1
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Lu W, Zhao X, Li M, Li Y, Zhang C, Xiong Y, Li J, Zhou H, Ye X, Li X, Wang J, Liang X, Qing G. Precise Structural Analysis of Neutral Glycans Using Aerolysin Mutant T240R Nanopore. ACS NANO 2024; 18:12412-12426. [PMID: 38693619 DOI: 10.1021/acsnano.4c01571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Glycans play vital roles in nearly all life processes of multicellular organisms, and understanding these activities is inseparable from elucidating the biological significance of glycans. However, glycan research has lagged behind that of DNA and protein due to the challenges posed by structural heterogeneity and isomerism (i.e., structures with equal molecular weights) the lack of high-efficiency structural analysis techniques. Nanopore technology has emerged as a sensitive single-molecule biosensor, shining a light on glycan analysis. However, a significant number of glycans are small and uncharged, making it challenging to elicit identifiable nanopore signals. Here we introduce a R-binaphthyl tag into glycans, which enhances the cation-π interaction between the derivatized glycan molecules and the nanopore interface, enabling the detection of neutral glycans with an aerolysin nanopore. This approach allows for the distinction of di-, tri-, and tetrasaccharides with monosaccharide resolution and has the potential for group discrimination, the monitoring of enzymatic transglycosylation reactions. Notably, the aerolysin mutant T240R achieves unambiguous identification of six disaccharide isomers, trisaccharide and tetrasaccharide linkage isomers. Molecular docking simulations reveal that multiple noncovalent interactions occur between residues R282, K238, and R240 and the glycans and R-binaphthyl tag, significantly slowing down their translocation across the nanopore. Importantly, we provide a demonstration of the kinetic translocation process of neutral glycan isomers, establishing a solid theoretical foundation for glycan nanopore analysis. The development of our technology could promote the analysis of glycan structural isomers and has the potential for nanopore-based glycan structural determination and sequencing.
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Affiliation(s)
- Wenqi Lu
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xinjia Zhao
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Minmin Li
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yuting Li
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Chen Zhang
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Yuting Xiong
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Jiaqi Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Han Zhou
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Xianlong Ye
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Xiaonong Li
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Jing Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xinmiao Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Guangyan Qing
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
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2
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Ju H, Cheng L, Li M, Mei K, He S, Jia C, Guo X. Single-Molecule Electrical Profiling of Peptides and Proteins. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401877. [PMID: 38639403 DOI: 10.1002/advs.202401877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/03/2024] [Indexed: 04/20/2024]
Abstract
In recent decades, there has been a significant increase in the application of single-molecule electrical analysis platforms in studying proteins and peptides. These advanced analysis methods have the potential for deep investigation of enzymatic working mechanisms and accurate monitoring of dynamic changes in protein configurations, which are often challenging to achieve in ensemble measurements. In this work, the prominent research progress in peptide and protein-related studies are surveyed using electronic devices with single-molecule/single-event sensitivity, including single-molecule junctions, single-molecule field-effect transistors, and nanopores. In particular, the successful commercial application of nanopores in DNA sequencing has made it one of the most promising techniques in protein sequencing at the single-molecule level. From single peptides to protein complexes, the correlation between their electrical characteristics, structures, and biological functions is gradually being established. This enables to distinguish different molecular configurations of these biomacromolecules through real-time electrical monitoring of their life activities, significantly improving the understanding of the mechanisms underlying various life processes.
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Affiliation(s)
- Hongyu Ju
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Li Cheng
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Mengmeng Li
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Kunrong Mei
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Suhang He
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Chuancheng Jia
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Xuefeng Guo
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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3
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Shepherd JW, Guilbaud S, Zhou Z, Howard JAL, Burman M, Schaefer C, Kerrigan A, Steele-King C, Noy A, Leake MC. Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA. Nat Commun 2024; 15:2748. [PMID: 38553446 PMCID: PMC10980717 DOI: 10.1038/s41467-024-47126-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 03/21/2024] [Indexed: 04/02/2024] Open
Abstract
Biopolymer topology is critical for determining interactions inside cell environments, exemplified by DNA where its response to mechanical perturbation is as important as biochemical properties to its cellular roles. The dynamic structures of chiral biopolymers exhibit complex dependence with extension and torsion, however the physical mechanisms underpinning the emergence of structural motifs upon physiological twisting and stretching are poorly understood due to technological limitations in correlating force, torque and spatial localization information. We present COMBI-Tweez (Combined Optical and Magnetic BIomolecule TWEEZers), a transformative tool that overcomes these challenges by integrating optical trapping, time-resolved electromagnetic tweezers, and fluorescence microscopy, demonstrated on single DNA molecules, that can controllably form and visualise higher order structural motifs including plectonemes. This technology combined with cutting-edge MD simulations provides quantitative insight into complex dynamic structures relevant to DNA cellular processes and can be adapted to study a range of filamentous biopolymers.
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Affiliation(s)
- Jack W Shepherd
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
- Department of Biology, University of York, York, YO10 5DD, England
| | - Sebastien Guilbaud
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Zhaokun Zhou
- Guangdong Provincial Key Lab of Robotics and Intelligent System, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jamieson A L Howard
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Matthew Burman
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Charley Schaefer
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Adam Kerrigan
- The York-JEOL Nanocentre, University of York, York, YO10 5BR, England
| | - Clare Steele-King
- Bioscience Technology Facility, University of York, York, YO10 5DD, England
| | - Agnes Noy
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Mark C Leake
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England.
- Department of Biology, University of York, York, YO10 5DD, England.
