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Namani S, Kavetsky K, Lin CY, Maharjan S, Gamper HB, Li NS, Piccirilli JA, Hou YM, Drndic M. Unraveling RNA Conformation Dynamics in Mitochondrial Encephalomyopathy, Lactic Acidosis, and Stroke-like Episode Syndrome with Solid-State Nanopores. ACS NANO 2024; 18:17240-17250. [PMID: 38906834 DOI: 10.1021/acsnano.4c04625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/23/2024]
Abstract
This study investigates transfer ribonucleic acid (tRNA) conformational dynamics in the context of MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) using solid-state silicon nitride (SiN) nanopore technology. SiN nanopores in thin membranes with specific dimensions exhibit high signal resolution, enabling real-time and single-molecule electronic detection of tRNA conformational changes. We focus on human mitochondrial tRNALeu(UAA) (mt-Leu(UAA)) that decodes Leu codons UUA/UUG (UUR) during protein synthesis on the mt-ribosome. The single A14G substitution in mt-Leu(UAA) is the major cause of MELAS disease. Measurements of current blockades and dwell times reveal distinct conformational dynamics of the wild-type (WT) and the A14G variant of mt-Leu(UAA) in response to the conserved post-transcriptional m1G9 methylation. While the m1G9-modified WT transcript adopts a more stable structure relative to the unmodified transcript, the m1G9-modified MELAS transcript adopts a less stable structure relative to the unmodified transcript. Notably, these differential features were observed at 0.4 M KCl, but not at 3 M KCl, highlighting the importance of experimental settings that are closer to physiological conditions. This work demonstrates the feasibility of the nanopore platform to discern tRNA molecules that differ by a single-nucleotide substitution or by a single methylation event, providing an important step forward to explore changes in the conformational dynamics of other RNA molecules in human diseases.
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Affiliation(s)
- Srilahari Namani
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Kyril Kavetsky
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chih-Yuan Lin
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Sunita Maharjan
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Howard B Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Nan-Sheng Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Marija Drndic
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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Rao YF, Sun LZ, Luo MB. Na +-Mg 2+ ion effects on conformation and translocation dynamics of single-stranded RNA: Cooperation and competition. Int J Biol Macromol 2024; 267:131273. [PMID: 38569994 DOI: 10.1016/j.ijbiomac.2024.131273] [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] [Received: 02/04/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024]
Abstract
The nanopore-based translocation of a single-stranded RNA (ssRNA) in mixed salt solution has garnered increasing interest for its biological and technological significance. However, it is challenging to comprehensively understand the effects of the mixed ion species on the translocation dynamics due to their cooperation and competition, which can be directly reflected by the ion screening and neutralizing effects, respectively. In this study, Langevin dynamics simulation is employed to investigate the properties of ssRNA conformation and translocation in mixed Na+-Mg2+ ion environments. Simulation results reveal that the ion screening effect dominates the change in the ssRNA conformational size, the ion neutralizing effect controls the capture rate of the ssRNA by the nanopore, and both of them take charge of the different changes in translocation time of the ssRNA under various mixed ion environments. Under high Na+ ion concentration, as Mg2+ concentration increases, the ion neutralizing effect strengthens, weakening the driving force inside the nanopore, leading to longer translocation time. Conversely, at low Na+ concentration, an increase in Mg2+ concentration enhances the ion screening effect, aiding in faster translocation. Furthermore, these simulation results will be explained by quantitative analysis, advancing a deeper understanding of the complicated effects of the mixed Na+-Mg2+ ions.
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Affiliation(s)
- Yi-Fan Rao
- School of Physics, Zhejiang University, Hangzhou 310027, China; Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Meng-Bo Luo
- School of Physics, Zhejiang University, Hangzhou 310027, China.
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3
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de Blois C, Engel M, Rejou MA, Molcrette B, Favier A, Montel F. Optical single molecule characterisation of natural and synthetic polymers through nanopores. NANOSCALE 2023; 16:138-151. [PMID: 38054974 DOI: 10.1039/d3nr04915a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Nanopore techniques are now widely used to sequence DNA, RNA and even oligopeptide molecules at the base pair level by measuring the ionic current. In order to build a more versatile characterisation system, optical methods for the detection of a single molecule translocating through a nanopore have been developed, achieving very promising results. In this work, we developed a series of tools to interpret the optical signals in terms of the physical behaviour of various types of natural and synthetic polymers, with high throughput. We show that the measurement of the characteristic time of a translocation event gives access to the apparent molecular weight of an object, and allows us to quantify the concentration ratio of two DNA samples of different molecular weights in solution. Using the same tools for smaller synthetic polymers, we were able to obtain information about their molecular weight distribution depending on the synthesis method.
