Nanoconfinement-Enhanced Conformational Response of Single DNA Molecules to Changes in Ionic Environment

Reisner, Walter; Beech, Jason P.; Larsen, Niels Bent; Flyvbjerg, Henrik; Kristensen, Anders; Tegenfeldt, Jonas O.

doi:10.1103/physrevlett.99.058302

Cited by 169 publications

(275 citation statements)

References 30 publications

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“…14 The latter authors also interpreted their results with the scaling model of de Gennes, but they used the Flory radius for the blob size which is exclusively valid for long chain segments. We have used the relevant combination of the unperturbed radius of gyration and swelling factor for shorter chains, in accordance with the relatively small correlation lengths imposed by the channel cross-sectional diameters.…”

Section: B Effects Of Ionic Strengthmentioning

confidence: 99%

“…The scaling relations for the extension of DNA molecules confined in nanochannels of various diameters have been verified by Reisner et al 12 The effects of electrostatic screening on the conformation of DNA molecules inside nanoslits and nanochannels of various dimensions also have been reported before. 13,14 In general, the DNA molecule has been observed to stretch out with decreased screening of Coulomb interaction. The variation in extension with the ionic strength of the supporting medium was interpreted in terms of a variation in the persistence length.…”

Section: Introductionmentioning

confidence: 99%

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Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

Zhang

Kan

et al. 2008

The Journal of Chemical Physics

100

154

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Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with fluorescence microscopy as a function of the ionic strength and composition of the buffer as well as the DNA intercalation level by the YOYO-1 dye. The data were interpreted with scaling theory for a wormlike polymer in good solvent, including the effects of confinement, charge, and self-avoidance. It was found that the elongation of the DNA molecules with decreasing ionic strength can be interpreted in terms of an increase of the persistence length. Self-avoidance effects on the extension are moderate, due to the small correlation length imposed by the channel cross-sectional diameter.Intercalation of the dye results in an increase of the DNA contour length and a partial neutralization of the DNA charge, but besides effects of electrostatic origin it has no significant effect on the bare bending rigidity. In the presence of divalent cations, the DNA molecules were observed to contract, but they do not collapse into a condensed structure. It is proposed that this contraction results from a divalent counterion mediated attractive force between the segments of the DNA molecule.

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Section: B Effects Of Ionic Strengthmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

Zhang

Kan

et al. 2008

The Journal of Chemical Physics

100

154

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“…DNA has played a key role in the experimental tests of theories of a polymer confined to a slit [1][2][3][4][5][6][7][8][9][10][11][12][13][14] or a channel [15][16][17][18][19][20][21][22][23][24][25][26][27], in particular the models by de Gennes and coworkers for weak confinement [28,29] and Odijk for strong confinement [30,31]. The key results of this body of work have been summarized in several recent reviews [32][33][34].…”

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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“…The polymer physics of confined DNA molecules has been studied intensively during the last decade [6,7] and the effects of solvent characteristics [8,9] and molecular crowding [10,11] have been analyzed in detail. Recently, several groups have used nanofluidic channels to investigate the physical properties of nanoconfined DNA-protein complexes [12][13][14][15][16] and for optical mapping of single DNA molecules [17][18][19][20][21] .…”

Section: Introductionmentioning

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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Nanoconfinement-Enhanced Conformational Response of Single DNA Molecules to Changes in Ionic Environment

Cited by 169 publications

References 30 publications

Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

Wall depletion length of a channel-confined polymer

Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics

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