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4
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Liu J, Zhao B, Zhang X, Guan D, Sun K, Zhang Y, Liu Q. Thiolation for Enhancing Photostability of Fluorophores at the Single-Molecule Level. Angew Chem Int Ed Engl 2024; 63:e202316192. [PMID: 37975636 DOI: 10.1002/anie.202316192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023]
Abstract
Fluorescent probes are essential for single-molecule imaging. However, their application in biological systems is often limited by the short photobleaching lifetime. To overcome this, we developed a novel thiolation strategy for squaraine dyes. By introducing thiolation of the central cyclobutene of squaraine (thio-squaraine), we observed a ≈5-fold increase in photobleaching lifetime. Our single-molecule data analysis attributes this improvement to improved photostability resulting from thiolation. Interestingly, bulk measurements show rapid oxidation of thio-squaraine to its oxo-analogue under irradiation, giving the perception of inferior photostability. This discrepancy between bulk and single-molecule environments can be ascribed to the factors in the latter, including larger intermolecular distances and restricted mobility, which reduce the interactions between a fluorophore and reactive oxygen species produced by other fluorophores, ultimately impacting photobleaching and photoconversion rate. We demonstrate the remarkable performance of thio-squaraine probes in various imaging buffers, such as glucose oxidase with catalase (GLOX) and GLOX+trolox. We successfully employed these photostable probes for single-molecule tracking of CD56 membrane protein and monitoring mitochondria movements in live neurons. CD56 tracking revealed distinct motion states and the corresponding protein fractions. This investigation is expected to propel the development of single-molecule imaging probes, particularly in scenarios where bulk measurements show suboptimal performance.
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Affiliation(s)
- Jinyang Liu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China
| | - Bingjie Zhao
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China
| | - Xuebo Zhang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China
| | - Daoming Guan
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China
| | - Kuangshi Sun
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China
| | - Yunxiang Zhang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China
| | - Qian Liu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China
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5
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Yang J, Kamai H, Wang Y, Xu Y. Nanofluidic Aptamer Nanoarray to Enable Stochastic Capture of Single Proteins at Normal Concentrations. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2301013. [PMID: 37350189 DOI: 10.1002/smll.202301013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 05/18/2023] [Indexed: 06/24/2023]
Abstract
Single-molecule experiments allow understanding of the diversity, stochasticity, and heterogeneity of molecular behaviors and properties hidden by conventional ensemble-averaged measurements. They hence have great importance and significant impacts in a wide range of fields. Despite significant advances in single-molecule experiments at ultralow concentrations, the capture of single molecules in solution at normal concentrations within natural biomolecular processes remains a formidable challenge. Here, a high-density, well-defined nanofluidic aptamer nanoarray (NANa) formed via site-specific self-assembly of well-designed aptamer molecules in nanochannels with nano-in-nano gold nanopatterns is presented. The nanofluidic aptamer nanoarray exhibits a high capability to specifically capture target proteins (e.g., platelet-derived growth factor BB; PDGF-BB) to form uniform protein nanoarrays under optimized nanofluidic conditions. Owing to these fundamental features, the nanofluidic aptamer nanoarray enables the stochastic capture of single PDGF-BB molecules at a normal concentration from a sample with an ultrasmall volume equivalent to a single cell by following Poisson statistics, forming a readily addressable single-protein nanoarray. This approach offers a methodology and device to surpass both the concentration and volume limits of single-protein capture in most conventional methodologies of single-molecule experiments, thus opening an avenue to explore the behavior of individual biomolecules in a manner close to their natural forms, which remains largely unexplored to date.
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Affiliation(s)
- Jinbin Yang
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8570, Japan
| | - Hiroki Kamai
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8570, Japan
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, 26 CBEB, University Park, PA, 16802-6804, USA
| | - Yan Xu
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8570, Japan
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Metropolitan University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8570, Japan
- Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
- Japan Science and Technology Agency (JST), CREST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
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6
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Squires AH. Electrokinetic manipulation of a nanowire. NATURE NANOTECHNOLOGY 2023; 18:1128-1129. [PMID: 37500781 DOI: 10.1038/s41565-023-01459-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Affiliation(s)
- Allison H Squires
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA.
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7
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Kümmerlin M, Mazumder A, Kapanidis AN. Bleaching-resistant, Near-continuous Single-molecule Fluorescence and FRET Based on Fluorogenic and Transient DNA Binding. Chemphyschem 2023; 24:e202300175. [PMID: 37043705 PMCID: PMC10946581 DOI: 10.1002/cphc.202300175] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/16/2023] [Indexed: 04/14/2023]
Abstract
Photobleaching of fluorescent probes limits the observation span of typical single-molecule fluorescence measurements and hinders observation of dynamics at long timescales. Here, we present a general strategy to circumvent photobleaching by replenishing fluorescent probes via transient binding of fluorogenic DNAs to complementary DNA strands attached to a target molecule. Our strategy allows observation of near-continuous single-molecule fluorescence for more than an hour, a timescale two orders of magnitude longer than the typical photobleaching time of single fluorophores under our conditions. Using two orthogonal sequences, we show that our method is adaptable to Förster Resonance Energy Transfer (FRET) and that can be used to study the conformational dynamics of dynamic structures, such as DNA Holliday junctions, for extended periods. By adjusting the temporal resolution and observation span, our approach enables capturing the conformational dynamics of proteins and nucleic acids over a wide range of timescales.
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Affiliation(s)
- Mirjam Kümmerlin
- Department of PhysicsUniversity of OxfordOxfordOX1 3PUUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordDorothy Crowfoot Hodgkin BuildingOxfordOX1 3QUUK
| | - Abhishek Mazumder
- Department of PhysicsUniversity of OxfordOxfordOX1 3PUUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordDorothy Crowfoot Hodgkin BuildingOxfordOX1 3QUUK
- Structural Biology and Bioinformatics DivisionCSIR-Indian Institute of Chemical Biology4, Raja S. C. Mullick RoadKolkata700 032India
| | - Achillefs N. Kapanidis
- Department of PhysicsUniversity of OxfordOxfordOX1 3PUUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordDorothy Crowfoot Hodgkin BuildingOxfordOX1 3QUUK
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8
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Islam F, Purkait D, Mishra PP. Insights into the Dynamics and Helicase Activity of RecD2 of Deinococcus radiodurans during DNA Repair: A Single-Molecule Perspective. J Phys Chem B 2023; 127:4351-4363. [PMID: 37163679 DOI: 10.1021/acs.jpcb.3c00778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
While the double helix is the most stable conformation of DNA inside cells, its transient unwinding and subsequent partial separation of the two complementary strands yields an intermediate single-stranded DNA (ssDNA). The ssDNA is involved in all major DNA transactions such as replication, transcription, recombination, and repair. The process of DNA unwinding and translocation is shouldered by helicases that transduce the chemical energy derived from nucleotide triphosphate (NTP) hydrolysis to mechanical energy and utilize it to destabilize hydrogen bonds between complementary base pairs. Consequently, a comprehensive understanding of the molecular mechanisms of these enzymes is essential. In the last few decades, a combination of single-molecule techniques (force-based manipulation and visualization) have been employed to study helicase action. These approaches have allowed researchers to study the single helicase-DNA complex in real-time and the free energy landscape of their interaction together with the detection of conformational intermediates and molecular heterogeneity during the course of helicase action. Furthermore, the unique ability of these techniques to resolve helicase motion at nanometer and millisecond spatial and temporal resolutions, respectively, provided surprising insights into their mechanism of action. This perspective outlines the contribution of single-molecule methods in deciphering molecular details of helicase activities. It also exemplifies how each technique was or can be used to study the helicase action of RecD2 in recombination DNA repair.
