1
|
Zhong J, Sun Z, Zhang L, Whitehead GFS, Vitorica-Yrezabal IJ, Leigh DA. Folding a Molecular Strand into a Trefoil Knot of Single Handedness with Co(II)/Co(III) Chaperones. J Am Chem Soc 2024; 146:21762-21768. [PMID: 39060953 PMCID: PMC11311214 DOI: 10.1021/jacs.4c05953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/01/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024]
Abstract
We report the synthesis of a right-handed (Δ-stereochemistry of strand crossings) trefoil knot from a single molecular strand containing three pyrazine-2,5-dicarboxamide units adjacent to point-chiral centers and six pyridine moieties. The oligomeric ligand strand folds into an overhand (open-trefoil) knot through the assistance of coordinatively dynamic Co(II) "chaperones" that drive the formation of a three-metal-ion circular helicate. The entangled structure is kinetically locked by oxidation to Co(III) and covalently captured by ring-closing olefin metathesis to generate a trefoil knot of single topological handedness. The stereochemistry of the strand crossings in the metal-coordinated overhand knot is governed by the stereochemistry of the point-chiral carbon centers in the ligand strand. The overhand and trefoil knots were characterized by NMR spectroscopy, mass spectrometry, and X-ray crystallography. Removal of the metal ions from the knot, followed by hydrogenation of the alkene, yielded the wholly organic trefoil knot. The metal-free knot and parent ligand were investigated by circular dichroism (CD) spectroscopy. The CD spectra indicate that the topological stereochemistry of the knot has a greater effect on the asymmetry of the chromophore environment than do the point-chiral centers of the strand.
Collapse
Affiliation(s)
- Jiankang Zhong
- Department
of Chemistry, University of Manchester, Manchester M13 9PL, U.K.
| | - Zhanhu Sun
- School
of Chemistry and Molecular Engineering, East China Normal University, 200062 Shanghai, China
| | - Liang Zhang
- School
of Chemistry and Molecular Engineering, East China Normal University, 200062 Shanghai, China
| | | | | | - David A. Leigh
- School
of Chemistry and Molecular Engineering, East China Normal University, 200062 Shanghai, China
- Department
of Chemistry, University of Manchester, Manchester M13 9PL, U.K.
| |
Collapse
|
2
|
Cui Y, Ying C, Huang XY, Ye Q, Tian J, Liu Z. Electrical Transport and Dynamics of Confined DNA through Highly Conductive 2D Graphene Nanochannels. NANO LETTERS 2024; 24:4485-4492. [PMID: 38578031 DOI: 10.1021/acs.nanolett.4c00403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Confining DNA in nanochannels is an important approach to studying its structure and transportation dynamics. Graphene nanochannels are particularly attractive for studying DNA confinement due to their atomic flatness, precise height control, and excellent mechanical strength. Here, using femtosecond laser etching and wetting transfer, we fabricate graphene nanochannels down to less than 4.3 nm in height, with the length-to-height ratios up to 103. These channels exhibit high stability, low noise, and self-cleaning ability during the long-term ionic current recording. We report a clear linear relationship between DNA length and the residence time in the channel and further utilize this relationship to differentiate DNA fragments based on their lengths, ranging widely from 200 bps to 48.5 kbps. The graphene nanochannel presented here provides a potential platform for label-free analyses and reveals fundamental insights into the conformational dynamics of DNA and proteins in confined space.
Collapse
Affiliation(s)
- Yangjun Cui
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Cuifeng Ying
- Advanced Optics & Photonics Laboratory, Department of Engineering, School of Science & Technology, Nottingham Trent University, Nottingham NG11 8NS, U.K
| | - Xiao-Yu Huang
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Qing Ye
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Jianguo Tian
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
- Renewable Energy Conversion and Storage Center, Nankai University, Tianjin 300071, China
| | - Zhibo Liu
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
- Renewable Energy Conversion and Storage Center, Nankai University, Tianjin 300071, China
- The Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| |
Collapse
|
3
|
Zeng L, Capaldi X, Liu Z, Reisner WW. Transient physics in the compression and mixing dynamics of two nanochannel-confined polymer chains. Phys Rev E 2024; 109:024501. [PMID: 38491709 DOI: 10.1103/physreve.109.024501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/16/2024] [Indexed: 03/18/2024]
Abstract
We use molecular dynamics (MD) simulation and nanofluidic experiments to probe the non-equilibrium transient physics of two nanochannel-confined polymers driven against a permeable barrier in a flow field. For chains with a persistence length P smaller than the channel diameter D, both simulation and experiment with dsDNA reveal nonuniform mixing of the two chains, with one chain dominating locally in what we term "aggregates." Aggregates undergo stochastic dynamics, persisting for a limited time, then disappearing and reforming. Whereas aggregate-prone mixing occurs immediately at sufficiently high flow speeds, chains stay segregated at intermediate flow for some time, often attempting to mix multiple times, before suddenly successfully mixing. Observation of successful mixing nucleation events in nanofluidic experiments reveal that they arise through a peculiar "back-propagation" mechanism whereby the upstream chain, closest to the barrier, penetrates and passes through the downstream chain (farthest from the barrier) moving against the flow direction. Simulations suggest that the observed back-propagation nucleation mechanism is favored at intermediate flow speeds and arises from a special configuration where the upstream chain exhibits one or more folds facing the downstream chain, while the downstream chain has an unfolded chain end facing upstream.
Collapse
Affiliation(s)
- Lili Zeng
- Department of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 2T8, Canada
| | - Xavier Capaldi
- Department of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 2T8, Canada
| | - Zezhou Liu
- Department of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 2T8, Canada
| | - Walter W Reisner
- Department of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 2T8, Canada
| |
Collapse
|
4
|
Rusková R, Račko D. Knot Formation on DNA Pushed Inside Chiral Nanochannels. Polymers (Basel) 2023; 15:4185. [PMID: 37896430 PMCID: PMC10611388 DOI: 10.3390/polym15204185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
We performed coarse-grained molecular dynamics simulations of DNA polymers pushed inside infinite open chiral and achiral channels. We investigated the behavior of the polymer metrics in terms of span, monomer distributions and changes of topological state of the polymer in the channels. We also compared the regime of pushing a polymer inside the infinite channel to the case of polymer compression in finite channels of knot factories investigated in earlier works. We observed that the compression in the open channels affects the polymer metrics to different extents in chiral and achiral channels. We also observed that the chiral channels give rise to the formation of equichiral knots with the same handedness as the handedness of the chiral channels.
