1
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Hosseini II, Hamidi SV, Capaldi X, Liu Z, Silva Pessoa MA, Mahshid S, Reisner W. Tunable nanofluidic device for digital nucleic acid analysis. NANOSCALE 2024. [PMID: 38682564 DOI: 10.1039/d3nr05553a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Nano/microfluidic-based nucleic acid tests have been proposed as a rapid and reliable diagnostic technology. Two key steps for many of these tests are target nucleic acid (NA) immobilization followed by an enzymatic reaction on the captured NAs to detect the presence of a disease-associated sequence. NA capture within a geometrically confined volume is an attractive alternative to NA surface immobilization that eliminates the need for sample pre-treatment (e.g. label-based methods such as lateral flow assays) or use of external actuators (e.g. dielectrophoresis) that are required for most nano/microfluidic-based NA tests. However, geometrically confined spaces hinder sample loading while making it challenging to capture, subsequently, retain and simultaneously expose target NAs to required enzymes. Here, using a nanofluidic device that features real-time confinement control via pneumatic actuation of a thin membrane lid, we demonstrate the loading of digital nanocavities by target NAs and exposure of target NAs to required enzymes/co-factors while the NAs are retained. In particular, as proof of principle, we amplified single-stranded DNAs (M13mp18 plasmid vector) in an array of nanocavities via two isothermal amplification approaches (loop-mediated isothermal amplification and rolling circle amplification).
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Affiliation(s)
- Imman I Hosseini
- Department of Biomedical Engineering, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada.
| | - Seyed Vahid Hamidi
- Department of Biomedical Engineering, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada.
| | - Xavier Capaldi
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada.
| | - Zezhou Liu
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada.
| | | | - Sara Mahshid
- Department of Biomedical Engineering, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada.
| | - Walter Reisner
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada.
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2
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Kk S, Persson F, Fritzsche J, Beech JP, Tegenfeldt JO, Westerlund F. Fluorescence Microscopy of Nanochannel-Confined DNA. Methods Mol Biol 2024; 2694:175-202. [PMID: 37824005 DOI: 10.1007/978-1-0716-3377-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level, and the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments, and analyze the data.
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Affiliation(s)
- Sriram Kk
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Joachim Fritzsche
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Jason P Beech
- NanoLund and Department of Physics, Lund University, Lund, Sweden
| | | | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
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3
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Sasanian N, Sharma R, Lubart Q, Kk S, Ghaeidamini M, Dorfman KD, Esbjörner EK, Westerlund F. Probing physical properties of single amyloid fibrils using nanofluidic channels. NANOSCALE 2023; 15:18737-18744. [PMID: 37953701 DOI: 10.1039/d3nr02740f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Amyloid fibril formation is central to the pathology of many diseases, including neurodegenerative disorders such as Alzheimer's and Parkinson's disease. Amyloid fibrils can also have functional and scaffolding roles, for example in bacterial biofilms, and have also been exploited as useful biomaterials. Despite being linear protein homopolymers, amyloid fibrils can exhibit significant structural and morphological polymorphism, making it relevant to study them on the single fibril level. We here introduce the concept of nanofluidic channel analysis to the study of single, fluorescently-labeled amyloid fibrils in solution, monitoring the extension and emission intensity of individual fibrils confined in nanochannels with a depth of 300 nm and a width that gradually increases from 300 to 3000 nm. The change in fibril extension with channel width permitted accurate determination of the persistence length of individual fibrils using Odijk's theory for strongly confined polymers. The technique was applied to amyloid fibrils prepared from the Alzheimer's related peptide amyloid-β(1-42) and the Parkinson's related protein α-synuclein, obtaining mean persistence lengths of 5.9 ± 4.5 μm and 3.0 ± 1.6 μm, respectively. The broad distributions of fibril persistence lengths indicate that amyloid fibril polymorphism can manifest in their physical properties. Interestingly, the α-synuclein fibrils had lower persistence lengths than the amyloid-β(1-42) fibrils, despite being thicker. Furthermore, there was no obvious within-sample correlation between the fluorescence emission intensity per unit length of the labelled fibrils and their persistence lengths, suggesting that stiffness may not be proportional to thickness. We foresee that the nanofluidics methodology established here will be a useful tool to study amyloid fibrils on the single fibril level to gain information on heterogeneity in their physical properties and interactions.
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Affiliation(s)
- Nima Sasanian
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
| | - Rajhans Sharma
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
| | - Quentin Lubart
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
| | - Sriram Kk
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
| | - Marziyeh Ghaeidamini
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Elin K Esbjörner
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
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4
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Che B, Sun D, Zhang C, Hou J, Zhao W, Jing G, Mu Y, Cao Y, Dai L, Zhang C. Gradient Nanoconfinement Facilitates Binding of Transcriptional Factor NF-κB to Histone- and Protamine-DNA Complexes. NANO LETTERS 2023; 23:2388-2396. [PMID: 36857512 DOI: 10.1021/acs.nanolett.3c00325] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Mechanically induced chromosome reorganization plays important roles in transcriptional regulation. However, the interplay between chromosome reorganization and transcription activities is complicated, such that it is difficult to decipher the regulatory effects of intranuclear geometrical cues. Here, we simplify the system by introducing DNA, packaging proteins (i.e., histone and protamine), and transcription factor NF-κB into a well-defined fluidic chip with changing spatical confinement ranging from 100 to 500 nm. It is uncovered that strong nanoconfinement suppresses higher-order folding of histone- and protamine-DNA complexes, the fracture of which exposes buried DNA segments and causes increased quantities of NF-κB binding to the DNA chain. Overall, these results reveal a pathway of how intranuclear geometrical cues alter the open/closed state of a DNA-protein complex and therefore affect transcription activities: i.e., NF-κB binding.
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Affiliation(s)
- Bingchen Che
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, People's Republic of China
- School of Physics, Northwest University, Xi'an 710069, People's Republic of China
| | - Dan Sun
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, People's Republic of China
| | - Chen Zhang
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, People's Republic of China
| | - Jiaqing Hou
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, People's Republic of China
| | - Wei Zhao
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, People's Republic of China
| | - Guangyin Jing
- School of Physics, Northwest University, Xi'an 710069, People's Republic of China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore 639798, Singapore
| | - Yaoyu Cao
- Institute of Photonics Technology, Jinan University, 510632, Guangzhou, People's Republic of China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Hong Kong 999077, People's Republic of China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, People's Republic of China
| | - Ce Zhang
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, People's Republic of China
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5
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Crowding and confinement act in concert to slow DNA diffusion within cell-sized droplets. iScience 2022; 25:105122. [PMID: 36185357 PMCID: PMC9523355 DOI: 10.1016/j.isci.2022.105122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/27/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
Dynamics of biological macromolecules, such as DNA, in crowded and confined environments are critical to understanding cellular processes such as transcription, infection, and replication. However, the combined effects of cellular confinement and crowding on macromolecular dynamics remain poorly understood. Here, we use differential dynamic microscopy to investigate the diffusion of large DNA molecules confined in cell-sized droplets and crowded by dextran polymers. We show that confined and crowded DNA molecules exhibit universal anomalous subdiffusion with scaling that is insensitive to the degree of confinement and crowding. However, effective DNA diffusion coefficients Deff decrease up to 2 orders of magnitude as droplet size decreases—an effect that is enhanced by increased crowding. We mathematically model the coupling of crowding and confinement by combining polymer scaling theories with confinement-induced depletion effects. The generality and tunability of our system and models render them applicable to elucidating wide-ranging crowded and confined systems. DNA diffusion measured in cell-sized droplets with differential dynamic microscopy Combination of crowding and confinement leads to subdiffusion and slowing Diffusion coefficients of DNA decrease strongly with decreasing droplet size Polymer scaling theories and depletion effects predict observed dynamics
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6
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Zhu Y, Kumar PBS, Laradji M. Conformational behavior and self-assembly of disjoint semi-flexible ring polymers adsorbed on solid substrates. SOFT MATTER 2021; 17:5427-5435. [PMID: 33969850 DOI: 10.1039/d1sm00500f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The conformational behavior and spatial organization of self-avoiding semi-flexible ring polymers, that are fully adsorbed on solid substrates, are investigated via systematic coarse-grained molecular dynamics simulations. Our results show that both conformations and spatial organization of the polymers depend strongly on their bending stiffness, κ, and on their areal number density, ρ. For ρ < ρ*, where ρ* is the overlap density, and for low values of κ, thermal fluctuations lead to weakly anisotropic instantaneous conformations of the polymers. The interplay between thermal fluctuations and polymer stiffness leads to a non-monotonic dependence of the polymers elongation on κ with a maximum elongation at some intermediate κ. Regardless of κ, the polymers elongation is almost independent of ρ for ρ ⪅ ρ*, then increases with ρ. At ρ ≈ ρ* and high κ, the almost circularly-shaped polymers self-assemble into a triangular lattice with quasi-long range order. For ρ above ρ* and high κ, crowding of the polymers leads to their self-assembly into liquid-crystalline phases. In particular, for ρ moderately above ρ* and high κ, the polymer conformations are obround and self-assemble into domains with smectic-A-like order. At higher densities, the polymer have a biconcave geometry and self-assemble into domains with smectic-C-like order.