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Affiliation(s)
- Farhana Islam
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
| | - Debayan Purkait
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
| | - Padmaja Prasad Mishra
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
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9
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Kitta K, Sakamoto M, Hayakawa K, Nukazuka A, Kano K, Yamamoto T. Nanopore Impedance Spectroscopy Reveals Electrical Properties of Single Nanoparticles for Detecting and Identifying Pathogenic Viruses. ACS OMEGA 2023; 8:14684-14693. [PMID: 37125101 PMCID: PMC10134219 DOI: 10.1021/acsomega.3c00628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
In the conventional nanopore method, direct current (DC) is used to study molecules and nanoparticles; however, it cannot easily discriminate between materials with similarly sized particles. Herein, we developed an alternating current (AC)-based nanopore method to measure the impedance of a single nanoparticle and distinguish between particles of the same size based on their material characteristics. We demonstrated the performance of this method using impedance measurements to determine the size and frequency characteristics of various particles, ranging in diameter from 200 nm to 1 μm. Furthermore, the alternating current method exhibited high accuracy for biosensing applications, identifying viruses with over 85% accuracy using single-particle measurement and machine learning. Therefore, this novel nanopore method is useful for applications in materials science, biology, and medicine.
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Affiliation(s)
- Kazuki Kitta
- Mechanical
Engineering, Tokyo Institute of Technology, Ishikawadai 1-314, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Maami Sakamoto
- Mechanical
Engineering, Tokyo Institute of Technology, Ishikawadai 1-314, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Kei Hayakawa
- Material
Research and Innovation Division, DENSO
CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Akira Nukazuka
- Material
Research and Innovation Division, DENSO
CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Kazuhiko Kano
- Material
Research and Innovation Division, DENSO
CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Takatoki Yamamoto
- Mechanical
Engineering, Tokyo Institute of Technology, Ishikawadai 1-314, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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10
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Choosing the Probe for Single-Molecule Fluorescence Microscopy. Int J Mol Sci 2022; 23:ijms232314949. [PMID: 36499276 PMCID: PMC9735909 DOI: 10.3390/ijms232314949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.
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11
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Artsimovitch I, Ramírez-Sarmiento CA. Metamorphic proteins under a computational microscope: Lessons from a fold-switching RfaH protein. Comput Struct Biotechnol J 2022; 20:5824-5837. [PMID: 36382197 PMCID: PMC9630627 DOI: 10.1016/j.csbj.2022.10.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/28/2022] Open
Abstract
Metamorphic proteins constitute unexpected paradigms of the protein folding problem, as their sequences encode two alternative folds, which reversibly interconvert within biologically relevant timescales to trigger different cellular responses. Once considered a rare aberration, metamorphism may be common among proteins that must respond to rapidly changing environments, exemplified by NusG-like proteins, the only transcription factors present in every domain of life. RfaH, a specialized paralog of bacterial NusG, undergoes an all-α to all-β domain switch to activate expression of virulence and conjugation genes in many animal and plant pathogens and is the quintessential example of a metamorphic protein. The dramatic nature of RfaH structural transformation and the richness of its evolutionary history makes for an excellent model for studying how metamorphic proteins switch folds. Here, we summarize the structural and functional evidence that sparked the discovery of RfaH as a metamorphic protein, the experimental and computational approaches that enabled the description of the molecular mechanism and refolding pathways of its structural interconversion, and the ongoing efforts to find signatures and general properties to ultimately describe the protein metamorphome.
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Affiliation(s)
- Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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12
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Li Y, Wong IY, Guo M. Reciprocity of Cell Mechanics with Extracellular Stimuli: Emerging Opportunities for Translational Medicine. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107305. [PMID: 35319155 PMCID: PMC9463119 DOI: 10.1002/smll.202107305] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Human cells encounter dynamic mechanical cues in healthy and diseased tissues, which regulate their molecular and biophysical phenotype, including intracellular mechanics as well as force generation. Recent developments in bio/nanomaterials and microfluidics permit exquisitely sensitive measurements of cell mechanics, as well as spatiotemporal control over external mechanical stimuli to regulate cell behavior. In this review, the mechanobiology of cells interacting bidirectionally with their surrounding microenvironment, and the potential relevance for translational medicine are considered. Key fundamental concepts underlying the mechanics of living cells as well as the extracelluar matrix are first introduced. Then the authors consider case studies based on 1) microfluidic measurements of nonadherent cell deformability, 2) cell migration on micro/nano-topographies, 3) traction measurements of cells in three-dimensional (3D) matrix, 4) mechanical programming of organoid morphogenesis, as well as 5) active mechanical stimuli for potential therapeutics. These examples highlight the promise of disease diagnosis using mechanical measurements, a systems-level understanding linking molecular with biophysical phenotype, as well as therapies based on mechanical perturbations. This review concludes with a critical discussion of these emerging technologies and future directions at the interface of engineering, biology, and medicine.