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Affiliation(s)
- Charlotte de Blois
- Univ. Lyon, ENS de Lyon, CNRS, Laboratoire de Physique, F-69342 Lyon, France.
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, INSA Lyon, Université Jean Monnet, UMR 5233, Ingénierie des Matériaux Polymères, F-69621 Villeurbanne, France.
| | - Marie Engel
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, INSA Lyon, Université Jean Monnet, UMR 5233, Ingénierie des Matériaux Polymères, F-69621 Villeurbanne, France.
| | - Marie-Amélie Rejou
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, INSA Lyon, Université Jean Monnet, UMR 5233, Ingénierie des Matériaux Polymères, F-69621 Villeurbanne, France.
| | - Bastien Molcrette
- Univ. Lyon, ENS de Lyon, CNRS, Laboratoire de Physique, F-69342 Lyon, France.
| | - Arnaud Favier
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, INSA Lyon, Université Jean Monnet, UMR 5233, Ingénierie des Matériaux Polymères, F-69621 Villeurbanne, France.
| | - Fabien Montel
- Univ. Lyon, ENS de Lyon, CNRS, Laboratoire de Physique, F-69342 Lyon, France.
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Maharjan S, Gamper H, Yamaki Y, Henley RY, Li NS, Suzuki T, Suzuki T, Piccirilli JA, Wanunu M, Seifert E, Wallace DC, Hou YM. Post-Transcriptional Methylation of Mitochondrial-tRNA Differentially Contributes to Mitochondrial Pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.09.569632. [PMID: 38106193 PMCID: PMC10723379 DOI: 10.1101/2023.12.09.569632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Human mitochondrial tRNAs (mt-tRNAs), critical for mitochondrial biogenesis, are frequently associated with pathogenic mutations. These mt-tRNAs have unusual sequence motifs and require post-transcriptional modifications to stabilize their fragile structures. However, whether a modification that stabilizes a wild-type (WT) mt-tRNA structure would also stabilize its pathogenic variants is unknown. Here we show that the N 1 -methylation of guanosine at position 9 (m 1 G9) of mt-Leu(UAA), while stabilizing the WT tRNA, has an opposite and destabilizing effect on variants associated with MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes). This differential effect is further demonstrated by the observation that demethylation of m 1 G9, while damaging to the WT tRNA, is beneficial to the major pathogenic variant, improving its structure and activity. These results have new therapeutic implications, suggesting that the N 1 -methylation of mt-tRNAs at position 9 is a determinant of pathogenicity and that controlling the methylation level is an important modulator of mt-tRNA-associated diseases.
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Haghizadeh A, Iftikhar M, Dandpat SS, Simpson T. Looking at Biomolecular Interactions through the Lens of Correlated Fluorescence Microscopy and Optical Tweezers. Int J Mol Sci 2023; 24:2668. [PMID: 36768987 PMCID: PMC9916863 DOI: 10.3390/ijms24032668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
Understanding complex biological events at the molecular level paves the path to determine mechanistic processes across the timescale necessary for breakthrough discoveries. While various conventional biophysical methods provide some information for understanding biological systems, they often lack a complete picture of the molecular-level details of such dynamic processes. Studies at the single-molecule level have emerged to provide crucial missing links to understanding complex and dynamic pathways in biological systems, which are often superseded by bulk biophysical and biochemical studies. Latest developments in techniques combining single-molecule manipulation tools such as optical tweezers and visualization tools such as fluorescence or label-free microscopy have enabled the investigation of complex and dynamic biomolecular interactions at the single-molecule level. In this review, we present recent advances using correlated single-molecule manipulation and visualization-based approaches to obtain a more advanced understanding of the pathways for fundamental biological processes, and how this combination technique is facilitating research in the dynamic single-molecule (DSM), cell biology, and nanomaterials fields.
