DNA-DNA interaction beyond the ground state

D. J. Lee, A. Wynveen, A. A. Kornyshev

Research output: Contribution to journalArticlepeer-review

23 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)12
Number of pages1
JournalPhysical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics
Issue number5
StatePublished - 2004

Bibliographical note

Funding Information:
Numerous discussions with Dr. S. Leikin are gratefully acknowledged. This work was made possible via the Royal Society Wolfson Research Merit Grant to A.A.K. and the EPSRC Grant No. GR/S31068/01.


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