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Affiliation(s)
- Yiwei Li
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, Hubei, 430074, China
| | - Ian Y Wong
- School of Engineering, Center for Biomedical Engineering, Joint Program in Cancer Biology, Brown University, 184 Hope St Box D, Providence, RI, 02912, USA
| | - Ming Guo
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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13
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Kausar F, Rasheed T, Tuoqeer Anwar M, Ali J. Revisiting the Role of Sulfur based Compounds in monitoring of Various analytes through spectroscopical investigations. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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14
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Strobl K, Selivanovitch E, Ibáñez-Freire P, Moreno-Madrid F, Schaap IAT, Delgado-Buscalioni R, Douglas T, de Pablo PJ. Electromechanical Photophysics of GFP Packed Inside Viral Protein Cages Probed by Force-Fluorescence Hybrid Single-Molecule Microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200059. [PMID: 35718881 PMCID: PMC9528512 DOI: 10.1002/smll.202200059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Packing biomolecules inside virus capsids has opened new avenues for the study of molecular function in confined environments. These systems not only mimic the highly crowded conditions in nature, but also allow their manipulation at the nanoscale for technological applications. Here, green fluorescent proteins are packed in virus-like particles derived from P22 bacteriophage procapsids. The authors explore individual virus cages to monitor their emission signal with total internal reflection fluorescence microscopy while simultaneously changing the microenvironment with the stylus of atomic force microscopy. The mechanical and electronic quenching can be decoupled by ≈10% each using insulator and conductive tips, respectively. While with conductive tips the fluorescence quenches and recovers regardless of the structural integrity of the capsid, with the insulator tips quenching only occurs if the green fluorescent proteins remain organized inside the capsid. The electronic quenching is associated with the coupling of the protein fluorescence emission with the tip surface plasmon resonance. In turn, the mechanical quenching is a consequence of the unfolding of the aggregated proteins during the mechanical disruption of the capsid.
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Affiliation(s)
- Klara Strobl
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | | | - Pablo Ibáñez-Freire
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Francisco Moreno-Madrid
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | | | - Rafael Delgado-Buscalioni
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, Madrid, 28049, Spain
- Institute of Condensed Matter Physics (IFIMAC), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Trevor Douglas
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Pedro J de Pablo
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, Madrid, 28049, Spain
- Institute of Condensed Matter Physics (IFIMAC), Universidad Autónoma de Madrid, Madrid, 28049, Spain
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15
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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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16
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Recent Advances in Fluorescence Recovery after Photobleaching for Decoupling Transport and Kinetics of Biomacromolecules in Cellular Physiology. Polymers (Basel) 2022; 14:polym14091913. [PMID: 35567083 PMCID: PMC9105003 DOI: 10.3390/polym14091913] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 12/16/2022] Open
Abstract
Among the new molecular tools available to scientists and engineers, some of the most useful include fluorescently tagged biomolecules. Tools, such as green fluorescence protein (GFP), have been applied to perform semi-quantitative studies on biological signal transduction and cellular structural dynamics involved in the physiology of healthy and disease states. Such studies focus on drug pharmacokinetics, receptor-mediated endocytosis, nuclear mechanobiology, viral infections, and cancer metastasis. In 1976, fluorescence recovery after photobleaching (FRAP), which involves the monitoring of fluorescence emission recovery within a photobleached spot, was developed. FRAP allowed investigators to probe two-dimensional (2D) diffusion of fluorescently-labelled biomolecules. Since then, FRAP has been refined through the advancements of optics, charged-coupled-device (CCD) cameras, confocal microscopes, and molecular probes. FRAP is now a highly quantitative tool used for transport and kinetic studies in the cytosol, organelles, and membrane of a cell. In this work, the authors intend to provide a review of recent advances in FRAP. The authors include epifluorescence spot FRAP, total internal reflection (TIR)/FRAP, and confocal microscope-based FRAP. The underlying mathematical models are also described. Finally, our understanding of coupled transport and kinetics as determined by FRAP will be discussed and the potential for future advances suggested.
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17
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Bell NAW, Molloy JE. Efficient golden gate assembly of DNA constructs for single molecule force spectroscopy and imaging. Nucleic Acids Res 2022; 50:e77. [PMID: 35489063 PMCID: PMC9303394 DOI: 10.1093/nar/gkac300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 03/18/2022] [Accepted: 04/13/2022] [Indexed: 01/01/2023] Open
Abstract
Single-molecule techniques such as optical tweezers and fluorescence imaging are powerful tools for probing the biophysics of DNA and DNA-protein interactions. The application of these methods requires efficient approaches for creating designed DNA structures with labels for binding to a surface or microscopic beads. In this paper, we develop a simple and fast technique for making a diverse range of such DNA constructs by combining PCR amplicons and synthetic oligonucleotides using golden gate assembly rules. We demonstrate high yield fabrication of torsionally-constrained duplex DNA up to 10 kbp in length and a variety of DNA hairpin structures. We also show how tethering to a cross-linked antibody substrate significantly enhances measurement lifetime under high force. This rapid and adaptable fabrication method streamlines the assembly of DNA constructs for single molecule biophysics.
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18
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Adhikari S, Orrit M. Progress and perspectives in single-molecule optical spectroscopy. J Chem Phys 2022; 156:160903. [PMID: 35489995 DOI: 10.1063/5.0087003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We review some of the progress of single-molecule optical experiments in the past 20 years and propose some perspectives for the coming years. We particularly focus on methodological advances in fluorescence, super-resolution, photothermal contrast, and interferometric scattering and briefly discuss a few of the applications. These advances have enabled the exploration of new emitters and quantum optics; the chemistry and biology of complex heterogeneous systems, nanoparticles, and plasmonics; and the detection and study of non-fluorescing and non-absorbing nano-objects. We conclude by proposing some ideas for future experiments. The field will move toward more and better signals of a broader variety of objects and toward a sharper view of the surprising complexity of the nanoscale world of single (bio-)molecules, nanoparticles, and their nano-environments.
