1
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Knot Factories with Helical Geometry Enhance Knotting and Induce Handedness to Knots. Polymers (Basel) 2022; 14:polym14194201. [PMID: 36236148 PMCID: PMC9572405 DOI: 10.3390/polym14194201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/25/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
We performed molecular dynamics simulations of DNA polymer chains confined in helical nano-channels under compression in order to explore the potential of knot-factories with helical geometry to produce knots with a preferred handedness. In our simulations, we explore mutual effect of the confinement strength and compressive forces in a range covering weak, intermediate and strong confinement together with weak and strong compressive forces. The results find that while the common metrics of polymer chain in cylindrical and helical channels are very similar, the DNA in helical channels exhibits greatly different topology in terms of chain knottedness, writhe and handedness of knots. The results show that knots with a preferred chirality in terms of average writhe can be produced by using channels with a chosen handedness.
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2
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Schotzinger RM, Menard LD, Ramsey JM. Single-Molecule DNA Extension in Rectangular and Square Profile Nanochannels in the Extended de Gennes Regime. Macromolecules 2020. [DOI: 10.1021/acs.macromol.9b02249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- R. Michael Schotzinger
- Department of Biomedical Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | | | - J. Michael Ramsey
- Department of Biomedical Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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3
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Bhandari AB, Dorfman KD. Limitations of the equivalent neutral polymer assumption for theories describing nanochannel-confined DNA. Phys Rev E 2020; 101:012501. [PMID: 32069627 PMCID: PMC7040977 DOI: 10.1103/physreve.101.012501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Indexed: 11/07/2022]
Abstract
The prevailing theories describing DNA confinement in a nanochannel are predicated on the assumption that wall-DNA electrostatic interactions are sufficiently short-ranged such that the problem can be mapped to an equivalent neutral polymer confined by hard walls with an appropriately reduced effective channel size. To determine when this hypothesis is valid, we leveraged a recently reported experimental data set for the fractional extension of DNA molecules in a 250-nm-wide poly(dimethyl siloxane) (PDMS) nanochannel with buffer ionic strengths between 0.075 and 48 mM. Evaluating these data in the context of the weakly correlated telegraph model of DNA confinement reveals that, at ionic strengths greater than 0.3 mM, the average fractional extension of the DNA molecules agree with theoretical predictions with a mean absolute error of 0.04. In contrast, experiments at ionic strengths below 0.3 mM produce average fractional extensions that are systematically smaller than the theoretical predictions with a larger mean absolute error of 0.15. The deviations between experiment and theory display a correlation coefficient of 0.82 with the decay length for the DNA-wall electrostatics, linking the deviations with a breakdown in approximating the DNA with an equivalent neutral polymer.
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Affiliation(s)
- Aditya Bikram Bhandari
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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4
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Jia J, Li K, Hofmann A, Heermann DW. The Effect of Bending Rigidity on Polymers. MACROMOL THEOR SIMUL 2019. [DOI: 10.1002/mats.201800071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jiying Jia
- Institute for Theoretical Physics Philosophenweg 12 69120 Heidelberg Germany
| | - Kunhe Li
- Institute for Theoretical Physics Philosophenweg 12 69120 Heidelberg Germany
| | - Andreas Hofmann
- Institute for Theoretical Physics Philosophenweg 12 69120 Heidelberg Germany
| | - Dieter W. Heermann
- Institute for Theoretical Physics Philosophenweg 19 69120 Heidelberg Germany
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5
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Krog J, Alizadehheidari M, Werner E, Bikkarolla SK, Tegenfeldt JO, Mehlig B, Lomholt MA, Westerlund F, Ambjörnsson T. Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysis. J Chem Phys 2019; 149:215101. [PMID: 30525714 DOI: 10.1063/1.5051319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Nanochannels provide a means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. Here we introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients are the entropic unfolding force and the friction coefficient for the unfolding process, and we describe the associated dynamics by a non-linear Langevin equation. By analyzing experimental data where DNA molecules are photo-cut and unfolded inside a nanochannel, our model allows us to extract values for the unfolding force as well as the friction coefficient for the first time. In order to extract numerical values for these physical quantities, we employ a recently introduced Bayesian inference framework. We find that the determined unfolding force is in agreement with estimates from a simple Flory-type argument. The estimated friction coefficient is in agreement with theoretical estimates for motion of a cylinder in a channel. We further validate the estimated friction constant by extracting this parameter from DNA's center-of-mass motion before and after unfolding, yielding decent agreement. We provide publically available software for performing the required image and Bayesian analysis.
