1
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Young TW, Kappler MP, Call ED, Brown QJ, Jacobson SC. Integrated In-Plane Nanofluidic Devices for Resistive-Pulse Sensing. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:221-242. [PMID: 38608295 DOI: 10.1146/annurev-anchem-061622-030223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Single-particle (or digital) measurements enhance sensitivity (10- to 100-fold improvement) and uncover heterogeneity within a population (one event in 100 to 10,000). Many biological systems are significantly influenced by rare or infrequent events, and determining what species is present, in what quantity, and the role of that species is critically important to unraveling many questions. To develop these measurement systems, resistive-pulse sensing is used as a label-free, single-particle detection technique and can be combined with a range of functional elements, e.g., mixers, reactors, filters, separators, and pores. Virtually, any two-dimensional layout of the micro- and nanofluidic conduits can be envisioned, designed, and fabricated in the plane of the device. Multiple nanopores in series lead to higher-precision measurements of particle size, shape, and charge, and reactions coupled directly with the particle-size measurements improve temporal response. Moreover, other detection techniques, e.g., fluorescence, are highly compatible with the in-plane format. These integrated in-plane nanofluidic devices expand the toolbox of what is possible with single-particle measurements.
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Affiliation(s)
- Tanner W Young
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - Michael P Kappler
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - Ethan D Call
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - Quintin J Brown
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
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2
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Mi Z, Chen X, Zhao X, Tang H, Wang W, Shan X, Lu X. High-precision high-speed nanopore ping-pong control system based on field programmable gate array. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2024; 95:073202. [PMID: 39016698 DOI: 10.1063/5.0213543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/02/2024] [Indexed: 07/18/2024]
Abstract
"Molecular ping-pong," emerging as a control strategy in solid-state nanopore technology, presents a highly promising approach for repetitive measurements of single biomolecules, such as DNA. This paper introduces a high-precision, high-speed nanopore molecular ping-pong control system consisting of a home-built trans-impedance amplifier (TIA), a control system based on a Field Programmable Gate Array (FPGA), and a LabVIEW program operating on the host personal computer. Through feedback compensation and post-stage boosting, the TIA achieves a high bandwidth of about 200 kHz with a gain of 100 MΩ, along with low input-referred current noise of 1.6 × 10-4 pA2/Hz at 1 kHz and 1.1 × 10-3 pA2/Hz at 100 kHz. The FPGA-based control system demonstrates a minimum overall response time (tdelay) of 6.5 μs from the analog input current signal trigger to the subsequent reversal of the analog output drive voltage signal, with a control precision of 1 μs. Additionally, a LabVIEW program has been developed to facilitate rapid data exchange and communication with the FPGA program, enabling real-time signal monitoring, parameter adjustment, and data storage. Successful recapture of individual DNA molecules at various tdelay, resulting in an improvement in capture rate by up to 2 orders of magnitude, has been demonstrated. With unprecedented control precision and capture efficiency, this system provides robust technical support and opens novel research avenues for nanopore single-molecule sensing and manipulation.
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Affiliation(s)
- Zhuang Mi
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoyu Chen
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xinjia Zhao
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Haitao Tang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Wenyu Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xinyan Shan
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xinghua Lu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
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3
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Gao Y, Yin M, Zhang H, Xu B. Electrically Suppressed Outflow of Confined Liquid in Hydrophobic Nanopores. ACS NANO 2022; 16:9420-9427. [PMID: 35658431 DOI: 10.1021/acsnano.2c02240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Confining liquid in a hydrophobic nanoenvironment has enabled a broad spectrum of applications in biomedical sensors, mechanical actuators, and energy storage and converters, where the outflow of confined liquid is spontaneous and fast due to the intrinsic hydrophobic nature of nanopores with extremely low interfacial friction, challenging design capacity and control tolerance of structures and devices. Here, we present a facile approach of suppressing the outflow of water confined in hydrophobic nanopores with an electric field. Extensive molecular dynamics simulations show that the presence of an electric field could significantly strengthen hydrogen bonds and retard degradations of the associated networks during the outflow. The outflow deformation and strength are extracted to quantitatively characterize the electrical suppression to outflow and agree well with simulations. This study proposes a practical means of impeding the fast liquid outflow in hydrophobic nanopores, potentially useful for devising nanofluidics-based functional structures and devices with controllable performance.