Collapse
Affiliation(s)
- Renáta Rusková
- Polymer Institute of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia
| | - Dušan Račko
- Polymer Institute of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia
| |
Collapse
|
5
|
Zeng L, Reisner WW. Mixing and demixing arising from compression of two semiflexible polymer chains in nanochannels. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:88. [PMID: 37755600 DOI: 10.1140/epje/s10189-023-00346-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/03/2023] [Indexed: 09/28/2023]
Abstract
We use molecular dynamics simulation to probe the non-equilibrium physics of two nanochannel-confined semiflexible polymers in a homogeneous flow field. We find that for sufficiently stiff chains the internal organization of the two chains takes the form of interwoven folds and circular coils. This organization can lead to mixing or demixing depending on chain stiffness and flow speed. At low and intermediate flow, the two chains adopt a folded configuration, which favours mixing. At high flow, the two chains adopt a predominantly coiled configuration. The coiled configuration results in demixing when the chains are compressed from an initially demixed condition and mixing when the chains are compressed from an initially mixed condition. We find that the mixing/demixing behaviour is governed by the ratio of the number of folded segments of one chain relative to the other at low flow and by the degree of coiling in both chains at high flow. For decreasing stiffness, the chains start to aggregate locally instead of mixing smoothly at low and intermediate flow. In the limit of completely flexible chains, the two chains either completely segregate at low flow, or adopt a locally demixed configuration consisting of large aggregates of one chain relative to the other that undergo complex stochastic dynamics, diffusing, disintegrating, and reforming at intermediate flow. The transition from complete segregation to the aggregate-dominated configuration occurs when the linear intra-chain ordering breaks down.
Collapse
Affiliation(s)
- Lili Zeng
- Department of Physics, McGill University, 3600 University Street, Montreal, QC, H3A 2T8, Canada.
| | - Walter W Reisner
- Department of Physics, McGill University, 3600 University Street, Montreal, QC, H3A 2T8, Canada
| |
Collapse
|
6
|
Radhakrishnan K, Singh SP. Compression of a confined semiflexible polymer under direct and oscillating fields. Phys Rev E 2023; 108:014501. [PMID: 37583203 DOI: 10.1103/physreve.108.014501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 06/19/2023] [Indexed: 08/17/2023]
Abstract
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long biopolymers tend to collapse under an external field, which is contrary to the previously reported stretching of the chain. In this work, we capture the compression of a confined semiflexible polymer under direct and oscillating fields using a coarse-grained computer simulation model in the presence of long-range hydrodynamics. In the case of a semiflexible polymer chain, the inhomogeneous hydrodynamic drag from the center to the periphery of the coil couples with the chain bending to cause a swirling movement of the chain segments, leading to structural intertwining and compaction. Contrarily, a flexible chain of the same length lacks such structural deformation and forms a well-established tadpole structure. While bending rigidity profoundly influences the chain's folding favorability, we also found that subject to the direct field, chains in stronger confinements exhibit substantial compaction, contrary to the one in moderate confinements or bulk where such compaction is absent. However, an alternating field within an optimum frequency can effectuate this compression even in moderate or no confinement. This field-induced collapse is a quintessential hydrodynamic phenomenon, resulting in intertwined knotted structures even for shorter chains, unlike other spontaneous knotting experiments where it happens exclusively for longer chains.
Collapse
Affiliation(s)
- Keerthi Radhakrishnan
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India
| | - Sunil P Singh
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India
| |
Collapse
|
7
|
Mao R, Dorfman KD. Diffusion of knots in nanochannel-confined DNA molecules. J Chem Phys 2023; 158:2890486. [PMID: 37184024 DOI: 10.1063/5.0151025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/03/2023] [Indexed: 05/16/2023] Open
Abstract
We used Langevin dynamics simulations without hydrodynamic interactions to probe knot diffusion mechanisms and the time scales governing the evolution and the spontaneous untying of trefoil knots in nanochannel-confined DNA molecules in the extended de Gennes regime. The knot untying follows an "opening up process," wherein the initially tight knot continues growing and fluctuating in size as it moves toward the end of the DNA molecule before its annihilation at the chain end. The mean knot size increases significantly and sub-linearly with increasing chain contour length. The knot diffusion in nanochannel-confined DNA molecules is subdiffusive, with the unknotting time scaling with chain contour length with an exponent of 2.64 ± 0.23 to within a 95% confidence interval. The scaling exponent for the mean unknotting time vs chain contour length, along with visual inspection of the knot conformations, suggests that the knot diffusion mechanism is a combination of self-reptation and knot region breathing for the simulated parameters.
Collapse
Affiliation(s)
- Runfang Mao
- 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
| |
Collapse
|
8
|
Cifra P, Bleha T. Pressure of Linear and Ring Polymers Confined in a Cavity. J Phys Chem B 2023; 127:4646-4657. [PMID: 37192395 DOI: 10.1021/acs.jpcb.3c01585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nanoscale confinement of polymers in a cavity is central to a variety of biological and nanotechnology processes. Using the discrete WLC model we simulate the compression of flexible and semiflexible polymers of linear and ring topology in a closed cavity. Simulation reveals that polymer pressure inside the cavity increases with the chain stiffness but is practically unaffected by the chain topology. For flexible polymers, the computed dependence of pressure on the cavity size and polymer concentration is consistent with the scaling behavior expected for bulk polymers in a good solvent. However, the scaling behavior of semiflexible polymers is only in partial agreement with the theory prediction, with discrepancies arising from a continuous transition between regimes in chains of moderate lengths. The computed segment density profiles endorse the propensity of semiflexible polymers to concentrate beneath the cavity surface and thus elevate the pressure. The compaction of polymers by compression into the disordered globule or growing toroidal structure is documented.
Collapse
Affiliation(s)
- Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
| | - Tomáš Bleha
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
| |
Collapse
|
9
|
Wettermann S, Datta R, Virnau P. Influence of ionic conditions on knotting in a coarse-grained model for DNA. Front Chem 2023; 10:1096014. [PMID: 36733610 PMCID: PMC9887150 DOI: 10.3389/fchem.2022.1096014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/23/2022] [Indexed: 01/18/2023] Open
Abstract
We investigate knotting probabilities of long double-stranded DNA strands in a coarse-grained Kratky-Porod model for DNA with Monte Carlo simulations. Various ionic conditions are implemented by adjusting the effective diameter of monomers. We find that the occurrence of knots in DNA can be reinforced considerably by high salt conditions and confinement between plates. Likewise, knots can almost be dissolved completely in a low salt scenario. Comparisons with recent experiments confirm that the coarse-grained model is able to capture and quantitatively predict topological features of DNA and can be used for guiding future experiments on DNA knots.
Collapse
|
10
|
Tagliabue A, Micheletti C, Mella M. Tuning Knotted Copolyelectrolyte Conformations via Solution Properties. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Andrea Tagliabue
- Dipartimento di Scienza ed Alta Tecnologia, Università degli Studi dell’Insubria, via Valleggio 11, 22100Como, Italy
- SISSA (Scuola Internazionale Superiore di Studi Avanzati), via Bonomea 265, 34136Trieste, Italy
| | - Cristian Micheletti
- SISSA (Scuola Internazionale Superiore di Studi Avanzati), via Bonomea 265, 34136Trieste, Italy
| | - Massimo Mella
- Dipartimento di Scienza ed Alta Tecnologia, Università degli Studi dell’Insubria, via Valleggio 11, 22100Como, Italy
| |
Collapse
|
11
|
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.
