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Rahman M, Islam KR, Islam MR, Islam MJ, Kaysir MR, Akter M, Rahman MA, Alam SMM. A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices. MICROMACHINES 2022; 13:968. [PMID: 35744582 PMCID: PMC9229244 DOI: 10.3390/mi13060968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023]
Abstract
Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.
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Affiliation(s)
- Mahmudur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Kazi Rafiqul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Rashedul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Jahirul Islam
- Department of Electrical and Electronic Engineering, Khulna University of Engineering & Technology, Khulna 9203, Bangladesh;
| | - Md. Rejvi Kaysir
- Department of Electrical and Computer Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada;
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Masuma Akter
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Arifur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - S. M. Mahfuz Alam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
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Promising Assays for Examining a Putative Role of Ribosomal Heterogeneity in COVID-19 Susceptibility and Severity. Life (Basel) 2022; 12:life12020203. [PMID: 35207490 PMCID: PMC8880406 DOI: 10.3390/life12020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 11/17/2022] Open
Abstract
The heterogeneity of ribosomes, characterized by structural variations, arises from differences in types, numbers, and/or post-translational modifications of participating ribosomal proteins (RPs), ribosomal RNAs (rRNAs) sequence variants plus post-transcriptional modifications, and additional molecules essential for forming a translational machinery. The ribosomal heterogeneity within an individual organism or a single cell leads to preferential translations of selected messenger RNA (mRNA) transcripts over others, especially in response to environmental cues. The role of ribosomal heterogeneity in SARS-CoV-2 coronavirus infection, propagation, related symptoms, or vaccine responses is not known, and a technique to examine these has not yet been developed. Tools to detect ribosomal heterogeneity or to profile translating mRNAs independently cannot identify unique or specialized ribosome(s) along with corresponding mRNA substrate(s). Concurrent characterizations of RPs and/or rRNAs with mRNA substrate from a single ribosome would be critical to decipher the putative role of ribosomal heterogeneity in the COVID-19 disease, caused by the SARS-CoV-2, which hijacks the host ribosome to preferentially translate its RNA genome. Such a protocol should be able to provide a high-throughput screening of clinical samples in a large population that would reach a statistical power for determining the impact of a specialized ribosome to specific characteristics of the disease. These characteristics may include host susceptibility, viral infectivity and transmissibility, severity of symptoms, antiviral treatment responses, and vaccine immunogenicity including its side effect and efficacy. In this study, several state-of-the-art techniques, in particular, chemical probing of ribosomal components or rRNA structures, proximity ligation to generate rRNA-mRNA chimeras for sequencing, nanopore gating of individual ribosomes, nanopore RNA sequencing and/or structural analyses, single-ribosome mass spectrometry, and microfluidic droplets for separating ribosomes or indexing rRNAs/mRNAs, are discussed. The key elements for further improvement and proper integration of the above techniques to potentially arrive at a high-throughput protocol for examining individual ribosomes and their mRNA substrates in a clinical setting are also presented.
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Rahman M, Sampad MJN, Hawkins A, Schmidt H. Recent advances in integrated solid-state nanopore sensors. LAB ON A CHIP 2021; 21:3030-3052. [PMID: 34137407 PMCID: PMC8372664 DOI: 10.1039/d1lc00294e] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The advent of single-molecule probing techniques has revolutionized the biomedical and life science fields and has spurred the development of a new class of labs-on-chip based on powerful biosensors. Nanopores represent one of the most recent and most promising single molecule sensing paradigms that is seeing increased chip-scale integration for improved convenience and performance. Due to their physical structure, nanopores are highly sensitive, require low sample volume, and offer label-free, amplification-free, high-throughput real-time detection and identification of biomolecules. Over the last 25 years, nanopores have been extensively employed to detect a variety of biomolecules with a growing range of applicatons ranging from nucleic acid sequencing to ultrasensitive diagnostics to single-molecule biophysics. Nanopores, in particular those in solid-state membranes, also have the potential for integration with other technologies such as optics, plasmonics, microfluidics, and optofluidics to perform more complex tasks for an ever-expanding demand. A number of breakthrough results using integrated nanopore platforms have already been reported, and more can be expected as nanopores remain the focus of innovative research and are finding their way into commercial instruments. This review provides an overview of different aspects and challenges of nanopore technology with a focus on chip-scale integration of solid-state nanopores for biosensing and bioanalytical applications.