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Affiliation(s)
- Subhasis Adhikari
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, P.O. Box 9504, 2333 CA Leiden, The Netherlands
| | - Michel Orrit
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, P.O. Box 9504, 2333 CA Leiden, The Netherlands
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19
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Volkán-Kacsó S, Marcus RA. F 1-ATPase Rotary Mechanism: Interpreting Results of Diverse Experimental Modes With an Elastic Coupling Theory. Front Microbiol 2022; 13:861855. [PMID: 35531282 PMCID: PMC9072658 DOI: 10.3389/fmicb.2022.861855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/28/2022] [Indexed: 11/19/2022] Open
Abstract
In this chapter, we review single-molecule observations of rotary motors, focusing on the general theme that their mechanical motion proceeds in substeps with each substep described by an angle-dependent rate constant. In the molecular machine F1-ATPase, the stepping rotation is described for individual steps by forward and back reaction rate constants, some of which depend strongly on the rotation angle. The rotation of a central shaft is typically monitored by an optical probe. We review our recent work on the theory for the angle-dependent rate constants built to treat a variety of single-molecule and ensemble experiments on the F1-ATPase, and relating the free energy of activation of a step to the standard free energy of reaction for that step. This theory, an elastic molecular transfer theory, provides a framework for a multistate model and includes the probe used in single-molecule imaging and magnetic manipulation experiments. Several examples of its application are the following: (a) treatment of the angle-dependent rate constants in stalling experiments, (b) use of the model to enhance the time resolution of the single-molecule imaging apparatus and to detect short-lived states with a microsecond lifetime, states hidden by the fluctuations of the imaging probe, (c) treatment of out-of-equilibrium "controlled rotation" experiments, (d) use of the model to predict, without adjustable parameters, the angle-dependent rate constants of nucleotide binding and release, using data from other experiments, and (e) insights obtained from correlation of kinetic and cryo-EM structural data. It is also noted that in the case where the release of ADP would be a bottleneck process, the binding of ATP to another site acts to accelerate the release by 5-6 orders of magnitude. The relation of the present set of studies to previous and current theoretical work in the field is described. An overall goal is to gain mechanistic insight into the biological function in relation to structure.
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Affiliation(s)
- Sándor Volkán-Kacsó
- Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA, United States
- Segerstrom Science Center, Azusa Pacific University, Azusa, CA, United States
| | - Rudolph A. Marcus
- Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA, United States
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20
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Chauhan N, Saxena K, Jain U. Single molecule detection; from microscopy to sensors. Int J Biol Macromol 2022; 209:1389-1401. [PMID: 35413320 DOI: 10.1016/j.ijbiomac.2022.04.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 01/31/2023]
Abstract
Single molecule detection is necessary to find out physical, chemical properties and their mechanism involved in the normal functioning of body cells. In this way, they can provide a new direction to the healthcare system. Various techniques have been developed and employed for their successful detection. Herein, we have emphasized various traditional methods as well as biosensing technology which offer single molecule sensitivity. The various methods including plasmonic resonance, nanopores, whispering gallery mode, Simoa assay and recognition tunneling are discussed in the initial part which has been followed by a discussion about biosensor-based detection. Plasmonic, SERS, CRISPR/Cas, and other types of biosensors are focused in this review and found to be highly sensitive for single molecule detection. This review provides an overview of progression in different techniques employed for single molecule detection.
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Affiliation(s)
- Nidhi Chauhan
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Noida 201313, U.P., India
| | - Kirti Saxena
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Noida 201313, U.P., India
| | - Utkarsh Jain
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Noida 201313, U.P., India.
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21
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Huang SH, Huang BC, Chao L. Development of Cell Membrane Electrophoresis to Measure the Diffusivity of a Native Transmembrane Protein. Anal Chem 2022; 94:4531-4537. [PMID: 35230091 DOI: 10.1021/acs.analchem.2c00211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The lateral diffusion of transmembrane proteins in cell membranes is an important process that controls the dynamics and functions of the cell membrane. Several fluorescence-based techniques have been developed to study the diffusivities of transmembrane proteins. However, it is challenging to measure the diffusivity of a transmembrane protein with slow diffusion because of the photobleaching effect caused by long exposure times or multiple exposures to light. In this study, we developed a cell membrane electrophoresis platform to measure diffusivity. We deposited cell membrane vesicles derived from HeLa cells to form supported cell membrane patches. We demonstrated that the electrophoresis platform can be used to drive the movement of not only a lipid probe but also a native transmembrane protein, GLUT1. The movements were halted by the boundaries of the membrane patches and the concentration profiles reached steady states when the diffusion mass flux was balanced with the electrical mass flux. We used the Nernst-Planck equation as the mass balance equation to describe the steady concentration profiles and fitted these equations to our data to obtain the diffusivities. The obtained diffusivities were comparable to those obtained by fluorescence recovery after photobleaching, suggesting the validity of this new method of diffusivity measurement. Only a single snapshot is required for the diffusivity measurement, addressing the problems associated with photobleaching and allowing researchers to measure the diffusivity of transmembrane proteins with slow diffusion.
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Affiliation(s)
- Sin-Han Huang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Bo-Chuan Huang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Ling Chao
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
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22
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Shaheen C, Hastie C, Metera K, Scott S, Zhang Z, Chen S, Gu G, Weber L, Munsky B, Kouzine F, Levens D, Benham C, Leslie S. Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation. Nucleic Acids Res 2022; 50:2754-2764. [PMID: 35188541 PMCID: PMC8934633 DOI: 10.1093/nar/gkac101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 12/12/2022] Open
Abstract
Many cellular processes occur out of equilibrium. This includes site-specific unwinding in supercoiled DNA, which may play an important role in gene regulation. Here, we use the Convex Lens-induced Confinement (CLiC) single-molecule microscopy platform to study these processes with high-throughput and without artificial constraints on molecular structures or interactions. We use two model DNA plasmid systems, pFLIP-FUSE and pUC19, to study the dynamics of supercoiling-induced secondary structural transitions after perturbations away from equilibrium. We find that structural transitions can be slow, leading to long-lived structural states whose kinetics depend on the duration and direction of perturbation. Our findings highlight the importance of out-of-equilibrium studies when characterizing the complex structural dynamics of DNA and understanding the mechanisms of gene regulation.
