DNA bending through large angles is aided by ionic screening

Justin Spiriti, Hiqmet Kamberaj, Adam M R De Graff, Michael Thorpe, Arjan Van Der Vaart

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

We used adaptive umbrella sampling on a modified version of the roll angle to simulate the bending of DNA dodecamers. Simulations were carried out with the AMBER and CHARMM force fields for 10 sequences in which the central base pair step was varied. On long length scales, the DNA behavior was found to be consistent with the worm-like chain model. Persistence lengths calculated directly from the simulated structures and indirectly through the use of sequence-independent coarse-grained models based on simulation data were similar to literature values. On short length scales, the free energy cost of bending DNA was found to be consistent with the worm-like chain model for small and intermediate bending angles. At large angles, the bending free energy as a function of the roll angle became linear, suggesting a relative increase in flexibility at larger roll angles. Counterions congregated on the concave side of the highly bent DNA and screened the repulsion of the phosphate groups, facilitating the bending.

Original languageEnglish (US)
Pages (from-to)2145-2156
Number of pages12
JournalJournal of Chemical Theory and Computation
Volume8
Issue number6
DOIs
StatePublished - Jun 12 2012

Fingerprint

Screening
DNA
screening
deoxyribonucleic acid
worms
Free energy
free energy
data simulation
Phosphates
field theory (physics)
Sampling
phosphates
flexibility
sampling
costs
Costs
simulation

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications

Cite this

Spiriti, J., Kamberaj, H., De Graff, A. M. R., Thorpe, M., & Van Der Vaart, A. (2012). DNA bending through large angles is aided by ionic screening. Journal of Chemical Theory and Computation, 8(6), 2145-2156. https://doi.org/10.1021/ct300177r

DNA bending through large angles is aided by ionic screening. / Spiriti, Justin; Kamberaj, Hiqmet; De Graff, Adam M R; Thorpe, Michael; Van Der Vaart, Arjan.

In: Journal of Chemical Theory and Computation, Vol. 8, No. 6, 12.06.2012, p. 2145-2156.

Research output: Contribution to journalArticle

Spiriti, J, Kamberaj, H, De Graff, AMR, Thorpe, M & Van Der Vaart, A 2012, 'DNA bending through large angles is aided by ionic screening', Journal of Chemical Theory and Computation, vol. 8, no. 6, pp. 2145-2156. https://doi.org/10.1021/ct300177r
Spiriti J, Kamberaj H, De Graff AMR, Thorpe M, Van Der Vaart A. DNA bending through large angles is aided by ionic screening. Journal of Chemical Theory and Computation. 2012 Jun 12;8(6):2145-2156. https://doi.org/10.1021/ct300177r
Spiriti, Justin ; Kamberaj, Hiqmet ; De Graff, Adam M R ; Thorpe, Michael ; Van Der Vaart, Arjan. / DNA bending through large angles is aided by ionic screening. In: Journal of Chemical Theory and Computation. 2012 ; Vol. 8, No. 6. pp. 2145-2156.
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