Fluctuations of a long, semiflexible polymer in a narrow channel

Burkhardt, Theodore W.; Yang, Yingzi; Gompper, Gerhard

doi:10.1103/physreve.82.041801

Cited by 75 publications

(142 citation statements)

References 25 publications

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“…The variance exhibits linear behavior over the central portion of the plot, consistent with the polymer models for confinement. 16,32,35 There is some deviation at the smaller molecular weights, which we can attribute to the difficulty in accurately measuring small distances between labels and the systematic error introduced by 250 bp bins for small molecular weights, and scatter at higher molecular weights, which arises from the sampling error (even after binning the data). It is possible that the deviation from linearity at smaller distances is physically relevant, since simulations clearly indicate that the asymptotic scaling for the variance in extension is not achieved until the chain is long enough, of the order of 185 kbp, and that the variance increases sub-linearly with molecular weight for small molecular weights.…”

Section: Resultsmentioning

confidence: 99%

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Reinhart

Reifenberger

Gupta

et al. 2015

The Journal of Chemical Physics

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We obtained experimental extension data for barcoded E. coli genomic DNA molecules confined in nanochannels from 40 nm to 51 nm in width. The resulting data set consists of 1 627 779 measurements of the distance between fluorescent probes on 25 407 individual molecules. The probability density for the extension between labels is negatively skewed, and the magnitude of the skewness is relatively insensitive to the distance between labels. The two Odijk theories for DNA confinement bracket the mean extension and its variance, consistent with the scaling arguments underlying the theories. We also find that a harmonic approximation to the free energy, obtained directly from the probability density for the distance between barcode labels, leads to substantial quantitative error in the variance of the extension data. These results suggest that a theory for DNA confinement in such channels must account for the anharmonic nature of the free energy as a function of chain extension. C 2015 AIP Publishing LLC. [http://dx

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Section: Resultsmentioning

confidence: 99%

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Reinhart

Reifenberger

Gupta

et al. 2015

The Journal of Chemical Physics

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“…Although there are challenges in using DNA beyond those discussed here, for example the inability to tune the system so that different confinement regimes span multiple decades in channel size [39,74], DNA remains the most convenient model system for studying confined polymers. While it may ultimately prove challenging to use DNA to test the existing models down to the prefactors for the scaling laws [23,25,[41][42][43], there is no better experimental system to directly visualize the effects of confinement at the single molecule level and investigate the universal properties of confined polymers at the scaling level.…”

Section: Discussionmentioning

confidence: 99%

“…In some cases, the prefactors for the scaling laws are known exactly [41][42][43]. These thermodynamic quantities depend on the contour length L of the polymer, its persistence length l p , the effective width w of the polymer backbone, and the channel size D. The persistence length and effective width of DNA, which are affected by the relative amount of screening of electrostatics by the ionic environment, can be obtained from polyelectrolyte theory [44][45][46][47], albeit with some uncertainty arising from the effect of the intercalating dye [48][49][50][51][52][53][54].…”

Section: Introductionmentioning

confidence: 99%

Wall depletion length of a channel-confined polymer

Cheong

Dorfman

2017

Phys. Rev. E

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Numerous experiments have taken advantage of DNA as a model system to test theories for a channel-confined polymer. A tacit assumption in analyzing these data is the existence of a well defined depletion length characterizing DNA-wall interactions such that the experimental system (a polyelectrolyte in a channel with charged walls) can be mapped to the theoretical model (a neutral polymer with hard walls). We test this assumption using pruned-enriched Rosenbluth method (PERM) simulations of a DNA-like semiflexible polymer confined in a tube. The polymer-wall interactions are modeled by augmenting a hard wall interaction with an exponentially decaying, repulsive soft potential. The free energy, mean span, and variance in the mean span obtained in the presence of a soft wall potential are compared to equivalent simulations in the absence of the soft wall potential to determine the depletion length. We find that the mean span and variance about the mean span have the same depletion length for all soft potentials we tested. In contrast, the depletion length for the confinement free energy approaches that for the mean span only when depletion length no longer depends on channel size. The results have implications for the interpretation of DNA confinement experiments under low ionic strengths. * dorfman@umn.edu

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“…[34] As in the extended de Gennes regime, circular DNA in the Odijk regime can be treated as two strands going in opposite directions.…”

Section: Theory For the Odijk Regimementioning

confidence: 99%

Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics

Alizadehheidari¹,

Werner

Noble³

et al. 2015

Macromolecules

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Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to linear configuration as a light-induced double strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to which extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.

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Fluctuations of a long, semiflexible polymer in a narrow channel

Cited by 75 publications

References 25 publications

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Wall depletion length of a channel-confined polymer

Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics

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