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Ma S, Payir A, McLoughlin N, Harris PL. Scientific and religious beliefs are primarily shaped by testimony. Trends Cogn Sci 2024:S1364-6613(24)00112-8. [PMID: 38806376 DOI: 10.1016/j.tics.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/30/2024]
Abstract
Understanding why individuals are more confident of the existence of invisible scientific phenomena (e.g., oxygen) than invisible religious phenomena (e.g., God) remains a puzzle. Departing from conventional explanations linking ontological beliefs to direct experience, we introduce a model positing that testimony predominantly shapes beliefs in both scientific and religious domains. Distinguishing direct experience (personal observation) from cultural input (testimony-based evidence), we argue that even apparently direct experiences often stem from others' testimony. Our analysis indicates that variability in direct experience cannot explain belief disparities between science and religion, within each domain, or across cultures. Instead, variability in testimony is the primary driver of ontological beliefs. We present developmental evidence for testimony-based beliefs and elucidate the mechanisms underlying their impact.
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Affiliation(s)
- Shaocong Ma
- Division of Social Science, Hong Kong University of Science and Technology, Hong Kong Special Administrative Region, People's Republic of China; Graduate School of Education, Harvard University, Cambridge, MA 02138, USA.
| | - Ayse Payir
- Department of Psychology, Union College, Schenectady, NY 12308, USA
| | - Niamh McLoughlin
- Department of Economics, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Paul L Harris
- Graduate School of Education, Harvard University, Cambridge, MA 02138, USA
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2
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Pal N, Walter NG. Using Single-Molecule FRET to Evaluate DNA Nanodevices at Work. Methods Mol Biol 2023; 2639:157-172. [PMID: 37166717 DOI: 10.1007/978-1-0716-3028-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The observation of DNA nanodevices at a single molecule (i.e., device) level and in real time provides rich information that is typically masked in ensemble measurements. Single-molecule fluorescence resonance energy transfer (smFRET) offers a means to directly follow dynamic conformational or compositional changes that DNA nanodevices undergo while operating, thereby retrieving insights critical for refining them toward optimal function. To be successful, smFRET measurements require careful execution and meticulous data analysis for robust statistics. Here we outline the elemental steps for smFRET experiments on DNA nanodevices, starting from microscope slide preparation for single-molecule observation to data acquisition and analysis.
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Affiliation(s)
- Nibedita Pal
- Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, India.
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
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3
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Schaub JM, Ruan Q, Tetin SY. Epifluorescent single-molecule counting with Streptavidin-Phycoerythrin conjugates. Anal Biochem 2022; 659:114955. [PMID: 36265689 DOI: 10.1016/j.ab.2022.114955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/10/2022] [Indexed: 12/14/2022]
Abstract
Single-molecule methods, specifically single-molecule counting, convey high sensitivity in research applications. However, single-molecule counting experiments require specialized equipment or consumables to perform. We demonstrate the utility of using bright Streptavidin-Phycoerythrin (SA-PE) conjugates and an epifluorescence microscope, for single-molecule counting applications. In this work, we show that we can visualize single-molecules on glass surfaces, perform single-molecule diagnostic assays on magnetic microparticles, and image individual foci on cell surfaces. This approach is simple and effective for researchers interested in single-molecule counting.
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Affiliation(s)
- Jeffrey M Schaub
- Applied Research and Technology, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL, 60064, USA
| | - Qiaoqiao Ruan
- Applied Research and Technology, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL, 60064, USA
| | - Sergey Y Tetin
- Applied Research and Technology, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL, 60064, USA.
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4
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Infrared nanospectroscopic imaging of DNA molecules on mica surface. Sci Rep 2022; 12:18972. [PMID: 36348038 PMCID: PMC9643503 DOI: 10.1038/s41598-022-23637-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Significant efforts have been done in last two decades to develop nanoscale spectroscopy techniques owning to their great potential for single-molecule structural detection and in addition, to resolve open questions in heterogeneous biological systems, such as protein-DNA complexes. Applying IR-AFM technique has become a powerful leverage for obtaining simultaneous absorption spectra with a nanoscale spatial resolution for studied proteins, however the AFM-IR investigation of DNA molecules on surface, as a benchmark for a nucleoprotein complexes nanocharacterization, has remained elusive. Herein, we demonstrate methodological approach for acquisition of AFM-IR mapping modalities with corresponding absorption spectra based on two different DNA deposition protocols on spermidine and Ni2+ pretreated mica surface. The nanoscale IR absorbance of distinctly formed DNA morphologies on mica are demonstrated through series of AFM-IR absorption maps with corresponding IR spectrum. Our results thus demonstrate the sensitivity of AFM-IR nanospectroscopy for a nucleic acid research with an open potential to be employed in further investigation of nucleoprotein complexes.
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5
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Yu P, Chen L, Zhang Y, Zhao S, Chen Z, Hu Y, Liu J, Yang Y, Shi J, Yao Z, Hong W. Single-Molecule Tunneling Sensors for Nitrobenzene Explosives. Anal Chem 2022; 94:12042-12050. [PMID: 35971273 DOI: 10.1021/acs.analchem.2c01592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tunneling current through the single-molecule junctions principally offers the ultimate solution for chemical and biochemical sensing via the interactions between probes and target analytes at the single-molecule level. However, it remains unexplored to achieve the sensitive and selective detection of targeted analytes using single-molecule junction techniques due to the challenge in quantitative evaluation of sensing sensitivity and selectivity. Herein, we demonstrate a single-molecule tunneling sensor for the highly sensitive and selective detection of nitrobenzene explosives using scanning tunneling microscope break junction (STM-BJ). Taking advantage of π-π stacking interactions between the molecular probes and nitrobenzene explosives, we use a spectral clustering algorithm to assign the signal of probes and π-stacked probes for sensitively detecting the targeted analytes and the distinguishable conductance change of probes when interacting with different nitroaromatic explosive compounds for selective detection. We find that pronounced conductance changes up to 0.8 orders of magnitude when the probes interact with TNT. Also, we obtain a sensitivity of up to ∼10 pM for TNT and high sensitivity for eight TNT analogues. Combined with theoretical calculations, we discover that the harness of the destructive quantum interference of the probe M1OH after interacting with TNT leads to high selectivity in sensing with TNT. Our work demonstrates the great potential of the single-molecule tunneling current for environmental sensing molecules with high selectivity and sensitivity.
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Affiliation(s)
- Peikai Yu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Lichuan Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Yanxi Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Shiqiang Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Zhixin Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Yong Hu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Junyang Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Yang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Jia Shi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Zhiyi Yao
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083 Beijing, China
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
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6
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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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7
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Molecular electronics sensors on a scalable semiconductor chip: A platform for single-molecule measurement of binding kinetics and enzyme activity. Proc Natl Acad Sci U S A 2022; 119:2112812119. [PMID: 35074874 PMCID: PMC8812571 DOI: 10.1073/pnas.2112812119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
Detection of molecular interactions is the foundation for many important biotechnology applications in society and industry, such as drug discovery, diagnostics, and DNA sequencing. This report describes a broadly applicable platform for detecting molecular interactions at the single-molecule scale, in real-time, label-free, and potentially highly multiplexable fashion, using single-molecule sensors on a highly scalable semiconductor sensor array chip. Such chips are both practically manufacturable in the near term, and have a durable long-term scaling roadmap, thus providing an ideal way to bring the power of modern chip technology to the broad area of biosensing. This work also realizes a 50-year-old scientific vision of integrating single molecules into electronic chips to achieve the ultimate miniaturization of electronics. For nearly 50 years, the vision of using single molecules in circuits has been seen as providing the ultimate miniaturization of electronic chips. An advanced example of such a molecular electronics chip is presented here, with the important distinction that the molecular circuit elements play the role of general-purpose single-molecule sensors. The device consists of a semiconductor chip with a scalable array architecture. Each array element contains a synthetic molecular wire assembled to span nanoelectrodes in a current monitoring circuit. A central conjugation site is used to attach a single probe molecule that defines the target of the sensor. The chip digitizes the resulting picoamp-scale current-versus-time readout from each sensor element of the array at a rate of 1,000 frames per second. This provides detailed electrical signatures of the single-molecule interactions between the probe and targets present in a solution-phase test sample. This platform is used to measure the interaction kinetics of single molecules, without the use of labels, in a massively parallel fashion. To demonstrate broad applicability, examples are shown for probe molecule binding, including DNA oligos, aptamers, antibodies, and antigens, and the activity of enzymes relevant to diagnostics and sequencing, including a CRISPR/Cas enzyme binding a target DNA, and a DNA polymerase enzyme incorporating nucleotides as it copies a DNA template. All of these applications are accomplished with high sensitivity and resolution, on a manufacturable, scalable, all-electronic semiconductor chip device, thereby bringing the power of modern chips to these diverse areas of biosensing.