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Affiliation(s)
- Yu Zhu
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
| | - P B Sunil Kumar
- Department of Physics, Indian Institute of Technology Palakkad, Palakkad-668557, Kerala, India
| | - Mohamed Laradji
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
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7
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Jeffet J, Margalit S, Michaeli Y, Ebenstein Y. Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale. Essays Biochem 2021; 65:51-66. [PMID: 33739394 PMCID: PMC8056043 DOI: 10.1042/ebc20200021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information content. This includes large-scale genetic aberrations, as well as diverse epigenetic patterns that are crucial for regulating specific cell functions. These genetic and epigenetic patterns operate in concert in order to maintain specific cellular functions in health and disease. Single-molecule optical genome mapping is a high-throughput genome analysis method that is based on imaging long chromosomal fragments stretched in nanochannel arrays. The access to long DNA molecules coupled with fluorescent tagging of various genomic information presents a unique opportunity to study genetic and epigenetic patterns in the genome at a single-molecule level over large genomic distances. Optical mapping entwines synergistically chemical, physical, and computational advancements, to uncover invaluable biological insights, inaccessible by sequencing technologies. Here we describe the method's basic principles of operation, and review the various available mechanisms to fluorescently tag genomic information. We present some of the recent biological and clinical impact enabled by optical mapping and present recent approaches for increasing the method's resolution and accuracy. Finally, we discuss how multiple layers of genomic information may be mapped simultaneously on the same DNA molecule, thus paving the way for characterizing multiple genomic observables on individual DNA molecules.
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Affiliation(s)
- Jonathan Jeffet
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sapir Margalit
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Michaeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
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8
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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.
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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.)
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9
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Schotzinger RM, Menard LD, Ramsey JM. Single-Molecule DNA Extension in Rectangular and Square Profile Nanochannels in the Extended de Gennes Regime. Macromolecules 2020. [DOI: 10.1021/acs.macromol.9b02249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- R. Michael Schotzinger
- Department of Biomedical Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | | | - J. Michael Ramsey
- Department of Biomedical Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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10
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Chuang HM, Reifenberger JG, Bhandari AB, Dorfman KD. Extension distribution for DNA confined in a nanochannel near the Odijk regime. J Chem Phys 2019; 151:114903. [PMID: 31542006 DOI: 10.1063/1.5121305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
DNA confinement in a nanochannel typically is understood via mapping to the confinement of an equivalent neutral polymer by hard walls. This model has proven to be effective for confinement in relatively large channels where hairpin formation is frequent. An analysis of existing experimental data for Escherichia coli DNA extension in channels smaller than the persistence length, combined with an additional dataset for λ-DNA confined in a 34 nm wide channel, reveals a breakdown in this approach as the channel size approaches the Odijk regime of strong confinement. In particular, the predicted extension distribution obtained from the asymptotic solution to the weakly correlated telegraph model for a confined wormlike chain deviates significantly from the experimental distribution obtained for DNA confinement in the 34 nm channel, and the discrepancy cannot be resolved by treating the alignment fluctuations or the effective channel size as fitting parameters. We posit that the DNA-wall electrostatic interactions, which are sensible throughout a significant fraction of the channel cross section in the Odijk regime, are the source of the disagreement between theory and experiment. Dimensional analysis of the wormlike chain propagator in channel confinement reveals the importance of a dimensionless parameter, reflecting the magnitude of the DNA-wall electrostatic interactions relative to thermal energy, which has not been considered explicitly in the prevailing theories for DNA confinement in a nanochannel.
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Affiliation(s)
- Hui-Min Chuang
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Jeffrey G Reifenberger
- Bionano Genomics, Inc., 9640 Towne Centre Drive, Suite 100, San Diego, California 92121, USA
| | - Aditya Bikram Bhandari
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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11
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Movahed S, Azad Z, Dangi S, Riehn R. Direct observation of confinement-induced diffusophoresis. NANOTECHNOLOGY 2019; 30:41LT01. [PMID: 31300622 PMCID: PMC6821566 DOI: 10.1088/1361-6528/ab31f7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nanofluidic devices have channel dimensions which come to within one order of magnitude of the Debye length of common aqueous solutions. Conventionally, external driving is used to create concentration polarization of ions and biomolecules in nanofluidic devices. Here we show that long-range ionic strength gradients intrinsic to all nanofluidic devices, even at equilibrium, also drive a drift of macromolecules. To demonstrate the effect, we confine long DNA to straight nanochannels of constant, rectangular cross-section (100 × 100 nm2) which are connected to large microfluidic reservoirs. The motion of DNA is observed in absence of any driving. We find that at low ionic strengths, molecules in nanochannels migrate toward the nano-micro interface, while they are undergoing purely diffusive motion in high salt. Using numerical models, we demonstrate that the motion is consistent with the ionic strength gradient at the micro-nano interface even at equilibrium, and that the dominant cause of the drift is diffusophoresis.
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12
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Krog J, Alizadehheidari M, Werner E, Bikkarolla SK, Tegenfeldt JO, Mehlig B, Lomholt MA, Westerlund F, Ambjörnsson T. Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysis. J Chem Phys 2019; 149:215101. [PMID: 30525714 DOI: 10.1063/1.5051319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Nanochannels provide a means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. Here we introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients are the entropic unfolding force and the friction coefficient for the unfolding process, and we describe the associated dynamics by a non-linear Langevin equation. By analyzing experimental data where DNA molecules are photo-cut and unfolded inside a nanochannel, our model allows us to extract values for the unfolding force as well as the friction coefficient for the first time. In order to extract numerical values for these physical quantities, we employ a recently introduced Bayesian inference framework. We find that the determined unfolding force is in agreement with estimates from a simple Flory-type argument. The estimated friction coefficient is in agreement with theoretical estimates for motion of a cylinder in a channel. We further validate the estimated friction constant by extracting this parameter from DNA's center-of-mass motion before and after unfolding, yielding decent agreement. We provide publically available software for performing the required image and Bayesian analysis.