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Affiliation(s)
- Yuan Gao
- Department of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Mengtian Yin
- Department of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Haozhe Zhang
- Department of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Baoxing Xu
- Department of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
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4
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Nakajima K, Tsujimura T, Doi K, Kawano S. Visualization of Optical Vortex Forces Acting on Au Nanoparticles Transported in Nanofluidic Channels. ACS OMEGA 2022; 7:2638-2648. [PMID: 35097262 PMCID: PMC8792943 DOI: 10.1021/acsomega.1c04855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
The optical manipulation of nanoscale objects via structured light has attracted significant attention for its various applications, as well as for its fundamental physics. In such cases, the detailed behavior of nano-objects driven by optical forces must be precisely predicted and controlled, despite the thermal fluctuation of small particles in liquids. In this study, the optical forces of an optical vortex acting on gold nanoparticles (Au NPs) are visualized using dark-field microscopic observations in a nanofluidic channel with strictly suppressed forced convection. Manipulating Au NPs with an optical vortex allows the evaluation of the three optical force components, namely, gradient, scattering, and absorption forces, from the in-plane trajectory. We develop a Langevin dynamics simulation model coupled with Rayleigh scattering theory and compare the theoretical results with the experimental ones. Experimental results using Au NPs with diameters of 80-150 nm indicate that our experimental method can determine the radial trapping stiffness and tangential force with accuracies on the order of 0.1 fN/nm and 1 fN, respectively. Our experimental method will contribute to broadening not only applications of the optical-vortex manipulation of nano-objects, but also investigations of optical properties on unknown nanoscale materials via optical force analyses.
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Affiliation(s)
- Kichitaro Nakajima
- Global
Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tempei Tsujimura
- Graduate
School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kentaro Doi
- Department
of Mechanical Engineering, Toyohashi University
of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Satoyuki Kawano
- Graduate
School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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5
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Zhou J, Zlotnick A, Jacobson SC. Disassembly of Single Virus Capsids Monitored in Real Time with Multicycle Resistive-Pulse Sensing. Anal Chem 2022; 94:985-992. [PMID: 34932317 PMCID: PMC8784147 DOI: 10.1021/acs.analchem.1c03855] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Virus assembly and disassembly are critical steps in the virus lifecycle; however, virus disassembly is much less well understood than assembly. For hepatitis B virus (HBV) capsids, disassembly of the virus capsid in the presence of guanidine hydrochloride (GuHCl) exhibits strong hysteresis that requires additional chemical energy to initiate disassembly and disrupt the capsid structure. To study disassembly of HBV capsids, we mixed T = 4 HBV capsids with 1.0-3.0 M GuHCl, monitored the reaction over time by randomly selecting particles, and measured their size with resistive-pulse sensing. Particles were cycled forward and backward multiple times to increase the observation time and likelihood of observing a disassembly event. The four-pore device used for resistive-pulse sensing produces four current pulses for each particle during translocation that improves tracking and identification of single particles and increases the precision of particle-size measurements when pulses are averaged. We studied disassembly at GuHCl concentrations below and above denaturing conditions of the dimer, the fundamental unit of HBV capsid assembly. As expected, capsids showed little disassembly at low GuHCl concentrations (e.g., 1.0 M GuHCl), whereas at higher GuHCl concentrations (≥1.5 M), capsids exhibited disassembly, sometimes as a complex series of events. In all cases, disassembly was an accelerating process, where capsids catastrophically disassembled within a few 100 ms of reaching critical stability; disassembly rates reached tens of dimers per second just before capsids fell apart. Some disassembly events exhibited metastable intermediates that appeared to lose one or more trimers of dimers in a stepwise fashion.
