Confinement Spectroscopy: Probing Single DNA Molecules with Tapered Nanochannels

Persson, Fredrik; Utko, Pawel; Reisner, Walter; Larsen, Niels Bent; Kristensen, Anders

doi:10.1021/nl803030e

Cited by 123 publications

(177 citation statements)

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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%

“…Intercalation also increases the DNA contour length relative to the rise of naked DNA [55]. However, uncertainties in contour length can be minimized by (i) ensuring uniform staining of the DNA [56] and (ii) using funnel-shaped channels that allow one to interrogate the properties the same DNA molecule in a range of confinement [18,22,23,25,57]. For long chains [31], the thermodynamic variables become extensive quantities, so funnel-shaped channels permit a single-molecule test of various scaling laws independent of the contour length.…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Wall depletion length of a channel-confined polymer

Cheong

Dorfman

2017

Phys. Rev. E

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“…3 Since that time, intense theoretical and simulation work on channel-confined DNA has produced a more nuanced understanding of confined semiflexible chains, but these new predictions now require experimental investigation. Confinement spectroscopy 4 is a potentially powerful approach. This method uses a nanochannel with a fixed depth and a variable channel width, thereby probing many different channel sizes in a single device.…”

Section: Introductionmentioning

confidence: 99%

Mixed confinement regimes during equilibrium confinement spectroscopy of DNA

Gupta

Sheats²,

Muralidhar

et al. 2014

The Journal of Chemical Physics

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We have used a combination of fluorescence microscopy experiments and Pruned Enriched Rosenbluth Method simulations of a discrete wormlike chain model to measure the mean extension and the variance in the mean extension of λ-DNA in 100 nm deep nanochannels with widths ranging from 100 nm to 1000 nm in discrete 100 nm steps. The mean extension is only weakly affected by the channel aspect ratio. In contrast, the fluctuations of the chain extension qualitatively differ between rectangular channels and square channels with the same cross-sectional area, owing to the "mixing" of different confinement regimes in the rectangular channels. The agreement between experiment and simulation is very good, using the extension due to intercalation as the only adjustable parameter.

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“…The behavior of confined circular chains remains also poorly understood, and only a few experiments explored this system [12]. Ring closure, and more generally topology, plays a key role in a wide range of biophysical contexts where DNA is constrained: segregation of the compacted circular genome of some bacteria [13], formation of chromosomal territories [14] in cell nuclei, compaction and ejection of the knotted DNA of a virus [15,16], migration of a circular DNA in an electrophoresis gel [17] or in a nanodevice such as a nanochannel [18], or localization of knots [3,19].…”

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confidence: 99%

Conformation of Ring Polymers in 2D Constrained Environments

et al. 2011

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The combination of ring closure and spatial constraints has a fundamental effect on the statistics of semiflexible polymers such as DNA. However, studies of the interplay between circularity and constraints are scarce and single-molecule experimental data concerning polymer conformations are missing. By means of atomic force microscopy we probe the conformation of circular DNA molecules in two dimensions and in the concentrated regime (above the overlap concentration c Ã ). Molecules in this regime experience a collapse, and their statistical properties agree very well with those of simulated vesicles under pressure. Some circular molecules also create confining regions in which other molecules are trapped. Thus we show further that spatially confined molecules fold into specific conformations close to those found for linear chains, and strongly dependent on the size of the confining box. DOI: 10.1103/PhysRevLett.106.248301 PACS numbers: 82.35.Gh, 87.64.Dz, 36.20.Ey, 87.14.gk Ring closure of a polymer is one of the important factors influencing its statistical mechanical properties [1], e.g., scaling [2,3], shape [4,5], and diffusion [6][7][8], because it restrains the accessible phase space. The theoretical description of circular chains (knots or catenanes) is a challenging problem, owing to the difficulties inherent to a systematic theoretical analysis of such objects constrained to a unique topology. The problem is particularly evident for systems of interacting chains, for example, in semidilute or confined states. Cates and Deutsch [9] pointed out that topological constraints act to alter quite dramatically the behavior of chains in a melt. This has been confirmed by experiments and simulations for the three-dimensional (3D) system [10], but to our knowledge not for the 2D case where studies are limited to the linear case [11].The behavior of confined circular chains remains also poorly understood, and only a few experiments explored this system [12]. Ring closure, and more generally topology, plays a key role in a wide range of biophysical contexts where DNA is constrained: segregation of the compacted circular genome of some bacteria [13], formation of chromosomal territories [14] in cell nuclei, compaction and ejection of the knotted DNA of a virus [15,16], migration of a circular DNA in an electrophoresis gel [17] or in a nanodevice such as a nanochannel [18], or localization of knots [3,19]. Therefore a better understanding of the basic properties of such systems is highly needed.In the present Letter, we would like to present experimental findings on ring polymers in the concentrated phase and in a confined environment obtained at the singlemolecule level by means of the atomic force microscope (AFM) as depicted in Fig. 1.A 10 l drop of nicked circular-plasmid DNA pBR322 (4361 base pairs) at a concentration of 0:5 mg=ml in 1 mM MgCl 2 was deposited for 5 minutes on a freshly cleaved mica surface, then rinsed with 10 ml of ultrapure water and dried. The samples were then imaged in tapping mode wit...

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Confinement Spectroscopy: Probing Single DNA Molecules with Tapered Nanochannels

Cited by 123 publications

References 26 publications

Wall depletion length of a channel-confined polymer

Wall depletion length of a channel-confined polymer

Mixed confinement regimes during equilibrium confinement spectroscopy of DNA

Conformation of Ring Polymers in 2D Constrained Environments

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