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Affiliation(s)
- Mahmudur Rahman
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA. and Dhaka University of Engineering & Technology, Gazipur, Bangladesh
| | | | - Aaron Hawkins
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT, 84602 USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA.
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Wright JG, Amin MN, Schmidt H, Hawkins AR. Performance Comparison of Flow-Through Optofluidic Biosensor Designs. BIOSENSORS 2021; 11:226. [PMID: 34356697 PMCID: PMC8301811 DOI: 10.3390/bios11070226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/01/2021] [Accepted: 07/03/2021] [Indexed: 12/04/2022]
Abstract
Optofluidic flow-through biosensors are being developed for single particle detection, particularly as a tool for pathogen diagnosis. The sensitivity of the biosensor chip depends on design parameters, illumination format (side vs. top), and flow configuration (parabolic, two- and three-dimensional hydrodynamic focused (2DHF and 3DHF)). We study the signal differences between various combinations of these design aspects. Our model is validated against a sample of physical devices. We find that side-illumination with 3DHF produces the strongest and consistent signal, but parabolic flow devices process a sample volume more quickly. Practical matters of optical alignment are also discussed, which may affect design choice.
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Affiliation(s)
- Joel G. Wright
- Electrical and Computer Engineering, Brigham Young University, 450 Engineering Building, Provo, UT 84602, USA;
| | - Md Nafiz Amin
- Electrical and Computer Engineering, University of California, 1156 High Street, Santa Cruz, CA 95064, USA; (M.N.A.); (H.S.)
| | - Holger Schmidt
- Electrical and Computer Engineering, University of California, 1156 High Street, Santa Cruz, CA 95064, USA; (M.N.A.); (H.S.)
| | - Aaron R. Hawkins
- Electrical and Computer Engineering, Brigham Young University, 450 Engineering Building, Provo, UT 84602, USA;
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Abstract
Nanopores hold great potential for the analysis of complex biological molecules at the single-entity level. One particularly interesting macromolecular machine is the ribosome, responsible for translating mRNAs into proteins. In this study, we use a solid-state nanopore to fingerprint 80S ribosomes and polysomes from a human neuronal cell line andDrosophila melanogaster cultured cells and ovaries. Specifically, we show that the peak amplitude and dwell time characteristics of 80S ribosomes are distinct from polysomes and can be used to discriminate ribosomes from polysomes in mixed samples. Moreover, we are able to distinguish large polysomes, containing more than seven ribosomes, from those containing two to three ribosomes, and demonstrate a correlation between polysome size and peak amplitude. This study highlights the application of solid-state nanopores as a rapid analytical tool for the detection and characterization of ribosomal complexes.
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Affiliation(s)
- Mukhil Raveendran
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K
| | - Anna Rose Leach
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K
| | - Tayah Hopes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
- LeedsOmics, University of Leeds, Leeds LS2 9JT, U.K
| | - Julie L. Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
- LeedsOmics, University of Leeds, Leeds LS2 9JT, U.K
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K
- LeedsOmics, University of Leeds, Leeds LS2 9JT, U.K
- Bragg Centre for Materials Research, Leeds LS2 9JT, U.K
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Advances in Continuous Microfluidics-Based Technologies for the Study of HIV Infection. Viruses 2020; 12:v12090982. [PMID: 32899657 PMCID: PMC7552050 DOI: 10.3390/v12090982] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/28/2020] [Accepted: 09/02/2020] [Indexed: 12/31/2022] Open
Abstract
HIV-1 is the causative agent of acquired immunodeficiency syndrome (AIDS). It affects millions of people worldwide and the pandemic persists despite the implementation of highly active antiretroviral therapy. A wide spectrum of techniques has been implemented in order to diagnose and monitor AIDS progression over the years. Besides the conventional approaches, microfluidics has provided useful methods for monitoring HIV-1 infection. In this review, we introduce continuous microfluidics as well as the fabrication and handling of microfluidic chips. We provide a review of the different applications of continuous microfluidics in AIDS diagnosis and progression and in the basic study of the HIV-1 life cycle.