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Affiliation(s)
- Jens Krog
- MEMPHYS-Center for Biomembrane Physics, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark
| | | | - Erik Werner
- Department of Physics, Gothenburg University, Gothenburg, Sweden
| | - Santosh Kumar Bikkarolla
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Bernhard Mehlig
- Department of Physics, Gothenburg University, Gothenburg, Sweden
| | - Michael A Lomholt
- MEMPHYS-Center for Biomembrane Physics, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
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13
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Öz R, Kk S, Westerlund F. A nanofluidic device for real-time visualization of DNA-protein interactions on the single DNA molecule level. NANOSCALE 2019; 11:2071-2078. [PMID: 30644945 DOI: 10.1039/c8nr09023h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Single DNA molecule techniques have revolutionized our understanding of DNA-protein interactions. Traditional techniques for such studies have the major drawback that the DNA molecule studied is attached to a bead or a surface. Stretching of DNA molecules in nanofluidic channels has enabled single-molecule studies of DNA-protein interactions without the need of tethering the molecule to a foreign entity. This in turn allows for studying reactions along the whole extension of the molecule, including the free DNA ends. However, existing studies either rely on measurements where all components are mixed before introduction into the nanochannels or where passive diffusion brings the reagents to the confined DNA molecule. We here present a new generation of nanofluidic devices, where active exchange of the local environment within the nanofluidic channel is possible, while keeping the DNA molecule stretched and in confinement. To demonstrate the functionality of this novel device we added different analytes, such as SDS, spermidine and DNase I, to YOYO-1 stained DNA and studied the response in real time. We also performed a FRET-based reaction, where two different analytes were added sequentially to the same DNA molecule. We believe that this design will enable in situ mapping of complex biochemical processes, involving multiple proteins and cofactors, on single DNA molecules as well as other biomacromolecules.
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Affiliation(s)
- Robin Öz
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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14
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Dangi S, Riehn R. Nanoplumbing with 2D Metamaterials. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1803478. [PMID: 30537130 PMCID: PMC6785347 DOI: 10.1002/smll.201803478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 11/09/2018] [Indexed: 06/09/2023]
Abstract
Complex manipulations of DNA in a nanofluidic device require channels with branches and junctions. However, the dynamic response of DNA in such nanofluidic networks is relatively unexplored. Here, the transport of DNA in a 2D metamaterial made by arrays of nanochannel junctions is investigated. The mechanism of transport is explained as Brownian motion through an energy landscape formed by the combination of the confinement free energy of DNA and the effective potential of hydrodynamic flow, which both can be tuned independently within the device. For the quantitative understanding of DNA transport, a dynamic mean-field model of DNA at a nanochannel junction is proposed. It is shown that the dynamics of DNA in a nanofluidic device with branched channels and junctions is well described by the model.
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15
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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.
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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.
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16
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Bhandari AB, Reifenberger JG, Chuang HM, Cao H, Dorfman KD. Measuring the wall depletion length of nanoconfined DNA. J Chem Phys 2018; 149:104901. [PMID: 30219022 PMCID: PMC6135644 DOI: 10.1063/1.5040458] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/20/2018] [Indexed: 12/14/2022] Open
Abstract
Efforts to study the polymer physics of DNA confined in nanochannels have been stymied by a lack of consensus regarding its wall depletion length. We have measured this quantity in 38 nm wide, square silicon dioxide nanochannels for five different ionic strengths between 15 mM and 75 mM. Experiments used the Bionano Genomics Irys platform for massively parallel data acquisition, attenuating the effect of the sequence-dependent persistence length and finite-length effects by using nick-labeled E. coli genomic DNA with contour length separations of at least 30 µm (88 325 base pairs) between nick pairs. Over 5 × 106 measurements of the fractional extension were obtained from 39 291 labeled DNA molecules. Analyzing the stretching via Odijk's theory for a strongly confined wormlike chain yielded a linear relationship between the depletion length and the Debye length. This simple linear fit to the experimental data exhibits the same qualitative trend as previously defined analytical models for the depletion length but now quantitatively captures the experimental data.
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Affiliation(s)
- Aditya Bikram Bhandari
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Jeffrey G Reifenberger
- Bionano Genomics, Inc., 9640 Towne Centre Drive, Suite 100, San Diego, California 92121, USA
| | - Hui-Min Chuang
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Han Cao
- Bionano Genomics, Inc., 9640 Towne Centre Drive, Suite 100, San Diego, California 92121, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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17
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Samadi Taheri F, Fazli H, Doi M, Habibi M. Granular chain escape from a pore in a wall in the presence of particles on one side: a comparison to polymer translocation. SOFT MATTER 2018; 14:5420-5427. [PMID: 29938271 DOI: 10.1039/c8sm00790j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Escape of a granular chain from a pore in a wall in the presence of diffusing granular particles on one side of the wall is studied experimentally. The escape time shows power-law behavior as a function of the chain length (τ ∝ Nα). A Langevin dynamics simulation of a polymer chain in a similar geometry is also performed and similar results to those for a granular system are obtained. A simple scaling argument and an energetic argument (based on the Onsager principle) are introduced which explain our results very well. Experiments (simulations) show that by increasing the number of particles on one side of the wall from zero, the exponent α decreases from 2.6 ± 0.1 (3.1 ± 0.1) to about 2. Both scaling and the Onsager principle argument predict α = 2 at high particle concentration, in agreement with the experiments and simulations. In the absence of particles, the scaling predicts τ = N2.5 (in agreement with the experimental result for the granular chain) and the Onsager principle predictsτ = N3 ln N, supporting the simulation result for the polymer chain. Experiments, simulations, scaling, and the Onsager principle confirm an inverse relation between τ and the density of particles on one side of the wall.
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Affiliation(s)
- Fereshteh Samadi Taheri
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
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18
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Yu M, Hou Y, Song R, Xu X, Yao S. Tunable Confinement for Bridging Single-Cell Manipulation and Single-Molecule DNA Linearization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1800229. [PMID: 29575689 DOI: 10.1002/smll.201800229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/07/2018] [Indexed: 06/08/2023]
Abstract
DNA linearization by nanoconfinement has offered a new avenue toward large-scale genome mapping. The ability to smoothly interface the widely different length scales from cell manipulation to DNA linearization is critical to the development of single-cell genomic mapping or sequencing technologies. Conventional nanochannel technologies for DNA analysis suffer from complex fabrication procedures, DNA stacking at the nanochannel entrance, and inefficient solution exchange. In this work, a dynamic and tunable confinement strategy is developed to manipulate and linearize genomic-length DNA molecules from a single cell. By leveraging pneumatic microvalve control and elastomeric collapse, an array of nanochannels with confining dimension down to 20 nm and length up to sub-millimeter is created and can be dynamically tuned in size. The curved edges of the microvalve form gradual transitions from microscale to nanoscale confinement, smoothly facilitating DNA entry into the nanochannels. A unified micro/nanofluidic device that integrates single-cell trapping and lysis, DNA extraction, purification, labeling, and linearization is developed based on dynamically controllable nanochannels. Mbp-long DNA molecules are extracted directly from a single cell and in situ linearized in the nanochannels. The device provides a facile and promising platform to achieve the ultimate goal of single-cell, single-genome analysis.
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Affiliation(s)
- Miao Yu
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
| | - Youmin Hou
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
| | - Ruyuan Song
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
| | - Xiaonan Xu
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
| | - Shuhuai Yao
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
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19
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Abstract
Long-read genomic applications, such as genome mapping in nanochannels, require long DNA that is free of small-DNA impurities. We have developed a chip-based system based on entropic trapping that can simultaneously concentrate and purify a long DNA sample under the alternating application of an applied pressure (for sample injection) and an electric field (for filtration and concentration). In contrast, short DNA tends to pass through the filter owing to its comparatively weak entropic penalty for entering the nanoslit. The single-stage prototype developed here, which operates in a continuous pulsatile manner, achieves selectivities of up to 3.5 for λ-phage DNA (48.5 kilobase pairs) compared to a 2 kilobase pair standard based on experimental data for the fraction filtered using pure samples of each species. The device is fabricated in fused silica using standard clean-room methods, making it compatible for integration with long-read genomics technologies.