Collapse
|
12
|
Zeng L, Reisner WW. Organized states arising from compression of single semiflexible polymer chains in nanochannels. Phys Rev E 2022; 105:064501. [PMID: 35854522 DOI: 10.1103/physreve.105.064501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
We use molecular dynamics simulation to probe the nonequilibrium physics of single nanochannel-confined semiflexible polymers in a homogeneous flow field. The flow field compresses the polymer against the end of the nanochannel, simulating an experiment of a nanochannel confined chain compressed against a slit barrier. The flow-based compression gives rise to a packing of the chain against the channel end that possesses a striking organization, consisting of interweaving of folds and circular coils. For stiff chains at low flow, we find that the organization is dominated by repeated hairpin folds. For stiff chains at higher flow, we observe that circular coils arise along with the folds, with folding and coiling domains becoming interwoven at the highest flow speeds. Chain organization is retained even when the chain persistence length is on order of the channel width. We show that the global polymer organization, consisting of a number of defined folds and coiled loops, arises from the minimization of the total chain free energy.
Collapse
Affiliation(s)
- Lili Zeng
- Department of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 2T8, Canada
| | - Walter W Reisner
- Department of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 2T8, Canada
| |
Collapse
|
13
|
Li F, Luo Y, Xi G, Fu J, Tu J. Single-Molecule Analysis of DNA structures using nanopore sensors. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
14
|
Rothörl J, Wettermann S, Virnau P, Bhattacharya A. Knot formation of dsDNA pushed inside a nanochannel. Sci Rep 2022; 12:5342. [PMID: 35351953 PMCID: PMC8964721 DOI: 10.1038/s41598-022-09242-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/17/2022] [Indexed: 12/23/2022] Open
Abstract
Recent experiments demonstrated that knots in single molecule dsDNA can be formed by compression in a nanochannel. In this manuscript, we further elucidate the underlying molecular mechanisms by carrying out a compression experiment in silico, where an equilibrated coarse-grained double-stranded DNA confined in a square channel is pushed by a piston. The probability of forming knots is a non-monotonic function of the persistence length and can be enhanced significantly by increasing the piston speed. Under compression knots are abundant and delocalized due to a backfolding mechanism from which chain-spanning loops emerge, while knots are less frequent and only weakly localized in equilibrium. Our in silico study thus provides insights into the formation, origin and control of DNA knots in nanopores.
Collapse
Affiliation(s)
- Jan Rothörl
- Institut für Physik, Johannes Gutenberg-Universität, Staudinger Weg 9, 55099, Mainz, Germany
| | - Sarah Wettermann
- Institut für Physik, Johannes Gutenberg-Universität, Staudinger Weg 9, 55099, Mainz, Germany
| | - Peter Virnau
- Institut für Physik, Johannes Gutenberg-Universität, Staudinger Weg 9, 55099, Mainz, Germany.
| | - Aniket Bhattacharya
- Department of Physics, University of Central Florida, Orlando, FL, 32816-2385, USA.
| |
Collapse
|
15
|
Zhu Y, Zhu H, Tian F, Qiu Q, Dai L. Quantifying the effects of slit confinement on polymer knots using the tube model. Phys Rev E 2022; 105:024501. [PMID: 35291068 DOI: 10.1103/physreve.105.024501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Knots can spontaneously form in DNA, proteins, and other polymers and affect their properties. These knots often experience spatial confinement in biological systems and experiments. While confinement dramatically affects the knot behavior, the physical mechanisms underlying the confinement effects are not fully understood. In this work, we provide a simple physical picture of the polymer knots in slit confinement using the tube model. In the tube model, the polymer segments in the knot core are assumed to be confined in a virtual tube due to the topological restriction. We first perform Monte Carlo simulation of a flexible knotted chain confined in a slit. We find that with the decrease of the slit height from H=+∞ (the 3D case) to H=2a (the 2D case), the most probable knot size L_{knot}^{*} dramatically shrinks from (L_{knot}^{*})_{3D}≈140a to (L_{knot}^{*})_{2D}≈26a, where a is the monomer diameter of the flexible chain. Then we quantitatively explain the confinement-induced knot shrinking and knot deformation using the tube model. Our results for H=2a can be applied to a polymer knot on a surface, which resembles DNA knots measured by atomic force microscopy under the conditions that DNA molecules are weakly absorbed on the surface and reach equilibrium 2D conformations. This work demonstrates the effectiveness of the tube model in understanding polymer knots.
Collapse
Affiliation(s)
- Yongjian Zhu
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, 999077, China and Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
| | - Haoqi Zhu
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, 999077, China and Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, 999077, China and Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
| | - Qiyuan Qiu
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, 999077, China and Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, 999077, China and Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
| |
Collapse
|
16
|
Chen W, Wei S. Compressive deformations of ring polymers in a confining channel. POLYMER 2021. [DOI: 10.1016/j.polymer.2021.124340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
17
|
Tagliabue A, Micheletti C, Mella M. Tunable Knot Segregation in Copolyelectrolyte Rings Carrying a Neutral Segment. ACS Macro Lett 2021; 10:1365-1370. [PMID: 35549022 DOI: 10.1021/acsmacrolett.1c00453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We use Langevin dynamics simulations to study the knotting properties of copolyelectrolyte rings carrying neutral segments. We show that by solely tuning the relative length of the neutral and charged blocks, one can achieve different combinations of knot contour position and size. Strikingly, the latter is shown to vary nonmonotonically with the length of the neutral segment; at the same time, the knot switches from being pinned at the block's edge to becoming trapped inside it. Model calculations relate both effects to the competition between two adversarial mechanisms: the energy gain of localizing one or more of the knot's essential crossings on the neutral segment and the entropic cost of such localization. Tuning the length of the neutral segment sets the balance between the two mechanisms and hence the number of localized essential crossings, which in turn modulates the knot's size. This general principle ought to be useful in more complex systems, such as multiblock copolyelectrolytes, to achieve a more granular control of topological constraints.
Collapse
Affiliation(s)
- Andrea Tagliabue
- Dipartimento di Scienza ed Alta Tecnologia, Universitá degli Studi dell’Insubria, via Valleggio 11, 22100, Como, Italy
| | - Cristian Micheletti
- SISSA (Scuola Internazionale Superiore di Studi Avanzati), via Bonomea 265, 34136, Trieste, Italy
| | - Massimo Mella
- Dipartimento di Scienza ed Alta Tecnologia, Universitá degli Studi dell’Insubria, via Valleggio 11, 22100, Como, Italy
| |
Collapse
|
18
|
Orlandini E, Micheletti C. Topological and physical links in soft matter systems. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 34:013002. [PMID: 34547745 DOI: 10.1088/1361-648x/ac28bf] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Linking, or multicomponent topological entanglement, is ubiquitous in soft matter systems, from mixtures of polymers and DNA filaments packedin vivoto interlocked line defects in liquid crystals and intertwined synthetic molecules. Yet, it is only relatively recently that theoretical and experimental advancements have made it possible to probe such entanglements and elucidate their impact on the physical properties of the systems. Here, we review the state-of-the-art of this rapidly expanding subject and organize it as follows. First, we present the main concepts and notions, from topological linking to physical linking and then consider the salient manifestations of molecular linking, from synthetic to biological ones. We next cover the main physical models addressing mutual entanglements in mixtures of polymers, both linear and circular. Finally, we consider liquid crystals, fluids and other non-filamentous systems where topological or physical entanglements are observed in defect or flux lines. We conclude with a perspective on open challenges.