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Fu J, Wu L, Qiao Y, Tu J, Lu Z. Microfluidic Systems Applied in Solid-State Nanopore Sensors. MICROMACHINES 2020; 11:mi11030332. [PMID: 32210148 PMCID: PMC7142662 DOI: 10.3390/mi11030332] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/08/2020] [Accepted: 03/20/2020] [Indexed: 01/04/2023]
Abstract
Microfluidic system, as a kind of miniature integrated operating platform, has been applied to solid-state nanopore sensors after many years of experimental study. In the process of introducing microfluidic into solid-state nanopore sensors, many novel device structures are designed due to the abundance of analytes and the diversity of detection methods. Here we review the fundamental setup of nanopore-based microfluidic systems and the developments and advancements that have been taking place in the field. The microfluidic systems with a multichannel strategy to elevate the throughput and efficiency of nanopore sensors are then presented. Multifunctional detection represented by optical-electrical detection, which is realized by microfluidic integration, is also described. A high integration microfluidic system with nanopore is further discussed, which shows the prototype of commercialization.
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Affiliation(s)
| | | | | | - Jing Tu
- Correspondence: (J.T.); (Z.L.); Tel.: +86-25-8379-2396 (J.T.); +86-25-8379-3779 (Z.L.)
| | - Zuhong Lu
- Correspondence: (J.T.); (Z.L.); Tel.: +86-25-8379-2396 (J.T.); +86-25-8379-3779 (Z.L.)
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Lepoitevin M, Ma T, Bechelany M, Janot JM, Balme S. Functionalization of single solid state nanopores to mimic biological ion channels: A review. Adv Colloid Interface Sci 2017; 250:195-213. [PMID: 28942265 DOI: 10.1016/j.cis.2017.09.001] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/01/2017] [Accepted: 09/06/2017] [Indexed: 10/18/2022]
Abstract
In nature, ion channels are highly selective pores and act as gate to ensure selective ion transport, allowing ions to cross the membrane. By mimicking them, single solid state nanopore devices emerge as a new, powerful class of molecule sensors that allow for the label-free detection of biomolecules (DNA, RNA, and proteins), non-biological polymers, as well as small molecules. In this review, we exhaustively describe the fabrication and functionalization techniques to design highly robust and selective solid state nanopores. First we outline the different materials and methods to design nanopores, we explain the ionic conduction in nanopores, and finally we summarize some techniques to modify and functionalize the surface in order to obtain biomimetic nanopores, responding to different external stimuli.
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Liu S, Hawkins AR, Schmidt H. Optofluidic devices with integrated solid-state nanopores. Mikrochim Acta 2016; 183:1275-1287. [PMID: 27046940 DOI: 10.1007/s00604-016-1758-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This review (with 90 refs.) covers the state of the art in optofluidic devices with integrated solid-state nanopores for use in detection and sensing. Following an introduction into principles of optofluidics and solid-state nanopore technology, we discuss features of solid-state nanopore based assays using optofluidics. This includes the incorporation of solid-state nanopores into optofluidic platforms based on liquid-core anti-resonant reflecting optical waveguides (ARROWs), methods for their fabrication, aspects of single particle detection and particle manipulation. We then describe the new functionalities provided by solid-state nanopores integrated into optofluidic chips, in particular acting as smart gates for correlated electro-optical detection and discrimination of nanoparticles. This enables the identification of viruses and λ-DNA, particle trajectory simulations, enhancing sensitivity by tuning the shape of nanopores. The review concludes with a summary and an outlook.
