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Li C, Chen Q, Ding M. Escape dynamics of active ring polymers in a cylindrical nanochannel. SOFT MATTER 2024; 20:1719-1724. [PMID: 38284326 DOI: 10.1039/d3sm01524f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
We explore the escape dynamics of active ring polymers confined in a cylindrical nanochannel using Brownian dynamics. Our simulation results show that the escape time decreases with the increase of the Péclet number, which is not noticeable between the two stages of the escape process, based on whether the center of mass of the polymer is inside or outside the nanochannel. However, the monomer motion trajectory of the active polymer is very different from that of the passive polymer, similar to the snake-like motion with uniform velocity. The passive polymer, however, is in constant fugitive motion with increased velocity at the tail end of the escape. Our work is vital for understanding the escape dynamics of active ring polymers in the confined nanochannel, which provides new perspectives on their characterization and analysis.
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Affiliation(s)
- Chuqiao Li
- Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, China
| | - Qiaoyue Chen
- Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, China
| | - Mingming Ding
- Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, China
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, China.
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2
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Chaudhuri D, Banerjee S, Chakraborty S, Chowdhury D, Haldar S. Direct Observation of the Mechanical Role of Bacterial Chaperones in Protein Folding. Biomacromolecules 2022; 23:2951-2967. [PMID: 35678300 DOI: 10.1021/acs.biomac.2c00451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein folding under force is an integral source of generating mechanical energy in various cellular processes, ranging from protein translation to degradation. Although chaperones are well known to interact with proteins under mechanical force, how they respond to force and control cellular energetics remains unknown. To address this question, we introduce a real-time magnetic tweezer technology herein to mimic the physiological force environment on client proteins, keeping the chaperones unperturbed. We studied two structurally distinct client proteins--protein L and talin with seven different chaperones─independently and in combination and proposed a novel mechanical activity of chaperones. We found that chaperones behave differently, while these client proteins are under force, than their previously known functions. For instance, tunnel-associated chaperones (DsbA and trigger factor), otherwise working as holdase without force, assist folding under force. This process generates an additional mechanical energy up to ∼147 zJ to facilitate translation or translocation. However, well-known cytoplasmic foldase chaperones (PDI, thioredoxin, or DnaKJE) do not possess the mechanical folding ability under force. Notably, the transferring chaperones (DnaK, DnaJ, and SecB) act as holdase and slow down the folding process, both in the presence and absence of force, to prevent misfolding of the client proteins. This provides an emerging insight of mechanical roles of chaperones: they can generate or consume energy by shifting the energy landscape of the client proteins toward a folded or an unfolded state, suggesting an evolutionary mechanism to minimize energy consumption in various biological processes.
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Affiliation(s)
- Deep Chaudhuri
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Souradeep Banerjee
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Soham Chakraborty
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Debojyoti Chowdhury
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Shubhasis Haldar
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
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3
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Chen J, Sun L, Wang S, Tian F, Zhu H, Zhang R, Dai L. Crowding-induced polymer trapping in a channel. Phys Rev E 2021; 104:054502. [PMID: 34942690 DOI: 10.1103/physreve.104.054502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 10/20/2021] [Indexed: 11/07/2022]
Abstract
In this work, we report an intriguing phenomenon: crowding-induced polymer trapping in a channel. Using Langevin dynamics simulations and analytical calculations, we find that for a polymer confined in a channel, crowding particles can push a polymer into the channel corner through inducing an effective polymer-corner attraction due to the depletion effect. This phenomenon is referred to as polymer trapping. The occurrence of polymer trapping requires a minimum volume fraction of crowders, ϕ^{*}, which scales as ϕ^{*}∼(a_{c}/L_{p})^{1/3} for a_{c}≫a_{m} and ϕ^{*}∼(a_{c}/L_{p})^{1/3}(a_{c}/a_{m})^{1/2} for a_{c}≪a_{m}, where a_{c} is the crowder diameter, a_{m} is the monomer diameter, and L_{p} is the polymer persistence length. For DNA, ϕ^{*} is estimated to be around 0.25 for crowders with a_{c}=2nm. We find that ϕ^{*} also strongly depends on the shape of the channel cross section, and ϕ^{*} is much smaller for a triangle channel than a square channel. The polymer trapping leads to a nearly fully stretched polymer conformation along a channel corner, which may have practical applications, such as full stretching of DNA for the nanochannel-based genome mapping technology.