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Orlandini E, Micheletti C. Topological and physical links in soft matter systems. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 34:013002. [PMID: 34547745 DOI: 10.1088/1361-648x/ac28bf] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Linking, or multicomponent topological entanglement, is ubiquitous in soft matter systems, from mixtures of polymers and DNA filaments packedin vivoto interlocked line defects in liquid crystals and intertwined synthetic molecules. Yet, it is only relatively recently that theoretical and experimental advancements have made it possible to probe such entanglements and elucidate their impact on the physical properties of the systems. Here, we review the state-of-the-art of this rapidly expanding subject and organize it as follows. First, we present the main concepts and notions, from topological linking to physical linking and then consider the salient manifestations of molecular linking, from synthetic to biological ones. We next cover the main physical models addressing mutual entanglements in mixtures of polymers, both linear and circular. Finally, we consider liquid crystals, fluids and other non-filamentous systems where topological or physical entanglements are observed in defect or flux lines. We conclude with a perspective on open challenges.
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Affiliation(s)
- Enzo Orlandini
- Department of Physics and Astronomy, University of Padova and Sezione INFN, Via Marzolo 8, Padova, Italy
| | - Cristian Micheletti
- SISSA, International School for Advanced Studies, via Bonomea 265, Trieste, Italy
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Becchi M, Chiarantoni P, Suma A, Micheletti C. RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration. J Phys Chem B 2021; 125:1098-1106. [PMID: 33497228 PMCID: PMC7875513 DOI: 10.1021/acs.jpcb.0c09966] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/19/2021] [Indexed: 11/28/2022]
Abstract
We use MD simulations to study the pore translocation properties of a pseudoknotted viral RNA. We consider the 71-nucleotide-long xrRNA from the Zika virus and establish how it responds when driven through a narrow pore by static or periodic forces applied to either of the two termini. Unlike the case of fluctuating homopolymers, the onset of translocation is significantly delayed with respect to the application of static driving forces. Because of the peculiar xrRNA architecture, activation times can differ by orders of magnitude at the two ends. Instead, translocation duration is much smaller than activation times and occurs on time scales comparable at the two ends. Periodic forces amplify significantly the differences at the two ends, for both activation times and translocation duration. Finally, we use a waiting-times analysis to examine the systematic slowing downs in xrRNA translocations and associate them to the hindrance of specific secondary and tertiary elements of xrRNA. The findings provide a useful reference to interpret and design future theoretical and experimental studies of RNA translocation.
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Affiliation(s)
- Matteo Becchi
- Physics
Area, Scuola Internazionale Superiore di
Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Pietro Chiarantoni
- Physics
Area, Scuola Internazionale Superiore di
Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Antonio Suma
- Dipartimento
di Fisica, Università di Bari and
Sezione INFN di Bari, via Amendola 173, 70126 Bari, Italy
| | - Cristian Micheletti
- Physics
Area, Scuola Internazionale Superiore di
Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
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Qiao L, Ignacio M, Slater GW. An efficient kinetic Monte Carlo to study analyte capture by a nanopore: transients, boundary conditions and time-dependent fields. Phys Chem Chem Phys 2021; 23:1489-1499. [PMID: 33400742 DOI: 10.1039/d0cp03638b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
To better understand the capture process by a nanopore, we introduce an efficient Kinetic Monte Carlo (KMC) algorithm that can simulate long times and large system sizes by mapping the dynamic of a point-like particle in a 3D spherically symmetric system onto the 1D biased random walk. Our algorithm recovers the steady-state analytical solution and allows us to study time-dependent processes such as transients. Simulation results show that the steady-state depletion zone near pore is barely larger than the pore radius and narrows at higher field intensities; as a result, the time to reach steady-state is much smaller than the time required to empty a zone of the size of the capture radius λe. When the sample reservoir has a finite size, a second depletion region propagates inward from the outer wall, and the capture rate starts decreasing when it reaches the capture radius λe. We also note that the flatness of the electric field near the pore, which is often neglected, induces a traffic jam that can increase the transient time by several orders of magnitude. Finally, we propose a new proof-of-concept scheme to separate two analytes of the same mobility but different diffusion coefficients using time-varying fields.