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Affiliation(s)
- Jinsheng Zhou
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, U.S.A
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7003, U.S.A
| | - Stephen C. Jacobson
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, U.S.A,Corresponding author.
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6
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Shrestha P, Yang D, Tomov TE, MacDonald JI, Ward A, Bergal HT, Krieg E, Cabi S, Luo Y, Nathwani B, Johnson-Buck A, Shih WM, Wong WP. Single-molecule mechanical fingerprinting with DNA nanoswitch calipers. NATURE NANOTECHNOLOGY 2021; 16:1362-1370. [PMID: 34675411 PMCID: PMC8678201 DOI: 10.1038/s41565-021-00979-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/16/2021] [Indexed: 05/31/2023]
Abstract
Decoding the identity of biomolecules from trace samples is a longstanding goal in the field of biotechnology. Advances in DNA analysis have substantially affected clinical practice and basic research, but corresponding developments for proteins face challenges due to their relative complexity and our inability to amplify them. Despite progress in methods such as mass spectrometry and mass cytometry, single-molecule protein identification remains a highly challenging objective. Towards this end, we combine DNA nanotechnology with single-molecule force spectroscopy to create a mechanically reconfigurable DNA nanoswitch caliper capable of measuring multiple coordinates on single biomolecules with atomic resolution. Using optical tweezers, we demonstrate absolute distance measurements with ångström-level precision for both DNA and peptides, and using multiplexed magnetic tweezers, we demonstrate quantification of relative abundance in mixed samples. Measuring distances between DNA-labelled residues, we perform single-molecule fingerprinting of synthetic and natural peptides, and show discrimination, within a heterogeneous population, between different posttranslational modifications. DNA nanoswitch calipers are a powerful and accessible tool for characterizing distances within nanoscale complexes that will enable new applications in fields such as single-molecule proteomics.
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Affiliation(s)
- Prakash Shrestha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Darren Yang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Toma E Tomov
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - James I MacDonald
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Andrew Ward
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Hans T Bergal
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Biophysics Program, Harvard University, Cambridge, MA, USA
| | - Elisha Krieg
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Serkan Cabi
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yi Luo
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Bhavik Nathwani
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander Johnson-Buck
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Biophysics Program, Harvard University, Cambridge, MA, USA
| | - William M Shih
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Wesley P Wong
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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7
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Nakajima K, Nakatsuka R, Tsuji T, Doi K, Kawano S. Synchronized resistive-pulse analysis with flow visualization for single micro- and nanoscale objects driven by optical vortex in double orifice. Sci Rep 2021; 11:9323. [PMID: 33927219 PMCID: PMC8085213 DOI: 10.1038/s41598-021-87822-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/15/2021] [Indexed: 11/09/2022] Open
Abstract
Resistive-pulse analysis is a powerful tool for identifying micro- and nanoscale objects. For low-concentration specimens, the pulse responses are rare, and it is difficult to obtain a sufficient number of electrical waveforms to clearly characterize the targets and reduce noise. In this study, we conducted a periodic resistive-pulse analysis using an optical vortex and a double orifice, which repetitively senses a single micro- or nanoscale target particle with a diameter ranging from 700 nm to 2 \documentclass[12pt]{minimal}
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\begin{document}$$\mu$$\end{document}μm. The periodic motion results in the accumulation of a sufficient number of waveforms within a short period. Acquired pulses show periodic ionic-current drops associated with the translocation events through each orifice. Furthermore, a transparent fluidic device allows us to synchronously average the waveforms by the microscopic observation of the translocation events and improve the signal-to-noise ratio. By this method, we succeed in distinguishing single particle diameters. Additionally, the results of measured signals and the simultaneous high-speed observations are used to quantitatively and systematically discuss the effect of the complex fluid flow in the orifices on the amplitude of the resistive pulse. The synchronized resistive-pulse analysis by the optical vortex with the flow visualization improves the pulse-acquisition rate for a single specific particle and accuracy of the analysis, refining the micro- and nanoscale object identification.