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Affiliation(s)
- Jens Krog
- MEMPHYS-Center for Biomembrane Physics, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark
| | | | - Erik Werner
- Department of Physics, Gothenburg University, Gothenburg, Sweden
| | - Santosh Kumar Bikkarolla
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Bernhard Mehlig
- Department of Physics, Gothenburg University, Gothenburg, Sweden
| | - Michael A Lomholt
- MEMPHYS-Center for Biomembrane Physics, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
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6
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Bhandari AB, Reifenberger JG, Chuang HM, Cao H, Dorfman KD. Measuring the wall depletion length of nanoconfined DNA. J Chem Phys 2018; 149:104901. [PMID: 30219022 PMCID: PMC6135644 DOI: 10.1063/1.5040458] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/20/2018] [Indexed: 12/14/2022] Open
Abstract
Efforts to study the polymer physics of DNA confined in nanochannels have been stymied by a lack of consensus regarding its wall depletion length. We have measured this quantity in 38 nm wide, square silicon dioxide nanochannels for five different ionic strengths between 15 mM and 75 mM. Experiments used the Bionano Genomics Irys platform for massively parallel data acquisition, attenuating the effect of the sequence-dependent persistence length and finite-length effects by using nick-labeled E. coli genomic DNA with contour length separations of at least 30 µm (88 325 base pairs) between nick pairs. Over 5 × 106 measurements of the fractional extension were obtained from 39 291 labeled DNA molecules. Analyzing the stretching via Odijk's theory for a strongly confined wormlike chain yielded a linear relationship between the depletion length and the Debye length. This simple linear fit to the experimental data exhibits the same qualitative trend as previously defined analytical models for the depletion length but now quantitatively captures the experimental data.
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Affiliation(s)
- Aditya Bikram Bhandari
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Jeffrey G Reifenberger
- Bionano Genomics, Inc., 9640 Towne Centre Drive, Suite 100, San Diego, California 92121, USA
| | - Hui-Min Chuang
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Han Cao
- Bionano Genomics, Inc., 9640 Towne Centre Drive, Suite 100, San Diego, California 92121, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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7
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Bleha T, Cifra P. Correlation anisotropy and stiffness of DNA molecules confined in nanochannels. J Chem Phys 2018; 149:054903. [PMID: 30089382 DOI: 10.1063/1.5034219] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The anisotropy of orientational correlations in DNA molecules confined in cylindrical channels is explored by Monte Carlo simulations using a coarse-grained model of double-stranded (ds) DNA. We find that the correlation function ⟨C(s)⟩⊥ in the transverse (confined) dimension exhibits a region of negative values in the whole range of channel sizes. Such a clear-cut sign of the opposite orientation of chain segments represents a microscopic validation of the Odijk deflection mechanism in narrow channels. At moderate-to-weak confinement, the negative ⟨C(s)⟩⊥ correlations imply a preference of DNA segments for transverse looping. The inclination for looping can explain a reduction of stiffness as well as the enhanced knotting of confined DNA relative to that detected earlier in bulk at some channel sizes. Furthermore, it is shown that the orientational persistence length Por fails to convey the apparent stiffness of DNA molecules in channels. Instead, correlation lengths P∥ and P⊥ in the axial and transverse directions, respectively, encompass the channel-induced modifications of DNA stiffness.
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Affiliation(s)
- Tomáš Bleha
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
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8
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Ödman D, Werner E, Dorfman KD, Doering CR, Mehlig B. Distribution of label spacings for genome mapping in nanochannels. BIOMICROFLUIDICS 2018; 12:034115. [PMID: 30018694 PMCID: PMC6019347 DOI: 10.1063/1.5038417] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 06/06/2018] [Indexed: 05/27/2023]
Abstract
In genome mapping experiments, long DNA molecules are stretched by confining them to very narrow channels, so that the locations of sequence-specific fluorescent labels along the channel axis provide large-scale genomic information. It is difficult, however, to make the channels narrow enough so that the DNA molecule is fully stretched. In practice, its conformations may form hairpins that change the spacings between internal segments of the DNA molecule, and thus the label locations along the channel axis. Here, we describe a theory for the distribution of label spacings that explains the heavy tails observed in distributions of label spacings in genome mapping experiments.