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Affiliation(s)
- Pranav Agrawal
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, USA.
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20
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Gupta D, Bhandari AB, Dorfman KD. Evaluation of Blob Theory for the Diffusion of DNA in Nanochannels. Macromolecules 2018; 51:1748-1755. [PMID: 29599567 DOI: 10.1021/acs.macromol.7b02270] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We have measured the diffusivity of λ-DNA molecules in approximately square nanochannels with effective sizes ranging from 117 nm to 260 nm at moderate ionic strength. The experimental results do not agree with the non-draining scaling predicted by blob theory. Rather, the data are consistent with the predictions of previous simulations of the Kirkwood diffusivity of a discrete wormlike chain model, without the need for any fitting parameters.
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Affiliation(s)
- Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Aditya Bikram Bhandari
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
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21
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Reifenberger JG, Cao H, Dorfman KD. Odijk excluded volume interactions during the unfolding of DNA confined in a nanochannel. Macromolecules 2018; 51:1172-1180. [PMID: 29479117 PMCID: PMC5823525 DOI: 10.1021/acs.macromol.7b02466] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report experimental data on the unfolding of human and E. coli genomic DNA molecules shortly after injection into a 45 nm nanochannel. The unfolding dynamics are deterministic, consistent with previous experiments and modeling in larger channels, and do not depend on the biological origin of the DNA. The measured entropic unfolding force per friction per unit contour length agrees with that predicted by combining the Odijk excluded volume with numerical calculations of the Kirkwood diffusivity of confined DNA. The time scale emerging from our analysis has implications for genome mapping in nanochannels, especially as the technology moves towards longer DNA, by setting a lower bound for the delay time before making a measurement.
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Affiliation(s)
| | - Han Cao
- BioNano Genomics Inc., 9640 Towne Centre Drive, Suite 100, San Diego, CA 92121
| | - 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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22
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Abstract
Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level and both the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments and analyze the data.
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23
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Werner E, Cheong GK, Gupta D, Dorfman KD, Mehlig B. One-Parameter Scaling Theory for DNA Extension in a Nanochannel. PHYSICAL REVIEW LETTERS 2017; 119:268102. [PMID: 29328690 PMCID: PMC5769985 DOI: 10.1103/physrevlett.119.268102] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Indexed: 05/27/2023]
Abstract
Experiments measuring DNA extension in nanochannels are at odds with even the most basic predictions of current scaling arguments for the conformations of confined semiflexible polymers such as DNA. We show that a theory based on a weakly self-avoiding, one-dimensional "telegraph" process collapses experimental data and simulation results onto a single master curve throughout the experimentally relevant region of parameter space and explains the mechanisms at play.
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Affiliation(s)
- E Werner
- Department of Physics, University of Gothenburg, SE-41296 Gothenburg, Sweden
| | - G K Cheong
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - D Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - K D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - B Mehlig
- Department of Physics, University of Gothenburg, SE-41296 Gothenburg, Sweden
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24
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Satarifard V, Heidari M, Mashaghi S, Tans SJ, Ejtehadi MR, Mashaghi A. Topology of polymer chains under nanoscale confinement. NANOSCALE 2017; 9:12170-12177. [PMID: 28805849 DOI: 10.1039/c7nr04220e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Spatial confinement limits the conformational space accessible to biomolecules but the implications for bimolecular topology are not yet known. Folded linear biopolymers can be seen as molecular circuits formed by intramolecular contacts. The pairwise arrangement of intra-chain contacts can be categorized as parallel, series or cross, and has been identified as a topological property. Using molecular dynamics simulations, we determine the contact order distributions and topological circuits of short semi-flexible linear and ring polymer chains with a persistence length of lp under a spherical confinement of radius Rc. At low values of lp/Rc, the entropy of the linear chain leads to the formation of independent contacts along the chain and accordingly, increases the fraction of series topology with respect to other topologies. However, at high lp/Rc, the fraction of cross and parallel topologies are enhanced in the chain topological circuits with cross becoming predominant. At an intermediate confining regime, we identify a critical value of lp/Rc, at which all topological states have equal probability. Confinement thus equalizes the probability of more complex cross and parallel topologies to the level of the more simple, non-cooperative series topology. Moreover, our topology analysis reveals distinct behaviours for ring- and linear polymers under weak confinement; however, we find no difference between ring- and linear polymers under strong confinement. Under weak confinement, ring polymers adopt parallel and series topologies with equal likelihood, while linear polymers show a higher tendency for series arrangement. The radial distribution analysis of the topology reveals a non-uniform effect of confinement on the topology of polymer chains, thereby imposing more pronounced effects on the core region than on the confinement surface. Additionally, our results reveal that over a wide range of confining radii, loops arranged in parallel and cross topologies have nearly the same contact orders. Such degeneracy implies that the kinetics and transition rates between the topological states cannot be solely explained by contact order. We expect these findings to be of general importance in understanding chaperone assisted protein folding, chromosome architecture, and the evolution of molecular folds.
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Affiliation(s)
- Vahid Satarifard
- Leiden Academic Centre for Drug Research, Faculty of Mathematics and Natural Sciences, Leiden University, Leiden, The Netherlands.
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25
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Benková Z, Rišpanová L, Cifra P. Structural Behavior of a Semiflexible Polymer Chain in an Array of Nanoposts. Polymers (Basel) 2017; 9:E313. [PMID: 30970991 PMCID: PMC6418663 DOI: 10.3390/polym9080313] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 11/27/2022] Open
Abstract
The structural properties of a flexible and semiflexible circular chain confined in an array of parallel nanoposts with a square lattice cross-sectional projection were studied using coarse-grained molecular dynamics simulations. To address the effect of the circular topology, a comparison with linear analogs was also carried out. In the interpretation of the chain structural properties, the geometry of the post array is considered as a combination of a channel approximating the interstitial volume with the diameter dc and a slit approximating the passage aperture with the width wp. The number of interstitial volumes occupied by a chain monotonically increases with the decreasing ratio dc/wp regardless of the way the geometry of the post array is varied. However, depending on how the array geometry is modified, the chain span along the posts displays a monotonic (constant post separation) or a non-monotonic behavior (constant passage width) when plotted as a function of the post diameter. In the case of monotonic trend, the width of interstitial spaces increases with the increasing chain occupation number, while, in the case of non-monotonic trend, the width of interstitial spaces decreases with the increasing chain occupation number. In comparison with linear topology, for circular topology, the stiffness affects more significantly the relative chain extension along the posts and less significantly the occupation number. The geometrical parameters of the post arrays are stored in the single-chain structure factors. The characteristic humps are recognized in the structure factor which ensue from the local increase in the density of segments in the circular chains presented in an interstitial volume or from the correlation of parallel chain fragments separated by a row of posts. Although the orientation correlations provide qualitative information about the chain topology and the character of confinement within a single interstitial volume, information about the array periodicity is missing.
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Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia.
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal.
| | - Lucia Rišpanová
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia.
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia.
