1
|
Singh SL, Chauhan K, Bharadwaj AS, Kishore V, Laux P, Luch A, Singh AV. Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges. Int J Mol Sci 2023; 24:6153. [PMID: 37047125 PMCID: PMC10094227 DOI: 10.3390/ijms24076153] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.
Collapse
Affiliation(s)
- Swarn Lata Singh
- Department of Physics, Mahila Mahavidyalaya (MMV), Banaras Hindu University, Varanasi 221005, UP, India
| | - Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Atul S. Bharadwaj
- Department of Physics, CMP Degree College, University of Allahabad, Prayagraj 211002, UP, India
| | - Vimal Kishore
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Peter Laux
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Ajay Vikram Singh
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| |
Collapse
|
2
|
Chen K, Choudhary A, Sandler SE, Maffeo C, Ducati C, Aksimentiev A, Keyser UF. Super-Resolution Detection of DNA Nanostructures Using a Nanopore. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2207434. [PMID: 36630969 DOI: 10.1002/adma.202207434] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/28/2022] [Indexed: 06/17/2023]
Abstract
High-resolution analysis of biomolecules has brought unprecedented insights into fundamental biological processes and dramatically advanced biosensing. Notwithstanding the ongoing resolution revolution in electron microscopy and optical imaging, only a few methods are presently available for high-resolution analysis of unlabeled single molecules in their native states. Here, label-free electrical sensing of structured single molecules with a spatial resolution down to single-digit nanometers is demonstrated. Using a narrow solid-state nanopore, the passage of a series of nanostructures attached to a freely translocating DNA molecule is detected, resolving individual nanostructures placed as close as 6 nm apart and with a surface-to-surface gap distance of only 2 nm. Such super-resolution ability is attributed to the nanostructure-induced enhancement of the electric field at the tip of the nanopore. This work demonstrates a general approach to improving the resolution of single-molecule nanopore sensing and presents a critical advance towards label-free, high-resolution DNA sequence mapping, and digital information storage independent of molecular motors.
Collapse
Affiliation(s)
- Kaikai Chen
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Adnan Choudhary
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, USA
| | - Sarah E Sandler
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, USA
| | - Caterina Ducati
- Department of Materials Science & Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge, CB3 0FS, UK
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Avenue, Urbana, IL 61801, USA
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| |
Collapse
|
3
|
Sharma A, Kapri R, Chaudhuri A. Driven translocation of a semiflexible polymer through a conical channel in the presence of attractive surface interactions. Sci Rep 2022; 12:19081. [PMID: 36351960 PMCID: PMC9646819 DOI: 10.1038/s41598-022-21845-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/04/2022] [Indexed: 11/11/2022] Open
Abstract
We study the translocation of a semiflexible polymer through a conical channel with attractive surface interactions and a driving force which varies spatially inside the channel. Using the results of the translocation dynamics of a flexible polymer through an extended channel as control, we first show that the asymmetric shape of the channel gives rise to non-monotonic features in the total translocation time as a function of the apex angle of the channel. The waiting time distributions of individual monomer beads inside the channel show unique features strongly dependent on the driving force and the surface interactions. Polymer stiffness results in longer translocation times for all angles of the channel. Further, non-monotonic features in the translocation time as a function of the channel angle changes substantially as the polymer becomes stiffer, which is reflected in the changing features of the waiting time distributions. We construct a free energy description of the system incorporating entropic and energetic contributions in the low force regime to explain the simulation results.