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8
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Su Z, Li T, Wu D, Wu Y, Li G. Recent Progress on Single-Molecule Detection Technologies for Food Safety. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:458-469. [PMID: 34985271 DOI: 10.1021/acs.jafc.1c06808] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rapid and sensitive detection technologies for food contaminants play vital roles in food safety. Due to the complexity of the food matrix and the trace amount distribution, traditional methods often suffer from unsatisfying accuracy, sensitivity, or specificity. In past decades, single-molecule detection (SMD) has emerged as a way to realize the rapid and ultrasensitive measurement with low sample consumption, showing a great potential in food contaminants detection. For instance, based on the nanopore technique, simple and effective methods for single-molecule analysis of food contaminants have been developed. To our knowledge, there has been a rare review that focuses on SMD techniques for food safety. The present review attempts to cover some typical SMD methods in food safety, including electrochemistry, optical spectrum, and atom force microscopy. Then, recent applications of these techniques for detecting food contaminants such as biotoxins, pesticides, heavy metals, and illegal additives are reviewed. Finally, existing research challenges and future trends of SMD in food safety are also tentatively proposed.
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Affiliation(s)
- Zhuoqun Su
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Tong Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, United Kingdom
| | - Yongning Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
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9
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Sobhy MA, Tehseen M, Takahashi M, Bralić A, De Biasio A, Hamdan SM. Implementing fluorescence enhancement, quenching, and FRET for investigating flap endonuclease 1 enzymatic reaction at the single-molecule level. Comput Struct Biotechnol J 2021; 19:4456-4471. [PMID: 34471492 PMCID: PMC8385120 DOI: 10.1016/j.csbj.2021.07.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 11/24/2022] Open
Abstract
Flap endonuclease 1 (FEN1) is an important component of the intricate molecular machinery for DNA replication and repair. FEN1 is a structure-specific 5' nuclease that cleaves nascent single-stranded 5' flaps during the maturation of Okazaki fragments. Here, we review our research primarily applying single-molecule fluorescence to resolve important mechanistic aspects of human FEN1 enzymatic reaction. The methodology presented in this review is aimed as a guide for tackling other biomolecular enzymatic reactions by fluorescence enhancement, quenching, and FRET and their combinations. Using these methods, we followed in real-time the structures of the substrate and product and 5' flap cleavage during catalysis. We illustrate that FEN1 actively bends the substrate to verify its features and continues to mold it to induce a protein disorder-to-order transitioning that controls active site assembly. This mechanism suppresses off-target cleavage of non-cognate substrates and promotes their dissociation with an accuracy that was underestimated from bulk assays. We determined that product release in FEN1 after the 5' flap release occurs in two steps; a brief binding to the bent nicked-product followed by longer binding to the unbent nicked-product before dissociation. Based on our cryo-electron microscopy structure of the human lagging strand replicase bound to FEN1, we propose how this two-step product release mechanism may regulate the final steps during the maturation of Okazaki fragments.
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Affiliation(s)
- Mohamed A Sobhy
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Muhammad Tehseen
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Masateru Takahashi
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Amer Bralić
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Alfredo De Biasio
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester LE1 7HB, UK
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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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: 19] [Impact Index Per Article: 6.3] [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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11
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Ghosh D, Sugimoto H, Lee JY, Qian M. Targeted Mass Spectrometry-Based Approach for the Determination of Intrinsic Internalization Kinetics of Cell-Surface Membrane Protein Targets. Anal Chem 2021; 93:10005-10012. [PMID: 34255494 DOI: 10.1021/acs.analchem.1c00146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Successful development of targeted therapeutics aimed at the elimination of diseased cells relies on the target properties and the therapeutics that target them. Currently, target properties have been evaluated through antibody-dependent semiquantitative approaches such as flow cytometry, Western blotting, or microscopy. Since antibodies can alter target properties following binding, antibody-dependent approaches provide at best skewed measurements for target intrinsic properties. To circumvent, here we attempted to develop an antibody-free targeted mass spectrometry-based (ATM) strategy to measure the surface densities and the intrinsic rates (Kint) of CD38 internalization in multiple myeloma cell lines. Using cell-surface biotinylation in conjunction with differential mass tagging to separate inward CD38 molecules from the outbound and nascent ones, the ATM approach revealed diversities in measured CD38 Kint values of 0.239 min-1 S.E. ± 0.076, 0.109 min-1 S.E. ± 0.032, and 0.058 min-1 S.E. ± 0.001 for LP1, NCIH929, and MOLP8 cell lines, respectively. Together with CD38 surface densities, intrinsic Kint values aligned well with the tumor penetration model and supported the outcomes for tumor regression in mouse xenografts upon drug treatment. Additionally, the ATM approach can evaluate molecules with fast Kint as we determined for CTLA4 protein. We believe that the ATM approach has the potential to evaluate diverse cell-surface targets as part of the pharmacological assessment in drug discovery.
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Affiliation(s)
- Dhimankrishna Ghosh
- Preclinical and Translational Sciences/Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals Inc., Cambridge, Massachusetts 02139, United States
| | - Hiroshi Sugimoto
- Preclinical and Translational Sciences/Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals Inc., Cambridge, Massachusetts 02139, United States
| | - Janice Y Lee
- Preclinical and Translational Sciences/Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals Inc., Cambridge, Massachusetts 02139, United States
| | - Mark Qian
- Preclinical and Translational Sciences/Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals Inc., Cambridge, Massachusetts 02139, United States
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12
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Jordan JW, Fung KLY, Skowron ST, Allen CS, Biskupek J, Newton GN, Kaiser U, Khlobystov AN. Single-molecule imaging and kinetic analysis of intermolecular polyoxometalate reactions. Chem Sci 2021; 12:7377-7387. [PMID: 34163827 PMCID: PMC8171355 DOI: 10.1039/d1sc01874d] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 04/12/2021] [Indexed: 11/21/2022] Open
Abstract
We induce and study reactions of polyoxometalate (POM) molecules, [PW12O40]3- (Keggin) and [P2W18O62]6- (Wells-Dawson), at the single-molecule level. Several identical carbon nanotubes aligned side by side within a bundle provided a platform for spatiotemporally resolved imaging of ca. 100 molecules encapsulated within the nanotubes by transmission electron microscopy (TEM). Due to the entrapment of POM molecules their proximity to one another is effectively controlled, limiting molecular motion in two dimensions but leaving the third dimension available for intermolecular reactions between pairs of neighbouring molecules. By coupling the information gained from high resolution structural and kinetics experiments via the variation of key imaging parameters in the TEM, we shed light on the reaction mechanism. The dissociation of W-O bonds, a key initial step of POM reactions, is revealed to be reversible by the kinetic analysis, followed by an irreversible bonding of POM molecules to their nearest neighbours, leading to a continuous tungsten oxide nanowire, which subsequently transforms into amorphous tungsten-rich clusters due to progressive loss of oxygen atoms. The overall intermolecular reaction can therefore be described as a step-wise reductive polycondensation of POM molecules, via an intermediate state of an oxide nanowire. Kinetic analysis enabled by controlled variation of the electron flux in TEM revealed the reaction to be highly flux-dependent, which leads to reaction rates too fast to follow under the standard TEM imaging conditions. Although this presents a challenge for traditional structural characterisation of POM molecules, we harness this effect by controlling the conditions around the molecules and tuning the imaging parameters in TEM, which combined with theoretical modelling and image simulation, can shed light on the atomistic mechanisms of the reactions of POMs. This approach, based on the direct space and real time chemical reaction analysis by TEM, adds a new method to the arsenal of single-molecule kinetics techniques.