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Affiliation(s)
- D Ödman
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - E Werner
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - K D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - C R Doering
- Center for the Study of Complex Systems, University of Michigan, Ann Arbor, Michigan 48109-1042, USA
| | - B Mehlig
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
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9
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Gupta D, Bhandari AB, Dorfman KD. Evaluation of Blob Theory for the Diffusion of DNA in Nanochannels. Macromolecules 2018; 51:1748-1755. [PMID: 29599567 DOI: 10.1021/acs.macromol.7b02270] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We have measured the diffusivity of λ-DNA molecules in approximately square nanochannels with effective sizes ranging from 117 nm to 260 nm at moderate ionic strength. The experimental results do not agree with the non-draining scaling predicted by blob theory. Rather, the data are consistent with the predictions of previous simulations of the Kirkwood diffusivity of a discrete wormlike chain model, without the need for any fitting parameters.
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Affiliation(s)
- Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Aditya Bikram Bhandari
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
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10
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Bleha T, Cifra P. Stretching and compression of DNA by external forces under nanochannel confinement. SOFT MATTER 2018; 14:1247-1259. [PMID: 29363709 DOI: 10.1039/c7sm02413d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mechanical deformation of dsDNA molecules inside square nanochannels is investigated using simulations based on a coarse-grained model of DNA. The combined action of confinement and weak external forces is explored in a variety of confinement regimes, including the transition zone relevant to nanofluidic experiments. The computed free energy and force profiles are markedly affected by the channel size. Effective elastic softening of confined DNA molecules relative to the bulk DNA is observed in the channels of intermediate widths. The extension of DNA from its bulk equilibrium length in nanofluidic devices is resolved into contributions from the passive extension due to confinement and from the active stretching induced by force. Potential implications of the very different energy costs computed for the two extension modes (extension by confinement takes much more free energy than stretching by force) for behavior of DNA in nanofluidic chips are indicated.
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Affiliation(s)
- Tomáš Bleha
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia.
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11
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Werner E, Cheong GK, Gupta D, Dorfman KD, Mehlig B. One-Parameter Scaling Theory for DNA Extension in a Nanochannel. PHYSICAL REVIEW LETTERS 2017; 119:268102. [PMID: 29328690 PMCID: PMC5769985 DOI: 10.1103/physrevlett.119.268102] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Indexed: 05/27/2023]
Abstract
Experiments measuring DNA extension in nanochannels are at odds with even the most basic predictions of current scaling arguments for the conformations of confined semiflexible polymers such as DNA. We show that a theory based on a weakly self-avoiding, one-dimensional "telegraph" process collapses experimental data and simulation results onto a single master curve throughout the experimentally relevant region of parameter space and explains the mechanisms at play.
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Affiliation(s)
- E Werner
- Department of Physics, University of Gothenburg, SE-41296 Gothenburg, Sweden
| | - G K Cheong
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - D Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - K D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - B Mehlig
- Department of Physics, University of Gothenburg, SE-41296 Gothenburg, Sweden
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12
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Sean D, Slater GW. Highly driven polymer translocation from a cylindrical cavity with a finite length. J Chem Phys 2017; 146:054903. [DOI: 10.1063/1.4975091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- David Sean
- University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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13
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Smithe TSC, Iarko V, Muralidhar A, Werner E, Dorfman KD, Mehlig B. Finite-size corrections for confined polymers in the extended de Gennes regime. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:062601. [PMID: 26764718 PMCID: PMC4714778 DOI: 10.1103/physreve.92.062601] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Indexed: 06/01/2023]
Abstract
Theoretical results for the extension of a polymer confined to a channel are usually derived in the limit of infinite contour length. But experimental studies and simulations of DNA molecules confined to nanochannels are not necessarily in this asymptotic limit. We calculate the statistics of the span and the end-to-end distance of a semiflexible polymer of finite length in the extended de Gennes regime, exploiting the fact that the problem can be mapped to a one-dimensional weakly self-avoiding random walk. The results thus obtained compare favorably with pruned-enriched Rosenbluth method (PERM) simulations of a three-dimensional discrete wormlike chain model of DNA confined in a nanochannel. We discuss the implications for experimental studies of linear λ-DNA confined to nanochannels at the high ionic strengths used in many experiments.
