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Cui Y, Ying C, Huang XY, Ye Q, Tian J, Liu Z. Electrical Transport and Dynamics of Confined DNA through Highly Conductive 2D Graphene Nanochannels. NANO LETTERS 2024; 24:4485-4492. [PMID: 38578031 DOI: 10.1021/acs.nanolett.4c00403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Confining DNA in nanochannels is an important approach to studying its structure and transportation dynamics. Graphene nanochannels are particularly attractive for studying DNA confinement due to their atomic flatness, precise height control, and excellent mechanical strength. Here, using femtosecond laser etching and wetting transfer, we fabricate graphene nanochannels down to less than 4.3 nm in height, with the length-to-height ratios up to 103. These channels exhibit high stability, low noise, and self-cleaning ability during the long-term ionic current recording. We report a clear linear relationship between DNA length and the residence time in the channel and further utilize this relationship to differentiate DNA fragments based on their lengths, ranging widely from 200 bps to 48.5 kbps. The graphene nanochannel presented here provides a potential platform for label-free analyses and reveals fundamental insights into the conformational dynamics of DNA and proteins in confined space.
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Affiliation(s)
- Yangjun Cui
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Cuifeng Ying
- Advanced Optics & Photonics Laboratory, Department of Engineering, School of Science & Technology, Nottingham Trent University, Nottingham NG11 8NS, U.K
| | - Xiao-Yu Huang
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Qing Ye
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Jianguo Tian
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
- Renewable Energy Conversion and Storage Center, Nankai University, Tianjin 300071, China
| | - Zhibo Liu
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
- Renewable Energy Conversion and Storage Center, Nankai University, Tianjin 300071, China
- The Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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Theeyancheri L, Chaki S, Bhattacharjee T, Chakrabarti R. Migration of active rings in porous media. Phys Rev E 2022; 106:014504. [PMID: 35974648 DOI: 10.1103/physreve.106.014504] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Inspired by how the shape deformations in active organisms help them to migrate through disordered porous environments, we simulate active ring polymers in two-dimensional random porous media. Flexible and inextensible active ring polymers navigate smoothly through the disordered media. In contrast, semiflexible rings undergo transient trapping inside the pore space; the degree of trapping is inversely correlated with the increase in activity. We discover that flexible rings swell while inextensible and semiflexible rings monotonically shrink upon increasing the activity. Together, our findings identify the optimal migration of active ring polymers through porous media.
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Affiliation(s)
- Ligesh Theeyancheri
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Subhasish Chaki
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Tapomoy Bhattacharjee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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Bucci G, Gadelrab K, Spakowitz AJ. Free Energy and Dynamics of Annihilation of Topological Defects in Nanoconfined DNA. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Giovanna Bucci
- Robert Bosch LLC, 384 Santa Trinita Ave, Sunnyvale, California 94085, United States
| | - Karim Gadelrab
- Robert Bosch LLC, 1 Kendall Square, Suite 7-101, Cambridge, Massachusetts 02139, United States
| | - Andrew J. Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
- Department of Applied Physics, Stanford University, Stanford, California 94305, United States
- Biophysics Program, Stanford University, Stanford, California 94305, United States
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Yong H, Molcrette B, Sperling M, Montel F, Sommer JU. Regulating the Translocation of DNA through Poly( N-isopropylacrylamide)-Decorated Switchable Nanopores by Cononsolvency Effect. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Huaisong Yong
- Leibniz-Institut für Polymerforschung Dresden e.V., Dresden 01069, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden 01069, Germany
| | - Bastien Molcrette
- Université de Lyon, École Normale Supérieure de Lyon, Université Claude Bernard, CNRS, Laboratoire de Physique, Lyon F-69342, France
| | - Marcel Sperling
- Fraunhofer-Institut für Angewandte Polymerforschung, Potsdam-Golm 14476, Germany
| | - Fabien Montel
- Université de Lyon, École Normale Supérieure de Lyon, Université Claude Bernard, CNRS, Laboratoire de Physique, Lyon F-69342, France
| | - Jens-Uwe Sommer
- Leibniz-Institut für Polymerforschung Dresden e.V., Dresden 01069, Germany
- Institute for Theoretical Physics, Technische Universität Dresden, Dresden 01069, Germany
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