Collapse
Affiliation(s)
- Enzo Orlandini
- Department of Physics and Astronomy, University of Padova and Sezione INFN, Via Marzolo 8, Padova, Italy
| | - Cristian Micheletti
- SISSA, International School for Advanced Studies, via Bonomea 265, Trieste, Italy
| |
Collapse
|
19
|
Ma Z, Dorfman KD. Interactions between two knots in nanochannel-confined DNA molecules. J Chem Phys 2021; 155:154901. [PMID: 34686050 DOI: 10.1063/5.0067076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Experimental data on the interaction between two knots in deoxyribonucleic acid (DNA) confined in nanochannels produced two particular behaviors of knot pairs along the DNA molecules: (i) widely separated knots experience an attractive interaction but only remain in close proximity for several seconds and (ii) knots tend to remain separated until one of the knots unravels at the chain end. The associated free energy profile of the knot-knot separation distance for an ensemble of DNA knots exhibits a global minimum when knots are separated, indicating that the separated knot state is more stable than the intertwined knot state, with dynamics in the separated knot state that are consistent with independent diffusion. The experimental observations of knot-knot interactions under nanochannel confinement are inconsistent with previous simulation-based and experimental results for stretched polymers under tension wherein the knots attract and then stay close to each other. This inconsistency is postulated to result from a weaker fluctuation-induced attractive force between knots under confinement when compared to the knots under tension, the latter of which experience larger fluctuations in transverse directions.
Collapse
Affiliation(s)
- Zixue Ma
- 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
| |
Collapse
|
20
|
Affiliation(s)
- Peter Cifra
- Polymer Institute Slovak Academy of Sciences Bratislava 84541 Slovakia
| | - Tomáš Bleha
- Polymer Institute Slovak Academy of Sciences Bratislava 84541 Slovakia
| |
Collapse
|
21
|
Sharma RK, Agrawal I, Dai L, Doyle P, Garaj S. DNA Knot Malleability in Single-Digit Nanopores. NANO LETTERS 2021; 21:3772-3779. [PMID: 33661654 DOI: 10.1021/acs.nanolett.0c05142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Knots in long DNA molecules are prevalent in biological systems and serve as a model system for investigating static and dynamic properties of biopolymers. We explore the dynamics of knots in double-stranded DNA in a new regime of nanometer-scale confinement, large forces, and short time scales, using solid-state nanopores. We show that DNA knots undergo isomorphic translocation through a nanopore, retaining their equilibrium morphology by swiftly compressing in a lateral direction to fit the constriction. We observe no evidence of knot tightening or jamming, even for single-digit nanopores. We explain the observations as the malleability of DNA, characterized by sharp buckling of the DNA in nanopores, driven by the transient disruption of base pairing. Our molecular dynamics simulations support the model. These results are relevant not only for the understanding of DNA packing and manipulation in living cells but also for the polymer physics of DNA and the development of nanopore-based sequencing technologies.
Collapse
Affiliation(s)
- Rajesh Kumar Sharma
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602, Singapore
- Centre for Advanced 2D Materials, National University of Singapore, Singapore 117546, Singapore
| | - Ishita Agrawal
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, P. R. China
| | - Patrick Doyle
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602, Singapore
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Slaven Garaj
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
- Centre for Advanced 2D Materials, National University of Singapore, Singapore 117546, Singapore
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
| |
Collapse
|
22
|
Ma Z, Dorfman KD. Diffusion of Knotted DNA Molecules in Nanochannels in the Extended de Gennes Regime. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00143] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zixue Ma
- Department of Chemical Engineering and Materials Science, University of Minnesota−Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, United States
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota−Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
23
|
Pan M, Cai J, Li S, Xu L, Ma W, Xu C, Kuang H. Aptamer-Gated Ion Channel for Ultrasensitive Mucin 1 Detection. Anal Chem 2021; 93:4825-4831. [PMID: 33688720 DOI: 10.1021/acs.analchem.0c04137] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Detection of cancer markers is important for early diagnosis and timely treatment of cancer. In this study, we fabricated a tailorable gold nanofilm-anodized aluminum oxide (Au-AAO) ion channel through nanoparticle self-assembly and proposed a highly sensitive and selective Mucin 1 (MUC1) detection method. By engineering the optimal layers of the Au-AAO ion channel and encoding the aptamer between the interlayers, a highly controllable ion rectification phenomenon was observed. From this, the relationship between the rectification ratio (RR) and the concentration of MUC1 was established and the highly sensitive detection of MUC1 is achieved. We found that the aptamer-modified Au-AAO ion channel has a good linear range within the MUC1 concentration of 1-104 fg mL-1 and the limit of detection (LOD) was as low as 0.0364 fg mL-1 (0.0025 aM). Thus, this research opens a new horizon for fabricating multi-functional ion channels as well as developing ultrasensitive detection technologies.
Collapse
Affiliation(s)
- Mengying Pan
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Jiarong Cai
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Si Li
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Liguang Xu
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Wei Ma
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Chuanlai Xu
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Hua Kuang
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| |
Collapse
|
24
|
Zhu H, Tian F, Sun L, Wang S, Dai L. Revisiting the Non-monotonic Dependence of Polymer Knotting Probability on the Bending Stiffness. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haoqi Zhu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, P. R. China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, P. R. China
| | - Liang Sun
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, P. R. China
| | - Simin Wang
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, P. R. China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, P. R. China
| |
Collapse
|
25
|
Song Y, Schaufelberger F, Ashbridge Z, Pirvu L, Vitorica-Yrezabal IJ, Leigh DA. Effects of turn-structure on folding and entanglement in artificial molecular overhand knots. Chem Sci 2020; 12:1826-1833. [PMID: 34163946 PMCID: PMC8179330 DOI: 10.1039/d0sc05897a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The length and constitution of spacers linking three 2,6-pyridinedicarboxamide units in a molecular strand influence the tightness of the resulting overhand (open-trefoil) knot that the strand folds into in the presence of lanthanide(iii) ions. The use of β-hairpin forming motifs as linkers enables a metal-coordinated pseudopeptide with a knotted tertiary structure to be generated. The resulting pseudopeptide knot has one of the highest backbone-to-crossing ratios (BCR)—a measure of knot tightness (a high value corresponding to looseness)—for a synthetic molecular knot to date. Preorganization in the crossing-free turn section of the knot affects aromatic stacking interactions close to the crossing region. The metal-coordinated pseudopeptide knot is compared to overhand knots with other linkers of varying tightness and turn preorganization, and the entangled architectures characterized by NMR spectroscopy, ESI-MS, CD spectroscopy and, in one case, X-ray crystallography. The results show how it is possible to program specific conformational properties into different key regions of synthetic molecular knots, opening the way to systems where knotting can be systematically incorporated into peptide-like chains through design. Spacers linking 2,6-pyridinedicarboxamide units influence the tightness of the corresponding lanthanide-coordinated overhand knot. β-Hairpin forming motifs generate a metal-coordinated pseudopeptide with a knotted tertiary structure.![]()
Collapse
Affiliation(s)
- Yiwei Song
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 PR China
| | | | - Zoe Ashbridge
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | - Lucian Pirvu
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | | | - David A Leigh
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 PR China .,Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| |
Collapse
|
26
|
Lu L, Zhu H, Yuyuan Lu, An L, Dai L. Application of the Tube Model to Explain the Unexpected Decrease in Polymer Bending Energy Induced by Knot Formation. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luwei Lu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, P.R. China
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- University of Science and Technology of China, Chinese Academy of Sciences, Hefei 230026, P.R. China
| | - Haoqi Zhu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, P.R. China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
| | - Yuyuan Lu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Lijia An
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- University of Science and Technology of China, Chinese Academy of Sciences, Hefei 230026, P.R. China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, P.R. China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
| |
Collapse
|
27
|
Caraglio M, Marcone B, Baldovin F, Orlandini E, Stella AL. Topological Disentanglement of Linear Polymers under Tension. Polymers (Basel) 2020; 12:E2580. [PMID: 33153057 PMCID: PMC7692779 DOI: 10.3390/polym12112580] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 01/01/2023] Open
Abstract
We develop a theoretical description of the topological disentanglement occurring when torus knots reach the ends of a semiflexible polymer under tension. These include decays into simpler knots and total unknotting. The minimal number of crossings and the minimal knot contour length are the topological invariants playing a key role in the model. The crossings behave as particles diffusing along the chain and the application of appropriate boundary conditions at the ends of the chain accounts for the knot disentanglement. Starting from the number of particles and their positions, suitable rules allow reconstructing the type and location of the knot moving on the chain Our theory is extensively benchmarked with corresponding molecular dynamics simulations and the results show a remarkable agreement between the simulations and the theoretical predictions of the model.
