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The "sugar" coarse-grained DNA model.

N A Kovaleva1, I P Koroleva Kikot2, M A Mazo2

  • 1N.N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow, 119991, Russia. natkov@polymer.chph.ras.ru.

Journal of Molecular Modeling
|February 11, 2017
PubMed
Summary

A new coarse-grained DNA model captures ribose flexibility, accurately simulating B-DNA and A-DNA forms and their transitions. This advances DNA nanotechnology and biophysics simulations.

Keywords:
Coarse grainingDNAPhase transition

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Area of Science:

  • Computational Biology
  • Biophysics
  • Nanotechnology

Background:

  • Over 20 coarse-grained (CG) DNA models exist for simulations.
  • Existing models fail to reproduce DNA polymorphism due to ribose ring conformational changes.
  • Ribose flexibility is crucial for DNA local deformability and B- to A-form transitions.

Purpose of the Study:

  • To develop a CG DNA model that includes ribose conformational flexibility.
  • To accurately represent DNA polymorphism and B- to A-form transitions.

Main Methods:

  • Developed a "sugar" CG DNA model with six sites per nucleotide.
  • Derived CG interaction potentials using a "bottom-up" approach with the AMBER force field.
  • Incorporated explicit ions and sequence dependence into the model.

Main Results:

  • The model requires novel non-harmonic and three-particle potentials for ribose flexibility.
  • The CG model successfully reproduces both B-DNA and A-DNA forms.
  • The model demonstrates reversible A to B and B to A phase transitions.

Conclusions:

  • The proposed CG DNA model accurately captures essential DNA polymorphism.
  • This model enables the simulation of B- to A-form transitions crucial for biological interactions and nanotechnology.
  • The model provides a more realistic representation of DNA behavior in simulations.