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Dynamic studies of the unwinding of a DNA‐like strand
Author(s) -
Ree Francis H.,
Chay Teresa Ree
Publication year - 1972
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.1972.360110505
Subject(s) - brownian dynamics , brownian motion , inverse , helix (gastropod) , chemistry , cylinder , work (physics) , physics , langevin dynamics , amplitude , statistical physics , classical mechanics , quantum mechanics , geometry , mathematics , ecology , snail , biology
Following Simon and Zimm's recent work, both molecular dynamic and Monte Carlo methods are used to simulate on a computer the unwinding of a DNA‐like ( N + 1)‐unit helical strand. The strand unwinding is assumed to obey ( N + 1)‐coupled Langevin equations of motion ( N = 10–50). The present computer “experiment” was done to elaborate dependence of unwinding behavior of the helix upon (i) configurations of its complementary strand [represented here by a square cylinder (Simon‐Zimm model), a circular cylinder, and a fixed helix (double‐helical model)]; (ii) interstrand potentials (a hard‐cylinder potential, an inverse twelfth‐power soft repulsion with or without an inverse third‐power attractive tail); (iii) amplitudes of the Brownian motions, and (iv) the molecular weights of the unwinding strand. We found that (i) the Brownian motions strongly couple with the interstrand potentials to produce a shorter “unwinding time” (τ 0 ) (which characterizes an expotential decay of the unwinding) for a longer renged repulsive potential (without the Brownian motions, no such effect was present); (ii) addition of an attractive tail to the repulsive potentials further reinforces the unwinding, thereby giving a reduced value of τ 0 ; (iii) τ 0 can be expressed as a product of two factors–unwinding time for a one‐dimensional spring‐bead model, which mostly accounts for the N 2 ‐dependence in τ 0 , and a factor which depends on the Brownian motions and the interstrand potentials; (iv) among the three models described above, under similar situations, the three‐dimensional double‐helical model has the smallest τ 0 ; and (v) unless the maximum Brownian displacement exceeds a certain value, the unwinding around a square cylinder takes place in a (unrealistic) stair‐step manner whose τ 0 decreases with increase in the Brownian displacements. The N 2 ‐dependence of τ 0 agrees with the Simon and Zimm's machine results as well as Crother's experimental data on T2 DNA; however, it contradicts experimental data of Massie and Zimm, and others. Further possible improvements in connection with the computer simulation are suggested.