Collapse
Affiliation(s)
- Michele Caraglio
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Boris Marcone
- Istituto Tecnico Economico Tecnologico Statale ‘L. Einaudi’, via Tommaso D’Aquino 8, I-36061 Bassano del Grappa, Italy;
| | - Fulvio Baldovin
- Dipartimento di Fisica e Astronomia and Sezione INFN Università di Padova, Via Marzolo 8, I-35131 Padova, Italy; (F.B.); (E.O.); (A.L.S.)
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN Università di Padova, Via Marzolo 8, I-35131 Padova, Italy; (F.B.); (E.O.); (A.L.S.)
| | - Attilio L. Stella
- Dipartimento di Fisica e Astronomia and Sezione INFN Università di Padova, Via Marzolo 8, I-35131 Padova, Italy; (F.B.); (E.O.); (A.L.S.)
| |
Collapse
|
28
|
Polson JM, Hastie CG. Free energy of a knotted polymer confined to narrow cylindrical and conical channels. Phys Rev E 2020; 102:052502. [PMID: 33327190 DOI: 10.1103/physreve.102.052502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/16/2020] [Indexed: 06/12/2023]
Abstract
Monte Carlo simulations are used to study the conformational behavior of a semiflexible polymer confined to cylindrical and conical channels. The channels are sufficiently narrow that the conditions for the Odijk regime are marginally satisfied. For cylindrical confinement, we examine polymers with a single knot of topology 3_{1}, 4_{1}, or 5_{1}, as well as unknotted polymers that are capable of forming S loops. We measure the variation of the free energy F with the end-to-end polymer extension length X and examine the effect of varying the polymer topology, persistence length P, and cylinder diameter D on the free-energy functions. Similarly, we characterize the behavior of the knot span along the channel. We find that increasing the knot complexity increases the typical size of the knot. In the regime of low X, where the knot/S-loop size is large, the conformational behavior is independent of polymer topology. In addition, the scaling properties of the free energy and knot span are in agreement with predictions from a theoretical model constructed using known properties of interacting polymers in the Odijk regime. We also examine the variation of F with the position of a knot in conical channels for various values of the cone angle α. The free energy decreases as the knot moves in a direction where the cone widens, and it also decreases with increasing α and with increasing knot complexity. The behavior is in agreement with predictions from a theoretical model in which the dominant contribution to the change in F is the change in the size of the hairpins as the knot moves to the wider region of the channel.
Collapse
Affiliation(s)
- James M Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island, C1A 4P3, Canada
| | - Cameron G Hastie
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island, C1A 4P3, Canada
| |
Collapse
|
29
|
Abstract
The properties of knots are exploited in a range of applications, from shoelaces to the knots used for climbing, fishing and sailing1. Although knots are found in DNA and proteins2, and form randomly in other long polymer chains3,4, methods for tying5 different sorts of knots in a synthetic nanoscale strand are lacking. Molecular knots of high symmetry have previously been synthesized by using non-covalent interactions to assemble and entangle molecular chains6-15, but in such instances the template and/or strand structure intrinsically determines topology, which means that only one type of knot is usually possible. Here we show that interspersing coordination sites for different metal ions within an artificial molecular strand enables it to be tied into multiple knots. Three topoisomers-an unknot (01) macrocycle, a trefoil (31) knot6-15, and a three-twist (52) knot-were each selectively prepared from the same molecular strand by using transition-metal and lanthanide ions to guide chain folding in a manner reminiscent of the action of protein chaperones16. We find that the metal-ion-induced folding can proceed with stereoinduction: in the case of one knot, a lanthanide(III)-coordinated crossing pattern formed only with a copper(I)-coordinated crossing of particular handedness. In an unanticipated finding, metal-ion coordination was also found to translocate an entanglement from one region of a knotted molecular structure to another, resulting in an increase in writhe (topological strain) in the new knotted conformation. The knot topology affects the chemical properties of the strand: whereas the tighter 52 knot can bind two different metal ions simultaneously, the looser 31 isomer can bind only either one copper(I) ion or one lutetium(III) ion. The ability to tie nanoscale chains into different knots offers opportunities to explore the modification of the structure and properties of synthetic oligomers, polymers and supramolecules.
Collapse
|
30
|
Michieletto D, Orlandini E, Turner MS, Micheletti C. Separation of Geometrical and Topological Entanglement in Confined Polymers Driven out of Equilibrium. ACS Macro Lett 2020; 9:1081-1085. [PMID: 35653213 DOI: 10.1021/acsmacrolett.0c00366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We use Brownian dynamics simulations and advanced topological profiling methods to characterize the out-of-equilibrium evolution of self-entanglement in linear polymers confined into nanochannels and under periodic compression. By introducing suitable observables, we can distinguish two main forms of entanglement that we term geometrical and topological. The latter is measured by the number of (essential) crossings of the physical knot detected after a suitable bridging of the chain termini. The former is instead measured as the average number of times a linear chain appears to cross itself when viewed under all projections and is irrespective of the physical knotted state. The key discovery of our work is that these two forms of entanglement are uncoupled and evolve with distinct dynamics. While geometrical entanglement is typically in phase with the compression-elongation cycles and it is primarily sensitive to its force f, the topological measure is mildly sensitive to cyclic modulation but strongly depends on both compression force f and duration k. The findings could assist the interpretation of experiments using fluorescence molecular tracers to track physical knots in polymers. Furthermore, we identify optimal regions in the experimentally controllable parameter space in which to obtain more/less topological and geometrical entanglement; this may help designing polymers with targeted topology.