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Affiliation(s)
- Kichitaro Nakajima
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan
| | - Ryoji Nakatsuka
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan
| | - Tetsuro Tsuji
- Graduate School of Informatics, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Kentaro Doi
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan
| | - Satoyuki Kawano
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan.
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8
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Zhou J, Kondylis P, Haywood DG, Harms ZD, Lee LS, Zlotnick A, Jacobson SC. Characterization of Virus Capsids and Their Assembly Intermediates by Multicycle Resistive-Pulse Sensing with Four Pores in Series. Anal Chem 2018; 90:7267-7274. [PMID: 29708733 PMCID: PMC6039186 DOI: 10.1021/acs.analchem.8b00452] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Virus self-assembly is a critical step in the virus lifecycle. Understanding how viruses assemble and disassemble provides needed insight into developing antiviral pharmaceuticals. Few tools offer sufficient resolution to study assembly intermediates that differ in size by a few dimers. Our goal is to improve resistive-pulse sensing on nanofluidic devices to offer better particle-size and temporal resolution to study intermediates and capsids generated along the assembly pathway. To increase the particle-size resolution of the resistive-pulse technique, we measured the same, single virus particles up to a thousand times, cycling them back and forth across a series of nanopores by switching the polarity of the applied potential, i.e., virus ping-pong. Multiple pores in series provide a unique multipulse signature during each cycle that improves particle tracking and, therefore, identification of a single particle and reduces the number of cycles needed to make the requisite number of measurements. With T = 3 and T = 4 hepatitis B virus (HBV) capsids, we showed the standard deviation of the particle-size distribution decreased with the square root of the number of measurements and approached discriminating particles differing in size by single dimers. We then studied in vitro assembly of HBV capsids and observed that the ensemble of intermediates shift to larger sizes over 2 days of annealing. On the contrary, assembly reactions diluted to lower dimer concentrations an hour after initiation had fewer intermediates that persisted after the 2 day incubation and had a higher ratio of T = 4 to T = 3 capsids. These reactions indicate that labile T = 4 intermediates are formed rapidly, and dependent on conditions, intermediates may be trapped as metastable species or progress to yield complete capsids.
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Affiliation(s)
- Jinsheng Zhou
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | | | | | - Zachary D. Harms
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Lye Siang Lee
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
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9
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Kondylis P, Zhou J, Harms ZD, Kneller AR, Lee LS, Zlotnick A, Jacobson SC. Nanofluidic Devices with 8 Pores in Series for Real-Time, Resistive-Pulse Analysis of Hepatitis B Virus Capsid Assembly. Anal Chem 2017; 89:4855-4862. [PMID: 28322548 PMCID: PMC5549943 DOI: 10.1021/acs.analchem.6b04491] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To improve the precision of resistive-pulse measurements, we have used a focused ion beam instrument to mill nanofluidic devices with 2, 4, and 8 pores in series and compared their performance. The in-plane design facilitates the fabrication of multiple pores in series which, in turn, permits averaging of the series of pulses generated from each translocation event. The standard deviations (σ) of the pulse amplitude distributions decrease by 2.7-fold when the average amplitudes of eight pulses are compared to the amplitudes of single pulses. Similarly, standard deviations of the pore-to-pore time distributions decrease by 3.2-fold when the averages of the seven measurements from 8-pore devices are contrasted to single measurements from 2-pore devices. With signal averaging, the inherent uncertainty in the measurements decreases; consequently, the resolution (mean/σ) improves by a factor equal to the square root of the number of measurements. We took advantage of the improved size resolution of the 8-pore devices to analyze in real time the assembly of Hepatitis B Virus (HBV) capsids below the pseudocritical concentration. We observe that abundances of assembly intermediates change over time. During the first hour of the reaction, the abundance of smaller intermediates decreased, whereas the abundance of larger intermediates with sizes closer to a T = 4 capsid remained constant.