Collapse
Affiliation(s)
- Andri Sharma
- grid.458435.b0000 0004 0406 1521Department of Physical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, S. A. S. Nagar, Mohali, 140306 Punjab India
| | - Rajeev Kapri
- grid.458435.b0000 0004 0406 1521Department of Physical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, S. A. S. Nagar, Mohali, 140306 Punjab India
| | - Abhishek Chaudhuri
- grid.458435.b0000 0004 0406 1521Department of Physical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, S. A. S. Nagar, Mohali, 140306 Punjab India
| |
Collapse
|
4
|
Zhou Y, Wang H. Molecular Dynamics Simulation of a Single Carbon Chain through an Asymmetric Double-Layer Graphene Nanopore for Prolonging the Translocation Time. ACS OMEGA 2022; 7:16422-16429. [PMID: 35601336 PMCID: PMC9118202 DOI: 10.1021/acsomega.2c00438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
In recent years, sensing technology based on nanopores has become one of the trustworthy options for characterization and even identification of a single biomolecule. In nanopore based DNA sequencing technology, the DNA strand in the electrolyte solution passes through the nanopore under an applied bias electric field. Commonly, the ionic current signals carrying the sequence information are difficult to detect effectively due to the fast translocation speed of the DNA strand, so that slowing down the translocation speed is expected to make the signals easier to distinguish and improve the sequencing accuracy. Modifying the nanopore structure is one of the effective methods. Through all-atom molecular dynamics simulations, we designed an asymmetric double-layer graphene nanopore structure to regulate the translocation speed of a single carbon chain. The structure consists of two nanopores with different sizes located on two layers. The simulation results indicate that the asymmetric nanopore structure will affect the chain's translocation speed and the ionic current value. When the single carbon chain passes from the smaller pore to the larger pore, the translocation time is significantly prolonged, which is about three times as long as the chain passing from the larger pore to the smaller pore. These results provide a new idea for designing more accurate and effective single-molecule solid-state nanopore sensors.
Collapse
|
5
|
Sun LZ, Qian JL, Cai P, Hu HX, Xu X, Luo MB. Mg2+ effects on the single-stranded DNA conformations and nanopore translocation dynamics. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.124895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
6
|
Domański Z, Grzybowski AZ. Simulation Study of Chain-like Body Translocation through Conical Pores in Thick Membranes. MEMBRANES 2022; 12:membranes12020138. [PMID: 35207060 PMCID: PMC8878698 DOI: 10.3390/membranes12020138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/08/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023]
Abstract
Artificial membranes with conical pores and controllable thickness reveal ionic-transport capabilities that are superior compared with those offered by cylindrical pores. By simulating the translocation of an abstract chain-like body through a conical pore in a membrane with a variable thickness, we formulate a statistical model of the translocation time τ. Our rough model encodes the biochemical details of a given real chain-like molecule as evolving sequences of the allowed chain-like body’s conformations. In our simulation experiments, we focus primarily on pore geometry and kinetic aspects of the translocation process. We study the impact of the membrane thickness L, and both conical-pore diameters ϕcis,ϕtrans on the probability distribution of τ. We have found that for all considered simulation setups, the randomness of τ is accurately described by the family of Moyal distributions while its expected value τ is proportional to Lξ, with ξ being dependent on ϕcis,ϕtrans.
Collapse
|
7
|
Sun LZ, Cao WP, Wang CH, Xu X. The translocation dynamics of the polymer through a conical pore: Non-stuck, weak-stuck, and strong-stuck modes. J Chem Phys 2021; 154:054903. [PMID: 33557527 DOI: 10.1063/5.0033689] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The external voltage-driven polymer translocation through a conical pore (with a large opening at the entry and a small tip at the exit) is studied by using the Langevin dynamics simulation in this paper. The entire translocation process is divided into an approaching stage and a threading stage. First, the approaching stage starts from the polymer entering the large opening and ends up at a terminal monomer reaching the pore tip. In this stage, the polymer will undergo the conformation adjustment to fit the narrowed cross-sectional area of the pore, leading to three approaching modes: the non-stuck mode with a terminal monomer arriving at the pore tip smoothly, the weak-stuck mode for the polymer stuck inside the pore for a short duration with minor conformational adjustments, and the strong-stuck mode with major conformational changes and a long duration. The approaching times (the duration of the approaching stage) of the three approaching modes show different behavior as a function of the pore apex angle. Second, the threading stage describes that the polymer threads through the pore tip with a linear fashion. In this stage, an increase in the apex angle causes the reduction of the threading time (the duration of the threading stage) due to the increase in the driving force with the apex angle at the tip. Moreover, we also find that with the increase in the apex angle or the polymer length, the polymer threading dynamics will change from the quasi-equilibrium state to the non-equilibrium state.