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Affiliation(s)
- Jialu Chen
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Liang Sun
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Simin Wang
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Haoqi Zhu
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Ruiqin Zhang
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Hong Kong, China
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4
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Teng Y, Andersen NT, Chen JZY. Statistical Properties of a Slit-Confined Wormlike Chain of Finite Length. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Yue Teng
- Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Nigel T. Andersen
- Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jeff Z. Y. Chen
- Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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5
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Eckels EC, Chaudhuri D, Chakraborty S, Echelman DJ, Haldar S. DsbA is a redox-switchable mechanical chaperone. Chem Sci 2021; 12:11109-11120. [PMID: 34522308 PMCID: PMC8386657 DOI: 10.1039/d1sc03048e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 07/17/2021] [Indexed: 12/18/2022] Open
Abstract
DsbA is a ubiquitous bacterial oxidoreductase that associates with substrates during and after translocation, yet its involvement in protein folding and translocation remains an open question. Here we demonstrate a redox-controlled chaperone activity of DsbA, on both cysteine-containing and cysteine-free substrates, using magnetic tweezers-based single molecule force spectroscopy that enables independent measurements of oxidoreductase activity and chaperone behavior. Interestingly we found that this chaperone activity is tuned by the oxidation state of DsbA; oxidized DsbA is a strong promoter of folding, but the effect is weakened by the reduction of the catalytic CXXC motif. We further localize the chaperone binding site of DsbA using a seven-residue peptide which effectively blocks the chaperone activity. We found that the DsbA assisted folding of proteins in the periplasm generates enough mechanical work to decrease the ATP consumption needed for periplasmic translocation by up to 33%.
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Affiliation(s)
- Edward C Eckels
- Department of Biological Sciences, Columbia University New York NY 10027 USA
- Department of Internal Medicine, Columbia University Medical Center New York NY 10032 USA
| | - Deep Chaudhuri
- Department of Biological Sciences, Ashoka University Sonepat Haryana 131029 India
| | - Soham Chakraborty
- Department of Biological Sciences, Ashoka University Sonepat Haryana 131029 India
| | - Daniel J Echelman
- Department of Biological Sciences, Columbia University New York NY 10027 USA
| | - Shubhasis Haldar
- Department of Biological Sciences, Ashoka University Sonepat Haryana 131029 India
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6
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Pezzuoli D, Angeli E, Repetto D, Ferrera F, Guida P, Firpo G, Repetto L. Nanofluidic-Based Accumulation of Antigens for Miniaturized Immunoassay. SENSORS 2020; 20:s20061615. [PMID: 32183234 PMCID: PMC7146560 DOI: 10.3390/s20061615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 01/29/2023]
Abstract
The continuous advances of Nanofluidics have been stimulating the development of novel nanostructures and strategies to accumulate very diluted analytes, for implementing a new class of high sensitivity miniaturized polymeric sensors. We take advantage of the electrokinetic properties of these structures, which allow accumulating analytes inside asymmetric microfluidic structures to implement miniaturized sensors able to detect diluted solutions down to nearly 1.2 pg/mL. In particular, exploiting polydimethylsiloxane devices, fabricated by using the junction gap breakdown technique, we concentrate antigens inside a thin microfunnel functionalized with specific antibodies to favor the interaction and, if it is the case, the recognition between antigens in solution and antibodies anchored to the surface. The transduction mechanism consists in detecting the fluorescence signal of labeled avidin when it binds to biotinylated antigens. Here, we demonstrate that exploiting these electrokinetic phenomena, typical of nanofluidic structures, we succeeded in concentrating biomolecules in correspondence of a 1 pL sensing region, a strategy that grants to the device performance comparable to standard immunoassays.