Collapse
Affiliation(s)
- Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, United Kingdom.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, North Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Universitá degli Studi di Padova, I-35131 Padova, Italy
| | - Matthew S Turner
- Department of Physics and Centre for Complexity Science, University of Warwick, Coventry, CV4 7AL, U.K.,Department of Chemical Engineering, Kyoto University, Kyoto, Japan
| | - Cristian Micheletti
- SISSA (Scuola Internazionale Superiore di Studi Avanzati), Via Bonomea 265, 34136 Trieste, Italy
| |
Collapse
|
31
|
Affiliation(s)
- Zixue Ma
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
32
|
Shoura MJ, Giovan SM, Vetcher AA, Ziraldo R, Hanke A, Levene SD. Loop-closure kinetics reveal a stable, right-handed DNA intermediate in Cre recombination. Nucleic Acids Res 2020; 48:4371-4381. [PMID: 32182357 PMCID: PMC7192630 DOI: 10.1093/nar/gkaa153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 02/24/2020] [Accepted: 02/29/2020] [Indexed: 11/12/2022] Open
Abstract
In Cre site-specific recombination, the synaptic intermediate is a recombinase homotetramer containing a pair of loxP DNA target sites. The enzyme system's strand-exchange mechanism proceeds via a Holliday-junction (HJ) intermediate; however, the geometry of DNA segments in the synapse has remained highly controversial. In particular, all crystallographic structures are consistent with an achiral, planar Holliday-junction (HJ) structure, whereas topological assays based on Cre-mediated knotting of plasmid DNAs are consistent with a right-handed chiral junction. We use the kinetics of loop closure involving closely spaced (131-151 bp) loxP sites to investigate the in-aqueo ensemble of conformations for the longest-lived looped DNA intermediate. Fitting the experimental site-spacing dependence of the loop-closure probability, J, to a statistical-mechanical theory of DNA looping provides evidence for substantial out-of-plane HJ distortion, which unequivocally stands in contrast to the square-planar intermediate geometry from Cre-loxP crystal structures and those of other int-superfamily recombinases. J measurements for an HJ-isomerization-deficient Cre mutant suggest that the apparent geometry of the wild-type complex is consistent with temporal averaging of right-handed and achiral structures. Our approach connects the static pictures provided by crystal structures and the natural dynamics of macromolecules in solution, thus advancing a more comprehensive dynamic analysis of large nucleoprotein structures and their mechanisms.
Collapse
Affiliation(s)
- Massa J Shoura
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Stefan M Giovan
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Alexandre A Vetcher
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Riccardo Ziraldo
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Andreas Hanke
- Department of Physics, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA
| | - Stephen D Levene
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
- Physics, University of Texas at Dallas, Richardson, TX 75080, USA
| |
Collapse
|
33
|
Vandans O, Yang K, Wu Z, Dai L. Identifying knot types of polymer conformations by machine learning. Phys Rev E 2020; 101:022502. [PMID: 32168694 DOI: 10.1103/physreve.101.022502] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/14/2020] [Indexed: 02/04/2023]
Abstract
We investigate the use of artificial neural networks (NNs) as an alternative tool to current analytical methods for recognizing knots in a given polymer conformation. The motivation is twofold. First, it is of interest to examine whether NNs are effective at learning the global and sequential properties that uniquely define a knot. Second, knot classification is an important and unsolved problem in mathematical and physical sciences, and NNs may provide insights into this problem. Motivated by these points, we generate millions of polymer conformations for five knot types: 0, 3_{1}, 4_{1}, 5_{1}, and 5_{2}, and we design various NN models for classification. Our best model achieves a five-class classification accuracy of above 99% on a polymer of 100 monomers. We find that the sequential modeling ability of recurrent NNs is crucial for this result, as it outperforms feed-forward NNs and successfully generalizes to differently sized conformations as well. We present our methods and suggest that deep learning may be used in specific applications of knot detection where some error is permissible. Hopefully, with further development, NNs can offer an alternative computational method for knot identification and facilitate knot research in mathematical and physical sciences.
Collapse
Affiliation(s)
- Olafs Vandans
- Department of Physics, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Kaiyuan Yang
- Department of Computer Science, School of Computing, National University of Singapore, Singapore 117417, Singapore
| | - Zhongtao Wu
- Department of Mathematics, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China.,Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China
| |
Collapse
|
34
|
Bleha T, Cifra P. Compression and Stretching of Single DNA Molecules under Channel Confinement. J Phys Chem B 2020; 124:1691-1702. [PMID: 32045238 DOI: 10.1021/acs.jpcb.9b11602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We study the compression and extension response of single dsDNA (double-stranded DNA) molecules confined in cylindrical channels by means of Monte Carlo simulations. The elastic response of micrometer-sized DNA to the external force acting through the chain ends or through the piston is markedly affected by the size of the channel. The interpretation of the force (f)-displacement (R) functions under quasi-one-dimensional confinement is facilitated by resolving the overall change of displacement ΔR into the confinement contribution ΔRD and the force contribution ΔRf. The external stretching of confined DNA results in a characteristic pattern of f-R functions involving their shift to the larger extensions due to the channel-induced pre-stretching ΔRD. A smooth end-chain compression into loop-like conformations observed in moderately confined DNA can be accounted for by the relationship valid for a Gaussian chain in bulk. In narrow channels, the considerably pre-stretched DNA molecules abruptly buckle on compression by the backfolding into hairpins. On the contrary, the piston compression of DNA is characterized by a gradual reduction of the chain span S and by smooth f-S functions in the whole spatial range from the 3d near to 1d limits. The observed discrepancy between the shape of the f-R and f-S functions from two compression methods can be important for designing nanopiston experiments of compaction and knotting of single DNA in nanochannels.
Collapse
Affiliation(s)
- Tomáš Bleha
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
| |
Collapse
|
35
|
Kumar Sharma R, Agrawal I, Dai L, Doyle PS, Garaj S. Complex DNA knots detected with a nanopore sensor. Nat Commun 2019; 10:4473. [PMID: 31578328 PMCID: PMC6775256 DOI: 10.1038/s41467-019-12358-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/27/2019] [Indexed: 01/15/2023] Open
Abstract
Equilibrium knots are common in biological polymers-their prevalence, size distribution, structure, and dynamics have been extensively studied, with implications to fundamental biological processes and DNA sequencing technologies. Nanopore microscopy is a high-throughput single-molecule technique capable of detecting the shape of biopolymers, including DNA knots. Here we demonstrate nanopore sensors that map the equilibrium structure of DNA knots, without spurious knot tightening and sliding. We show the occurrence of both tight and loose knots, reconciling previous contradictory results from different experimental techniques. We evidence the occurrence of two quantitatively different modes of knot translocation through the nanopores, involving very different tension forces. With large statistics, we explore the complex knots and, for the first time, reveal the existence of rare composite knots. We use parametrized complexity, in concert with simulations, to test the theoretical assumptions of the models, further asserting the relevance of nanopores in future investigation of knots.
Collapse
Affiliation(s)
- Rajesh Kumar Sharma
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
- Singapore-MIT Alliance for Research and Technology Centre, 1 CREATE Way, Singapore, 138602, Singapore
- Centre for Advanced 2D Materials, National University of Singapore, 6 Science Drive 2, Singapore, 117546, Singapore
| | - Ishita Agrawal
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
| | - Liang Dai
- Department of Physics, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Patrick S Doyle
- Singapore-MIT Alliance for Research and Technology Centre, 1 CREATE Way, Singapore, 138602, Singapore.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Slaven Garaj
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore.
