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Modeling of long‐range electrostatic interactions in DNA
Author(s) -
Vologodskii Alexander,
Cozzarelli Nicholas
Publication year - 1995
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360350304
Subject(s) - chemistry , range (aeronautics) , electrostatic interaction , electrostatics , dna , chemical physics , nanotechnology , biophysics , computational chemistry , biochemistry , aerospace engineering , biology , engineering , materials science
We used a Monte Carlo approach to compute the statistical properties of closed DNA chains with different descriptions of the electrostatic interactions. We compared these computed results with experimentally measured knotting probabilities, which are very sensitive to intersegment interactions. The calculated results based on the Debye‐Hückel approximation of the solution of the Poisson‐Boltzmann equation agreed very well with the published experimental data, while potential based on counterion condensation theory was clearly less satisfactory. We then compared the simpler hard‐core approximation of electrostatic interactions to the Debye‐Hückel potential. The hard‐core approximation, specified in terms of a DNA effective diameter, gives the same conformational properties of random coils as the Debye‐Hückel approximation. We found clear but relatively small differences between the two potentials for the conformational properties of supercoiled DNA. © 1995 John Wiley & Sons, Inc.