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Affiliation(s)
- Le Qiao
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
| | - Maxime Ignacio
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
| | - Gary W Slater
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
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Yan H, Zhang Z, Weng T, Zhu L, Zhang P, Wang D, Liu Q. Recognition of Bimolecular Logic Operation Pattern Based on a Solid-State Nanopore. SENSORS (BASEL, SWITZERLAND) 2020; 21:s21010033. [PMID: 33374742 PMCID: PMC7793508 DOI: 10.3390/s21010033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 05/17/2023]
Abstract
Nanopores have a unique advantage for detecting biomolecules in a label-free fashion, such as DNA that can be synthesized into specific structures to perform computations. This method has been considered for the detection of diseased molecules. Here, we propose a novel marker molecule detection method based on DNA logic gate by deciphering a variable DNA tetrahedron structure using a nanopore. We designed two types of probes containing a tetrahedron and a single-strand DNA tail which paired with different parts of the target molecule. In the presence of the target, the two probes formed a double tetrahedron structure. As translocation of the single and the double tetrahedron structures under bias voltage produced different blockage signals, the events could be assigned into four different operations, i.e., (0, 0), (0, 1), (1, 0), (1, 1), according to the predefined structure by logic gate. The pattern signal produced by the AND operation is obviously different from the signal of the other three operations. This pattern recognition method has been differentiated from simple detection methods based on DNA self-assembly and nanopore technologies.
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Affiliation(s)
- Han Yan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China; (H.Y.); (Z.Z.); (L.Z.)
| | - Zhen Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China; (H.Y.); (Z.Z.); (L.Z.)
| | - Ting Weng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (T.W.); (P.Z.); (D.W.)
| | - Libo Zhu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China; (H.Y.); (Z.Z.); (L.Z.)
| | - Pang Zhang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (T.W.); (P.Z.); (D.W.)
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (T.W.); (P.Z.); (D.W.)
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China; (H.Y.); (Z.Z.); (L.Z.)
- Correspondence:
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10
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Suma A, Coronel L, Bussi G, Micheletti C. Directional translocation resistance of Zika xrRNA. Nat Commun 2020; 11:3749. [PMID: 32719310 PMCID: PMC7385498 DOI: 10.1038/s41467-020-17508-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022] Open
Abstract
xrRNAs from flaviviruses survive in host cells because of their exceptional dichotomic response to the unfolding action of different enzymes. They can be unwound, and hence copied, by replicases, and yet can resist degradation by exonucleases. How the same stretch of xrRNA can encode such diverse responses is an open question. Here, by using atomistic models and translocation simulations, we uncover an elaborate and directional mechanism for how stress propagates when the two xrRNA ends, [Formula: see text] and [Formula: see text], are driven through a pore. Pulling the [Formula: see text] end, as done by replicases, elicits a progressive unfolding; pulling the [Formula: see text] end, as done by exonucleases, triggers a counterintuitive molecular tightening. Thus, in what appears to be a remarkable instance of intra-molecular tensegrity, the very pulling of the [Formula: see text] end is what boosts resistance to translocation and consequently to degradation. The uncovered mechanistic principle might be co-opted to design molecular meta-materials.
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Affiliation(s)
- Antonio Suma
- Dipartimento di Fisica, Università di Bari and INFN Sezione di Bari, via Amendola 173, 70126, Bari, Italy
- Institute for Computational Molecular Science (ICMS), Temple University, 19122, Philadelphia, PA, Italy
| | - Lucia Coronel
- Physics Area, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136, Trieste, Italy
| | - Giovanni Bussi
- Physics Area, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136, Trieste, Italy
| | - Cristian Micheletti
- Physics Area, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136, Trieste, Italy.
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Qiao L, Slater GW. Capture of rod-like molecules by a nanopore: Defining an "orientational capture radius". J Chem Phys 2020; 152:144902. [PMID: 32295359 DOI: 10.1063/5.0002044] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Both the translational diffusion coefficient D and the electrophoretic mobility μ of a short rod-like molecule (such as dsDNA) that is being pulled toward a nanopore by an electric field should depend on its orientation. Since a charged rod-like molecule tends to orient in the presence of an inhomogeneous electric field, D and μ will change as the molecule approaches the nanopore, and this will impact the capture process. We present a simplified study of this problem using theoretical arguments and Langevin dynamics simulations. In particular, we introduce a new orientational capture radius, which we compare to the capture radius for the equivalent point-like particle, and we discuss the different physical regimes of orientation during capture and the impact of initial orientations on the capture time.
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Affiliation(s)
- Le Qiao
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Gary W Slater
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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