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Sedimentation coefficients of DNA topoisomers: The helical wormlike chain
Author(s) -
Shimada Jiro,
Yamakawa Hiromi
Publication year - 1988
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.360270410
Subject(s) - chain (unit) , monte carlo method , chemistry , function (biology) , cylinder , helix (gastropod) , sedimentation coefficient , sedimentation , dna , tensor (intrinsic definition) , physics , molecular physics , geometry , mathematics , quantum mechanics , statistics , geology , sediment , paleontology , biochemistry , evolutionary biology , snail , biology , enzyme
The sedimentation coefficient s N of the DNA topoisomer with the linking number N is evaluated as a function of N and chain length on the basis of a (circular) twisted wormlike chain, i.e., a special case of the helical wormlike chain. Evaluation is carried out by an application of the Oseen–Burgers procedure of hydrodynamics to the cylinder model with the preaveraged Oseen tensor. The necessary mean reciprocal distance between two contour points is obtained by a Monte Carlo method. It is shown that s N increases as |Δ N | is increased from 0 in the range of small |Δ N |, where Δ N = N − N , with N the number of helix turns in the linear DNA chain in the undeformed state. It is found that there is semiquantitative agreement between the Monte Carlo values and the experimental data obtained by Wang for s N .