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Affiliation(s)
- T. St Clere Smithe
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Göteborg, Sweden
| | - V. Iarko
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Göteborg, Sweden
| | - A. Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - E. Werner
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Göteborg, Sweden
| | - K. D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - B. Mehlig
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Göteborg, Sweden
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14
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Iarko V, Werner E, Nyberg LK, Müller V, Fritzsche J, Ambjörnsson T, Beech JP, Tegenfeldt JO, Mehlig K, Westerlund F, Mehlig B. Extension of nanoconfined DNA: Quantitative comparison between experiment and theory. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:062701. [PMID: 26764721 DOI: 10.1103/physreve.92.062701] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Indexed: 05/27/2023]
Abstract
The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose, we performed experiments measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic strength of the buffer. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths, the agreement is less good. We discuss possible reasons. In principle, our approach allows us to measure the Kuhn length and the effective width of a single DNA molecule and more generally of semiflexible polymers in solution.
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Affiliation(s)
- V Iarko
- Department of Physics, University of Gothenburg, 412 96 Göteborg, Sweden
| | - E Werner
- Department of Physics, University of Gothenburg, 412 96 Göteborg, Sweden
| | - L K Nyberg
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - V Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - J Fritzsche
- Department of Applied Physics, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - T Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, 22 100 Lund, Sweden
| | - J P Beech
- Department of Physics, Division of Solid State Physics, Lund University, 22 100 Lund, Sweden
| | - J O Tegenfeldt
- Department of Physics, Division of Solid State Physics, Lund University, 22 100 Lund, Sweden
- NanoLund, Lund University, 22 100 Lund, Sweden
| | - K Mehlig
- Department of Public Health and Community Medicine, University of Gothenburg, 413 46 Göteborg, Sweden
| | - F Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - B Mehlig
- Department of Physics, University of Gothenburg, 412 96 Göteborg, Sweden
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15
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McGinn S, Bauer D, Brefort T, Dong L, El-Sagheer A, Elsharawy A, Evans G, Falk-Sörqvist E, Forster M, Fredriksson S, Freeman P, Freitag C, Fritzsche J, Gibson S, Gullberg M, Gut M, Heath S, Heath-Brun I, Heron AJ, Hohlbein J, Ke R, Lancaster O, Le Reste L, Maglia G, Marie R, Mauger F, Mertes F, Mignardi M, Moens L, Oostmeijer J, Out R, Pedersen JN, Persson F, Picaud V, Rotem D, Schracke N, Sengenes J, Stähler PF, Stade B, Stoddart D, Teng X, Veal CD, Zahra N, Bayley H, Beier M, Brown T, Dekker C, Ekström B, Flyvbjerg H, Franke A, Guenther S, Kapanidis AN, Kaye J, Kristensen A, Lehrach H, Mangion J, Sauer S, Schyns E, Tost J, van Helvoort JMLM, van der Zaag PJ, Tegenfeldt JO, Brookes AJ, Mir K, Nilsson M, Willcocks JP, Gut IG. New technologies for DNA analysis--a review of the READNA Project. N Biotechnol 2015; 33:311-30. [PMID: 26514324 DOI: 10.1016/j.nbt.2015.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/17/2015] [Indexed: 01/09/2023]
Abstract
The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 41/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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Affiliation(s)
- Steven McGinn
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - David Bauer
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Thomas Brefort
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Liqin Dong
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Afaf El-Sagheer
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK; Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK; Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Abdou Elsharawy
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany; Faculty of Sciences, Division of Biochemistry, Chemistry Department, Damietta University, New Damietta City, Egypt
| | - Geraint Evans
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Elin Falk-Sörqvist
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | | | - Peter Freeman
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Camilla Freitag
- Department of Physics, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Joachim Fritzsche
- Department of Applied Physics, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden
| | - Spencer Gibson
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Mats Gullberg
- Olink AB, Dag Hammarskjölds väg 52A, 752 37 Uppsala, Sweden
| | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Simon Heath
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Isabelle Heath-Brun
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Andrew J Heron
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Johannes Hohlbein
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Rongqin Ke
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Owen Lancaster
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Ludovic Le Reste
