DNA stretching and multivalent-cation-induced condensation

Mamasakhlisov, Y. Sh.; Todd, Brian A.; Badasyan, Artem; Mkrtchyan, Anna F.; Morozov, V. F.; Parsegian, V. Adrian

doi:10.1103/physreve.80.031915

Cited by 14 publications

(14 citation statements)

References 33 publications

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“…In our one-dimensional continuum description of the DNA molecule, we account for DNA elasticity, DNA-DNA interactions, fluctuations, and configurational entropy in the tails, helices, and toroidal loops. For the description of the toroidal structures, we have added the twist effects to a well-established model (22,23). And for the description of the supercoiled structures, we follow the treatment in Argudo and Purohit (11) including the effects of multivalent cations in the internal energy.…”

Section: Introductionmentioning

confidence: 99%

Competition between Supercoils and Toroids in Single Molecule DNA Condensation

Argudo

Purohit

2012

Biophysical Journal

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The condensation of free DNA into toroidal structures in the presence of multivalent ions and polypeptides is well known. Recent single molecule experiments have shown that condensation into toroids occurs even when the DNA molecule is subjected to tensile forces. Here we show that the combined tension and torsion of DNA in the presence of condensing agents dramatically modifies this picture by introducing supercoiled DNA as a competing structure in addition to toroids. We combine a fluctuating elastic rod model of DNA with phenomenological models for DNA interaction in the presence of condensing agents to compute the minimum energy configuration for given tension and end-rotations. We show that for each tension there is a critical number of end-rotations above which the supercoiled solution is preferred and below which toroids are the preferred state. Our results closely match recent extension rotation experiments on DNA in the presence of spermine and other condensing agents. Motivated by this, we construct a phase diagram for the preferred DNA states as a function of tension and applied end-rotations and identify a region where new experiments or simulations are needed to determine the preferred state.

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Section: Introductionmentioning

confidence: 99%

Competition between Supercoils and Toroids in Single Molecule DNA Condensation

Argudo

Purohit

2012

Biophysical Journal

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“…Following Refs. [23,24] we estimate the free energy of the WLC at a given value of the extending external force f = ql p E s , where q is the effective linear charge density. A similar approach has been developed initially for the end forces.…”

Section: B the Free Energy Change Due To Wlc Stretchingmentioning

confidence: 99%

Long charged macromolecule in an entropic trap with rough surfaces

Mamasakhlisov

Hayryan²,

Hu³

2012

Phys. Rev. E

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The kinetics of the flux of a charged macromolecular solution through an environment of changing geometry with wide and constricted regions is investigated analytically. A model device consisting of alternating deep and shallow slits known as an "entropic trap" is used to represent the environment. The flux is supported by the external electrostatic field. The "wormlike chain" model is used for the macromolecule (dsDNA in the present study). The chain entropy in both the deep and the shallow slits, the work by the electric field, and the energy of the elastic bending of the chain are taken into account accurately. Based on the calculated free energy, the kinetics and the scaling behavior of the chain escaping from the entropic trap are studied. We find that the escape process occurs in two kinetic stages with different time scales and discuss the possible influence of the surface roughness. The scope of the accuracy of the proposed model is discussed.

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“…We investigate the conditions affecting the orientational order formation of short double-strand DNA fragments, immersed in the flexible polymer. It is shown that short double-strand DNA fragments exhibit the formation of a liquid crystalline ordered phase, in dependence on the value of the Flory-Huggins parameter, aspect ratio , and the attraction energy (Mamasakhlisov et al, 2009;Todd et al, 2008) Metropolis Monte Carlo method based on the extended cluster approach (Danilov, Dailidonis, van Mourik, & Fruchtl, 2011a, 2011bDailidonis, Danilov, Früchtl, & van Mourik, 2011) is used to investigate adenine-adenine (AA), guanine-guanine (GG), thymine-thymine (TT), and cytosine-cytosine (CC) homoassociates in a cluster consisting of 400 water molecules. The starting structures taken were AA N(7) amino symmetric, TT N (3) -O(4) symmetric, GG N(1) -O(6) symmetric, and CC N(3) amino symmetric base pairs.…”

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confidence: 99%