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Affiliation(s)
- Cynthia Shaheen
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Michael Smith Laboratories, University of British Columbia, BC V6T 1Z4, Canada
- Department of Physics and Astronomy, University of British Columbia, BC V6T 1Z1, Canada
| | - Cameron Hastie
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Michael Smith Laboratories, University of British Columbia, BC V6T 1Z4, Canada
- Department of Physics and Astronomy, University of British Columbia, BC V6T 1Z1, Canada
| | - Kimberly Metera
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Shane Scott
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Institute of Materials Science, Kiel University, 24142 Kiel, Germany
| | - Zhi Zhang
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Sitong Chen
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Gracia Gu
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Lisa Weber
- Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Brian Munsky
- Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Fedor Kouzine
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - David Levens
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Craig Benham
- Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Sabrina Leslie
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Michael Smith Laboratories, University of British Columbia, BC V6T 1Z4, Canada
- Department of Physics and Astronomy, University of British Columbia, BC V6T 1Z1, Canada
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23
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Lim W, Randisi F, Doye JPK, Louis AA. The interplay of supercoiling and thymine dimers in DNA. Nucleic Acids Res 2022; 50:2480-2492. [PMID: 35188542 PMCID: PMC8934635 DOI: 10.1093/nar/gkac082] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/21/2022] [Accepted: 02/04/2022] [Indexed: 11/16/2022] Open
Abstract
Thymine dimers are a major mutagenic photoproduct induced by UV radiation. While they have been the subject of extensive theoretical and experimental investigations, questions of how DNA supercoiling affects local defect properties, or, conversely, how the presence of such defects changes global supercoiled structure, are largely unexplored. Here, we introduce a model of thymine dimers in the oxDNA forcefield, parametrized by comparison to melting experiments and structural measurements of the thymine dimer induced bend angle. We performed extensive molecular dynamics simulations of double-stranded DNA as a function of external twist and force. Compared to undamaged DNA, the presence of a thymine dimer lowers the supercoiling densities at which plectonemes and bubbles occur. For biologically relevant supercoiling densities and forces, thymine dimers can preferentially segregate to the tips of the plectonemes, where they enhance the probability of a localized tip-bubble. This mechanism increases the probability of highly bent and denatured states at the thymine dimer site, which may facilitate repair enzyme binding. Thymine dimer-induced tip-bubbles also pin plectonemes, which may help repair enzymes to locate damage. We hypothesize that the interplay of supercoiling and local defects plays an important role for a wider set of DNA damage repair systems.
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Affiliation(s)
- Wilber Lim
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Ferdinando Randisi
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
- FabricNano Limited, 192 Drummond St, London NW1 3HP, UK
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
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24
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Chandra S, Gunasinghe Pattiya Arachchillage KG, Kliuchnikov E, Maksudov F, Ayoub S, Barsegov V, Artés Vivancos JM. Single-molecule conductance of double-stranded RNA oligonucleotides. NANOSCALE 2022; 14:2572-2577. [PMID: 35107112 DOI: 10.1039/d1nr06925j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
RNA oligonucleotides are crucial for a range of biological functions and in many biotechnological applications. Herein, we measured, for the first time, the conductance of individual double-stranded (ds)RNA molecules and compared it with the conductance of single DNA : RNA hybrids. The average conductance values are similar for both biomolecules, but the distribution of conductance values shows an order of magnitude higher variability for dsRNA, indicating higher molecular flexibility of dsRNA. Microsecond Molecular Dynamics simulations explain this difference and provide structural insights into the higher stability of DNA : RNA duplex with atomic level of detail. The rotations of 2'-OH groups of the ribose rings and the bases in RNA strands destabilize the duplex structure by weakening base stacking interactions, affecting charge transport, and making single-molecule conductance of dsRNA more variable (dynamic disorder). The results demonstrate that a powerful combination of state-of-the-art biomolecular electronics techniques and computational approaches can provide valuable insights into biomolecules' biophysics with unprecedented spatial resolution.
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Affiliation(s)
- Subrata Chandra
- Department of Chemistry, University of Massachusetts, Lowell, 01854 MA, USA.
| | | | - Evgenii Kliuchnikov
- Department of Chemistry, University of Massachusetts, Lowell, 01854 MA, USA.
| | - Farkhad Maksudov
- Department of Chemistry, University of Massachusetts, Lowell, 01854 MA, USA.
| | - Steven Ayoub
- Department of Chemistry, University of Massachusetts, Lowell, 01854 MA, USA.
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, 01854 MA, USA.
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25
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Rico-Pasto M, Alemany A, Ritort F. Force-Dependent Folding Kinetics of Single Molecules with Multiple Intermediates and Pathways. J Phys Chem Lett 2022; 13:1025-1032. [PMID: 35072478 PMCID: PMC9882750 DOI: 10.1021/acs.jpclett.1c03521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply the Kramers kinetic diffusive model to derive the force-dependent kinetic rates of intermediate states from nonequilibrium pulling experiments. From the kinetic rates, we also extract the force-dependent kinetic barriers and the equilibrium folding energies. We apply our method to DNA hairpins with multiple folding pathways and intermediates. The experimental results agree with theoretical predictions. Furthermore, the proposed nonequilibrium single-molecule approach permits us to characterize kinetic and thermodynamic properties of native, unfolded, and intermediate states that cannot be derived from equilibrium hopping experiments.
