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Becerra D, Klotz AR, Hall LM. Single-molecule analysis of solvent-responsive mechanically interlocked ring polymers and the effects of nanoconfinement from coarse-grained simulations. J Chem Phys 2024; 160:114906. [PMID: 38511659 DOI: 10.1063/5.0191295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/02/2024] [Indexed: 03/22/2024] Open
Abstract
In this study, we simulate mechanically interlocked semiflexible ring polymers inspired by the minicircles of kinetoplast DNA (kDNA) networks. Using coarse-grained molecular dynamics simulations, we investigate the impact of molecular topological linkage and nanoconfinement on the conformational properties of two- and three-ring polymer systems in varying solvent qualities. Under good-quality solvents, for two-ring systems, a higher number of crossing points lead to a more internally constrained structure, reducing their mean radius of gyration. In contrast, three-ring systems, which all had the same crossing number, exhibited more similar sizes. In unfavorable solvents, structures collapse, forming compact configurations with increased contacts. The morphological diversity of structures primarily arises from topological linkage rather than the number of rings. In three-ring systems with different topological conformations, structural uniformity varies based on link types. Extreme confinement induces isotropic and extended conformations for catenated polymers, aligning with experimental results for kDNA networks and influencing the crossing number and overall shape. Finally, the flat-to-collapse transition in extreme confinement occurs earlier (at relatively better solvent conditions) compared to non-confined systems. This study offers valuable insights into the conformational behavior of mechanically interlocked ring polymers, highlighting challenges in extrapolating single-molecule analyses to larger networks such as kDNA.
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Affiliation(s)
- Diego Becerra
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, USA
| | - Alexander R Klotz
- Department of Physics and Astronomy, California State University, Long Beach, California 90840, USA
| | - Lisa M Hall
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, USA
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Xie W, He S, Fang S, Liang L, Shi B, Wang D. Visualizing of AuNPs protection aptamer from DNase I enzyme digestion based on Nanopipette and its use for Microcystin-LR detection. Anal Chim Acta 2021; 1173:338698. [PMID: 34172149 DOI: 10.1016/j.aca.2021.338698] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/11/2021] [Accepted: 05/23/2021] [Indexed: 11/20/2022]
Abstract
A simple and effective fluorescence platform has been established for visualizing nanomaterials' protective effect of DNA from cellular enzyme digestion based on nanopipette. In a proof-of-concept trial, gold nanoparticles (AuNPs) protect aptamer was designed, and it used for Microcystin-LR (MC-LR) sensitive detection. In the absence of MC-LR, FAM-labeled aptamers were combined on AuNPs, resulting in weak fluorescence emission. In the presence of MC-LR, aptamer bound with MC-LR. The formed complex leaves the surface of AuNPs. With the addition of the deoxyribonuclease I (DNase I) enzyme, the aptamer was selectively cleavaged, and MC-LR was released as an additional target molecule to achieve signal amplification and obtain strong fluorescence intensity. At the optimized conditions, a wide linear range (0.25 nM-20 nM) of fluorescence response for MC-LR was obtained. Further, by electrochemically manipulation MC-LR and DNase I inside confining nanopipette, which is filled with aptamer/AuNPs. The fluorescence intensity change with the aptamer and AuNPs interaction, these results directly visualize the process of DNA cleavage, and the interaction with AuNPs can effectively prevent the cleavage at the nanoscale confinement. This convenient nanoscale device provides new kinetic information about the dynamic chemical processes at a single-molecule level.
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Affiliation(s)
- Wanyi Xie
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Shixuan He
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China; Physics Department, Sichuan University, Chengdu, Sichuan, 610065, China.
| | - Shaoxi Fang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Liyuan Liang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Biao Shi
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China.
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Klotz AR, Soh BW, Doyle PS. Equilibrium structure and deformation response of 2D kinetoplast sheets. Proc Natl Acad Sci U S A 2020; 117:121-127. [PMID: 31811027 PMCID: PMC6955370 DOI: 10.1073/pnas.1911088116] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The considerable interest in two-dimensional (2D) materials and complex molecular topologies calls for a robust experimental system for single-molecule studies. In this work, we study the equilibrium properties and deformation response of a complex DNA structure called a kinetoplast, a 2D network of thousands of linked rings akin to molecular chainmail. Examined in good solvent conditions, kinetoplasts appear as a wrinkled hemispherical sheet. The conformation of each kinetoplast is dictated by its network topology, giving it a unique shape, which undergoes small-amplitude thermal fluctuations at subsecond timescales, with a wide separation between fluctuation and diffusion timescales. They deform elastically when weakly confined and swell to their equilibrium dimensions when the confinement is released. We hope that, in the same way that linear DNA became a canonical model system on the first investigations of its polymer-like behavior, kinetoplasts can serve that role for 2D and catenated polymer systems.
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Affiliation(s)
- Alexander R Klotz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
- Department of Physics and Astronomy, California State University, Long Beach, CA 90840
| | - Beatrice W Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Patrick S Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142;
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Wang Y, Wang R, Gao T, Yang G. The Mixing Counterion Effect on DNA Compaction and Charge Neutralization at Low Ionic Strength. Polymers (Basel) 2018; 10:E244. [PMID: 30966279 PMCID: PMC6415083 DOI: 10.3390/polym10030244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 02/24/2018] [Accepted: 02/26/2018] [Indexed: 12/18/2022] Open
Abstract
DNA compaction and charge neutralization in a mixing counterion solution involves competitive and cooperative electrostatic binding, and sometimes counterion complexation. At normal ionic strength, it has been found that the charge neutralization of DNA by the multivalent counterion is suppressed when being added extra mono- and di-valent counterions. Here, we explore the effect mixing counterion on DNA compaction and charge neutralization under the condition of low ionic strength. Being quite different from normal ionic strength, the electrophoretic mobility of DNA in multivalent counterion solution (octalysine, spermine) increases the presence of mono- and di-valent cations, such as sodium and magnesium ions. It means that the charge neutralization of DNA by the multivalent counterion is promoted rather than suppressed when introducing extra mono- and di-valent counterions into solution. This conclusion is also supported by the measurement of condensing and unraveling forces of DNA condensates under the same condition by single molecular magnetic tweezers. This mixing effect can be attributed to the cooperative electrostatic binding of counterions to DNA when the concentration of counterions in solution is below a critical concentration.
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Affiliation(s)
- Yanwei Wang
- College of Mathematical, Physics and Electronic Information Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Ruxia Wang
- College of Mathematical, Physics and Electronic Information Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Tianyong Gao
- College of Mathematical, Physics and Electronic Information Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Guangcan Yang
- College of Mathematical, Physics and Electronic Information Engineering, Wenzhou University, Wenzhou 325035, China.
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