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Giovanni Maglia
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Rodolphe Marie
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Florence Mauger
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - Florian Mertes
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Marco Mignardi
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Lotte Moens
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | | | - Ruud Out
- FlexGen BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
| | | | - Fredrik Persson
- Department of Physics, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Vincent Picaud
- CEA-Saclay, Bât DIGITEO 565 - Pt Courrier 192, 91191 Gif-sur-Yvette Cedex, France
| | - Dvir Rotem
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Nadine Schracke
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Jennifer Sengenes
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - Peer F Stähler
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Björn Stade
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | - David Stoddart
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Xia Teng
- FlexGen BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
| | - Colin D Veal
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Nathalie Zahra
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Markus Beier
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Tom Brown
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK; Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Björn Ekström
- Olink AB, Dag Hammarskjölds väg 52A, 752 37 Uppsala, Sweden
| | - Henrik Flyvbjerg
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | - Simone Guenther
- Thermo Fisher Scientific Frankfurter Straße 129B, 64293 Darmstadt, Germany
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Jane Kaye
- HeLEX - Centre for Health, Law and Emerging Technologies, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Anders Kristensen
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Jonathan Mangion
- Thermo Fisher Scientific Frankfurter Straße 129B, 64293 Darmstadt, Germany
| | - Sascha Sauer
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Emile Schyns
- PHOTONIS France S.A.S. Avenue Roger Roncier, 19100 Brive B.P. 520, 19106 BRIVE Cedex, France
| | - Jörg Tost
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | | | - Pieter J van der Zaag
- Philips Research Laboratories, High Tech Campus 11, 5656 AE Eindhoven, The Netherlands
| | - Jonas O Tegenfeldt
- Division of Solid State Physics and NanoLund, Lund University, Box 118, 22100 Lund, Sweden
| | | | - Kalim Mir
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - James P Willcocks
- Oxford Nanopore Technologies, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford Science Park, Oxford OX4 4GA, UK
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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16
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Gupta D, Miller JJ, Muralidhar A, Mahshid S, Reisner W, Dorfman KD. Experimental evidence of weak excluded volume effects for nanochannel confined DNA. ACS Macro Lett 2015; 4:759-763. [PMID: 26664782 PMCID: PMC4671635 DOI: 10.1021/acsmacrolett.5b00340] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present experimental demonstration that weak excluded volume effects arise in DNA nanochannel confinement. In particular, by performing measurements of the variance in chain extension as a function of nanochannel dimension for effective channel size ranging from 305 nm to 453 nm, we show that the scaling of the variance in extension with channel size rejects the de Gennes scaling δ2X ~ D1/3 in favor of δ2X ~ D0 using uncertainty at the 95% confidence level. We also show how simulations and confinement spectroscopy can be combined to reduce molecular weight dispersity effects arising from shearing, photocleavage, and nonuniform staining of DNA.
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Affiliation(s)
- Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Jeremy J. Miller
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Sara Mahshid
- Physics Department, McGill University, 3600 rue University, Montreal QC H3A 2T8, Canada
| | - Walter Reisner
- Physics Department, McGill University, 3600 rue University, Montreal QC H3A 2T8, Canada
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
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17
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Werner E, Mehlig B. Scaling regimes of a semiflexible polymer in a rectangular channel. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:050601. [PMID: 26066107 DOI: 10.1103/physreve.91.050601] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Indexed: 06/04/2023]
Abstract
We derive scaling relations for the extension statistics and the confinement free energy for a semiflexible polymer confined to a channel with a rectangular cross section. Our motivation is recent numerical results [Gupta et al., J. Chem. Phys. 140, 214901 (2014)] indicating that extensional fluctuations are quite different in rectangular channels compared to square channels. Our results are of direct relevance for interpreting current experiments on DNA molecules confined to nanochannels, as many experiments are performed for rectangular channels with large aspect ratios, while theoretical and simulation results are usually obtained for square channels.