- Centre for Advanced 2D Materials, National University of Singapore, 6 Science Drive 2, Singapore, 117546, Singapore.
- Department of Physics, National University of Singapore, Singapore, Science Drive 3, Singapore, 117551, Singapore.
| |
Collapse
|
36
|
Affiliation(s)
- Liang Dai
- Department of Physics, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Beatrice W. Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
37
|
Soh BW, Klotz AR, Robertson-Anderson RM, Doyle PS. Long-Lived Self-Entanglements in Ring Polymers. PHYSICAL REVIEW LETTERS 2019; 123:048002. [PMID: 31491263 DOI: 10.1103/physrevlett.123.048002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/03/2019] [Indexed: 06/10/2023]
Abstract
The entanglement of ring polymers remains mysterious in many aspects. In this Letter, we use electric fields to induce self-entanglements in circular DNA molecules, which serve as a minimal system for studying chain entanglements. We show that self-threadings give rise to entanglements in ring polymers and can slow down polymer dynamics significantly. We find that strongly entangled circular molecules remain kinetically arrested in a compact state for very long times, thereby providing experimental evidence for the severe topological constraints imposed by threadings.
Collapse
Affiliation(s)
- Beatrice W Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Alexander R Klotz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Patrick S Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
38
|
Bleha T, Cifra P. Force-displacement relations at compression of dsDNA macromolecules. J Chem Phys 2019; 151:014901. [PMID: 31272182 DOI: 10.1063/1.5099522] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The elasticity of dsDNA molecules is investigated by Monte Carlo simulations based on a coarse-grained model of DNA. The force-displacement (f-r) curves are computed under the constraints of the constant force (Gibbs) or the constant length (Helmholtz) ensemble. Particular attention was paid to the compressional (negative) and weak tensile forces. It was confirmed that simulations using the vector Gibbs ensemble fail to represent the compression behavior of polymers. Simulations using the scalar Gibbs protocol resulted in a qualitatively correct compressional response of DNA provided that the quadratic averages of displacements were employed. Furthermore, a well-known shortcoming of the popular Marko-Siggia relation for DNA elasticity at weak tensile forces is elucidated. Conversely, the function f-r from the simulation at the constant length constraint, as well as the new closed-form expressions, provides a realistic depiction of the DNA elasticity over the wide range of negative and positive forces. Merely a qualitative resemblance of the compression functions f-r predicted by the employed approaches supports the notion that the elastic response of DNA molecules may be greatly affected by the specifics of the experimental setups and the kind of averaging of the measured variable.
Collapse
Affiliation(s)
- Tomáš Bleha
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
| |
Collapse
|
39
|
Kim YS, Dincau BM, Kwon YT, Kim JH, Yeo WH. Directly Accessible and Transferrable Nanofluidic Systems for Biomolecule Manipulation. ACS Sens 2019; 4:1417-1423. [PMID: 31062586 DOI: 10.1021/acssensors.9b00470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular detection and manipulation via nanofluidic systems offers new routes for single-molecule analysis to study epigenetic mechanisms and genetic mutation of disease. For detection of single biological molecule, many types of nanomicrofluidic systems have been utilized. Typically, mechanical tethering, fluidic pressure, chemical interactions, or electrical forces allow controllable attraction, enrichment, confinement, and elongation of target molecules. The currently available methods, however, are unable to offer both molecular manipulation and direct and concurrent assessment of target molecules in the system due to the nature of enclosed channels and associated fluidic components. Here, we introduce a wafer-scale nanofluidic system that incorporates an array of accessible open nanochannels and nano-microtrappers to enrich and elongate target molecules (DNA) via the combination of an electric field and hydrodynamic force. The open nanofluidic system allows easy access, direct observation, and manipulation of molecules in the nanochannels. The presence of a stretched single DNA and the efficacy of the nanofluidic system are studied by fluorescence microscopy and atomic force microscopy. Hybrid integration of the nanodevice fabrication with a material transfer printing technique enables to design a highly flexible and transferrable nanofluidic system after molecular concentration.
Collapse
Affiliation(s)
| | - Brian M. Dincau
- School of Engineering and Computer Science, Washington State University, Vancouver, Washington 98686, United States
| | | | - Jong-Hoon Kim
- School of Engineering and Computer Science, Washington State University, Vancouver, Washington 98686, United States
| | | |
Collapse
|
40
|
Weiss LB, Marenda M, Micheletti C, Likos CN. Hydrodynamics and Filtering of Knotted Ring Polymers in Nanochannels. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00516] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Lisa B. Weiss
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Mattia Marenda
- SISSA, International School of Advanced Studies, via Bonomea 265, I-34136 Trieste, Italy
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, U.K
| | - Cristian Micheletti
- SISSA, International School of Advanced Studies, via Bonomea 265, I-34136 Trieste, Italy
| | - Christos N. Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| |
Collapse
|
41
|
Caraglio M, Baldovin F, Marcone B, Orlandini E, Stella AL. Topological Disentanglement Dynamics of Torus Knots on Open Linear Polymers. ACS Macro Lett 2019; 8:576-581. [PMID: 35619367 DOI: 10.1021/acsmacrolett.9b00055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We simulate and study the topological disentanglement occurring when torus knots reach the ends of a semiflexible open polymer (decay into simpler knots or unknotting). Through a rescaling procedure and the application of appropriate boundary conditions, we show that the full unknotting process can be understood in terms of point-like particles representing essential crossings, diffusing on the support [0, 1]. We address the bending and configurational free energy drives on the diffusion process, together with the scaling properties of the effective diffusion and friction coefficients. Agreement with simulations suggests universal features for these two model parameters.
Collapse
Affiliation(s)
- Michele Caraglio
- KU Leuven, Soft Matter and Biophysics Section, Celestijnenlaan 200D, 3001 Leuven, Belgium
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Fulvio Baldovin
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy
- INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - Boris Marcone
- Center of Excellence for Stability Police Units, via Medici 87, 36100 Vicenza, Italy
| | - Enzo Orlandini
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy
- INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - Attilio L. Stella
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy
- INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
| |
Collapse
|
42
|
Wang J, Yan Y, Geng Y, Gan Y, Fang Z. Fabrication of polydimethylsiloxane nanofluidic chips under AFM tip-based nanomilling process. NANOSCALE RESEARCH LETTERS 2019; 14:136. [PMID: 30997583 PMCID: PMC6470239 DOI: 10.1186/s11671-019-2962-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 04/01/2019] [Indexed: 05/03/2023]
Abstract
In current research realm, polydimethylsiloxane (PDMS)-based nanofluidic devices are widely used in medical, chemical, and biological applications. In the present paper, a novel nanomilling technique (consisting of an AFM system and a piezoelectric actuator) was proposed to fabricate nanochannels (with controllable sizes) on PDMS chips, and nanochannel size was controlled by the driving voltage and frequency inputted to the piezoelectric actuator. Moreover, microchannel and nanochannel molds were respectively fabricated by UV lithography and AFM tip-based nanomilling, and finally, PDMS slabs with micro/nanochannels were obtained by transfer process. The influences of PDMS weight ratio on nanochannel size were also investigated. The bonding process of microchannel and nanochannel slabs was conducted on a homemade alignment system consisted of an optical monocular microscope and precision stages. Furthermore, the effects of nanochannel size on electrical characteristics of KCl solution (concentration of 1 mM) were analyzed. Therefore, it can be concluded that PDMS nanofluidic devices with multiple nanochannels of sub-100-nm depth can be efficiently and economically fabricated by the proposed method.