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Affiliation(s)
- Marc Rico-Pasto
- Small
Biosystems Lab, Condensed Matter Physics Department, University of Barcelona, C/Martí i Franqués 1, Barcelona, 08028, Spain
| | - Anna Alemany
- Department
of Anatomy and Embryology, Leiden University
Medical Center, Leiden, 2333ZC, The Netherlands
| | - Felix Ritort
- Small
Biosystems Lab, Condensed Matter Physics Department, University of Barcelona, C/Martí i Franqués 1, Barcelona, 08028, Spain
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26
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Nemashkalo A, Phipps ME, Hennelly SP, Goodwin PM. Real-time, single-molecule observation of biomolecular interactions inside nanophotonic zero mode waveguides. NANOTECHNOLOGY 2022; 33:165101. [PMID: 34959227 DOI: 10.1088/1361-6528/ac467c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
Living cells rely on numerous protein-protein, RNA-protein and DNA-protein interactions for processes such as gene expression, biomolecular assembly, protein and RNA degradation. Single-molecule microscopy and spectroscopy are ideal tools for real-time observation and quantification of nucleic acids-protein and protein-protein interactions. One of the major drawbacks of conventional single-molecule imaging methods is low throughput. Methods such as sequencing by synthesis utilizing nanofabrication and single-molecule spectroscopy have brought high throughput into the realm of single-molecule biology. The Pacific Biosciences RS2 sequencer utilizes sequencing by synthesis within nanophotonic zero mode waveguides. A number of years ago this instrument was unlocked by Pacific Biosciences for custom use by researchers allowing them to monitor biological interactions at the single-molecule level with high throughput. In this capability letter we demonstrate the use of the RS2 sequencer for real-time observation of DNA-to-RNA transcription and RNA-protein interactions. We use a relatively complex model-transcription of structured ribosomal RNA fromE. coliand interactions of ribosomal RNA with ribosomal proteins. We also show evidence of observation of transcriptional pausing without the application of an external force (as is required for single-molecule pausing studies using optical traps). Overall, in the unlocked, custom mode, the RS2 sequencer can be used to address a wide variety of biological assembly and interaction questions at the single-molecule level with high throughput. This instrument is available for use at the Center for Integrated Nanotechnologies Gateway located at Los Alamos National Laboratory.
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Affiliation(s)
- A Nemashkalo
- MPA-CINT (Materials Physics and Applications, Center for Integrated Nanotechnologies, Los Alamos National Laboratory), United States of America
| | - M E Phipps
- MPA-CINT (Materials Physics and Applications, Center for Integrated Nanotechnologies, Los Alamos National Laboratory), United States of America
| | - S P Hennelly
- B-11 (Bioenergy and Biome Sciences, Los Alamos National Laboratory), United States of America
| | - P M Goodwin
- MPA-CINT (Materials Physics and Applications, Center for Integrated Nanotechnologies, Los Alamos National Laboratory), United States of America
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Blanc T, Verdier H, Regnier L, Planchon G, Guérinot C, El Beheiry M, Masson JB, Hajj B. Towards Human in the Loop Analysis of Complex Point Clouds: Advanced Visualizations, Quantifications, and Communication Features in Virtual Reality. FRONTIERS IN BIOINFORMATICS 2022; 1:775379. [PMID: 36303735 PMCID: PMC9580855 DOI: 10.3389/fbinf.2021.775379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
Multiple fields in biological and medical research produce large amounts of point cloud data with high dimensionality and complexity. In addition, a large set of experiments generate point clouds, including segmented medical data or single-molecule localization microscopy. In the latter, individual molecules are observed within their natural cellular environment. Analyzing this type of experimental data is a complex task and presents unique challenges, where providing extra physical dimensions for visualization and analysis could be beneficial. Furthermore, whether highly noisy data comes from single-molecule recordings or segmented medical data, the necessity to guide analysis with user intervention creates both an ergonomic challenge to facilitate this interaction and a computational challenge to provide fluid interactions as information is being processed. Several applications, including our software DIVA for image stack and our platform Genuage for point clouds, have leveraged Virtual Reality (VR) to visualize and interact with data in 3D. While the visualization aspects can be made compatible with different types of data, quantifications, on the other hand, are far from being standard. In addition, complex analysis can require significant computational resources, making the real-time VR experience uncomfortable. Moreover, visualization software is mainly designed to represent a set of data points but lacks flexibility in manipulating and analyzing the data. This paper introduces new libraries to enhance the interaction and human-in-the-loop analysis of point cloud data in virtual reality and integrate them into the open-source platform Genuage. We first detail a new toolbox of communication tools that enhance user experience and improve flexibility. Then, we introduce a mapping toolbox allowing the representation of physical properties in space overlaid on a 3D mesh while maintaining a point cloud dedicated shader. We introduce later a new and programmable video capture tool in VR and desktop modes for intuitive data dissemination. Finally, we highlight the protocols that allow simultaneous analysis and fluid manipulation of data with a high refresh rate. We illustrate this principle by performing real-time inference of random walk properties of recorded trajectories with a pre-trained Graph Neural Network running in Python.
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Affiliation(s)
- Thomas Blanc
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Paris, France
| | - Hippolyte Verdier
- Decision and Bayesian Computation, CNRS USR 3756, Department of Computational Biology and Neuroscience, CNRS UMR 3571, Université de Paris, Institut Pasteur, Université de Paris, Paris, France
| | - Louise Regnier
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Paris, France
| | - Guillaume Planchon
- Decision and Bayesian Computation, CNRS USR 3756, Department of Computational Biology and Neuroscience, CNRS UMR 3571, Université de Paris, Institut Pasteur, Université de Paris, Paris, France
| | - Corentin Guérinot
- Decision and Bayesian Computation, CNRS USR 3756, Department of Computational Biology and Neuroscience, CNRS UMR 3571, Université de Paris, Institut Pasteur, Université de Paris, Paris, France
- Sorbonne Universités, Collège Doctoral, Paris, France
| | - Mohamed El Beheiry
- Decision and Bayesian Computation, CNRS USR 3756, Department of Computational Biology and Neuroscience, CNRS UMR 3571, Université de Paris, Institut Pasteur, Université de Paris, Paris, France
| | - Jean-Baptiste Masson
- Decision and Bayesian Computation, CNRS USR 3756, Department of Computational Biology and Neuroscience, CNRS UMR 3571, Université de Paris, Institut Pasteur, Université de Paris, Paris, France
- *Correspondence: Jean-Baptiste Masson, ; Bassam Hajj,
| | - Bassam Hajj
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Paris, France
- *Correspondence: Jean-Baptiste Masson, ; Bassam Hajj,
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Aicart-Ramos C, Hormeno S, Wilkinson OJ, Dillingham MS, Moreno-Herrero F. Long DNA constructs to study helicases and nucleic acid translocases using optical tweezers. Methods Enzymol 2022; 673:311-358. [DOI: 10.1016/bs.mie.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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29
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Shepherd JW, Leake MC. The End Restraint Method for Mechanically Perturbing Nucleic Acids In Silico. Methods Mol Biol 2022; 2476:249-262. [PMID: 35635708 DOI: 10.1007/978-1-0716-2221-6_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Far from being a passive information store, the genome is a mechanically dynamic and diverse system in which torsion and tension fluctuate and combine to determine structure and help regulate gene expression. Much of this mechanical perturbation is due to molecular machines such as topoisomerases which must stretch and twist DNA as part of various functions including DNA repair and replication. While the broad-scale mechanical response of nucleic acids to tension and torsion is well characterized, detail at the single base pair level is beyond the limits of even super-resolution imaging. Here, we present a straightforward, flexible, and extensible umbrella-sampling protocol to twist and stretch nucleic acids in silico using the popular biomolecular simulation package Amber-though the principles we describe are applicable also to other packages such as GROMACS. We discuss how to set up the simulation system, decide force fields and solvation models, and equilibrate. We then introduce the torsionally constrained stretching protocol, and finally we present some analysis techniques we have used to characterize structural motif formation. Rather than defining forces or fictional pseudoatoms, we instead define a fixed translation of specified atoms between each umbrella-sampling step, which allows comparison with experiment without needing to estimate applied forces by simply using the fractional end-to-end displacement as a comparison metric. We hope that this easy-to-implement solution will be valuable for interrogating optical and magnetic tweezers data on nucleic acids at base pair resolution.
