DNA-DNA interaction beyond the ground state

The electrostatic interaction potential between DNA duplexes in solution is a basis for the statistical mechanics of columnar DNA assemblies. It may also play an important role in recombination of homologous genes. We develop a theory of this interaction that includes thermal torsional fluctuations...

Full description

Saved in:
Bibliographic Details
Published in:Physical review. E, Statistical, nonlinear, and soft matter physics Statistical, nonlinear, and soft matter physics, 2004-11, Vol.70 (5 Pt 1), p.051913-051913, Article 051913
Main Authors: Lee, D J, Wynveen, A, Kornyshev, A A
Format: Article
Language:English
Subjects:
Base Pairing
Base Sequence
Binding Sites
Computer Simulation
Crystallization - methods
DNA - analysis
DNA - chemistry
Macromolecular Substances - chemistry
Models, Chemical
Models, Molecular
Models, Statistical
Molecular Sequence Data
Monte Carlo Method
Quantum Theory
Sequence Analysis, DNA - methods
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:The electrostatic interaction potential between DNA duplexes in solution is a basis for the statistical mechanics of columnar DNA assemblies. It may also play an important role in recombination of homologous genes. We develop a theory of this interaction that includes thermal torsional fluctuations of DNA using field-theoretical methods and Monte Carlo simulations. The theory extends and rationalizes the earlier suggested variational approach which was developed in the context of a ground state theory of interaction of nonhomologous duplexes. It shows that the heuristic variational theory is equivalent to the Hartree self-consistent field approximation. By comparison of the Hartree approximation with an exact solution based on the QM analogy of path integrals, as well as Monte Carlo simulations, we show that this easily analytically-tractable approximation works very well in most cases. Thermal fluctuations do not remove the ability of DNA molecules to attract each other at favorable azimuthal conformations, neither do they wash out the possibility of electrostatic "snap-shot" recognition of homologous sequences, considered earlier on the basis of ground state calculations. At short distances DNA molecules undergo a "torsional alignment transition," which is first order for nonhomologous DNA and weaker order for homologous sequences.
ISSN:1539-3755
1550-2376
DOI:10.1103/PhysRevE.70.051913