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Affiliation(s)
| | - Jinsheng Zhou
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Zachary D. Harms
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | | | - Lye Siang Lee
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
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10
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Friedrich SM, Zec HC, Wang TH. Analysis of single nucleic acid molecules in micro- and nano-fluidics. LAB ON A CHIP 2016; 16:790-811. [PMID: 26818700 PMCID: PMC4767527 DOI: 10.1039/c5lc01294e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nucleic acid analysis has enhanced our understanding of biological processes and disease progression, elucidated the association of genetic variants and disease, and led to the design and implementation of new treatment strategies. These diverse applications require analysis of a variety of characteristics of nucleic acid molecules: size or length, detection or quantification of specific sequences, mapping of the general sequence structure, full sequence identification, analysis of epigenetic modifications, and observation of interactions between nucleic acids and other biomolecules. Strategies that can detect rare or transient species, characterize population distributions, and analyze small sample volumes enable the collection of richer data from biosamples. Platforms that integrate micro- and nano-fluidic operations with high sensitivity single molecule detection facilitate manipulation and detection of individual nucleic acid molecules. In this review, we will highlight important milestones and recent advances in single molecule nucleic acid analysis in micro- and nano-fluidic platforms. We focus on assessment modalities for single nucleic acid molecules and highlight the role of micro- and nano-structures and fluidic manipulation. We will also briefly discuss future directions and the current limitations and obstacles impeding even faster progress toward these goals.
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Affiliation(s)
- Sarah M Friedrich
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Helena C Zec
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tza-Huei Wang
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA. and Mechanical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA
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11
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Navarkar A, Amiroudine S, Demekhin EA. On two-liquid AC electroosmotic system for thin films. Electrophoresis 2016; 37:727-35. [PMID: 26773725 DOI: 10.1002/elps.201500132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 12/15/2015] [Accepted: 01/06/2016] [Indexed: 11/12/2022]
Abstract
Lab-on-chip devices employ EOF for transportation and mixing of liquids. However, when a steady (DC) electric field is applied to the liquids, there are undesirable effects such as degradation of sample, electrolysis, bubble formation, etc. due to large magnitude of electric potential required to generate the flow. These effects can be averted by using a time-periodic or AC electric field. Transport and mixing of nonconductive liquids remain a problem even with this technique. In the present study, a two-liquid system bounded by two rigid plates, which act as substrates, is considered. The potential distribution is derived by assuming a Boltzmann charge distribution and using the Debye-Hückel linearization. Analytical solution of this time-periodic system shows some effects of viscosity ratio and permittivity ratio on the velocity profile. Interfacial electrostatics is also found to play a significant role in deciding velocity gradients at the interface. High frequency of the applied electric field is observed to generate an approximately static velocity profile away from the Electric Double Layer (EDL).
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Affiliation(s)
- Abhishek Navarkar
- Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, India
| | - Sakir Amiroudine
- Université de Bordeaux, Institut de Mécanique et d'Ingénieries, I2M, UMR CNRS 5295, Pessac, France
| | - Evgeny A Demekhin
- Laboratory of Electro-Hydrodynamics of Micro- and Nanoscales, Department of Mathematics and Computer Science, Financial University, Krasnodar, Russia.,Laboratory of General Aeromechanics, Institute of Mechanics, Moscow State University, Moscow, Russia
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12
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Edwards MA, German SR, Dick JE, Bard AJ, White HS. High-Speed Multipass Coulter Counter with Ultrahigh Resolution. ACS NANO 2015; 9:12274-12282. [PMID: 26549738 DOI: 10.1021/acsnano.5b05554] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Coulter counters measure the size of particles in solution by passing them through an orifice and measuring a resistive pulse, i.e., a drop in the ionic current flowing between two electrodes placed on either side of the orifice. The magnitude of the pulse gives information on the size of the particle; however, resolution is limited by variability in the path of the translocation, due to the Brownian motion of the particle. We present a simple yet powerful modified Coulter counter that uses programmable data acquisition hardware to switch the voltage after sensing the resistive pulse of a nanoparticle passing through the orifice of a nanopipet. Switching the voltage reverses the direction of the driving force on the particle and, when this detect-switch cycle is repeated, allows us to pass an individual nanoparticle through the orifice thousands of times. By measuring individual particles more than 100 times per second we rapidly determine the distribution of the resistive pulses for each particle, which allows us to accurately determine the mean pulse amplitude and deliver considerably improved size resolution over a conventional Coulter counter. We show that single polystyrene nanoparticles can be shuttled back and forth and monitored for minutes, leading to a precisely determined mean blocking current equating to sub-angstrom size resolution.
