Theory of the influence of changes in salt concentration on the configuration of intrinsically curved, impenetrable, rod-like structures modeling DNA minicircles

Biton, Yoav Y.; Coleman, Bernard D.

doi:10.1016/j.ijnonlinmec.2010.05.004

Cited by 8 publications

(21 citation statements)

References 23 publications

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“…However, Manning et al studied the effect of electrostatic repulsion of the phosphate groups on the flexibility of DNA and considered it to be the dominant factor (38). Biton et al have developed a more complete theoretical model of DNA that considers both the elasticity and the electrostatic interactions and have nicely shown the effect of NaCl concentration on the structure of a 549 bp DNA minicircle (41). In a recent article, Savelyev et al suggested that both elasticity and electrostatics contribute equally to the flexibility of DNA in the presence of monovalent ions (42).…”

Section: Mean-square Excursion Versus [Kcl]mentioning

confidence: 99%

Enhanced Tethered-Particle Motion Analysis Reveals Viscous Effects

Kumar

Manzo

Zurla

et al. 2014

Biophysical Journal

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Tethered-particle motion experiments do not require expensive or technically complex hardware, and increasing numbers of researchers are adopting this methodology to investigate the topological effects of agents that act on the tethering polymer or the characteristics of the polymer itself. These investigations depend on accurate measurement and interpretation of changes in the effective length of the tethering polymer (often DNA). However, the bead size, tether length, and buffer affect the confined diffusion of the bead in this experimental system. To evaluate the effects of these factors, improved measurements to calibrate the two-dimensional range of motion (excursion) versus DNA length were carried out. Microspheres of 160 or 240 nm in radius were tethered by DNA molecules ranging from 225 to 3477 basepairs in length in aqueous buffers containing 100 mM potassium glutamate and 8 mM MgCl2 or 10 mM Tris-HCl and 200 mM KCl, with or without 0.5% Tween added to the buffer, and the motion was recorded. Different buffers altered the excursion of beads on identical DNA tethers. Buffer with only 10 mM NaCl and >5 mM magnesium greatly reduced excursion. Glycerol added to increase viscosity slowed confined diffusion of the tethered beads but did not change excursion. The confined-diffusion coefficients for all tethered beads were smaller than those expected for freely diffusing beads and decreased for shorter tethers. Tethered-particle motion is a sensitive framework for diffusion experiments in which small beads on long leashes most closely resemble freely diffusing, untethered beads.

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Section: Mean-square Excursion Versus [Kcl]mentioning

confidence: 99%

Enhanced Tethered-Particle Motion Analysis Reveals Viscous Effects

Kumar

Manzo

Zurla

et al. 2014

Biophysical Journal

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“…Our theoretical model is based on the familiar naturally discrete model for DNA elasticity [23] , [34] , [28] in which the intramolecular electrostatic interactions and their dependence on the ionic strength in the aqueous media are taken into account [28] , [33] . In our simulations of TPM experiments all the excluded volume effects such as the impenetrability of the DNA molecule, the bead, and the plate, are taken into account.…”

Section: Methodsmentioning

confidence: 99%

“…We here employ the theory presented in [23] , [28] , [33] , in which the energy of a DNA molecule with base pairs is determined when there is given, for each , both the location of the barycenter of the -th base pair and an orthonormal triad that is embedded in the base pair as shown in Figure 1 . The total energy, , of a DNA configuration is taken to be the sum of elastic energy and electrostatic energy , …”

Section: Methodsmentioning

confidence: 99%

“…This algorithm utilizes explicit expression for the Jacobian of the mapping between DNA deformational parameters and end-to-end conditions, derived in [33], and successfully overcomes a significant difficulty: applying reversible perturbations that preserve the given geometric constraints. This scheme differs from other Monte Carlo schemes utilizing local perturbations such as the crankshaft move and global perturbations such as the slithering move, introduced in [29], which cannot be used for a non-homogenous sequences and are limited for circularized molecules or molecules subject to fully clamped end conditions.…”

Section: Introductionmentioning

confidence: 99%

“…In this paper we describe a new Metropolis Monte Carlo algorithm which enables us to generate large canonical ensembles of DNA configurations subject to any composition of geometric and topological constraints, including looped configurations of given topology, closed configurations, and configurations with preassigned end-to-end (or, more generally, site-to-site) distance. This algorithm utilizes explicit expression for the Jacobian of the mapping between DNA deformational parameters and end-to-end conditions, derived in [33] , and successfully overcomes a significant difficulty: applying reversible perturbations that preserve the given geometric constraints. This scheme differs from other Monte Carlo schemes utilizing local perturbations such as the crankshaft move and global perturbations such as the slithering move, introduced in [29] , which cannot be used for a non-homogenous sequences and are limited for circularized molecules or molecules subject to fully clamped end conditions.…”

Section: Introductionmentioning

confidence: 99%

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Lac Repressor Mediated DNA Looping: Monte Carlo Simulation of Constrained DNA Molecules Complemented with Current Experimental Results

et al. 2014

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Tethered particle motion (TPM) experiments can be used to detect time-resolved loop formation in a single DNA molecule by measuring changes in the length of a DNA tether. Interpretation of such experiments is greatly aided by computer simulations of DNA looping which allow one to analyze the structure of the looped DNA and estimate DNA-protein binding constants specific for the loop formation process. We here present a new Monte Carlo scheme for accurate simulation of DNA configurations subject to geometric constraints and apply this method to Lac repressor mediated DNA looping, comparing the simulation results with new experimental data obtained by the TPM technique. Our simulations, taking into account the details of attachment of DNA ends and fluctuations of the looped subsegment of the DNA, reveal the origin of the double-peaked distribution of RMS values observed by TPM experiments by showing that the average RMS value for anti-parallel loop types is smaller than that of parallel loop types. The simulations also reveal that the looping probabilities for the anti-parallel loop types are significantly higher than those of the parallel loop types, even for loops of length 600 and 900 base pairs, and that the correct proportion between the heights of the peaks in the distribution can only be attained when loops with flexible Lac repressor conformation are taken into account. Comparison of the in silico and in vitro results yields estimates for the dissociation constants characterizing the binding affinity between O1 and Oid DNA operators and the dimeric arms of the Lac repressor.

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A singularity free approach for Kirchhoff rods having uniformly distributed electrostatic charge

Singh

Kumar

2020

Computer Methods in Applied Mechanics and Engineering

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Theory of the influence of changes in salt concentration on the configuration of intrinsically curved, impenetrable, rod-like structures modeling DNA minicircles

Cited by 8 publications

References 23 publications

Enhanced Tethered-Particle Motion Analysis Reveals Viscous Effects

Enhanced Tethered-Particle Motion Analysis Reveals Viscous Effects

Lac Repressor Mediated DNA Looping: Monte Carlo Simulation of Constrained DNA Molecules Complemented with Current Experimental Results

A singularity free approach for Kirchhoff rods having uniformly distributed electrostatic charge

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