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Lee JH, Chiu JHC, Ginga NJ, Ahmed T, Thouless MD, Liu Y, Takayama S. Super-resolution imaging of linearized chromatin in tunable nanochannels. NANOSCALE HORIZONS 2023; 8:1043-1053. [PMID: 37221952 DOI: 10.1039/d3nh00096f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Nanofluidic linearization and optical mapping of naked DNA have been reported in the research literature, and implemented in commercial instruments. However, the resolution with which DNA features can be resolved is still inherently limited by both Brownian motion and diffraction-limited optics. Direct analysis of native chromatin is further hampered by difficulty in electrophoretic manipulation, which is routinely used for DNA analysis. This paper describes the development of a three-layer, tunable, nanochannel system that enables non-electrophoretic linearization and immobilization of native chromatin. Furthermore, through careful selection of self-blinking fluorescent dyes and the design of the nanochannel system, we achieve direct stochastic optical reconstruction microscopy (dSTORM) super-resolution imaging of the linearized chromatin. As an initial demonstration, rDNA chromatin extracted from Tetrahymena is analyzed by multi-color imaging of total DNA, newly synthesized DNA, and newly synthesized histone H3. Our analysis reveals a relatively even distribution of newly synthesized H3 across two halves of the rDNA chromatin with palindromic symmetry, supporting dispersive nucleosome segregation. As a proof-of-concept study, our work achieves super-resolution imaging of native chromatin fibers linearized and immobilized in tunable nanochannels. It opens up a new avenue for collecting long-range and high-resolution epigenetic information as well as genetic information.
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Affiliation(s)
- Ji-Hoon Lee
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joyce Han-Ching Chiu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nicholas J Ginga
- Department of Mechanical and Aerospace Engineering, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Tasdiq Ahmed
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - M D Thouless
- Department of Mechanical Engineering and Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yifan Liu
- Department of Biochemistry and Molecular Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA.
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Han J, Liu S, Wang Z, Wu Y. Micro/nanofluidic-electrochemical biosensors for in situ tumor cell analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Chen X, Zhang S, Gan Y, Liu R, Wang RQ, Du K. Understanding microbeads stacking in deformable Nano-Sieve for Efficient plasma separation and blood cell retrieval. J Colloid Interface Sci 2022; 606:1609-1616. [PMID: 34500162 PMCID: PMC8572169 DOI: 10.1016/j.jcis.2021.08.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/06/2021] [Accepted: 08/17/2021] [Indexed: 01/17/2023]
Abstract
Efficient separation of blood cells and plasma is key for numerous molecular diagnosis and therapeutics applications. Despite various microfluidics-based separation strategies having been developed, there is still a need for a simple, reliable, and multiplexing separation device that can process a large volume of blood. Here we show a microbead-packed deformable microfluidic system that can efficiently separate highly purified plasma from whole blood, as well as retrieve blocked blood cells from the device. To support and rationalize the experimental validation of the proposed device, a highly accurate model is constructed to help understand the link between the mechanical properties of the microfluidics, flow rate, and microbeads packing/leaking based on the microscope imaging and the optical coherence tomography (OCT) scanning. This deformable nano-sieve device is expected to offer a new solution for centrifuge-free diagnosis and treatment of bloodborne diseases and contribute to the design of next-generation deformable microfluidics for separation applications.
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Affiliation(s)
- Xinye Chen
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, NY 14623, United States, Department of Microsystems Engineering, Rochester Institute of Technology, Rochester, NY 14623, United States
| | - Shuhuan Zhang
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, NY 14623, United States
| | - Yu Gan
- Department of Electrical and Computer Engineering, University of Alabama, Tuscaloosa, AL 35401 United States
| | - Rui Liu
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, NY 14623, United States
| | - Ruo-Qian Wang
- Department of Civil and Environmental Engineering, Rutgers, The State University of New Jersey, NJ 08854 USA, Corresponding authors ;
| | - Ke Du
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, NY 14623, United States, Department of Microsystems Engineering, Rochester Institute of Technology, Rochester, NY 14623, United States, Chemistry and Materials Science, Rochester Institute of Technology, Rochester, NY 14623, United States, Corresponding authors ;
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Seetasang S, Xu Y. Recent progress and perspectives in applications of 2-methacryloyloxyethyl phosphorylcholine polymers in biodevices at small scales. J Mater Chem B 2022; 10:2323-2337. [DOI: 10.1039/d1tb02675e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bioinspired materials have attracted attention in a wide range of fields. Among these materials, a polymer family containing 2-methacryloyloxyethyl phosphorylcholine (MPC), which has a zwitterionic phosphorylcholine headgroup inspired by the...
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Wang M, Hou Y, Yu L, Hou X. Anomalies of Ionic/Molecular Transport in Nano and Sub-Nano Confinement. NANO LETTERS 2020; 20:6937-6946. [PMID: 32852959 DOI: 10.1021/acs.nanolett.0c02999] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Understanding and exploring the transport behaviors of ions and molecules in the nano and sub-nano confinement has great meaning in the fields of nanofluidics and basic transport physics. With the rapid progress in nanofabrication technology and effective characterization protocols, more and more anomalous transport behaviors have been observed and the ions/molecules inside small confinement can behave dramatically differently from bulk systems and present new mechanisms. In this Mini Review, we summarize the recent advances in the anomalous ionic/molecular transport behaviors in nano and sub-nano confinement. Our discussion includes the ionic/molecular transport of various confinement with different surface properties, static structures, and dynamic structures. Furthermore, we provide a brief overview of the latest applications of nanofluidics in membrane separation and energy conversion.