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26
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Japaridze A, Orlandini E, Smith KB, Gmür L, Valle F, Micheletti C, Dietler G. Spatial confinement induces hairpins in nicked circular DNA. Nucleic Acids Res 2017; 45:4905-4914. [PMID: 28201616 PMCID: PMC5605231 DOI: 10.1093/nar/gkx098] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/25/2017] [Accepted: 02/06/2017] [Indexed: 01/05/2023] Open
Abstract
In living cells, DNA is highly confined in space with the help of condensing agents, DNA binding proteins and high levels of supercoiling. Due to challenges associated with experimentally studying DNA under confinement, little is known about the impact of spatial confinement on the local structure of the DNA. Here, we have used well characterized slits of different sizes to collect high resolution atomic force microscopy images of confined circular DNA with the aim of assessing the impact of the spatial confinement on global and local conformational properties of DNA. Our findings, supported by numerical simulations, indicate that confinement imposes a large mechanical stress on the DNA as evidenced by a pronounced anisotropy and tangent-tangent correlation function with respect to non-constrained DNA. For the strongest confinement we observed nanometer sized hairpins and interwound structures associated with the nicked sites in the DNA sequence. Based on these findings, we propose that spatial DNA confinement in vivo can promote the formation of localized defects at mechanically weak sites that could be co-opted for biological regulatory functions.
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Affiliation(s)
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Universita di Padova, Via Marzolo 8, 35131 Padova, Italy
| | | | - Lucas Gmür
- Laboratory of Physics of Living Matter, EPFL, 1015 Lausanne, Switzerland
| | - Francesco Valle
- Consiglio Nazionale delle Ricerche (CNR), Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Via P.Gobetti 101, Bologna 40129, Italy
| | - Cristian Micheletti
- SISSA - Scuola Internazionale Superiore di Studi Avanzati and CNR-IOM Democritos, Via Bonomea 265, 34136 Trieste, Italy
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter, EPFL, 1015 Lausanne, Switzerland
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27
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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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28
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Müller V, Westerlund F. Optical DNA mapping in nanofluidic devices: principles and applications. LAB ON A CHIP 2017; 17:579-590. [PMID: 28098301 DOI: 10.1039/c6lc01439a] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Optical DNA mapping has over the last decade emerged as a very powerful tool for obtaining long range sequence information from single DNA molecules. In optical DNA mapping, intact large single DNA molecules are labeled, stretched out, and imaged using a fluorescence microscope. This means that sequence information ranging over hundreds of kilobasepairs (kbp) can be obtained in one single image. Nanochannels offer homogeneous and efficient stretching of DNA that is crucial to maximize the information that can be obtained from optical DNA maps. In this review, we highlight progress in the field of optical DNA mapping in nanochannels. We discuss the different protocols for sequence specific labeling and divide them into two main categories, enzymatic labeling and affinity-based labeling. Examples are highlighted where optical DNA mapping is used to gain information on length scales that would be inaccessible with traditional techniques. Enzymatic labeling has been commercialized and is mainly used in human genetics and assembly of complex genomes, while the affinity-based methods have primarily been applied in bacteriology, for example for rapid analysis of plasmids encoding antibiotic resistance. Next, we highlight how the design of nanofluidic channels can been altered in order to obtain the desired information and discuss how recent advances in the field make it possible to retrieve information beyond DNA sequence. In the outlook section, we discuss future directions of optical DNA mapping, such as fully integrated devices and portable microscopes.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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29
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Frykholm K, Nyberg LK, Westerlund F. Exploring DNA–protein interactions on the single DNA molecule level using nanofluidic tools. Integr Biol (Camb) 2017; 9:650-661. [DOI: 10.1039/c7ib00085e] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This review highlights the use of nanofluidic channels for studying DNA–protein interactions on the single DNA molecule level.
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Affiliation(s)
- Karolin Frykholm
- Department of Biology and Biological Engineering
- Chalmers University of Technology
- Gothenburg
- Sweden
| | - Lena K. Nyberg
- Department of Biology and Biological Engineering
- Chalmers University of Technology
- Gothenburg
- Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering
- Chalmers University of Technology
- Gothenburg
- Sweden
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30
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Benková Z, Námer P, Cifra P. Comparison of a stripe and slab confinement for ring and linear macromolecules in nanochannel. SOFT MATTER 2016; 12:8425-8439. [PMID: 27722460 DOI: 10.1039/c6sm01507g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The combined effects of the channel asymmetry and the closed chain topology on the chain extension, structure factor, and the orientation correlations were studied using coarse-grained molecular dynamics simulations for moderate chain lengths. These effects are related to applications in linearization experiments with a DNA molecule in nanofluidic devices. According to the aspect ratio, the channels are classified as a stripe or slabs. The chain segments do not have any freedom to move in the direction of the narrowest stripe size, being approximately the same size as the segment size. The chains of both ring and linear topologies are extended more in a stripe than in a slab; this effect is strengthened for a ring. For a ring in a stripe, the extension-confinement strength dependence leads to effective Flory exponents even larger than 3/4, which is characteristic for a self-avoiding two-dimensional chain. While the chain extension-confinement strength dependence for both topologies conforms to the de Gennes regime in a stripe, a linear chain undergoes gradual transition to the pseudoideal regime as the slab height increases in the slab-like confinement. For a confined circle, the onset of the pseudoideal regime is shifted to larger slab heights. The structure factor confirms the absence of the pseudoideal and extended de Gennes regime in a stripe and the transition from the extended to the pseudoideal regime of a circular and linear chain upon increasing the slab heights.
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Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia. and LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal
| | - Pavol Námer
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
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31
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Mortazavi F, Habibi M, Nedaaee Oskoee E. Translocation of a granular chain in a horizontally vibrated saw-tooth channel. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2016; 39:93. [PMID: 27761780 DOI: 10.1140/epje/i2016-16093-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 09/27/2016] [Indexed: 06/06/2023]
Abstract
We study the translocation mechanism of a granular chain in a horizontally vibrated saw-tooth channel using MD simulations and macro-scale experiments and show that the translocation speed is independent of the chain length as long as the chain length is larger than the spatial period of the saw-tooth. With the help of simulation, we explore the effect of geometry of the container and frequency and amplitude of vibration as well as chain flexibility on the chain drift speed. We observe that the most efficient transport is achieved when one of the channel walls is shifted with respect to the other wall by an amount equal to half the spatial period of the saw-tooth. We define a persistence length for the chain and show that the translocation speed depends on the ratio of persistence length over the spatial period of the saw-tooth. The optimum translocation occurs when this ratio is about 0.4. We also determine the optimum saw-tooth angle for the translocation of the chain as well as the optimum distance between the two walls. Some properties of this system are similar to those of polymer systems.
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Affiliation(s)
- Fariba Mortazavi
- Institute for Advanced Studies in Basic Sciences, Gava Zang, 45195-159, Zanjan, Iran
| | - Mehdi Habibi
- Institute for Advanced Studies in Basic Sciences, Gava Zang, 45195-159, Zanjan, Iran.
- Van der Waals-Zeeman Institute, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands.
| | - Ehsan Nedaaee Oskoee
- Institute for Advanced Studies in Basic Sciences, Gava Zang, 45195-159, Zanjan, Iran
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32
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Huang A, Reisner W, Bhattacharya A. Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket. Polymers (Basel) 2016; 8:E352. [PMID: 30974628 PMCID: PMC6432381 DOI: 10.3390/polym8100352] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 11/16/2022] Open
Abstract
We use Brownian dynamics (BD) simulation of a coarse-grained (CG) bead-spring model of DNA to study the nonequilibrim dynamics of a single DNA molecule confined inside a rectangular nanochannel being squeezed with a sliding gasket piston or "nanodozer". From our simulations we extract the nonequilibrim density profile c ( x , t ) of the squeezed molecule along the channel axis (x-coordinate) and then analyze the non-equilibrium profile using a recently introduced phenomenological Nonlinear Partial Differential Equation (NPDE) model. Since the NPDE approach also fits the experimental results well and is numerically efficient to implement, the combined BD + NPDE methods can be a powerful approach to analyze details of the confined molecular dynamics. In particular, the overall excellent agreement between the two complementary sets of data provides a strategy for carrying out large scale simulation on semi-flexible biopolymers in confinement at biologically relevant length scales.
