Structure of DNA Coils in Dilute and Semidilute Solutions

Nepal, Manish; Yaniv, Alon; Shafran, Eyal; Krichevsky, Oleg

doi:10.1103/physrevlett.110.058102

Cited by 18 publications

(31 citation statements)

References 26 publications

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“…Moreover, the length at which the divergence away from the WLC behavior occurs (the length where the dashed green and dotted red lines separate) is highly dependent on the width parameter w b . This result is consistent with experimental observations [10] and simulation [12].…”

Section: A Dna End-to-end Distance Analysis and Comparison To Rg Ressupporting

confidence: 93%

“…Since DNA is anisotropic with an effective aspect ratio that is estimated to be in the range of 0.03 − 0.09 [11], the power-law exponent for the endto-end distance of DNA was predicted [12] to not deviate substantially from the Gaussian chain prediction for lengths as high as ∼100 kb. This prediction was recently confirmed experimentally, showing a radius of gyration power-law of 0.52 ± 0.02 [10], that is very close to the Gaussian chain prediction of 0.5.…”

Section: Introductionsupporting

confidence: 79%

“…At large lengths, dsDNA becomes a swollen chain due to excluded volume effects that emerge from the inability of DNA to cross itself [2,8]. A recent set of theoretical studies [9,10] showed that the DNA length, at which the transition from the ideal to the swollen chain occurs is highly dependent on the effective aspect ratio of DNA, which we define as the ratio of the effective width or cross-section of DNA w to the Kuhn length b. As w b → 0, the DNA transition length becomes larger, which implies that the polymer behaves * Also at Russell Berrie Nanotechnology Institute, Technion † roeeamit@technion.ac.il; Also at Russell Berrie Nanotechnology Institute, Technion like an ideal chain for an ever increasing length.…”

Section: Introductionmentioning

confidence: 99%

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Self-avoiding wormlike chain model for double-stranded-DNA loop formation

2014

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We compute for the first time the effects of excluded volume on the probability for double-stranded DNA to form a loop. We utilize a Monte-Carlo algorithm for generation of large ensembles of selfavoiding worm-like chains, which are used to compute the J-factor for varying lengthscales. In the entropic regime, we confirm the scaling-theory prediction of a power-law drop off of −1.92, which is significantly stronger than the −1.5 power-law predicted by the non-self-avoiding worm-like chain model. In the elastic regime, we find that the angle-independent end-to-end chain distribution is highly anisotropic. This anisotropy, combined with the excluded volume constraints, lead to an increase in the J-factor of the self-avoiding worm-like chain by about half an order of magnitude relative to its non-self-avoiding counterpart. This increase could partially explain the anomalous results of recent cyclization experiments, in which short dsDNA molecules were found to have an increased propensity to form a loop.

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Section: A Dna End-to-end Distance Analysis and Comparison To Rg Ressupporting

confidence: 93%

Section: Introductionsupporting

confidence: 79%

Section: Introductionmentioning

confidence: 99%

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Self-avoiding wormlike chain model for double-stranded-DNA loop formation

2014

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“…The weak excluded volume interactions, at high salt, are in agreement with the ideal chain behavior for DNA < 100 kbp in solution (33)(34)(35) but disagree with the observed self-avoiding scaling R ∝ N 3/5 in DNA (36,37).…”

Section: Discussionmentioning

confidence: 42%

Entropy-driven collective interactions in DNA brushes on a biochip

Bracha

Karzbrun

Shemer

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Cell-free gene expression in localized DNA brushes on a biochip has been shown to depend on gene density and orientation, suggesting that brushes form compartments with partitioned conditions. At high density, the interplay of DNA entropic elasticity, electrostatics, and excluded volume interactions leads to collective conformations that affect the function of DNA-associated proteins. Hence, measuring the collective interactions in dense DNA, free of proteins, is essential for understanding crowded cellular environments and for the design of cell-free synthetic biochips. Here, we assembled dense DNA polymer brushes on a biochip along a density gradient and directly measured the collective extension of DNA using evanescent fluorescence. DNA of 1 kbp in a brush undergoes major conformational changes, from a relaxed random coil to a stretched configuration, following a universal function of density to ionic strength ratio with scaling exponent of 1/3. DNA extends because of the swelling force induced by the osmotic pressure of ions, which are trapped in the brush to maintain local charge neutrality, in competition with the restoring force of DNA entropic elasticity. The measurements reveal in DNA crossover between regimes of osmotic, salted, mushroom, and quasineutral brush. It is surprising to note that, at physiological ionic strength, DNA density does not induce collective stretch despite significant chain overlap, which implies that excluded volume interactions in DNA are weak.DNA biophysics | synthetic biology D ouble-helix DNA polymers exhibit relaxed random-walk configurations at lengths beyond the persistence scale l p = 50 nm, occupying volume to maximize their entropy. Unfolding DNA entropic degrees of freedom to full contour-length stretch requires large forces of 500 k B T/l p (50 pN) using a force-extension apparatus (1, 2). However, the transition of DNA into an ordered stretched state can also result from an entropy increase in a coupled system when chains experience significant overlap. Such is the case of polymer brushes where individual polymers stretch to minimize the free energy of the brush (3). For charged polymers, such as DNA, the collective extension also increases the mixing entropy of the ions that are trapped within the brush to maintain local charge neutrality (4-7).In the past two decades, DNA brushes have become useful in a range of applications such as next-generation sequencing (8, 9), hybridization arrays (10-14), protein biosynthesis compartments (15-18), and coated particle assembly (19,20). The utility of the diverse DNA-based reactions carried out in such brushes requires an in-depth understanding of their basic materials properties. To date, the focus has been on short DNA brushes (∼100 bp) (21, 22) having negligible polymer degrees of freedom. The compression of a few kilobase-pair DNA brushes on beads, as deduced from optical trapping force measurement and Brownian motion analysis (23, 24), was shown to behave as a power of −1/3 with ionic strength. For flexible polyelectrol...

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“…For instance, some authors have claimed that even a very long molecule like λ-DNA is “ideal”, being too short and stiff to experience excluded volume interactions. 2,7 However other studies suggest that excluded volume interactions indeed have an impact at similar contour lengths. 8–10 Further confounding the issue, the oft-cited measurements of the diffusion coefficient of concatamers of λ-DNA by Smith et al 11 suggested that dsDNA had already reached a universal limit.…”

Section: Introductionmentioning

confidence: 99%

Is DNA a Good Model Polymer?

et al. 2013

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The details surrounding the cross-over from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular weight, focusing on persistence lengths and effective widths that represent single-stranded and double-stranded DNA in a high ionic strength buffer. To do so, we use a chain-growth Monte Carlo algorithm, the Pruned-Enriched Rosenbluth Method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties of wormlike chains over an extremely large range of contour lengths. From our calculations, we find that very large DNA chains (≈ 1,000,000 base pairs depending on the choice of size metric) are required to reach flexible, swollen non-draining coils. Furthermore, our results indicate that the commonly used model polymer λ-DNA (48,500 base pairs) does not exhibit “ideal” scaling, but exists in the middle of the transition to long-chain behavior. We subsequently conclude that typical DNA used in experiments are too short to serve as an accurate model of long-chain, universal polymer behavior.

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Structure of DNA Coils in Dilute and Semidilute Solutions

Cited by 18 publications

References 26 publications

Self-avoiding wormlike chain model for double-stranded-DNA loop formation

Self-avoiding wormlike chain model for double-stranded-DNA loop formation

Entropy-driven collective interactions in DNA brushes on a biochip

Is DNA a Good Model Polymer?

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