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Affiliation(s)
- Denise Pezzuoli
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
| | - Elena Angeli
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
- Correspondence:
| | - Diego Repetto
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
| | - Francesca Ferrera
- Centre of Excellence for Biomedical Research, University of Genoa, viale Benedetto XV 9, 16132 Genoa, Italy
| | - Patrizia Guida
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
| | - Giuseppe Firpo
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
| | - Luca Repetto
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
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7
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Pezzuoli D, Angeli E, Repetto D, Guida P, Firpo G, Repetto L. Increased Flexibility in Lab-on-Chip Design with a Polymer Patchwork Approach. NANOMATERIALS 2019; 9:nano9121678. [PMID: 31775220 PMCID: PMC6955689 DOI: 10.3390/nano9121678] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 12/14/2022]
Abstract
Nanofluidic structures are often the key element of many lab-on-chips for biomedical and environmental applications. The demand for these devices to be able to perform increasingly complex tasks triggers a request for increasing the performance of the fabrication methods. Soft lithography and poly(dimethylsiloxane) (PDMS) have since long been the basic ingredients for producing low-cost, biocompatible and flexible devices, replicating nanostructured masters. However, when the desired functionalities require the fabrication of shallow channels, the “roof collapse” phenomenon, that can occur when sealing the replica, can impair the device functionalities. In this study, we demonstrate that a “focused drop-casting” of h-PDMS (hard PDMS) on nanostructured regions, provides the necessary stiffness to avoid roof collapse, without increasing the probability of deep cracks formation, a drawback that shows up in the peel-off step, when h-PDMS is used all over the device area. With this new approach, we efficiently fabricate working devices with reproducible sub-100 nm structures. We verify the absence of roof collapse and deep cracks by optical microscopy and, in order to assess the advantages that are introduced by the proposed technique, the acquired images are compared with those of cracked devices, whose top layer, of h-PDMS, and with those of collapsed devices, made of standard PDMS. The geometry of the critical regions is studied by atomic force microscopy of their resin casts. The electrical resistance of the nanochannels is measured and shown to be compatible with the estimates that can be obtained from the geometry. The simplicity of the method and its reliability make it suitable for increasing the fabrication yield and reducing the costs of nanofluidic polymeric lab-on-chips.
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8
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Zhang Y, Huang Z, He Y, Miao X. Enhancing the efficiency of energy harvesting from salt gradient with ion-selective nanochannel. NANOTECHNOLOGY 2019; 30:295402. [PMID: 30861495 DOI: 10.1088/1361-6528/ab0ed8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The development of a nanofluidic energy harvesting system plays a fundamental role in harvesting osmotic power from Gibbs free energy within the salt concentration gradient, which is considered to be a clean and renewable energy source for the future. In this study, a silica-nanochannel based nanofluidic energy harvesting system was fabricated and the output power density reached 705 W m-2 under suitable KCl concentration bias which exceeded-by almost two orders of magnitude-the results obtained by previous work. The enhancement of energy harvesting was mainly ascribed to the appropriate length of nanochannel that provides a good balance between the desirable ion selectivity and the unfavorable large resistance from the nanochannel. This high-performance nanofluidic energy device could be used in a variety of applications, including to power tiny biomedical devices or for constructing future clean-energy recovery plants.