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Affiliation(s)
- Martin A Edwards
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - Sean R German
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
- Revalesio Corporation , 1200 East D Street, Tacoma, Washington 98421, United States
| | - Jeffrey E Dick
- Center for Electrochemistry, Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Allen J Bard
- Center for Electrochemistry, Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Henry S White
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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Carson S, Wick ST, Carr PA, Wanunu M, Aguilar CA. Direct Analysis of Gene Synthesis Reactions Using Solid-State Nanopores. ACS NANO 2015; 9:12417-24. [PMID: 26580227 PMCID: PMC5154552 DOI: 10.1021/acsnano.5b05782] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Synthetic nucleic acids offer rich potential to understand and engineer new cellular functions, yet an unresolved limitation in their production and usage is deleterious products, which restrict design complexity and add cost. Herein, we employ a solid-state nanopore to differentiate molecules of a gene synthesis reaction into categories of correct and incorrect assemblies. This new method offers a solution that provides information on gene synthesis reactions in near-real time with higher complexity and lower costs. This advance can permit insights into gene synthesis reactions such as kinetics monitoring, real-time tuning, and optimization of factors that drive reaction-to-reaction variations as well as open venues between nanopore-sensing, synthetic biology, and DNA nanotechnology.
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Affiliation(s)
- Spencer Carson
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Scott T. Wick
- Massachusetts Institute of Technology Lincoln Laboratory, Massachusetts Institute of Technology, 244 Wood Street, Lexington, Massachusetts 02420, United States
| | - Peter A. Carr
- Massachusetts Institute of Technology Lincoln Laboratory, Massachusetts Institute of Technology, 244 Wood Street, Lexington, Massachusetts 02420, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Carlos A. Aguilar
- Massachusetts Institute of Technology Lincoln Laboratory, Massachusetts Institute of Technology, 244 Wood Street, Lexington, Massachusetts 02420, United States
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14
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German SR, Hurd TS, White HS, Mega TL. Sizing Individual Au Nanoparticles in Solution with Sub-Nanometer Resolution. ACS NANO 2015; 9:7186-7194. [PMID: 26083098 DOI: 10.1021/acsnano.5b01963] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Resistive-pulse sensing has generated considerable interest as a technique for characterizing nanoparticle suspensions. The size, charge, and shape of individual particles can be estimated from features of the resistive pulse, but the technique suffers from an inherent variability due to the stochastic nature of particles translocating through a small orifice or channel. Here, we report a method, and associated automated instrumentation, that allows repeated pressure-driven translocation of individual particles back and forth across the orifice of a conical nanopore, greatly reducing uncertainty in particle size that results from streamline path distributions, particle diffusion, particle asphericity, and electronic noise. We demonstrate ∼0.3 nm resolution in measuring the size of nominally 30 and 60 nm radius Au nanoparticles of spherical geometry; Au nanoparticles in solution that differ by ∼1 nm in radius are readily distinguished. The repetitive translocation method also allows differentiating particles based on surface charge density, and provides insights into factors that determine the distribution of measured particle sizes.