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Affiliation(s)
- Jack W Jordan
- School of Chemistry, University of Nottingham University Park Nottingham NG7 2RD UK
| | - Kayleigh L Y Fung
- School of Chemistry, University of Nottingham University Park Nottingham NG7 2RD UK
| | - Stephen T Skowron
- School of Chemistry, University of Nottingham University Park Nottingham NG7 2RD UK
| | - Christopher S Allen
- Electron Physical Science Imaging Center, Diamond Light Source Ltd. Didcot OX11 0DE UK
- Department of Materials, University of Oxford Oxford OX1 3HP UK
| | - Johannes Biskupek
- Electron Microscopy Group of Materials Science, Ulm University 89081 Ulm Germany
| | - Graham N Newton
- GSK Carbon Neutral Laboratories for Sustainable Chemistry, University of Nottingham Nottingham NG7 2TU UK
| | - Ute Kaiser
- Electron Microscopy Group of Materials Science, Ulm University 89081 Ulm Germany
| | - Andrei N Khlobystov
- School of Chemistry, University of Nottingham University Park Nottingham NG7 2RD UK
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13
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Takahashi S, Oshige M, Katsura S. DNA Manipulation and Single-Molecule Imaging. Molecules 2021; 26:1050. [PMID: 33671359 PMCID: PMC7922115 DOI: 10.3390/molecules26041050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 11/22/2022] Open
Abstract
DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein.
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Affiliation(s)
- Shunsuke Takahashi
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Hatoyama-cho, Hiki-gun, Saitama 350-0394, Japan;
| | - Masahiko Oshige
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan;
- Gunma University Center for Food Science and Wellness (GUCFW), Maebashi, Gunma 371-8510, Japan
| | - Shinji Katsura
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan;
- Gunma University Center for Food Science and Wellness (GUCFW), Maebashi, Gunma 371-8510, Japan
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Zhuang X, Wu Q, Zhang A, Liao L, Fang B. Single-molecule biotechnology for protein researches. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.10.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Platnich CM, Rizzuto FJ, Cosa G, Sleiman HF. Single-molecule methods in structural DNA nanotechnology. Chem Soc Rev 2021; 49:4220-4233. [PMID: 32538403 DOI: 10.1039/c9cs00776h] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Single molecules can now be visualised with unprecedented precision. As the resolution of single-molecule experiments improves, so too does the breadth, quantity and quality of information that can be extracted using these methodologies. In the field of DNA nanotechnology, we use programmable interactions between nucleic acids to generate complex, multidimensional structures. We can use single-molecule techniques - ranging from electron and fluorescence microscopies to electrical and force spectroscopies - to report on the structure, morphology, robustness, sample heterogeneity and other properties of these DNA nanoconstructs. In this Tutorial Review, we will detail how complementarity between static and dynamic single-molecule techniques can provide a unified image of DNA nanoarchitectures. The single-molecule methods that we discuss provide unprecedented insight into chemical and structural behaviour, yielding not just an average outcome but reporting on the distribution of values, ultimately showing how bulk properties arise from the collective behaviour of individual structures. As the fields of both DNA nanotechnology and single-molecule characterisation intertwine, a feedback loop is generated between disciplines, providing new opportunities for the development and operation of DNA-based materials as sensors, delivery vehicles, machinery and structural scaffolds.
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Affiliation(s)
- Casey M Platnich
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
| | - Felix J Rizzuto
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
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Abstract
Nanorobotics, which has long been a fantasy in the realm of science fiction, is now a reality due to the considerable developments in diverse fields including chemistry, materials, physics, information and nanotechnology in the past decades. Not only different prototypes of nanorobots whose sizes are nanoscale are invented for various biomedical applications, but also robotic nanomanipulators which are able to handle nano-objects obtain substantial achievements for applications in biomedicine. The outstanding achievements in nanorobotics have significantly expanded the field of medical robotics and yielded novel insights into the underlying mechanisms guiding life activities, remarkably showing an emerging and promising way for advancing the diagnosis & treatment level in the coming era of personalized precision medicine. In this review, the recent advances in nanorobotics (nanorobots, nanorobotic manipulations) for biomedical applications are summarized from several facets (including molecular machines, nanomotors, DNA nanorobotics, and robotic nanomanipulators), and the future perspectives are also presented.
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17
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Calebiro D, Koszegi Z, Lanoiselée Y, Miljus T, O'Brien S. G protein-coupled receptor-G protein interactions: a single-molecule perspective. Physiol Rev 2020; 101:857-906. [PMID: 33331229 DOI: 10.1152/physrev.00021.2020] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs) regulate many cellular and physiological processes, responding to a diverse range of extracellular stimuli including hormones, neurotransmitters, odorants, and light. Decades of biochemical and pharmacological studies have provided fundamental insights into the mechanisms of GPCR signaling. Thanks to recent advances in structural biology, we now possess an atomistic understanding of receptor activation and G protein coupling. However, how GPCRs and G proteins interact in living cells to confer signaling efficiency and specificity remains insufficiently understood. The development of advanced optical methods, including single-molecule microscopy, has provided the means to study receptors and G proteins in living cells with unprecedented spatio-temporal resolution. The results of these studies reveal an unexpected level of complexity, whereby GPCRs undergo transient interactions among themselves as well as with G proteins and structural elements of the plasma membrane to form short-lived signaling nanodomains that likely confer both rapidity and specificity to GPCR signaling. These findings may provide new strategies to pharmaceutically modulate GPCR function, which might eventually pave the way to innovative drugs for common diseases such as diabetes or heart failure.
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Affiliation(s)
- Davide Calebiro
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Zsombor Koszegi
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Yann Lanoiselée
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Tamara Miljus
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Shannon O'Brien
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
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18
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Vahid MR, Hanzon B, Ober RJ. Effect of Pixelation on the Parameter Estimation of Single Molecule Trajectories. IEEE TRANSACTIONS ON COMPUTATIONAL IMAGING 2020; 7:98-113. [PMID: 33604418 PMCID: PMC7879562 DOI: 10.1109/tci.2020.3039951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 08/13/2020] [Accepted: 11/15/2020] [Indexed: 06/12/2023]
Abstract
The advent of single molecule microscopy has revolutionized biological investigations by providing a powerful tool for the study of intercellular and intracellular trafficking processes of protein molecules which was not available before through conventional microscopy. In practice, pixelated detectors are used to acquire the images of fluorescently labeled objects moving in cellular environments. Then, the acquired fluorescence microscopy images contain the numbers of the photons detected in each pixel, during an exposure time interval. Moreover, instead of having the exact locations of detection of the photons, we only know the pixel areas in which the photons impact the detector. These challenges make the analysis of single molecule trajectories, from pixelated images, a complex problem. Here, we investigate the effect of pixelation on the parameter estimation of single molecule trajectories. In particular, we develop a stochastic framework to calculate the maximum likelihood estimates of the parameters of a stochastic differential equation that describes the motion of the molecule in living cells. We also calculate the Fisher information matrix for this parameter estimation problem. The analytical results are complicated through the fact that the observation process in a microscope prohibits the use of standard Kalman filter type approaches. The analytical framework presented here is illustrated with examples of low photon count scenarios for which we rely on Monte Carlo methods to compute the associated probability distributions.
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Affiliation(s)
- Milad R. Vahid
- Department of Biomedical EngineeringTexas A&M UniversityCollege StationTX77843USA
- Department of Biomedical Data ScienceStanford UniversityStanfordCA94305USA
| | - Bernard Hanzon
- Department of MathematicsUniversity College CorkT12YX86CorkIreland
| | - Raimund J. Ober
- Centre for Cancer ImmunologyFaculty of Medicine, University of SouthamptonSouthamptonSO16 6YDU.K.