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Affiliation(s)
- Yan Zhang
- Wuhan National Research Center for Optoelectronics, School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
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9
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Fernandez-Cuesta I, West MM, Montinaro E, Schwartzberg A, Cabrini S. A nanochannel through a plasmonic antenna gap: an integrated device for single particle counting. LAB ON A CHIP 2019; 19:2394-2403. [PMID: 31204419 DOI: 10.1039/c9lc00186g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Plasmonic nanoantennas are ideal for single molecule detection since they nano-focus the light beyond diffraction and enhance the optical fields by several orders of magnitude. But delivering the molecules into these nanometric hot-spots is a real challenge. Here, we present a dynamic sensor, with label-free real-time detection capabilities, which can detect and count molecules and particles one by one in their native environment independently of their concentration. To this end, we have integrated a 35 nm gap plasmonic bowtie antenna with a 30 nm × 30 nm nanochannel. The channel runs through the antenna gap, and delivers the analyte directly into the hot spot. We show how the antenna probes into zeptoliter volumes inside the nanochannel by observing the dark field resonance shift during the filling process of a non-fluorescent liquid. Moreover, we detect and count single quantum dots, one by one, at ultra-high concentrations of up to 25 mg mL-1. The nano-focusing of light, reduces the observation volume in five orders of magnitude compared to the diffraction limited spot, beating the diffraction limit. These results prove the unique sensitivity of the device and in the future can be extended to detection of a variety of molecules for biomedical applications.
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10
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Polson JM. Free Energy of a Folded Semiflexible Polymer Confined to a Nanochannel of Various Geometries. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01148] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- James M. Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island C1A 4P3, Canada
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11
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Cheong GK, Li X, Dorfman KD. Wall depletion length of a channel-confined polymer. Phys Rev E 2017; 95:022501. [PMID: 28297899 DOI: 10.1103/physreve.95.022501] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Indexed: 11/07/2022]
Abstract
Numerous experiments have taken advantage of DNA as a model system to test theories for a channel-confined polymer. A tacit assumption in analyzing these data is the existence of a well-defined depletion length characterizing DNA-wall interactions such that the experimental system (a polyelectrolyte in a channel with charged walls) can be mapped to the theoretical model (a neutral polymer with hard walls). We test this assumption using pruned-enriched Rosenbluth method (PERM) simulations of a DNA-like semiflexible polymer confined in a tube. The polymer-wall interactions are modeled by augmenting a hard wall interaction with an exponentially decaying, repulsive soft potential. The free energy, mean span, and variance in the mean span obtained in the presence of a soft wall potential are compared to equivalent simulations in the absence of the soft wall potential to determine the depletion length. We find that the mean span and variance about the mean span have the same depletion length for all soft potentials we tested. In contrast, the depletion length for the confinement free energy approaches that for the mean span only when depletion length no longer depends on channel size. The results have implications for the interpretation of DNA confinement experiments under low ionic strengths.
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Affiliation(s)
- Guo Kang Cheong
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - Xiaolan Li
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - 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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12
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Han M, Kim BC, Matsuoka T, Thouless MD, Takayama S. Dynamic simulations show repeated narrowing maximizes DNA linearization in elastomeric nanochannels. BIOMICROFLUIDICS 2016; 10:064108. [PMID: 27965731 PMCID: PMC5123996 DOI: 10.1063/1.4967963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 01/03/2017] [Accepted: 11/04/2016] [Indexed: 06/06/2023]
Abstract
This paper uses computer simulations to reveal unprecedented details about linearization of deoxyribonucleic acid (DNA) inside dynamic nanochannels that can be repeatedly widened and narrowed. We first analyze the effect of rate of channel narrowing on DNA linearization dynamics. Quick (∼0.1 s) narrowing of nanoscale channels results in rapid overstretching of the semi-flexible chain followed by a slower (∼0.1-10 s) relaxation to an equilibrium extension. Two phenomena that induce linearization during channel narrowing, namely, elongational-flow and confinement, occur simultaneously, regardless of narrowing speed. Interestingly, although elongational flow is a minimum at the mid-point of the channel and increases towards the two ends, neither the linearization dynamics nor the degree of DNA extension varies significantly with the center-of-mass of the polymer projected on the channel axis. We also noticed that there was a significant difference in time to reach the equilibrium length, as well as the degree of DNA linearization at short times, depending on the initial conformation of the biopolymer. Based on these observations, we tested a novel linearization protocol where the channels are narrowed and widened repeatedly, allowing DNA to explore multiple conformations. Repeated narrowing and widening, something uniquely enabled by the elastomeric nanochannels, significantly decrease the time to reach the equilibrium-level of stretch when performed within periods comparable to the chain relaxation time and more effectively untangle chains into more linearized biopolymers.