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Affiliation(s)
- Shuo Liu
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Aaron R Hawkins
- ECEn Department, 459 Clyde Building, Brigham Young University, Provo, UT 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
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10
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Pederson ED, Barbalas J, Drown BS, Culbertson MJ, Keranen Burden LM, Kasianowicz JJ, Burden DL. Proximal Capture Dynamics for a Single Biological Nanopore Sensor. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b04955] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Jonathan Barbalas
- Chemistry
Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Bryon S. Drown
- Chemistry
Department, Wheaton College, Wheaton, Illinois 60187, United States
| | | | | | - John J. Kasianowicz
- Semiconductor
Electronics Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8120, United States
| | - Daniel L. Burden
- Chemistry
Department, Wheaton College, Wheaton, Illinois 60187, United States
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11
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Liu S, Wall TA, Ozcelik D, Parks JW, Hawkins AR, Schmidt H. Electro-optical detection of single λ-DNA. Chem Commun (Camb) 2015; 51:2084-7. [PMID: 25533516 PMCID: PMC4304986 DOI: 10.1039/c4cc07591a] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single λ-DNA molecules are detected on a nanopore-gated optofluidic chip electrically and optically. Statistical variations in the single particle trajectories are used to predict the intensity distribution of the fluorescence signals.
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Affiliation(s)
- Shuo Liu
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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12
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Liu S, Zhao Y, Parks J, Deamer DW, Hawkins AR, Schmidt H. Correlated electrical and optical analysis of single nanoparticles and biomolecules on a nanopore-gated optofluidic chip. NANO LETTERS 2014; 14:4816-20. [PMID: 25006747 PMCID: PMC4134182 DOI: 10.1021/nl502400x] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The analysis of individual biological nanoparticles has significantly advanced our understanding of fundamental biological processes but is also rapidly becoming relevant for molecular diagnostic applications in the emerging field of personalized medicine. Both optical and electrical methods for the detection and analysis of single biomolecules have been developed, but they are generally not used in concert and in suitably integrated form to allow for multimodal analysis with high throughput. Here we report on a dual-mode electrical and optical single-nanoparticle sensing device with capabilities that would not be available with each technique individually. The new method is based on an optofluidic chip with an integrated nanopore that serves as a smart gate to control the delivery of individual nanoparticles to an optical excitation region for ensemble-free optical analysis in rapid succession. We demonstrate electro-optofluidic size discrimination of fluorescent nanobeads, electro-optical detection of single fluorescently labeled influenza viruses, and the identification of single viruses within a mixture of equally sized fluorescent nanoparticles with up to 100% fidelity.
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Affiliation(s)
- Shuo Liu
- School
of Engineering, University of California,
Santa Cruz, 1156 High
Street, Santa Cruz, California 95064, United States
| | - Yue Zhao
- Department
of Electrical & Computer Engineering, Brigham Young University, 459 Clyde Building, Provo, Utah 84602, United
States
| | - Joshua
W. Parks
- School
of Engineering, University of California,
Santa Cruz, 1156 High
Street, Santa Cruz, California 95064, United States
| | - David W. Deamer
- School
of Engineering, University of California,
Santa Cruz, 1156 High
Street, Santa Cruz, California 95064, United States
| | - Aaron R. Hawkins
- Department
of Electrical & Computer Engineering, Brigham Young University, 459 Clyde Building, Provo, Utah 84602, United
States
| | - Holger Schmidt
- School
of Engineering, University of California,
Santa Cruz, 1156 High
Street, Santa Cruz, California 95064, United States
- E-mail: . Phone: 831-459-1482
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