa molecule with 10 contacts established and with distorted termini.After 1.7 ns a full helix with all native base–base contactswas formed. This type of folding mechanism is referred to as slithering.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 slithering mechanism of thefoldingprocess of the Drew–Dickerson dodecamer.
© Copyright Policy
Related In: Results  -  Collection

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

fig12: Snapshots of trajectory of a slithering mechanism of thefoldingprocess of the Drew–Dickerson dodecamer.
Mentions: A different and less common folding process (65 of 158 trajectories)is shown in Figure 12. It was started fromtwo separated ssDNA chains, which were heated to 600 K and, after0.3 ns (T = 500 K), evolved into a completely randomconformation. First, contacts between the bases of the 5′-endsof the chains were established after 0.49 ns. It should be noted thatthese are non-native Watson–Crick G/C contacts. After that,the chains started to slide with respect to each other along a Watson–Crickinterface. After 0.89 ns, two G/C contacts were estabilished but alsoA/C and A/G mismatched pairs were formed. A 1.4 ns snapshot showsa molecule with 10 contacts established and with distorted termini.After 1.7 ns a full helix with all native base–base contactswas formed. This type of folding mechanism is referred to as slithering.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