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Affiliation(s)
- Miao Wang
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, Jiujiang Research Institute, College of Physical Science and Technology, Xiamen University, Xiamen 361005, China
| | - Yaqi Hou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Lejian Yu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xu Hou
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, Jiujiang Research Institute, College of Physical Science and Technology, Xiamen University, Xiamen 361005, China
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen 361005, China
- Tan Kah Kee Innovation Laboratory, Xiamen 361102, Fujian, China
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Kim YS, Dincau BM, Kwon YT, Kim JH, Yeo WH. Directly Accessible and Transferrable Nanofluidic Systems for Biomolecule Manipulation. ACS Sens 2019; 4:1417-1423. [PMID: 31062586 DOI: 10.1021/acssensors.9b00470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular detection and manipulation via nanofluidic systems offers new routes for single-molecule analysis to study epigenetic mechanisms and genetic mutation of disease. For detection of single biological molecule, many types of nanomicrofluidic systems have been utilized. Typically, mechanical tethering, fluidic pressure, chemical interactions, or electrical forces allow controllable attraction, enrichment, confinement, and elongation of target molecules. The currently available methods, however, are unable to offer both molecular manipulation and direct and concurrent assessment of target molecules in the system due to the nature of enclosed channels and associated fluidic components. Here, we introduce a wafer-scale nanofluidic system that incorporates an array of accessible open nanochannels and nano-microtrappers to enrich and elongate target molecules (DNA) via the combination of an electric field and hydrodynamic force. The open nanofluidic system allows easy access, direct observation, and manipulation of molecules in the nanochannels. The presence of a stretched single DNA and the efficacy of the nanofluidic system are studied by fluorescence microscopy and atomic force microscopy. Hybrid integration of the nanodevice fabrication with a material transfer printing technique enables to design a highly flexible and transferrable nanofluidic system after molecular concentration.
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Affiliation(s)
| | - Brian M. Dincau
- School of Engineering and Computer Science, Washington State University, Vancouver, Washington 98686, United States
| | | | - Jong-Hoon Kim
- School of Engineering and Computer Science, Washington State University, Vancouver, Washington 98686, United States
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Wang M, Meng H, Wang D, Yin Y, Stroeve P, Zhang Y, Sheng Z, Chen B, Zhan K, Hou X. Dynamic Curvature Nanochannel-Based Membrane with Anomalous Ionic Transport Behaviors and Reversible Rectification Switch. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1805130. [PMID: 30633407 DOI: 10.1002/adma.201805130] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/29/2018] [Indexed: 05/08/2023]
Abstract
Biological nanochannels control the movements of different ions through cell membranes depending on not only those channels' static inherent configurations, structures, inner surface's physicochemical properties but also their dynamic shape changes, which are required in various essential functions of life processes. Inspired by ion channels, many artificial nanochannel-based membranes for nanofluidics and biosensing applications have been developed to regulate ionic transport behaviors by using the functional molecular modifications at the inner surface of nanochannel to achieve a stimuli-responsive layer. Here, the concept of a dynamic nanochannel system is further developed, which is a new way to regulate ion transport in nanochannels by using the dynamic change in the curvature of channels to adjust ionic rectification in real time. The dynamic curvature nanochannel-based membrane displays the advanced features of the anomalous effect of voltage, concentration, and ionic size for applying simultaneous control over the curvature-tunable asymmetric and reversible ionic rectification switching properties. This dynamic approach can be used to build smart nanochannel-based systems, which have strong implications for flexible nanofluidics, ionic rectifiers, and power generators.
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Affiliation(s)
- Miao Wang
- Research Institute for Soft Matter and Biomimetics, College of Physical Science and Technology, Xiamen University, Xiamen, 361005, P. R. China
| | - Haiqiang Meng
- Research Institute for Soft Matter and Biomimetics, College of Physical Science and Technology, Xiamen University, Xiamen, 361005, P. R. China
| | - Dan Wang
- State Key Laboratory of Mechanics and Control of Mechanical Structures, College of Aerospace Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, P. R. China
| | - Yajun Yin
- School of Aerospace Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Pieter Stroeve
- Department of Chemical Engineering and Materials Science, University of California, Davis, Davis, CA, 95616, USA
| | - Yunmao Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Zhizhi Sheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Baiyi Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Kan Zhan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Xu Hou
- Research Institute for Soft Matter and Biomimetics, College of Physical Science and Technology, Xiamen University, Xiamen, 361005, P. R. China
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
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Abstract
A number of outstanding problems in genomics, such as identifying structural variations and sequencing through centromeres and telomeres, stand poised to benefit tremendously from emerging long-read genomics technologies such as nanopore sequencing and genome mapping in nanochannels. However, optimal application of these new genomics technologies requires facile methods for extracting long DNA from cells. These sample preparation tools should be amenable to automation and minimize fragmentation of the long DNA molecules by shear. We present one such approach in a poly(dimethylsiloxane) device, where gel-based high molecular weight DNA extraction and continuous flow purification in a 3D cell culture-inspired geometry is followed by electrophoretic extraction of the long DNA from the miniaturized gel. Molecular combing reveals that the device produces molecules that are typically in excess of 100 kilobase pairs in size, with the longest molecule extending up to 4 megabase pairs. The microfluidic format reduces the standard day-long and labor-intensive DNA extraction process to 4 hours, making it a promising prototype platform for routine long DNA sample preparation.
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Affiliation(s)
- Paridhi 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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