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Affiliation(s)
- E Werner
- Department of Physics, University of Gothenburg, Sweden
| | - B Mehlig
- Department of Physics, University of Gothenburg, Sweden
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18
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Alizadehheidari M, Werner E, Noble C, Reiter-Schad M, Nyberg LK, Fritzsche J, Mehlig B, Tegenfeldt JO, Ambjörnsson T, Persson F, Westerlund F. Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics. Macromolecules 2015. [DOI: 10.1021/ma5022067] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | - Erik Werner
- Department
of Physics, Gothenburg University, Gothenburg, Sweden
| | | | | | | | | | - Bernhard Mehlig
- Department
of Physics, Gothenburg University, Gothenburg, Sweden
| | | | | | - Fredrik Persson
- Department of Cell and
Molecular Biology, Uppsala University, Uppsala, Sweden
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19
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Werner E, Mehlig B. Confined polymers in the extended de Gennes regime. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:062602. [PMID: 25615121 DOI: 10.1103/physreve.90.062602] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Indexed: 05/27/2023]
Abstract
We show that the problem of describing the conformations of a semiflexible polymer confined to a channel can be mapped onto an exactly solvable model in the so-called extended de Gennes regime. This regime (where the polymer is neither weakly nor strongly confined) has recently been intensively studied experimentally and by means of computer simulations. The exact solution predicts precisely how the conformational fluctuations depend upon the channel width and upon the microscopic parameters characterizing the physical properties of the polymer.
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Affiliation(s)
- E Werner
- Department of Physics, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - B Mehlig
- Department of Physics, University of Gothenburg, SE-40530 Gothenburg, Sweden
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20
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Gupta D, Sheats J, Muralidhar A, Miller JJ, Huang DE, Mahshid S, Dorfman KD, Reisner W. Mixed confinement regimes during equilibrium confinement spectroscopy of DNA. J Chem Phys 2014; 140:214901. [PMID: 24908035 PMCID: PMC4048444 DOI: 10.1063/1.4879515] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/12/2014] [Indexed: 11/14/2022] Open
Abstract
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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Affiliation(s)
- Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Julian Sheats
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Jeremy J Miller
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Derek E Huang
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Sara Mahshid
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Walter Reisner
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
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21
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Dai L, van der Maarel J, Doyle PS. Extended de Gennes Regime of DNA Confined in a Nanochannel. Macromolecules 2014. [DOI: 10.1021/ma500326w] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Liang Dai
- BioSystems
and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Republic of Singapore 138602
| | - Johan van der Maarel
- BioSystems
and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Republic of Singapore 138602
- Department
of Physics, National University of Singapore, 2 Science Drive 3, Republic of Singapore 117551
| | - Patrick S. Doyle
- BioSystems
and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Republic of Singapore 138602
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, United States
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22
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Frykholm K, Alizadehheidari M, Fritzsche J, Wigenius J, Modesti M, Persson F, Westerlund F. Probing physical properties of a DNA-protein complex using nanofluidic channels. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:884-7. [PMID: 24382826 DOI: 10.1002/smll.201302028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/08/2013] [Indexed: 05/28/2023]
Abstract
A method to investigate physical properties of a DNA-protein complex in solution is demonstrated. By using tapered nanochannels and lipid passivation the persistence length of a RecA filament formed on double-stranded DNA is determined to 1.15 μm, in agreement with the literature, without attaching protein or DNA to any handles or surfaces.