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Affiliation(s)
- Minsub Han
- Department of Mechanical Engineering, College of Engineering, Incheon National University , Songdo-dong, Yeonsu-gu, Incheon 406-772, South Korea
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13
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Jain A, Sheats J, Reifenberger JG, Cao H, Dorfman KD. Modeling the relaxation of internal DNA segments during genome mapping in nanochannels. BIOMICROFLUIDICS 2016; 10:054117. [PMID: 27795749 PMCID: PMC5065570 DOI: 10.1063/1.4964927] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 10/04/2016] [Indexed: 06/01/2023]
Abstract
We have developed a multi-scale model describing the dynamics of internal segments of DNA in nanochannels used for genome mapping. In addition to the channel geometry, the model takes as its inputs the DNA properties in free solution (persistence length, effective width, molecular weight, and segmental hydrodynamic radius) and buffer properties (temperature and viscosity). Using pruned-enriched Rosenbluth simulations of a discrete wormlike chain model with circa 10 base pair resolution and a numerical solution for the hydrodynamic interactions in confinement, we convert these experimentally available inputs into the necessary parameters for a one-dimensional, Rouse-like model of the confined chain. The resulting coarse-grained model resolves the DNA at a length scale of approximately 6 kilobase pairs in the absence of any global hairpin folds, and is readily studied using a normal-mode analysis or Brownian dynamics simulations. The Rouse-like model successfully reproduces both the trends and order of magnitude of the relaxation time of the distance between labeled segments of DNA obtained in experiments. The model also provides insights that are not readily accessible from experiments, such as the role of the molecular weight of the DNA and location of the labeled segments that impact the statistical models used to construct genome maps from data acquired in nanochannels. The multi-scale approach used here, while focused towards a technologically relevant scenario, is readily adapted to other channel sizes and polymers.
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Affiliation(s)
- Aashish Jain
- 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
| | | | - Han Cao
- BioNano Genomics , 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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14
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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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15
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Angeli E, Volpe A, Fanzio P, Repetto L, Firpo G, Guida P, Savio RL, Wanunu M, Valbusa U. Simultaneous Electro-Optical Tracking for Nanoparticle Recognition and Counting. NANO LETTERS 2015; 15:5696-5701. [PMID: 26225640 PMCID: PMC5146980 DOI: 10.1021/acs.nanolett.5b01243] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We present the first detailed experimental observation and analysis of nanoparticle electrophoresis through a nanochannel obtained with synchronous high-bandwidth electrical and camera recordings. Optically determined particle diffusion coefficients agree with values extracted from fitting electrical transport measurements to distributions from 1D Fokker-Planck diffusion-drift theory. This combined tracking strategy enables optical recognition and electrical characterization of nanoparticles in solution, which can have a broad range of applications in biology and materials science.
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Affiliation(s)
- Elena Angeli
- Nanomed Laboratories, Dipartimento di Fisica, Università di Genova, 16146 Genova, Italy
- Corresponding Authors. ,
| | - Andrea Volpe
- Nanomed Laboratories, Dipartimento di Fisica, Università di Genova, 16146 Genova, Italy
| | - Paola Fanzio
- Nanomed Laboratories, Dipartimento di Fisica, Università di Genova, 16146 Genova, Italy
| | - Luca Repetto
- Nanomed Laboratories, Dipartimento di Fisica, Università di Genova, 16146 Genova, Italy
| | - Giuseppe Firpo
- Nanomed Laboratories, Dipartimento di Fisica, Università di Genova, 16146 Genova, Italy
| | - Patrizia Guida
- Nanomed Laboratories, Dipartimento di Fisica, Università di Genova, 16146 Genova, Italy
| | - Roberto Lo Savio
- Nanomed Laboratories, Dipartimento di Fisica, Università di Genova, 16146 Genova, Italy
| | - Meni Wanunu
- Department of Physics and Chemistry/Chemical Biology, Northeastern University, Boston 02115, Massachusetts, United States
- Corresponding Authors. ,
| | - Ugo Valbusa
- Nanomed Laboratories, Dipartimento di Fisica, Università di Genova, 16146 Genova, Italy
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16