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19
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Schueder F, Unterauer EM, Ganji M, Jungmann R. DNA-Barcoded Fluorescence Microscopy for Spatial Omics. Proteomics 2020; 20:e1900368. [PMID: 33030780 DOI: 10.1002/pmic.201900368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/24/2020] [Indexed: 12/18/2022]
Abstract
Innovation in genomics, transcriptomics, and proteomics research has created a plethora of state-of-the-art techniques such as nucleic acid sequencing and mass-spectrometry-based proteomics with paramount impact in the life sciences. While current approaches yield quantitative abundance analysis of biomolecules on an almost routine basis, coupling this high content to spatial information in a single cell and tissue context is challenging. Here, current implementations of spatial omics are discussed and recent developments in the field of DNA-barcoded fluorescence microscopy are reviewed. Light is shed on the potential of DNA-based imaging techniques to provide a comprehensive toolbox for spatial genomics and transcriptomics and discuss current challenges, which need to be overcome on the way to spatial proteomics using high-resolution fluorescence microscopy.
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Affiliation(s)
- Florian Schueder
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, Munich, 80539, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Eduard M Unterauer
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, Munich, 80539, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Mahipal Ganji
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, Munich, 80539, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Ralf Jungmann
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, Munich, 80539, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
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20
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Chatterjee T, Knappik A, Sandford E, Tewari M, Choi SW, Strong WB, Thrush EP, Oh KJ, Liu N, Walter NG, Johnson-Buck A. Direct kinetic fingerprinting and digital counting of single protein molecules. Proc Natl Acad Sci U S A 2020; 117:22815-22822. [PMID: 32868420 PMCID: PMC7502736 DOI: 10.1073/pnas.2008312117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The sensitive and accurate quantification of protein biomarkers plays important roles in clinical diagnostics and biomedical research. Sandwich ELISA and its variants accomplish the capture and detection of a target protein via two antibodies that tightly bind at least two distinct epitopes of the same antigen and have been the gold standard for sensitive protein quantitation for decades. However, existing antibody-based assays cannot distinguish between signal arising from specific binding to the protein of interest and nonspecific binding to assay surfaces or matrix components, resulting in significant background signal even in the absence of the analyte. As a result, they generally do not achieve single-molecule sensitivity, and they require two high-affinity antibodies as well as stringent washing to maximize sensitivity and reproducibility. Here, we show that surface capture with a high-affinity antibody combined with kinetic fingerprinting using a dynamically binding, low-affinity fluorescent antibody fragment differentiates between specific and nonspecific binding at the single-molecule level, permitting the direct, digital counting of single protein molecules with femtomolar-to-attomolar limits of detection (LODs). We apply this approach to four exemplary antigens spiked into serum, demonstrating LODs 55- to 383-fold lower than commercially available ELISA. As a real-world application, we establish that endogenous interleukin-6 (IL-6) can be quantified in 2-µL serum samples from chimeric antigen receptor T cell (CAR-T cell) therapy patients without washing away excess serum or detection probes, as is required in ELISA-based approaches. This kinetic fingerprinting thus exhibits great potential for the ultrasensitive, rapid, and streamlined detection of many clinically relevant proteins.
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Affiliation(s)
- Tanmay Chatterjee
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055
| | - Achim Knappik
- Life Science Group, Antibodies Division, Bio-Rad AbD Serotec GmbH, 82178 Puchheim, Germany
| | - Erin Sandford
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI 48109-1055
| | - Muneesh Tewari
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI 48109-1055
| | - Sung Won Choi
- Department of Pediatrics, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI 48109-1055
| | - William B Strong
- Life Science Group, Bio-Rad Laboratories, Inc., Hercules, CA 94547
| | - Evan P Thrush
- Life Science Group, Bio-Rad Laboratories, Inc., Hercules, CA 94547
| | - Kenneth J Oh
- Life Science Group, Bio-Rad Laboratories, Inc., Hercules, CA 94547
| | - Ning Liu
- Life Science Group, Bio-Rad Laboratories, Inc., Hercules, CA 94547
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055;
| | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055;
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI 48109-1055
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21
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Ruggeri FS, Mannini B, Schmid R, Vendruscolo M, Knowles TPJ. Single molecule secondary structure determination of proteins through infrared absorption nanospectroscopy. Nat Commun 2020; 11:2945. [PMID: 32522983 PMCID: PMC7287102 DOI: 10.1038/s41467-020-16728-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/11/2020] [Indexed: 12/21/2022] Open
Abstract
The chemical and structural properties of biomolecules determine their interactions, and thus their functions, in a wide variety of biochemical processes. Innovative imaging methods have been developed to characterise biomolecular structures down to the angstrom level. However, acquiring vibrational absorption spectra at the single molecule level, a benchmark for bulk sample characterization, has remained elusive. Here, we introduce off-resonance, low power and short pulse infrared nanospectroscopy (ORS-nanoIR) to allow the acquisition of infrared absorption spectra and chemical maps at the single molecule level, at high throughput on a second timescale and with a high signal-to-noise ratio (~10-20). This high sensitivity enables the accurate determination of the secondary structure of single protein molecules with over a million-fold lower mass than conventional bulk vibrational spectroscopy. These results pave the way to probe directly the chemical and structural properties of individual biomolecules, as well as their interactions, in a broad range of chemical and biological systems.
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Affiliation(s)
| | - Benedetta Mannini
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Roman Schmid
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | | | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK.
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22
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Quantitative Analysis of Single Quantum Dot Trajectories. Methods Mol Biol 2020. [PMID: 32246331 DOI: 10.1007/978-1-0716-0463-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Single quantum dot tracking (SQDT) is a powerful technique for interrogating biomolecular dynamics in living cells and tissue. SQDT has particularly excelled in driving discovery at the single-molecule level in the fields of neuronal communication, plasma membrane organization, viral infection, and immune system response. Here, we briefly characterize various elements of the SQDT analytical framework and provide the reader with a detailed set of executable commands to implement commonly used algorithms for SQDT data processing.
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23
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Menges JA, Grandjean A, Clasen A, Jung G. Kinetics of Palladium(0)‐Allyl Interactions in the Tsuji‐Trost Reaction, derived from Single‐Molecule Fluorescence Microscopy. ChemCatChem 2020. [DOI: 10.1002/cctc.202000032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Johannes A. Menges
- Department of Biophysical Chemistry Saarland University Building B2 2 66123 Saarbrücken Germany
| | - Alexander Grandjean
- Department of Biophysical Chemistry Saarland University Building B2 2 66123 Saarbrücken Germany
| | - Anne Clasen
- Department of Biophysical Chemistry Saarland University Building B2 2 66123 Saarbrücken Germany
| | - Gregor Jung
- Department of Biophysical Chemistry Saarland University Building B2 2 66123 Saarbrücken Germany
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Smith LD, Liu Y, Zahid MU, Canady TD, Wang L, Kohli M, Cunningham BT, Smith AM. High-Fidelity Single Molecule Quantification in a Flow Cytometer Using Multiparametric Optical Analysis. ACS NANO 2020; 14:2324-2335. [PMID: 31971776 PMCID: PMC7295608 DOI: 10.1021/acsnano.9b09498] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Microfluidic techniques are widely used for high-throughput quantification and discrete analysis of micron-scale objects but are difficult to apply to molecular-scale targets. Instead, single-molecule methods primarily rely on low-throughput microscopic imaging of immobilized molecules. Here we report that commercial-grade flow cytometers can detect single nucleic acid targets following enzymatic extension and dense labeling with multiple distinct fluorophores. We focus on microRNAs, short nucleic acids that can be extended by rolling circle amplification (RCA). We labeled RCA-extended microRNAs with multicolor fluorophores to generate repetitive nucleic acid products with submicron sizes and tunable multispectral profiles. By cross-correlating the multiparametric optical features, signal-to-background ratios were amplified 1600-fold to allow single-molecule detection across 4 orders of magnitude of concentration. The limit of detection was measured to be 47 fM, which is 100-fold better than gold-standard methods based on polymerase chain reaction. Furthermore, multiparametric analysis allowed discrimination of different microRNA sequences in the same solution using distinguishable optical barcodes. Barcodes can apply both ratiometric and colorimetric signatures, which could facilitate high-dimensional multiplexing. Because of the wide availability of flow cytometers, we anticipate that this technology can provide immediate access to high-throughput multiparametric single-molecule measurements and can further be adapted to the diverse range of molecular amplification methods that are continually emerging.