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Affiliation(s)
- Karolin Frykholm
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
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23
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Muralidhar A, Tree DR, Wang Y, Dorfman KD. Interplay between chain stiffness and excluded volume of semiflexible polymers confined in nanochannels. J Chem Phys 2014; 140:084905. [PMID: 24588196 PMCID: PMC3977884 DOI: 10.1063/1.4865965] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 02/05/2014] [Indexed: 11/14/2022] Open
Abstract
The properties of channel-confined semiflexible polymers are determined by a complicated interplay of chain stiffness and excluded volume effects. Using Pruned-Enriched Rosenbluth Method (PERM) simulations, we study the equilibrium properties of channel-confined polymers by systematically controlling chain stiffness and excluded volume. Our calculations of chain extension and confinement free energy for freely jointed chains with and without excluded volume show excellent agreement with theoretical predictions. For ideal wormlike chains, the extension is seen to crossover from Odijk behavior in strong confinement to zero-stretching, bulk-like behavior in weak confinement. In contrast, for self-avoiding wormlike chains, we always observe that the linear scaling of the extension with the contour length is valid in the long-chain limit irrespective of the regime of confinement, owing to the coexistence of stiffness and excluded volume effects. We further propose that the long-chain limit for the extension corresponds to chain lengths wherein the projection of the end-to-end distance along the axis of the channel is nearly equal to the mean span parallel to the axis. For DNA in nanochannels, this limit was identified using PERM simulations out to molecular weights of more than 1 megabase pairs; the molecular weight of λ-DNA is found to exhibit nearly asymptotic fractional extension for channels sizes used commonly in experiments.
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Affiliation(s)
- Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - Douglas R Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - Yanwei Wang
- Department of Polymer Science and Engineering, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 199 Ren-ai Road, Suzhou 215123, People's Republic of China
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
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24
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Tree DR, Wang Y, Dorfman KD. Modeling the relaxation time of DNA confined in a nanochannel. BIOMICROFLUIDICS 2013; 7:54118. [PMID: 24309551 PMCID: PMC3820670 DOI: 10.1063/1.4826156] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 10/07/2013] [Indexed: 05/12/2023]
Abstract
Using a mapping between a Rouse dumbbell model and fine-grained Monte Carlo simulations, we have computed the relaxation time of λ-DNA in a high ionic strength buffer confined in a nanochannel. The relaxation time thus obtained agrees quantitatively with experimental data [Reisner et al., Phys. Rev. Lett. 94, 196101 (2005)] using only a single O(1) fitting parameter to account for the uncertainty in model parameters. In addition to validating our mapping, this agreement supports our previous estimates of the friction coefficient of DNA confined in a nanochannel [Tree et al., Phys. Rev. Lett. 108, 228105 (2012)], which have been difficult to validate due to the lack of direct experimental data. Furthermore, the model calculation shows that as the channel size passes below approximately 100 nm (or roughly the Kuhn length of DNA) there is a dramatic drop in the relaxation time. Inasmuch as the chain friction rises with decreasing channel size, the reduction in the relaxation time can be solely attributed to the sharp decline in the fluctuations of the chain extension. Practically, the low variance in the observed DNA extension in such small channels has important implications for genome mapping.
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Affiliation(s)
- Douglas R Tree
- Department of Chemical Engineering and Material Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
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25
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Werner E, Westerlund F, Tegenfeldt JO, Mehlig B. Monomer Distributions and Intrachain Collisions of a Polymer Confined to a Channel. Macromolecules 2013. [DOI: 10.1021/ma400464c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- E. Werner
- Department of Physics, University of Gothenburg, Göteborg, Sweden
| | - F. Westerlund
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - J. O. Tegenfeldt
- Department of Physics, Division
of Solid State Physics, Lund University, Lund, Sweden
| | - B. Mehlig
- Department of Physics, University of Gothenburg, Göteborg, Sweden
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26
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Tree DR, Wang Y, Dorfman KD. Extension of DNA in a nanochannel as a rod-to-coil transition. PHYSICAL REVIEW LETTERS 2013; 110:208103. [PMID: 25167455 PMCID: PMC4156158 DOI: 10.1103/physrevlett.110.208103] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Indexed: 05/14/2023]
Abstract
DNA confinement in nanochannels is emerging as an important tool for genomics and an excellent platform for testing the theories of confined wormlike polymers. Using cutting-edge, large scale Monte Carlo simulations of asymptotically long wormlike chains, we show that, in analogy to the rod-to-coil transition for free wormlike polymers, there exists a universal, Gauss-de Gennes regime that connects the classic Odijk and de Gennes regimes of channel-confined chains. For DNA in a nanochannel, this Gauss-de Gennes regime spans practically the entire experimentally relevant range of channel sizes, including the nanochannels used in an incipient genome mapping technology.
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Affiliation(s)
- Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota ― Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455
| | - Yanwei Wang
- Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 199 Ren-ai Road, Suzhou, 215123, P.R. China
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota ― Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455
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