Collapse
Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Wei-Ping Cao
- Institute of Optoelectronic Technology, Lishui University, Lishui 323000, China
| | - Chang-Hui Wang
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
| |
Collapse
|
8
|
Nagarajan K, Chen SB. Polyelectrolyte Translocation through a Corrugated Nanopore. MACROMOL THEOR SIMUL 2020. [DOI: 10.1002/mats.202000042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Karthik Nagarajan
- Department of Chemical & Biomolecular EngineeringNational University of Singapore Singapore 117585 Singapore
| | - Shing Bor Chen
- Department of Chemical & Biomolecular EngineeringNational University of Singapore Singapore 117585 Singapore
| |
Collapse
|
9
|
Affiliation(s)
- Karthik Nagarajan
- K. Nagarajan, Prof. S. B. ChenDepartment of Chemical & Biomolecular EngineeringNational University of Singapore Singapore 117585 Singapore
| | - Shing Bor Chen
- K. Nagarajan, Prof. S. B. ChenDepartment of Chemical & Biomolecular EngineeringNational University of Singapore Singapore 117585 Singapore
| |
Collapse
|
10
|
Abstract
Although nanopores have shown tremendous promise for use in DNA sequencing, the rate of translocation through most pores studied previously is too rapid for the genetic information to be read accurately. In this study, dissipative particle dynamics simulations were employed to investigate the feasibility of using tortuous nanopores to control the rate of polyelectrolyte translocation. Unlike many previous studies, our simulation method incorporates the effects of hydrodynamic and electrostatic interactions and the spatial variation of electric field strength. The average translocation time, ⟨τ⟩, increases with the pore length and tortuosity but decreases as the pore width increases. For the longest pore investigated, the introduction of tortuosity results in ⟨τ⟩ increasing by as much as 187% as compared to a straight pore. The temporal variation of bond tension indicates that slower translocation in tortuous nanopores is caused by inhibition of tension propagation.
Collapse
Affiliation(s)
- Karthik Nagarajan
- Department of Chemical and Biomolecular Engineering , National University of Singapore , 117585 , Singapore
| | - Shing Bor Chen
- Department of Chemical and Biomolecular Engineering , National University of Singapore , 117585 , Singapore
| |
Collapse
|
11
|
Sun LZ, Wang CH, Luo MB, Li H. Trapped and non-trapped polymer translocations through a spherical pore. J Chem Phys 2019; 150:024904. [PMID: 30646715 DOI: 10.1063/1.5063331] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The polymer translocation through a spherical pore is studied using the Langevin dynamics simulation. The translocation events are classified into two types: one is the trapped translocation in which the entire polymer is trapped in the pore and the other is the non-trapped translocation where the pore cannot hold the whole polymer. We find that the trapped translocation is favored at large spheres and small external voltages. However, the monomer-pore attraction would lead to the non-monotonic behavior of the trapped translocation possibility out of all translocation events. Moreover, both the trapped and non-trapped translocation times are dependent on the polymer length, pore size, external voltage, and the monomer-pore attraction. There exist two pathways for the polymer in the trapped translocation: an actively trapped pathway for the polymer trapped in the pore before the head monomer arrives at the pore exit, and a passively trapped pathway for the polymer trapped in the pore while the head monomer is struggling to move out of the pore. The studies of trapped pathways can provide a deep understanding of the polymer translocation behavior.
Collapse
Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Chang-Hui Wang
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Haibin Li
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| |
Collapse
|