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Affiliation(s)
- Lucas D Smith
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Yang Liu
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Mohammad U Zahid
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Taylor D Canady
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Liang Wang
- Department of Tumor Biology , H. Lee Moffitt Cancer Center , Tampa , Florida 33612 , United States
| | - Manish Kohli
- Department of Genitourinary Oncology , H. Lee Moffitt Cancer Center , Tampa , Florida 33612 United States
| | - Brian T Cunningham
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Department of Electrical and Computer Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Cancer Center at Illinois , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Andrew M Smith
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Cancer Center at Illinois , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Department of Materials Science and Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Carle Illinois College of Medicine , Urbana , Illinois 61801 , United States
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26
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Chatterjee T, Li Z, Khanna K, Montoya K, Tewari M, Walter NG, Johnson-Buck A. Ultraspecific analyte detection by direct kinetic fingerprinting of single molecules. Trends Analyt Chem 2020; 123:115764. [PMID: 32863484 PMCID: PMC7451408 DOI: 10.1016/j.trac.2019.115764] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The detection and quantification of biomarkers have numerous applications in biological research and medicine. The most widely used methods to detect nucleic acids require amplification via the polymerase chain reaction (PCR). However, errors arising from the imperfect copying fidelity of DNA polymerases, limited specificity of primers, and heat-induced damage reduce the specificity of PCR-based methods, particularly for single-nucleotide variants. Furthermore, not all analytes can be amplified efficiently. While amplification-free methods avoid these pitfalls, the specificity of most such methods is strictly constrained by probe binding thermodynamics, which for example hampers detection of rare somatic mutations. In contrast, single-molecule recognition through equilibrium Poisson sampling (SiMREPS) provides ultraspecific detection with single-molecule and single-nucleotide sensitivity by monitoring the repetitive interactions of a fluorescent probe with surface-immobilized targets. In this review, we discuss SiMREPS in comparison with other analytical approaches, and describe its utility in quantifying a range of nucleic acids and other analytes.
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Affiliation(s)
- Tanmay Chatterjee
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zi Li
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kunal Khanna
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Karen Montoya
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Muneesh Tewari
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
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27
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Li Y, Yang C, Guo X. Single-Molecule Electrical Detection: A Promising Route toward the Fundamental Limits of Chemistry and Life Science. Acc Chem Res 2020; 53:159-169. [PMID: 31545589 DOI: 10.1021/acs.accounts.9b00347] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The ultimate limit of analytical chemistry is single-molecule detection, which allows one to visualize the dynamic processes of chemical/biological interactions with single-molecule or single-event sensitivity and hence enables the study of stochastic fluctuations under equilibrium conditions and the observation of time trajectories and reaction pathways of individual species in nonequilibrated systems. In addition, such studies may also allow the direct observation of novel microscopic quantum effects and fundamental discoveries of underlying molecular mechanisms in organic reactions and biological processes that are not accessible in ensemble experiments, thus providing unique opportunities to solve the key problems of physical, chemical, and life sciences. Consequently, the field of single-molecule detection has received considerable attention and has witnessed tremendous advances in different directions in combination with other disciplines. This Account describes our ongoing work on the development of groundbreaking methods (termed "single-molecule electrical approaches") of translating the detailed processes of chemical reactions or biological functions into detectable electrical signals at the single-event level on the platform of single-molecule electronic devices, with a particular focus on graphene-molecule-graphene single-molecule junctions (GMG-SMJs) and silicon-nanowire-based single-molecule electrical nanocircuits. These nanocircuit-based architectures are complementary to conventional optical or mechanical techniques but exhibit obvious advantages such as the absence of problems associated with bleaching and fluorescent labeling. Dash-line lithography (DLL) is an efficient lithographic method of cutting graphene and forming carboxylic-acid-functionalized nanogapped graphene point contact arrays developed to address the formidable challenges of molecular device fabrication difficulty and poor stability. Molecules of interest terminated by amines on both ends can be covalently sandwiched between graphene point contacts to create high-throughput robust GMG-SMJs containing only one molecule as the conductive element. In conjunction with the ease of device fabrication and device stability, this feature distinguishes GMG-SMJs as a new testbed platform for single-molecule analysis characterized by high temporal resolution and superior signal-to-noise ratios. By exploiting the DLL method, we have fabricated molecular devices that are sensitive to external stimuli and are capable of transducing chemical/biochemical events into electrical signals at the single-molecule level, with notable examples including host-guest interaction, hydrogen bond dynamics, DNA intercalation, photoinduced conformational transition, carbocation formation, nucleophilic addition, and stereoelectronic effect. In addition to GMG-SMJs and considering compatibility with the silicon-based industry, we have also developed a reliable method of point-functionalizing silicon-nanowire-based nanotransistors to afford single-molecule electrical nanocircuits. This approach proved to be a robust platform for single-molecule electrical analysis capable of probing fast dynamic processes such as single-protein detection, DNA hybridization/polymorphism, and motor rotation dynamics. The above systematic investigations emphasize the importance and unique advantages of universal single-molecule electrical approaches for realizing direct, label-free, real-time electrical measurements of reaction dynamics with single-event sensitivity. These approaches promise a fascinating mainstream platform to explore the dynamics of stochastic processes in chemical/biological systems as well as gain information in fields ranging from reaction chemistry for elucidating the intrinsic mechanisms to genomics or proteomics for accurate molecular and even point-of-care clinical diagnoses.
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Affiliation(s)
- Yu Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Chen Yang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
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Calebiro D, Grimes J. G Protein–Coupled Receptor Pharmacology at the Single-Molecule Level. Annu Rev Pharmacol Toxicol 2020; 60:73-87. [DOI: 10.1146/annurev-pharmtox-010919-023348] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
G protein–coupled receptors (GPCRs) mediate the effects of numerous hormones and neurotransmitters and are major pharmacological targets. Classical studies with crude cell lysates or membrane preparations have identified the main biochemical steps involved in GPCR signaling. Moreover, recent studies on purified proteins have provided astounding details at the atomic level of the 3-D structures of receptors in multiple conformations, including in complex with G proteins and β-arrestins. However, several fundamental questions remain regarding the highly specific effects and rapid nature of GPCR signaling. Recent developments in single-molecule microscopy are providing important contributions to answering these questions. Overall, single-molecule studies have revealed unexpected levels of complexity, with receptors existing in different conformations and dynamically interacting among themselves, their signaling partners, and structural elements of the plasma membrane to produce highly localized signals in space and time. These findings may provide a new basis to develop innovative strategies to modulate GPCR function for pharmacological purposes.
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Affiliation(s)
- Davide Calebiro
- Institute of Metabolism and Systems Research and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham B15 2TT, United Kingdom;,
| | - Jak Grimes
- Institute of Metabolism and Systems Research and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham B15 2TT, United Kingdom;,
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Li M, Xi N, Wang Y, Liu L. Atomic Force Microscopy as a Powerful Multifunctional Tool for Probing the Behaviors of Single Proteins. IEEE Trans Nanobioscience 2020; 19:78-99. [DOI: 10.1109/tnb.2019.2954099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Li Y, Zhao L, Yao Y, Guo X. Single-Molecule Nanotechnologies: An Evolution in Biological Dynamics Detection. ACS APPLIED BIO MATERIALS 2019; 3:68-85. [DOI: 10.1021/acsabm.9b00840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Lihua Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Yuan Yao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
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31
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Liu W, Guo Y, Wang K, Zhou X, Wang Y, Lü J, Shao Z, Hu J, Czajkowsky DM, Li B. Atomic force microscopy-based single-molecule force spectroscopy detects DNA base mismatches. NANOSCALE 2019; 11:17206-17210. [PMID: 31535117 DOI: 10.1039/c9nr05234h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Atomic force microscopy-based single-molecule-force spectroscopy is limited by low throughput. We introduce addressable DNA origami to study multiple target molecules. Six target DNAs that differed by only a single base-pair mismatch were clearly differentiated a rupture force of only 4 pN.