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Affiliation(s)
- Sean R German
- †Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- ‡Revalesio Corporation, 1200 East D Street, Tacoma, Washington 98421, United States
| | - Timothy S Hurd
- ‡Revalesio Corporation, 1200 East D Street, Tacoma, Washington 98421, United States
| | - Henry S White
- †Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Tony L Mega
- ‡Revalesio Corporation, 1200 East D Street, Tacoma, Washington 98421, United States
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15
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Harms ZD, Haywood DG, Kneller AR, Jacobson SC. Conductivity-based detection techniques in nanofluidic devices. Analyst 2015; 140:4779-91. [PMID: 25988434 PMCID: PMC4756766 DOI: 10.1039/c5an00075k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review covers conductivity detection in fabricated nanochannels and nanopores. Improvements in nanoscale sensing are a direct result of advances in fabrication techniques, which produce devices with channels and pores with reproducible dimensions and in a variety of materials. Analytes of interest are detected by measuring changes in conductance as the analyte accumulates in the channel or passes transiently through the pore. These detection methods take advantage of phenomena enhanced at the nanoscale, such as ion current rectification, surface conductance, and dimensions comparable to the analytes of interest. The end result is the development of sensing technologies for a broad range of analytes, e.g., ions, small molecules, proteins, nucleic acids, and particles.
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Affiliation(s)
- Zachary D Harms
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
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16
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Harms Z, Haywood DG, Kneller AR, Selzer L, Zlotnick A, Jacobson SC. Single-particle electrophoresis in nanochannels. Anal Chem 2015; 87:699-705. [PMID: 25489919 PMCID: PMC4287839 DOI: 10.1021/ac503527d] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/28/2014] [Indexed: 02/05/2023]
Abstract
Electrophoretic mobilities and particle sizes of individual Hepatitis B Virus (HBV) capsids were measured in nanofluidic channels with two nanopores in series. The channels and pores had three-dimensional topography and were milled directly in glass substrates with a focused ion beam instrument assisted by an electron flood gun. The nanochannel between the two pores was 300 nm wide, 100 nm deep, and 2.5 μm long, and the nanopores at each end had dimensions 45 nm wide, 45 nm deep, and 400 nm long. With resistive-pulse sensing, the nanopores fully resolved pulse amplitude distributions of T = 3 HBV capsids (32 nm outer diameter) and T = 4 HBV capsids (35 nm outer diameter) and had sufficient peak capacity to discriminate intermediate species from the T = 3 and T = 4 capsid distributions in an assembly reaction. Because the T = 3 and T = 4 capsids have a wiffle-ball geometry with a hollow core, the observed change in current due to the capsid transiting the nanopore is proportional to the volume of electrolyte displaced by the volume of capsid protein, not the volume of the entire capsid. Both the signal-to-noise ratio of the pulse amplitude and resolution between the T = 3 and T = 4 distributions of the pulse amplitudes increase as the electric field strength is increased. At low field strengths, transport of the larger T = 4 capsid through the nanopores is hindered relative to the smaller T = 3 capsid due to interaction with the pores, but at sufficiently high field strengths, the T = 3 and T = 4 capsids had the same electrophoretic mobilities (7.4 × 10(-5) cm(2) V(-1) s(-1)) in the nanopores and in the nanochannel with the larger cross-sectional area.