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Affiliation(s)
- Aiqun Huang
- University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.
| | - Walter Reisner
- McGill University, 845 Rue Sherbrooke O, Montréal, QC H3A 0G4, Canada.
| | - Aniket Bhattacharya
- University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.
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33
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Postigo PA, Alvaro R, Juarros A, Merino S. Optofluidic chips with nanochannels for dynamic molecular detection using enhanced fluorescence. BIOMEDICAL OPTICS EXPRESS 2016; 7:3289-3298. [PMID: 27699099 PMCID: PMC5030011 DOI: 10.1364/boe.7.003289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/08/2016] [Accepted: 07/17/2016] [Indexed: 06/06/2023]
Abstract
The fabrication of a novel optofluidic chip using nanochannels optimized for DNA-stretched molecules and optical detection by enhanced fluorescence is reported. The chips are composed of a series of microchannels that allow the transport of molecules in the femto-liter per second inside a fluid or gas. The nanochannels are surrounded by a photonic crystal structure to enhance the emission of fluorescent light from the molecules, which can travel along the nanochannel, allowing for enhanced optical detection of the molecules in motion. The photonic crystal structure provides an enhancement up to 2.5 times in the light emitted from fluorescent molecules inside the nanochannels which increases to around 250 when normalized to the area of the nanochannels emitting fluorescence. The results may help to the detection of fluorescent molecules (like marked-DNA) in series by speeding it and allowing the use of less sophisticated equipment.
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Affiliation(s)
- P. A. Postigo
- IMM-Instituto de Microelectrónica de Madrid, IMM-CNM-CSIC, Isaac Newton 8, PTM E-28760 Tres Cantos, Madrid, Spain
| | - R. Alvaro
- IMM-Instituto de Microelectrónica de Madrid, IMM-CNM-CSIC, Isaac Newton 8, PTM E-28760 Tres Cantos, Madrid, Spain
| | - A. Juarros
- Micro and Nanofabrication Unit, IK4-Tekniker, 20600 Eibar, Spain
| | - S. Merino
- Micro and Nanofabrication Unit, IK4-Tekniker, 20600 Eibar, Spain
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34
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Fornander LH, Frykholm K, Fritzsche J, Araya J, Nevin P, Werner E, Çakır A, Persson F, Garcin EB, Beuning PJ, Mehlig B, Modesti M, Westerlund F. Visualizing the Nonhomogeneous Structure of RAD51 Filaments Using Nanofluidic Channels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8403-8412. [PMID: 27479732 DOI: 10.1021/acs.langmuir.6b01877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
RAD51 is the key component of the homologous recombination pathway in eukaryotic cells and performs its task by forming filaments on DNA. In this study we investigate the physical properties of RAD51 filaments formed on DNA using nanofluidic channels and fluorescence microscopy. Contrary to the bacterial ortholog RecA, RAD51 forms inhomogeneous filaments on long DNA in vitro, consisting of several protein patches. We demonstrate that a permanent "kink" in the filament is formed where two patches meet if the stretch of naked DNA between the patches is short. The kinks are readily seen in the present microscopy approach but would be hard to identify using conventional single DNA molecule techniques where the DNA is more stretched. We also demonstrate that protein patches separated by longer stretches of bare DNA roll up on each other and this is visualized as transiently overlapping filaments. RAD51 filaments can be formed at several different conditions, varying the cation (Mg(2+) or Ca(2+)), the DNA substrate (single-stranded or double-stranded), and the RAD51 concentration during filament nucleation, and we compare the properties of the different filaments formed. The results provide important information regarding the physical properties of RAD51 filaments but also demonstrate that nanofluidic channels are perfectly suited to study protein-DNA complexes.
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Affiliation(s)
| | | | | | - Joshua Araya
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Philip Nevin
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Erik Werner
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Ali Çakır
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Fredrik Persson
- Department for Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , 751 24 Uppsala, Sweden
| | - Edwige B Garcin
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université , 13273 Marseille, France
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Bernhard Mehlig
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université , 13273 Marseille, France
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35
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Dai L, Renner CB, Doyle PS. The polymer physics of single DNA confined in nanochannels. Adv Colloid Interface Sci 2016; 232:80-100. [PMID: 26782150 DOI: 10.1016/j.cis.2015.12.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 12/01/2015] [Accepted: 12/01/2015] [Indexed: 11/17/2022]
Abstract
In recent years, applications and experimental studies of DNA in nanochannels have stimulated the investigation of the polymer physics of DNA in confinement. Recent advances in the physics of confined polymers, using DNA as a model polymer, have moved beyond the classic Odijk theory for the strong confinement, and the classic blob theory for the weak confinement. In this review, we present the current understanding of the behaviors of confined polymers while briefly reviewing classic theories. Three aspects of confined DNA are presented: static, dynamic, and topological properties. The relevant simulation methods are also summarized. In addition, comparisons of confined DNA with DNA under tension and DNA in semidilute solution are made to emphasize universal behaviors. Finally, an outlook of the possible future research for confined DNA is given.
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Affiliation(s)
- Liang Dai
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 138602, Singapore
| | - C Benjamin Renner
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, United States
| | - Patrick S Doyle
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 138602, Singapore; Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, United States.
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36
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Zinchenko A. DNA conformational behavior and compaction in biomimetic systems: Toward better understanding of DNA packaging in cell. Adv Colloid Interface Sci 2016; 232:70-79. [PMID: 26976700 DOI: 10.1016/j.cis.2016.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 02/05/2016] [Accepted: 02/11/2016] [Indexed: 10/22/2022]
Abstract
In a living cell, long genomic DNA is strongly compacted and exists in the environment characterized by a dense macromolecular crowding, high concentrations of mono- and divalent cations, and confinement of ca. 10μm size surrounded by a phospholipid membrane. Experimental modelling of such complex biological system is challenging but important to understand spatiotemporal dynamics and functions of the DNA in cell. The accumulated knowledge about DNA condensation/compaction in conditions resembling those in the real cell can be eventually used to design and construct partly functional "artificial cells" having potential applications in drug delivery systems, gene therapy, and production of synthetic cells. In this review, I would like to overview the past progress in our understanding of the DNA conformational behavior and, in particular, DNA condensation/compaction phenomenon and its relation to the DNA biological activity. This understanding was gained by designing relevant experimental models mimicking DNA behavior in the environment of living cell. Starting with a brief summary of classic experimental systems to study DNA condensation/compaction, in later parts, I highlight recent experimental methodologies to address the effects of macromolecular crowding and nanoscale and microscale confinements on DNA conformation dynamics. All the studies are discussed in the light of their relevance to DNA behavior in living cells, and future prospects of the field are outlined.
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Frykholm K, Berntsson RPA, Claesson M, de Battice L, Odegrip R, Stenmark P, Westerlund F. DNA compaction by the bacteriophage protein Cox studied on the single DNA molecule level using nanofluidic channels. Nucleic Acids Res 2016; 44:7219-27. [PMID: 27131370 PMCID: PMC5009727 DOI: 10.1093/nar/gkw352] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 03/30/2016] [Indexed: 01/10/2023] Open
Abstract
The Cox protein from bacteriophage P2 forms oligomeric filaments and it has been proposed that DNA can be wound up around these filaments, similar to how histones condense DNA. We here use fluorescence microscopy to study single DNA–Cox complexes in nanofluidic channels and compare how the Cox homologs from phages P2 and WΦ affect DNA. By measuring the extension of nanoconfined DNA in absence and presence of Cox we show that the protein compacts DNA and that the binding is highly cooperative, in agreement with the model of a Cox filament around which DNA is wrapped. Furthermore, comparing microscopy images for the wild-type P2 Cox protein and two mutants allows us to discriminate between compaction due to filament formation and compaction by monomeric Cox. P2 and WΦ Cox have similar effects on the physical properties of DNA and the subtle, but significant, differences in DNA binding are due to differences in binding affinity rather than binding mode. The presented work highlights the use of single DNA molecule studies to confirm structural predictions from X-ray crystallography. It also shows how a small protein by oligomerization can have great impact on the organization of DNA and thereby fulfill multiple regulatory functions.
