DNA curvature and flexibility<i>in vitro</i>and<i>in vivo</i>

Peters, Justin P.; Maher, L. James

doi:10.1017/s0033583510000077

Cited by 212 publications

(289 citation statements)

References 236 publications

(393 reference statements)

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“…Although this possibility was raised nearly 20 years ago 8 , there has been no direct experimental evidence to date. Importantly, support for such a model must be made quantitatively, because DNA loop formation makes explicit predictions on the loop size distribution [23][24][25][26] and thus the nucleosome transfer distance distribution. Transfer distances below 200 bp are energetically unfavourable as the persistence length of DNA is B150 bp, thus prohibiting the formation of small loops.…”

Section: Resultsmentioning

confidence: 99%

DNA Looping Mediates Nucleosome Transfer

Brennan

Forties²,

Patel

et al. 2017

Biophysical Journal

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Proper cell function requires preservation of the spatial organization of chromatin modifications. Maintenance of this epigenetic landscape necessitates the transfer of parental nucleosomes to newly replicated DNA, a process that is stringently regulated and intrinsically linked to replication fork dynamics. This creates a formidable setting from which to isolate the central mechanism of transfer. Here we utilized a minimal experimental system to track the fate of a single nucleosome following its displacement, and examined whether DNA mechanics itself, in the absence of any chaperones or assembly factors, may serve as a platform for the transfer process. We found that the nucleosome is passively transferred to available dsDNA as predicted by a simple physical model of DNA loop formation. These results demonstrate a fundamental role for DNA mechanics in mediating nucleosome transfer and preserving epigenetic integrity during replication.

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Section: Resultsmentioning

confidence: 99%

DNA Looping Mediates Nucleosome Transfer

Brennan

Forties²,

Patel

et al. 2017

Biophysical Journal

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“…Long double stranded DNA behaves as a continuous elastic rod with bending deformations described by the harmonic worm-like chain (WLC) model [1][2][3]. In many biological processes the DNA flexibility, notably its ability to wrap around proteins, plays a key role, therefore, the bendability of DNA is actively studied [4][5][6]. Recent experimental data indicate that the WLC model significantly underestimates the probability of strong bends on length scales shorter than the persistence length (l b =50nm) [7][8][9][10][11][12].…”

Section: Mounir Maaloummentioning

confidence: 99%

DNA Flexibility on Short Length Scales Probed by Atomic Force Microscopy

Mazur

Maaloum

2014

Phys. Rev. Lett.

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Unusually high bending flexibility has been recently reported for DNA on short length scales. We use atomic force microscopy (AFM) in solution to obtain a direct estimate of DNA bending statistics for scales down to one helical turn. It appears that DNA behaves as a Gaussian chain and is well described by the worm-like chain model at length scales beyond 3 helical turns (10.5nm). Below this threshold, the AFM data exhibit growing noise because of experimental limitations. This noise may hide small deviations from the Gaussian behavior, but they can hardly be significant.

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“…1 Mechanically, double-stranded (ds) DNA is a stiff chain molecule having the persistence length of about 50 nm or 150 bp. In a living cell, it is often tightly bent on nanometer scales for biological functions; [2][3][4] for example, in a nucleosome, a pivotal element for DNA packing in a nucleus is wrapped around proteins of about 10 nm size called histones; it can loop over a length of 10 nm mediated by transcription factors for gene regulation. 5 According to the worm-like chain (WLC) model, 6 in which the dsDNA is treated as an elastic rod, it is energetically improbable for the DNA to bend over the length scales much shorter than the persistence length.…”

Section: Introductionmentioning

confidence: 99%

How a short double-stranded DNA bends

Shin

Lee

Sung

2015

The Journal of Chemical Physics

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A recent experiment using fluorescence microscopy showed that double-stranded DNA fragments shorter than 100 base pairs loop with the probabilities higher by the factor of 10 2 -10 6 than predicted by the worm-like chain (WLC) model [R. Vafabakhsh and T. Ha, Science 337, 1101(2012)]. Furthermore, the looping probabilities were found to be nearly independent of the loop size. The results signify a breakdown of the WLC model for DNA mechanics which works well on long length scales and calls for fundamental understanding for stressed DNA on shorter length scales. We develop an analytical, statistical mechanical model to investigate what emerges to the short DNA under a tight bending. A bending above a critical level initiates nucleation of a thermally induced bubble, which could be trapped for a long time, in contrast to the bubbles in both free and uniformly bent DNAs, which are either transient or unstable. The trapped bubble is none other than the previously hypothesized kink, which releases the bending energy more easily as the contour length decreases. It leads to tremendous enhancement of the cyclization probabilities, in a reasonable agreement with experiment. C 2015 AIP Publishing LLC. [http://dx

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DNA curvature and flexibilityin vitroandin vivo

Cited by 212 publications

References 236 publications

DNA Looping Mediates Nucleosome Transfer

DNA Looping Mediates Nucleosome Transfer

DNA Flexibility on Short Length Scales Probed by Atomic Force Microscopy

How a short double-stranded DNA bends

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