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Affiliation(s)
- Zachary
D. Harms
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Daniel G. Haywood
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Andrew R. Kneller
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Lisa Selzer
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Stephen C. Jacobson
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
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17
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Niman CS, Zuckermann MJ, Balaz M, Tegenfeldt JO, Curmi PMG, Forde NR, Linke H. Fluidic switching in nanochannels for the control of Inchworm: a synthetic biomolecular motor with a power stroke. NANOSCALE 2014; 6:15008-15019. [PMID: 25367216 DOI: 10.1039/c4nr04701j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Synthetic molecular motors typically take nanometer-scale steps through rectification of thermal motion. Here we propose Inchworm, a DNA-based motor that employs a pronounced power stroke to take micrometer-scale steps on a time scale of seconds, and we design, fabricate, and analyze the nanofluidic device needed to operate the motor. Inchworm is a kbp-long, double-stranded DNA confined inside a nanochannel in a stretched configuration. Motor stepping is achieved through externally controlled changes in salt concentration (changing the DNA's extension), coordinated with ligand-gated binding of the DNA's ends to the functionalized nanochannel surface. Brownian dynamics simulations predict that Inchworm's stall force is determined by its entropic spring constant and is ∼ 0.1 pN. Operation of the motor requires periodic cycling of four different buffers surrounding the DNA inside a nanochannel, while keeping constant the hydrodynamic load force on the DNA. We present a two-layer fluidic device incorporating 100 nm-radius nanochannels that are connected through a few-nm-wide slit to a microfluidic system used for in situ buffer exchanges, either diffusionally (zero flow) or with controlled hydrodynamic flow. Combining experiment with finite-element modeling, we demonstrate the device's key performance features and experimentally establish achievable Inchworm stepping times of the order of seconds or faster.
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Affiliation(s)
- Cassandra S Niman
- Division of Solid State Physics, Lund University, Box 118, 22100 Lund, Sweden.
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18
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Hu Y, Zhou Z, Shan X, Lu X. Detection and analysis of DNA recapture through a solid-state nanopore. CHINESE SCIENCE BULLETIN-CHINESE 2014. [DOI: 10.1007/s11434-014-0662-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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Rassaei L, Mathwig K, Kang S, Heering HA, Lemay SG. Integrated biodetection in a nanofluidic device. ACS NANO 2014; 8:8278-84. [PMID: 25105352 DOI: 10.1021/nn502678t] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The sensing of enzymatic processes in volumes at or below the scale of single cells is challenging but highly desirable in the study of biochemical processes. Here we demonstrate a nanofluidic device that combines an enzymatic recognition element and electrochemical signal transduction within a six-femtoliter volume. Our approach is based on localized immobilization of the enzyme tyrosinase in a microfabricated nanogap electrochemical transducer. The enzymatic reaction product quinone is localized in the confined space of a nanochannel in which efficient redox cycling also takes place. Thus, the sensor allows the sensitive detection of minute amounts of product molecules generated by the enzyme in real time. This method is ideally suited for the study of ultra-small-volume systems such as the contents of individual biological cells or organelles.
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Aguilar CA, Craighead HG. Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics. NATURE NANOTECHNOLOGY 2013; 8:709-18. [PMID: 24091454 PMCID: PMC4072028 DOI: 10.1038/nnano.2013.195] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 08/28/2013] [Indexed: 05/05/2023]
Abstract
Deoxyribonucleic acid (DNA) is the blueprint on which life is based and transmitted, but the way in which chromatin - a dynamic complex of nucleic acids and proteins - is packaged and behaves in the cellular nucleus has only begun to be investigated. Epigenetic modifications sit 'on top of' the genome and affect how DNA is compacted into chromatin and transcribed into ribonucleic acid (RNA). The packaging and modifications around the genome have been shown to exert significant influence on cellular behaviour and, in turn, human development and disease. However, conventional techniques for studying epigenetic or conformational modifications of chromosomes have inherent limitations and, therefore, new methods based on micro- and nanoscale devices have been sought. Here, we review the development of these devices and explore their use in the study of DNA modifications, chromatin modifications and higher-order chromatin structures.
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Affiliation(s)
- Carlos A. Aguilar
- Massachusetts Institute of Technology - Lincoln Laboratory, 244 Wood St., Lexington, MA 02127
| | - Harold G. Craighead
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
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Halpern AR, Donavan KC, Penner RM, Corn RM. Wafer-Scale Fabrication of Nanofluidic Arrays and Networks Using Nanoimprint Lithography and Lithographically Patterned Nanowire Electrodeposition Gold Nanowire Masters. Anal Chem 2012; 84:5053-8. [DOI: 10.1021/ac3007285] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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