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Affiliation(s)
- Wenjing Liu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yourong Guo
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Kaizhe Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingfei Zhou
- School of Science, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Ying Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Junhong Lü
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Jun Hu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China and School of Physical Science and Technology, Shanghai Tech University, Shanghai 201204, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Bin Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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Schärfen L, Schlierf M. Real-time monitoring of protein-induced DNA conformational changes using single-molecule FRET. Methods 2019; 169:11-20. [DOI: 10.1016/j.ymeth.2019.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/21/2018] [Accepted: 02/11/2019] [Indexed: 12/11/2022] Open
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Li L, Yu Y, Wang C, Han Q, Su X. Transient Hybridization Directed Nanoflare for Single-Molecule miRNA Imaging. Anal Chem 2019; 91:11122-11128. [PMID: 31402644 DOI: 10.1021/acs.analchem.9b01766] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Accurate quantifications of cellular miRNAs are important not only for accelerating them becoming reliable diagnostics biomarkers but also for deeply understanding their influence on central signaling pathways. Although single-molecule miRNA imaging permits quantifying biomolecules at the single-molecule level, it is limited by the sensitivity and specificity of hybridization-based probes. We report a miRNA single-molecule imaging method by using conjugated polymer nanoparticle (CPN) labeled short DNA probe termed as a nanoflare. The transient hybridization of the nanoflares and target miRNAs yields a featured single-molecule kinetics signal rendering high single-molecule sensitivity and specificity. miRNA can be detected with a remarkable detection limit of 1 fM without using any amplification steps. The discrimination capability of homologous miRNAs was also demonstrated. Taking advantage of the featured single-molecule signal of the nanoflare, we can directly count single miR-21 molecules in single cells by using highly inclined and laminated optical sheet (HILO) microscopy. The statistics of the counting reveals miR-21's cell-to-cell fluctuation and differential expression of tumor cells and normal cells.
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Affiliation(s)
- Lina Li
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Yingjie Yu
- Institute of Translational Medicine , The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital , Shenzhen 518039 , China
| | - Congshan Wang
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Qianqian Han
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Xin Su
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China
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34
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Hashikawa Y, Murata Y. H2O/Olefinic-π Interaction inside a Carbon Nanocage. J Am Chem Soc 2019; 141:12928-12938. [DOI: 10.1021/jacs.9b06759] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Yoshifumi Hashikawa
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yasujiro Murata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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35
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Yang YJ, Song L, Zhao XC, Zhang C, Wu WQ, You HJ, Fu H, Zhou EC, Zhang XH. A Universal Assay for Making DNA, RNA, and RNA-DNA Hybrid Configurations for Single-Molecule Manipulation in Two or Three Steps without Ligation. ACS Synth Biol 2019; 8:1663-1672. [PMID: 31264849 DOI: 10.1021/acssynbio.9b00241] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite having a great variety of topologies, most DNA, RNA, and RNA-DNA hybrid (RDH) configurations for single-molecule manipulation are composed of several single-stranded (ss) DNA and ssRNA strands, with functional labels at the two ends for surface tethering. On this basis, we developed a simple, robust, and universal amplification-annealing (AA) assay for making all these configurations in two or three steps without inefficient digestion and ligation reactions. As examples, we made ssDNA, short ssDNA with double-stranded (ds) DNA handles, dsDNA with ssDNA handles, replication-fork shaped DNA/RDH/RNA, DNA holiday junction, three-site multiple-labeled and nicked DNA, torsion-constrained RNA/RDH, and short ssRNA with RDH handles. In addition to single-molecule manipulation techniques including optical tweezers, magnetic tweezers, and atomic force microscopy, these configurations can be applied in other surface-tethering techniques as well.
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Affiliation(s)
- Ya-Jun Yang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Lun Song
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Xiao-Cong Zhao
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Chen Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Wen-Qiang Wu
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Hui-Juan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hang Fu
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Er-Chi Zhou
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Xing-Hua Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
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36
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Lemay SG. Noise as Data: Nucleation of Electrochemically Generated Nanobubbles. ACS NANO 2019; 13:6141-6144. [PMID: 31149800 PMCID: PMC6595431 DOI: 10.1021/acsnano.9b03348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Single-entity electrochemistry aims to expand the toolkit for probing matter at the nanometer scale. Originally focused largely on electrochemically active systems, these methods are increasingly turning into versatile probes complementary to optical, electrical, or mechanical methods. Recent studies of the nucleation, structure, and stability of gas nanobubbles, which exploit electrochemistry at nanoelectrodes as generation and stabilization mechanisms, are prototypical examples. These measurements illustrate the interplay between advances in electrochemical methods and strategies for extracting microscopic information from the results.
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37
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Jalihal AP, Lund PE, Walter NG. Coming Together: RNAs and Proteins Assemble under the Single-Molecule Fluorescence Microscope. Cold Spring Harb Perspect Biol 2019; 11:11/4/a032441. [PMID: 30936188 DOI: 10.1101/cshperspect.a032441] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
RNAs, across their numerous classes, often work in concert with proteins in RNA-protein complexes (RNPs) to execute critical cellular functions. Ensemble-averaging methods have been instrumental in revealing many important aspects of these RNA-protein interactions, yet are insufficiently sensitive to much of the dynamics at the heart of RNP function. Single-molecule fluorescence microscopy (SMFM) offers complementary, versatile tools to probe RNP conformational and compositional changes in detail. In this review, we first outline the basic principles of SMFM as applied to RNPs, describing key considerations for labeling, imaging, and quantitative analysis. We then sample applications of in vitro and in vivo single-molecule visualization using the case studies of pre-messenger RNA (mRNA) splicing and RNA silencing, respectively. After discussing specific insights single-molecule fluorescence methods have yielded, we briefly review recent developments in the field and highlight areas of anticipated growth.
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Affiliation(s)
- Ameya P Jalihal
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan 48109.,Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Paul E Lund
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109.,Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109
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38
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Counting growth factors in single cells with infrared quantum dots to measure discrete stimulation distributions. Nat Commun 2019; 10:909. [PMID: 30796217 PMCID: PMC6385258 DOI: 10.1038/s41467-019-08754-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 01/29/2019] [Indexed: 12/20/2022] Open
Abstract
The distribution of single-cell properties across a population of cells can be measured using diverse tools, but no technology directly quantifies the biochemical stimulation events regulating these properties. Here we report digital counting of growth factors in single cells using fluorescent quantum dots and calibrated three-dimensional deconvolution microscopy (QDC-3DM) to reveal physiologically relevant cell stimulation distributions. We calibrate the fluorescence intensities of individual compact quantum dots labeled with epidermal growth factor (EGF) and demonstrate the necessity of near-infrared emission to overcome intrinsic cellular autofluoresence at the single-molecule level. When applied to human triple-negative breast cancer cells, we observe proportionality between stimulation and both receptor internalization and inhibitor response, reflecting stimulation heterogeneity contributions to intrinsic variability. We anticipate that QDC-3DM can be applied to analyze any peptidic ligand to reveal single-cell correlations between external stimulation and phenotypic variability, cell fate, and drug response. Measuring growth factors in single cells at physiologically relevant stimulation doses is challenging. Here the authors use fluorescent quantum dots and calibrated three-dimensional deconvolution microscopy to digitally count growth factors in single cells and reveal stimulation distributions in cancer cells.