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Affiliation(s)
- Karolin Frykholm
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Ronnie Per-Arne Berntsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691 Stockholm, Sweden
| | - Magnus Claesson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691 Stockholm, Sweden
| | - Laura de Battice
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Richard Odegrip
- Department of Molecular Biosciences, The Wenner-Gren Institute, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691 Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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38
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Abstract
Here, we present an experimental demonstration of slowing DNA translocation across a nanochannel by modulating the channel surface charge through an externally applied gate bias. The experiments were performed on a nanofluidic field-effect transistor, which is a monolithic integrated platform featuring a 50 nm-diameter in-plane alumina nanocapillary whose entire length is surrounded by a gate electrode. The field-effect transistor behavior was validated on the gating of ionic conductance and protein transport. The gating of DNA translocation was subsequently studied by measuring discrete current dips associated with single λ-DNA translocation events under a source-to-drain bias of 1 V. The translocation speeds under various gate bias conditions were extracted by fitting event histograms of the measured translocation time to the first passage time distributions obtained from a simple 1D biased diffusion model. A positive gate bias was observed to slow the translocation of single λ-DNA chains markedly; the translocation speed was reduced by an order of magnitude from 18.4 mm/s obtained under a floating gate down to 1.33 mm/s under a positive gate bias of 9 V. Therefore, a dynamic and flexible regulation of the DNA translocation speed, which is vital for single-molecule sequencing, can be achieved on this device by simply tuning the gate bias. The device is realized in a conventional semiconductor microfabrication process without the requirement of advanced lithography, and can be potentially further developed into a compact electronic single-molecule sequencer.
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Affiliation(s)
- Yifan Liu
- Department of Electronic and Computer Engineering, ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong S. A. R
| | - Levent Yobas
- Department of Electronic and Computer Engineering, ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong S. A. R
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39
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Muralidhar A, Quevillon MJ, Dorfman KD. The Backfolded Odijk Regime for Wormlike Chains Confined in Rectangular Nanochannels. Polymers (Basel) 2016; 8:polym8030079. [PMID: 30979173 PMCID: PMC6432538 DOI: 10.3390/polym8030079] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 02/05/2016] [Accepted: 03/07/2016] [Indexed: 11/16/2022] Open
Abstract
We confirm Odijk's scaling laws for (i) the average chain extension; (ii) the variance about the average extension; and (iii) the confinement free energy of a wormlike chain confined in a rectangular nanochannel smaller than its chain persistence length through pruned-enriched Rosenbluth method (PERM) simulations of asymptotically long, discrete wormlike chains. In the course of this analysis, we also computed the global persistence length of ideal wormlike chains for the modestly rectangular channels that are used in many experimental systems. The results are relevant to genomic mapping systems that confine DNA in channel sizes around 50 nm, since fabrication constraints generally lead to rectangular cross-sections.
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Affiliation(s)
- Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, USA.
| | - Michael J Quevillon
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, USA.
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, USA.
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40
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Nikoofard N, Mashaghi A. Topology sorting and characterization of folded polymers using nano-pores. NANOSCALE 2016; 8:4643-4649. [PMID: 26853059 DOI: 10.1039/c5nr08828c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied: one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the molecule passes through the nano-pore. The topology of a folded polymer chain is defined as the arrangement of the intramolecular contacts, known as circuit topology. In the case where intramolecular contacts remain intact, we show that the dynamics of passage through a nano-pore varies for molecules with differing topologies: a phenomenon that can be exploited to enrich certain topologies in mixtures. We find that the nano-pore allows reading of the topology for short chains. Moreover, when the passage is coupled with unfolding, the nano-pore enables discrimination between pure states, i.e., states in which the majority of contacts are arranged identically. In this case, as we show here, it is also possible to read the positions of the contact sites along a chain. Our results demonstrate the applicability of nano-pore technology to characterize and sort molecules based on their topology.
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Affiliation(s)
- Narges Nikoofard
- Institute of Nanoscience and Nanotechnology, University of Kashan, Kashan 51167-87317, Iran
| | - Alireza Mashaghi
- Harvard Medical School, Harvard University, Boston, MA 02115, USA.
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41
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Khorshid A, Amin S, Zhang Z, Sakaue T, Reisner WW. Nonequilibrium Dynamics of Nanochannel Confined DNA. Macromolecules 2016. [DOI: 10.1021/acs.macromol.5b02240] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Ahmed Khorshid
- Physics
Department, McGill University, Montreal, QC H3A 2T8, Canada
| | - Susan Amin
- Physics
Department, McGill University, Montreal, QC H3A 2T8, Canada
| | - Zhiyue Zhang
- Physics
Department, McGill University, Montreal, QC H3A 2T8, Canada
| | - Takahiro Sakaue
- Department
of Physics, Kyushu University, Fukuoka 819-0395, Japan
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42
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Iarko V, Werner E, Nyberg LK, Müller V, Fritzsche J, Ambjörnsson T, Beech JP, Tegenfeldt JO, Mehlig K, Westerlund F, Mehlig B. Extension of nanoconfined DNA: Quantitative comparison between experiment and theory. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:062701. [PMID: 26764721 DOI: 10.1103/physreve.92.062701] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Indexed: 05/27/2023]
Abstract
The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose, we performed experiments measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic strength of the buffer. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths, the agreement is less good. We discuss possible reasons. In principle, our approach allows us to measure the Kuhn length and the effective width of a single DNA molecule and more generally of semiflexible polymers in solution.
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Affiliation(s)
- V Iarko
- Department of Physics, University of Gothenburg, 412 96 Göteborg, Sweden
| | - E Werner
- Department of Physics, University of Gothenburg, 412 96 Göteborg, Sweden
| | - L K Nyberg
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - V Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - J Fritzsche
- Department of Applied Physics, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - T Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, 22 100 Lund, Sweden
| | - J P Beech
- Department of Physics, Division of Solid State Physics, Lund University, 22 100 Lund, Sweden
| | - J O Tegenfeldt
- Department of Physics, Division of Solid State Physics, Lund University, 22 100 Lund, Sweden
- NanoLund, Lund University, 22 100 Lund, Sweden
| | - K Mehlig
- Department of Public Health and Community Medicine, University of Gothenburg, 413 46 Göteborg, Sweden
| | - F Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - B Mehlig
- Department of Physics, University of Gothenburg, 412 96 Göteborg, Sweden
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43
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Reiter-Schad M, Werner E, Tegenfeldt JO, Mehlig B, Ambjörnsson T. How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model. J Chem Phys 2015; 143:115101. [DOI: 10.1063/1.4930220] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Michaela Reiter-Schad
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| | - Erik Werner
- Department of Physics, University of Gothenburg, Origovägen 6B, SE-412 96 Göteborg, Sweden
| | - Jonas O. Tegenfeldt
- Division of Solid State Physics, Department of Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Bernhard Mehlig
- Department of Physics, University of Gothenburg, Origovägen 6B, SE-412 96 Göteborg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
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44
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Suma A, Orlandini E, Micheletti C. Knotting dynamics of DNA chains of different length confined in nanochannels. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:354102. [PMID: 26291786 DOI: 10.1088/0953-8984/27/35/354102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Langevin dynamics simulations are used to characterize the typical mechanisms governing the spontaneous tying, untying and the dynamical evolution of knots in coarse-grained models of DNA chains confined in nanochannels. In particular we focus on how these mechanisms depend on the chain contour length, Lc, at a fixed channel width D = 56 nm corresponding to the onset of the Odijk scaling regime where chain backfoldings and hence knots are disfavoured but not suppressed altogether. We find that the lifetime of knots grows significantly with Lc, while that of unknots varies to a lesser extent. The underlying kinetic mechanisms are clarified by analysing the evolution of the knot position along the chain. At the considered confinement, in fact, knots are typically tied by local backfoldings of the chain termini where they are eventually untied after a stochastic motion along the chain. Consequently, the lifetime of unknots is mostly controlled by backfoldings events at the chain ends, which is largely independent of Lc. The lifetime of knots, instead, increases significantly with Lc because knots can, on average, travel farther along the chain before being untied. The observed interplay of knots and unknots lifetimes underpins the growth of the equilibrium knotting probability of longer and longer chains at fixed channel confinement.