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de Carvalho SJ, Metzler R, Cherstvy AG. Inverted critical adsorption of polyelectrolytes in confinement. SOFT MATTER 2015; 11:4430-4443. [PMID: 25940939 DOI: 10.1039/c5sm00635j] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
What are the fundamental laws for the adsorption of charged polymers onto oppositely charged surfaces, for convex, planar, and concave geometries? This question is at the heart of surface coating applications, various complex formation phenomena, as well as in the context of cellular and viral biophysics. It has been a long-standing challenge in theoretical polymer physics; for realistic systems the quantitative understanding is however often achievable only by computer simulations. In this study, we present the findings of such extensive Monte-Carlo in silico experiments for polymer-surface adsorption in confined domains. We study the inverted critical adsorption of finite-length polyelectrolytes in three fundamental geometries: planar slit, cylindrical pore, and spherical cavity. The scaling relations extracted from simulations for the critical surface charge density σc-defining the adsorption-desorption transition-are in excellent agreement with our analytical calculations based on the ground-state analysis of the Edwards equation. In particular, we confirm the magnitude and scaling of σc for the concave interfaces versus the Debye screening length 1/κ and the extent of confinement a for these three interfaces for small κa values. For large κa the critical adsorption condition approaches the known planar limit. The transition between the two regimes takes place when the radius of surface curvature or half of the slit thickness a is of the order of 1/κ. We also rationalize how σc(κ) dependence gets modified for semi-flexible versus flexible chains under external confinement. We examine the implications of the chain length for critical adsorption-the effect often hard to tackle theoretically-putting an emphasis on polymers inside attractive spherical cavities. The applications of our findings to some biological systems are discussed, for instance the adsorption of nucleic acids onto the inner surfaces of cylindrical and spherical viral capsids.
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Affiliation(s)
- Sidney J de Carvalho
- Institute of Biosciences, Letters and Exact Sciences, Sao Paulo State University, 15054-000 Sao Jose do Rio Preto, Brazil.
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Manneschi C, Fanzio P, Ala-Nissila T, Angeli E, Repetto L, Firpo G, Valbusa U. Stretching of DNA confined in nanochannels with charged walls. BIOMICROFLUIDICS 2014; 8:064121. [PMID: 25553196 PMCID: PMC4265123 DOI: 10.1063/1.4904008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/01/2014] [Indexed: 05/04/2023]
Abstract
There is currently a growing interest in control of stretching of DNA inside nanoconfined regions due to the possibility to analyze and manipulate single biomolecules for applications such as DNA mapping and barcoding, which are based on stretching the DNA in a linear fashion. In the present work, we couple Finite Element Methods and Monte Carlo simulations in order to study the conformation of DNA molecules confined in nanofluidic channels with neutral and charged walls. We find that the electrostatic forces become more and more important when lowering the ionic strength of the solution. The influence of the nanochannel cross section geometry is also studied by evaluating the DNA elongation in square, rectangular, and triangular channels. We demonstrate that coupling electrostatically interacting walls with a triangular geometry is an efficient way to stretch DNA molecules at the scale of hundreds of nanometers. The paper reports experimental observations of λ-DNA molecules in poly(dimethylsiloxane) nanochannels filled with solutions of different ionic strength. The results are in good agreement with the theoretical predictions, confirming the crucial role of the electrostatic repulsion of the constraining walls on the molecule stretching.
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Affiliation(s)
| | - Paola Fanzio
- Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy
| | - Tapio Ala-Nissila
- Department of Applied Physics and COMP Center of Excellence, Aalto University School of Science , P.O. Box 11100, FIN-00076 Aalto, Espoo, Finland and Department of Physics, Brown University , Providence, Rhode Island 02912-1843, USA
| | - Elena Angeli
- Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy
| | - Luca Repetto
- Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy
| | - Giuseppe Firpo
- Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy
| | - Ugo Valbusa
- Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy
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