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39
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Menges JA, Clasen A, Jourdain M, Beckmann J, Hoffmann C, König J, Jung G. Surface Preparation for Single-Molecule Chemistry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:2506-2516. [PMID: 30664351 DOI: 10.1021/acs.langmuir.8b03603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Immobilization procedures, intended to enable prolonged observation of single molecules by fluorescence microscopy, may generate heterogeneous microenvironments, thus inducing heterogeneity in the molecular behavior. On that account, we propose a straightforward surface preparation procedure for studying chemical reactions on the single-molecule level. Sensor fluorophores were developed, which exhibit dual-emissive characteristics in a homogeneously catalyzed showcase reaction. These molecules undergo a shift of fluorescence wavelength of about 100 nm upon Pd(0)-induced deallylation in the Tsuji-Trost reaction, allowing for separate visualization of the starting material and product. Whereas a simultaneous immobilization of dye and inert silane leads to strongly polydisperse reaction kinetics, a consecutive immobilization routine with deposition of dye molecules as the last step provides substrates underlying the kinetics of ensemble experiments. Also, the found kinetics are unaffected by the chemical variation of inert silanes, nearly uniform, and therefore well reproducible. Additional parameters like photostability, signal-to-noise ratio, dye-molecule density, and spatial distribution of dye molecules are, as well, hardly affected by surface modification in the successive immobilization scheme.
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Affiliation(s)
- Johannes A Menges
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Anne Clasen
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Matthias Jourdain
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Julian Beckmann
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Caroline Hoffmann
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Julien König
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Gregor Jung
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
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40
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Weng R, Lou S, Li L, Zhang Y, Qiu J, Su X, Qian Y, Walter NG. Single-Molecule Kinetic Fingerprinting for the Ultrasensitive Detection of Small Molecules with Aptasensors. Anal Chem 2019; 91:1424-1431. [PMID: 30562003 DOI: 10.1021/acs.analchem.8b04145] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aptamers have emerged as promising molecular tools for small-molecule analyte sensing. However, the performance of such aptasensors is generally limited by leakage since it has been difficult to completely suppress signal in the absence of analyte, resulting in a compromise between sensitivity and specificity. Here, we describe a methodology for the ultrasensitive detection of analytes combining aptasensors with single-molecule kinetic fingerprinting. A short, fluorescently labeled DNA probe is utilized to detect the structural changes upon ligand binding to the designed hairpin-shaped aptasensor probe. The Poisson statistics of binding and dissociation events of the DNA probe to single surface-immobilized aptasensor molecules is monitored by total internal reflection fluorescence microscopy, permitting the high-accuracy discrimination of the ligand bound and ligand-free states, resulting in zero background. The programmable dynamics of the hairpin enables fine-tuning of the hybridization kinetics of the fluorescent probe, rendering the acquisition time sufficiently flexible to optimize discrimination. Remarkable detection limits are achieved for a diverse set of analytes when spiked into chicken meat extract: the nucleotide adenosine (0.3 pM), the insecticide acetamiprid (0.35 pM), and the dioxin-like toxin PCB-77 (0.72 pM), which is superior to recently reported aptasensors. Our generalizable method significantly improves the performance of aptasensors, with the potential to extend to other molecular biomarkers.
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Affiliation(s)
- Rui Weng
- Key Laboratory of Agro-food Safety and Quality of Ministry of Agriculture and Rural Affairs, Institute of Quality Standards and Testing Technology for Agro-Products , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
| | - Shengting Lou
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Lidan Li
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Yi Zhang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Jing Qiu
- Key Laboratory of Agro-food Safety and Quality of Ministry of Agriculture and Rural Affairs, Institute of Quality Standards and Testing Technology for Agro-Products , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
| | - Xin Su
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Yongzhong Qian
- Key Laboratory of Agro-food Safety and Quality of Ministry of Agriculture and Rural Affairs, Institute of Quality Standards and Testing Technology for Agro-Products , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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41
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Fontana M, Fijen C, Lemay SG, Mathwig K, Hohlbein J. High-throughput, non-equilibrium studies of single biomolecules using glass-made nanofluidic devices. LAB ON A CHIP 2018; 19:79-86. [PMID: 30468446 DOI: 10.1039/c8lc01175c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Single-molecule detection schemes offer powerful means to overcome static and dynamic heterogeneity inherent to complex samples. However, probing biomolecular interactions and reactions with high throughput and time resolution remains challenging, often requiring surface-immobilized entities. Here, we introduce glass-made nanofluidic devices for the high-throughput detection of freely-diffusing single biomolecules by camera-based fluorescence microscopy. Nanochannels of 200 nm height and a width of several micrometers confine the movement of biomolecules. Using pressure-driven flow through an array of parallel nanochannels and by tracking the movement of fluorescently labelled DNA oligonucleotides, we observe conformational changes with high throughput. In a device geometry featuring a T-shaped junction of nanochannels, we drive steady-state non-equilibrium conditions by continuously mixing reactants and triggering chemical reactions. We use the device to probe the conformational equilibrium of a DNA hairpin as well as to continuously observe DNA synthesis in real time. Our platform offers a straightforward and robust method for studying reaction kinetics at the single-molecule level.
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Affiliation(s)
- Mattia Fontana
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
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Gibbs DR, Kaur A, Megalathan A, Sapkota K, Dhakal S. Build Your Own Microscope: Step-By-Step Guide for Building a Prism-Based TIRF Microscope. Methods Protoc 2018; 1:mps1040040. [PMID: 31164580 PMCID: PMC6481079 DOI: 10.3390/mps1040040] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/31/2018] [Accepted: 10/31/2018] [Indexed: 01/09/2023] Open
Abstract
Prism-based total internal reflection fluorescence (pTIRF) microscopy is one of the most widely used techniques for the single molecule analysis of a vast range of samples including biomolecules, nanostructures, and cells, to name a few. It allows for excitation of surface bound molecules/particles/quantum dots via evanescent field of a confined region of space, which is beneficial not only for single molecule detection but also for analysis of single molecule dynamics and for acquiring kinetics data. However, there is neither a commercial microscope available for purchase nor a detailed guide dedicated for building this microscope. Thus far, pTIRF microscopes are custom-built with the use of a commercially available inverted microscope, which requires high level of expertise in selecting and handling sophisticated instrument-parts. To directly address this technology gap, here we describe a step-by-step guide on how to build and characterize a pTIRF microscope for in vitro single-molecule imaging, nanostructure analysis and other life sciences research.
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Affiliation(s)
- Dalton R Gibbs
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
| | - Anisa Kaur
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
| | - Anoja Megalathan
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
| | - Kumar Sapkota
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
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Ray S, Chauvier A, Walter NG. Kinetics coming into focus: single-molecule microscopy of riboswitch dynamics. RNA Biol 2018; 16:1077-1085. [PMID: 30328748 DOI: 10.1080/15476286.2018.1536594] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Riboswitches are dynamic RNA motifs that are mostly embedded in the 5'-untranslated regions of bacterial mRNAs, where they regulate gene expression transcriptionally or translationally by undergoing conformational changes upon binding of a small metabolite or ion. Due to the small size of typical ligands, relatively little free energy is available from ligand binding to overcome the often high energetic barrier of reshaping RNA structure. Instead, most riboswitches appear to take advantage of the directional and hierarchical folding of RNA by employing the ligand as a structural 'linchpin' to adjust the kinetic partitioning between alternate folds. In this model, even small, local structural and kinetic effects of ligand binding can cascade into global RNA conformational changes affecting gene expression. Single-molecule (SM) microscopy tools are uniquely suited to study such kinetically controlled RNA folding since they avoid the ensemble averaging of bulk techniques that loses sight of unsynchronized, transient, and/or multi-state kinetic behavior. This review summarizes how SM methods have begun to unravel riboswitch-mediated gene regulation.