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Affiliation(s)
- Antonio Suma
- SISSA, International School for Advanced Studies, via Bonomea 265, I-34136 Trieste, Italy
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45
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Lee E, Jung Y. Segregated structures of ring polymer melts near the surface: a molecular dynamics simulation study. SOFT MATTER 2015; 11:6018-6028. [PMID: 26126895 DOI: 10.1039/c5sm01097g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We study structural properties of a ring polymeric melt confined in a film in comparison to a linear counterpart using molecular dynamics simulations. Local structure orderings of ring and linear polymers in the vicinity of the surface are similar to each other because the length scale of surface-monomer excluded volume interactions is smaller than the size of an ideal blob of the ring. In a long length scale, while the Silberberg hypothesis can be used to provide the physical origin of the confined linear polymer results, it no longer holds for the ring polymer case. We also present different structural properties of ring and linear polymers in a melt, including the size of polymers, the adsorbed amount, and the coordination number of a polymer. Our observation reveals that a confined ring in a melt adopts a highly segregated conformation due to a topological excluded volume repulsion, which may provide a new perspective to understand the nature of biological processes, such as territorial segregation of chromosomes in eukaryotic nuclei.
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Affiliation(s)
- Eunsang Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea.
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46
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Azad Z, Roushan M, Riehn R. DNA Brushing Shoulders: Targeted Looping and Scanning of Large DNA Strands. NANO LETTERS 2015; 15:5641-6. [PMID: 26156085 PMCID: PMC4684187 DOI: 10.1021/acs.nanolett.5b02476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present a nanofluidic device for targeted manipulations in the quarternary structure of single DNA molecules. We demonstrate the folding and unfolding of hairpin-shaped regions, similar to chromatin loops. These loops are stable for minutes at nanochannel junctions. We demonstrate continuous scanning of two DNA segments that occupy a common nanovolume. We present a model governing the stability of loop folds and discuss how the system achieves specific DNA configurations without operator intervention.
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47
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Alishahi M, Kamali R, Abouali O. Rigorous study of molecular dynamics of a single dsDNA confined in a nanochannel: Introduction of a critical mobility behaviour. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2015; 38:92. [PMID: 26314258 DOI: 10.1140/epje/i2015-15092-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 06/30/2015] [Accepted: 07/17/2015] [Indexed: 06/04/2023]
Abstract
The essential and effective characteristics of a double-stranded DNA (dsDNA) confined in a nanochannel is revisited by employing the rigorous full numerical approach of Molecular Dynamics (MD). The deformation of dsDNA and wall-biomolecule interaction which is critical in highly confined regime has been precisely imposed in numerical simulations. The numerical approach has been justified against available theoretical outcomes. A new and general expression for DNA electrophoretic mobility versus DNA length is extracted from numerical simulation which is out of reach of experimental methods due to practical shortcomings. The newly derived expression suggests an essential correction in the previously proposed expression for the critical case of small DNA molecules and reveals an astonishingly unbeknown trend of small DNA's mobility. Sub-molecular phenomenon of dsDNA melting under the condition of large external force is also studied. Assuming strong electric field exertion, the MD approach aptly demonstrates the elaborate melting phenomenon for dsDNA in sub-molecular scale.
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Affiliation(s)
- Marzieh Alishahi
- School of Mechanical Engineering, Shiraz University, Shiraz, Iran
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48
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Lee J, Kim Y, Lee S, Jo K. Visualization of large elongated DNA molecules. Electrophoresis 2015; 36:2057-71. [PMID: 25994517 DOI: 10.1002/elps.201400479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/08/2015] [Accepted: 04/27/2015] [Indexed: 12/26/2022]
Abstract
Long and linear DNA molecules are the mainstream single-molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA-protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.
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Affiliation(s)
- Jinyong Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Yongkyun Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
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49
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Gupta D, Miller JJ, Muralidhar A, Mahshid S, Reisner W, Dorfman KD. Experimental evidence of weak excluded volume effects for nanochannel confined DNA. ACS Macro Lett 2015; 4:759-763. [PMID: 26664782 PMCID: PMC4671635 DOI: 10.1021/acsmacrolett.5b00340] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present experimental demonstration that weak excluded volume effects arise in DNA nanochannel confinement. In particular, by performing measurements of the variance in chain extension as a function of nanochannel dimension for effective channel size ranging from 305 nm to 453 nm, we show that the scaling of the variance in extension with channel size rejects the de Gennes scaling δ2X ~ D1/3 in favor of δ2X ~ D0 using uncertainty at the 95% confidence level. We also show how simulations and confinement spectroscopy can be combined to reduce molecular weight dispersity effects arising from shearing, photocleavage, and nonuniform staining of DNA.
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Affiliation(s)
- Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Jeremy J. Miller
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Sara Mahshid
- Physics Department, McGill University, 3600 rue University, Montreal QC H3A 2T8, Canada
| | - Walter Reisner
- Physics Department, McGill University, 3600 rue University, Montreal QC H3A 2T8, Canada
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
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Sørensen KT, Lopacinska JM, Tommerup N, Silahtaroglu A, Kristensen A, Marie R. Automation of a single-DNA molecule stretching device. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:063702. [PMID: 26133839 DOI: 10.1063/1.4922068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We automate the manipulation of genomic-length DNA in a nanofluidic device based on real-time analysis of fluorescence images. In our protocol, individual molecules are picked from a microchannel and stretched with pN forces using pressure driven flows. The millimeter-long DNA fragments free flowing in micro- and nanofluidics emit low fluorescence and change shape, thus challenging the image analysis for machine vision. We demonstrate a set of image processing steps that increase the intrinsically low signal-to-noise ratio associated with single-molecule fluorescence microscopy. Furthermore, we demonstrate how to estimate the length of molecules by continuous real-time image stitching and how to increase the effective resolution of a pressure controller by pulse width modulation. The sequence of image-processing steps addresses the challenges of genomic-length DNA visualization; however, they should also be general to other applications of fluorescence-based microfluidics.
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Affiliation(s)
- Kristian Tølbøl Sørensen
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Joanna M Lopacinska
- Department of Cellular and Molecular Medicine, University of Copenhagen, København, Denmark
| | - Niels Tommerup
- Department of Cellular and Molecular Medicine, University of Copenhagen, København, Denmark
| | - Asli Silahtaroglu
- Department of Cellular and Molecular Medicine, University of Copenhagen, København, Denmark
| | - Anders Kristensen
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Rodolphe Marie
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kongens Lyngby, Denmark
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