Collapse
Affiliation(s)
- Jiqiang Wang
- Key Laboratory of Micro-systems and Micro-structures Manufacturing of Ministry of Education, Harbin Institute of Technology, Harbin, 150001 Heilongjiang People’s Republic of China
- Center for Precision Engineering, Harbin Institute of Technology, Harbin, 150001 Heilongjiang People’s Republic of China
| | - Yongda Yan
- Key Laboratory of Micro-systems and Micro-structures Manufacturing of Ministry of Education, Harbin Institute of Technology, Harbin, 150001 Heilongjiang People’s Republic of China
- Center for Precision Engineering, Harbin Institute of Technology, Harbin, 150001 Heilongjiang People’s Republic of China
| | - Yanquan Geng
- Key Laboratory of Micro-systems and Micro-structures Manufacturing of Ministry of Education, Harbin Institute of Technology, Harbin, 150001 Heilongjiang People’s Republic of China
- Center for Precision Engineering, Harbin Institute of Technology, Harbin, 150001 Heilongjiang People’s Republic of China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001 People’s Republic of China
| | - Yang Gan
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001 People’s Republic of China
| | - Zhuo Fang
- Center for Precision Engineering, Harbin Institute of Technology, Harbin, 150001 Heilongjiang People’s Republic of China
| |
Collapse
|
43
|
Abstract
We examine how channel confinement affects the equilibrium properties of topologically linked ring polymers and, by contrast, of equivalent unlinked rings, too. By performing extensive simulations of semiflexible rings of different chain length, N, and channel diameter, D, we discover three notable properties purely due to linking. First, upon entering the weak confinement regime, the length of the physically linked portion, lLKThe, becomes independent of chain length. Next, even when confinement is strong enough to pull apart and segregate unlinked rings, lLK stays much larger than in the highly stretched limit. Finally, at fixed N, lLK varies approximately as D0.5, and we provide a simple scaling argument for this power-law behavior. These properties, which may hold for different link topologies, can be tested by current experimental setups on DNA rings confined in microchannels. Moreover, they could be relevant for the efficient in vivo unlinking of newly replicated bacterial chromosomes.
Collapse
|
44
|
Lee S, Lee Y, Kim Y, Wang C, Park J, Jung GY, Chen Y, Chang R, Ikeda S, Sugiyama H, Jo K. Nanochannel-Confined TAMRA-Polypyrrole Stained DNA Stretching by Varying the Ionic Strength from Micromolar to Millimolar Concentrations. Polymers (Basel) 2018; 11:E15. [PMID: 30959999 PMCID: PMC6401831 DOI: 10.3390/polym11010015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022] Open
Abstract
Large DNA molecules have been utilized as a model system to investigate polymer physics. However, DNA visualization via intercalating dyes has generated equivocal results due to dye-induced structural deformation, particularly unwanted unwinding of the double helix. Thus, the contour length increases and the persistence length changes so unpredictably that there has been a controversy. In this paper, we used TAMRA-polypyrrole to stain single DNA molecules. Since this staining did not change the contour length of B-form DNA, we utilized TAMRA-polypyrrole stained DNA as a tool to measure the persistence length by changing the ionic strength. Then, we investigated DNA stretching in nanochannels by varying the ionic strength from 0.06 mM to 47 mM to evaluate several polymer physics theories proposed by Odijk, de Gennes and recent papers to deal with these regimes.
Collapse
Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| | - Yelin Lee
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| | - Yongkyun Kim
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| | - Cong Wang
- Department of Mechanical Engineering, Sogang University, Seoul 04107, Korea.
| | - Jungyul Park
- Department of Mechanical Engineering, Sogang University, Seoul 04107, Korea.
| | - Gun Young Jung
- School of Material Science and Engineering, GIST, Gwangju 61005, Korea.
| | - Yenglong Chen
- Institute of Physics, Academia Sinica and Department of Chemical Engineering, National Tsing-Hua University and Department of Physics, National Taiwan University, Taipei 10617, Taiwan.
| | - Rakwoo Chang
- Department of Chemistry, Kwangwoon University, Seoul 01897, Korea.
| | - Shuji Ikeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8501, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8501, Japan.
| | - Kyubong Jo
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| |
Collapse
|
45
|
Soh BW, Klotz AR, Doyle PS. Untying of Complex Knots on Stretched Polymers in Elongational Fields. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01879] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Beatrice W. Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alexander R. Klotz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
46
|
Berard DJ, Leslie SR. Miniaturized flow cell with pneumatically-actuated vertical nanoconfinement for single-molecule imaging and manipulation. BIOMICROFLUIDICS 2018; 12:054107. [PMID: 30344834 PMCID: PMC6167230 DOI: 10.1063/1.5052005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 09/17/2018] [Indexed: 05/06/2023]
Abstract
Convex Lens-induced Confinement (CLiC) is a single-molecule imaging technique that uses a deformable glass flow cell to gently trap, manipulate, and visualize single molecules within micro- and nano-structures, to enable a wide range of applications. Here, we miniaturize the CLiC flow cell, from 25 × 25 to 3 × 3 mm 2 and introduce pneumatic control of the confinement. Miniaturization of the flow cell improves fabrication throughput by almost two orders of magnitude and, advantageous for pharmaceutical and diagnostic applications where samples are precious, significantly lowers the internal volume from microliters to nanoliters. Pneumatic control of the device reduces the confinement gradient and improves mechanical stability while maintaining low autofluorescence and refractive index-matching with oil-immersion objectives. To demonstrate our "mini CLiC" system, we confine and image DNA in sub-50 nm nanogrooves, with high DNA extension consistent with the Odijk confinement regime.
Collapse
Affiliation(s)
- Daniel J Berard
- Department of Physics, McGill University, Montreal H3A 2T8, Canada
| | - Sabrina R Leslie
- Department of Physics, McGill University, Montreal H3A 2T8, Canada
| |
Collapse
|
47
|
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.
Collapse
Affiliation(s)
- Tomáš Bleha
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
| |
Collapse
|
48
|
Affiliation(s)
- Liang Dai
- BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore 117543
| | - Patrick S. Doyle
- BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore 117543
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, United States
| |
Collapse
|
49
|
Bernier S, Huang A, Reisner W, Bhattacharya A. Evolution of Nested Folding States in Compression of a Strongly Confined Semiflexible Chain. Macromolecules 2018. [DOI: 10.1021/acs.macromol.7b02748] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Simon Bernier
- Department of Physics, McGill University, 3600 rue university, Montreal, Quebec H3A 2T8, Canada
| | - Aiqun Huang
- Department of Physics, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
| | - Walter Reisner
- Department of Physics, McGill University, 3600 rue university, Montreal, Quebec H3A 2T8, Canada
| | - Aniket Bhattacharya
- Department of Physics, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
| |
Collapse
|