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Affiliation(s)
- Sujay Ray
- a Single Molecule Analysis Group, Department of Chemistry, University of Michigan , Ann Arbor , MI , USA
| | - Adrien Chauvier
- a Single Molecule Analysis Group, Department of Chemistry, University of Michigan , Ann Arbor , MI , USA
| | - Nils G Walter
- a Single Molecule Analysis Group, Department of Chemistry, University of Michigan , Ann Arbor , MI , USA
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Kovtun O, Tomlinson ID, Bailey DM, Thal LB, Ross EJ, Harris L, Frankland MP, Ferguson RS, Glaser Z, Greer J, Rosenthal SJ. Single Quantum Dot Tracking Illuminates Neuroscience at the Nanoscale. Chem Phys Lett 2018; 706:741-752. [PMID: 30270931 PMCID: PMC6157616 DOI: 10.1016/j.cplett.2018.06.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The use of nanometer-sized semiconductor crystals, known as quantum dots, allows us to directly observe individual biomolecular transactions through a fluorescence microscope. Here, we review the evolution of single quantum dot tracking over the past two decades, highlight key biophysical discoveries facilitated by quantum dots, briefly discuss biochemical and optical implementation strategies for a single quantum dot tracking experiment, and report recent accomplishments of our group at the interface of molecular neuroscience and nanoscience.
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Affiliation(s)
- Oleg Kovtun
- Departments of Chemistry, Chemical Biology, Vanderbilt University
- Departments of Vanderbilt Institute of Nanoscale Science and Engineering
| | - Ian D. Tomlinson
- Departments of Chemistry, Chemical Biology, Vanderbilt University
- Departments of Vanderbilt Institute of Nanoscale Science and Engineering
| | - Danielle M. Bailey
- Departments of Chemistry, Chemical Biology, Vanderbilt University
- Departments of Pharmacology, Chemical Biology, Vanderbilt University
- Departments of Vanderbilt Institute of Nanoscale Science and Engineering
| | - Lucas B. Thal
- Departments of Chemistry, Chemical Biology, Vanderbilt University
- Departments of Vanderbilt Institute of Nanoscale Science and Engineering
- Departments of Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN
| | - Emily J. Ross
- Departments of Hudson Alpha Institute for Biotechnology, Huntsville, AL
| | - Lauren Harris
- Departments of Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN
| | | | | | - Zachary Glaser
- Departments of Chemistry, Chemical Biology, Vanderbilt University
| | - Jonathan Greer
- Departments of Chemistry, Chemical Biology, Vanderbilt University
| | - Sandra J. Rosenthal
- Departments of Chemistry, Chemical Biology, Vanderbilt University
- Departments of Pharmacology, Chemical Biology, Vanderbilt University
- Departments of Chemical and Biomolecular Engineering, Chemical Biology, Vanderbilt University
- Departments of Physics and Astronomy, Chemical Biology, Vanderbilt University
- Departments of Vanderbilt Institute of Nanoscale Science and Engineering
- Departments of Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN
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Li J, Johnson-Buck A, Yang YR, Shih WM, Yan H, Walter NG. Exploring the speed limit of toehold exchange with a cartwheeling DNA acrobat. NATURE NANOTECHNOLOGY 2018; 13:723-729. [PMID: 29736034 DOI: 10.1038/s41565-018-0130-2] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/29/2018] [Indexed: 05/26/2023]
Abstract
Dynamic DNA nanotechnology has yielded nontrivial autonomous behaviours such as stimulus-guided locomotion, computation and programmable molecular assembly. Despite these successes, DNA-based nanomachines suffer from slow kinetics, requiring several minutes or longer to carry out a handful of operations. Here, we pursue the speed limit of an important class of reactions in DNA nanotechnology-toehold exchange-through the single-molecule optimization of a novel class of DNA walker that undergoes cartwheeling movements over a field of complementary oligonucleotides. After optimizing this DNA 'acrobat' for rapid movement, we measure a stepping rate constant approaching 1 s-1, which is 10- to 100-fold faster than prior DNA walkers. Finally, we use single-particle tracking to demonstrate movement of the walker over hundreds of nanometres within 10 min, in quantitative agreement with predictions from stepping kinetics. These results suggest that substantial improvements in the operating rates of broad classes of DNA nanomachines utilizing strand displacement are possible.
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Affiliation(s)
- Jieming Li
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Yuhe Renee Yang
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - William M Shih
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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Banerjee S, Maurya S, Roy R. Single-molecule fluorescence imaging: Generating insights into molecular interactions in virology. J Biosci 2018; 43:519-540. [PMID: 30002270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-molecule fluorescence methods remain a challenging yet information-rich set of techniques that allow one to probe the dynamics, stoichiometry and conformation of biomolecules one molecule at a time. Viruses are small (nanometers) in size, can achieve cellular infections with a small number of virions and their lifecycle is inherently heterogeneous with a large number of structural and functional intermediates. Single-molecule measurements that reveal the complete distribution of properties rather than the average can hence reveal new insights into virus infections and biology that are inaccessible otherwise. This article highlights some of the methods and recent applications of single-molecule fluorescence in the field of virology. Here, we have focused on new findings in virus-cell interaction, virus cell entry and transport, viral membrane fusion, genome release, replication, translation, assembly, genome packaging, egress and interaction with host immune proteins that underline the advantage of single-molecule approach to the question at hand. Finally, we discuss the challenges, outlook and potential areas for improvement and future use of single-molecule fluorescence that could further aid our understanding of viruses.
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Affiliation(s)
- Sunaina Banerjee
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
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Single-molecule fluorescence imaging: Generating insights into molecular interactions in virology. J Biosci 2018. [DOI: 10.1007/s12038-018-9769-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Ray S, Widom JR, Walter NG. Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World. Chem Rev 2018; 118:4120-4155. [PMID: 29363314 PMCID: PMC5918467 DOI: 10.1021/acs.chemrev.7b00519] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The emergence of single-molecule (SM) fluorescence techniques has opened up a vast new toolbox for exploring the molecular basis of life. The ability to monitor individual biomolecules in real time enables complex, dynamic folding pathways to be interrogated without the averaging effect of ensemble measurements. In parallel, modern biology has been revolutionized by our emerging understanding of the many functions of RNA. In this comprehensive review, we survey SM fluorescence approaches and discuss how the application of these tools to RNA and RNA-containing macromolecular complexes in vitro has yielded significant insights into the underlying biology. Topics covered include the three-dimensional folding landscapes of a plethora of isolated RNA molecules, their assembly and interactions in RNA-protein complexes, and the relation of these properties to their biological functions. In all of these examples, the use of SM fluorescence methods has revealed critical information beyond the reach of ensemble averages.
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Affiliation(s)
| | | | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA
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Calebiro D, Sungkaworn T. Single-Molecule Imaging of GPCR Interactions. Trends Pharmacol Sci 2018; 39:109-122. [DOI: 10.1016/j.tips.2017.10.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/23/2017] [Accepted: 10/25/2017] [Indexed: 02/07/2023]
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Pandey V, Gupta S, Elangovan R. Compact 3D printed module for fluorescence and label-free imaging using evanescent excitation. Methods Appl Fluoresc 2017; 6:015007. [PMID: 29076809 DOI: 10.1088/2050-6120/aa967a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Total internal reflection fluorescence (TIRF) microscopy is widely used for selective excitation and high-resolution imaging of fluorophores, and more recently label-free nanosized objects, with high vertical confinement near a liquid-solid interface. Traditionally, high numerical aperture objectives (>1.4) are used to simultaneously generate evanescent waves and collect fluorescence emission signals which limits their use to small area imaging (<0.1 mm2). Objective-based TIRFs are also expensive as they require dichroic mirrors and efficient notch filters to prevent specular reflection within the objective lenses. We have developed a compact 3D module called cTIRF that can generate evanescent waves in microscope glass slides via a planar waveguide illumination. The module can be attached as a fixture to any existing optical microscope, converting it into a TIRF and enabling high signal-to-noise ratio (SNR) fluorescence imaging using any magnification objective. As the incidence optics is perpendicular to the detector, label-free evanescent scattering-based imaging of submicron objects can also be performed without using emission filters. SNR is significantly enhanced in this case as compared to cTIRF alone, as seen through our model experiments performed on latex beads and mammalian cells. Extreme flexibility and the low cost of our approach makes it scalable for limited resource settings.
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Affiliation(s)
- Vikas Pandey
- Department of Chemical Engineering, Indian Institute of Technology, Delhi, 110016, India
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