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Affiliation(s)
| | - Mark C Leake
- Departments of Physics and Biology, University of York, York, UK
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30
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Vermeer B, Schmid S. Can DyeCycling break the photobleaching limit in single-molecule FRET? NANO RESEARCH 2022; 15:9818-9830. [PMID: 35582137 PMCID: PMC9101981 DOI: 10.1007/s12274-022-4420-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 05/03/2023]
Abstract
UNLABELLED Biomolecular systems, such as proteins, crucially rely on dynamic processes at the nanoscale. Detecting biomolecular nanodynamics is therefore key to obtaining a mechanistic understanding of the energies and molecular driving forces that control biomolecular systems. Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique to observe in real-time how a single biomolecule proceeds through its functional cycle involving a sequence of distinct structural states. Currently, this technique is fundamentally limited by irreversible photobleaching, causing the untimely end of the experiment and thus, a narrow temporal bandwidth of ≤ 3 orders of magnitude. Here, we introduce "DyeCycling", a measurement scheme with which we aim to break the photobleaching limit in smFRET. We introduce the concept of spontaneous dye replacement by simulations, and as an experimental proof-of-concept, we demonstrate the intermittent observation of a single biomolecule for one hour with a time resolution of milliseconds. Theoretically, DyeCycling can provide > 100-fold more information per single molecule than conventional smFRET. We discuss the experimental implementation of DyeCycling, its current and fundamental limitations, and specific biological use cases. Given its general simplicity and versatility, DyeCycling has the potential to revolutionize the field of time-resolved smFRET, where it may serve to unravel a wealth of biomolecular dynamics by bridging from milliseconds to the hour range. ELECTRONIC SUPPLEMENTARY MATERIAL Supplementary material is available for this article at 10.1007/s12274-022-4420-5 and is accessible for authorized users.
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Affiliation(s)
- Benjamin Vermeer
- NanoDynamicsLab, Laboratory of Biophysics, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Sonja Schmid
- NanoDynamicsLab, Laboratory of Biophysics, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
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31
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Pan J, Kmieciak T, Liu YT, Wildenradt M, Chen YS, Zhao Y. Quantifying molecular- to cellular-level forces in living cells. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2021; 54:483001. [PMID: 34866655 PMCID: PMC8635116 DOI: 10.1088/1361-6463/ac2170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mechanical cues have been suggested to play an important role in cell functions and cell fate determination, however, such physical quantities are challenging to directly measure in living cells with single molecule sensitivity and resolution. In this review, we focus on two main technologies that are promising in probing forces at the single molecule level. We review their theoretical fundamentals, recent technical advancements, and future directions, tailored specifically for interrogating mechanosensitive molecules in live cells.
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Affiliation(s)
- Jason Pan
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Tommy Kmieciak
- Department of Engineering Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Yen-Ting Liu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Matthew Wildenradt
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Yun-Sheng Chen
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Yang Zhao
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, 208 N. Wright Street, Urbana, IL 61801, United States of America
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32
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Zuckerman DM, Russo JD. A gentle introduction to the non-equilibrium physics of trajectories: Theory, algorithms, and biomolecular applications. AMERICAN JOURNAL OF PHYSICS 2021; 89:1048-1061. [PMID: 35530173 PMCID: PMC9075726 DOI: 10.1119/10.0005603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/25/2021] [Indexed: 06/14/2023]
Abstract
Despite the importance of non-equilibrium statistical mechanics in modern physics and related fields, the topic is often omitted from undergraduate and core-graduate curricula. Key aspects of non-equilibrium physics, however, can be understood with a minimum of formalism based on a rigorous trajectory picture. The fundamental object is the ensemble of trajectories, a set of independent time-evolving systems, which easily can be visualized or simulated (e.g., for protein folding) and which can be analyzed rigorously in analogy to an ensemble of static system configurations. The trajectory picture provides a straightforward basis for understanding first-passage times, "mechanisms" in complex systems, and fundamental constraints on the apparent reversibility of complex processes. Trajectories make concrete the physics underlying the diffusion and Fokker-Planck partial differential equations. Last but not least, trajectory ensembles underpin some of the most important algorithms that have provided significant advances in biomolecular studies of protein conformational and binding processes.
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33
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Bocanegra R, Plaza G A I, Ibarra B. In vitro single-molecule manipulation studies of viral DNA replication. Enzymes 2021; 49:115-148. [PMID: 34696830 DOI: 10.1016/bs.enz.2021.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Faithfull replication of genomic information relies on the coordinated activity of the multi-protein machinery known as the replisome. Several constituents of the replisome operate as molecular motors that couple thermal and chemical energy to a mechanical task. Over the last few decades, in vitro single-molecule manipulation techniques have been used to monitor and manipulate mechanically the activities of individual molecular motors involved in DNA replication with nanometer, millisecond, and picoNewton resolutions. These studies have uncovered the real-time kinetics of operation of these biological systems, the nature of their transient intermediates, and the processes by which they convert energy to work (mechano-chemistry), ultimately providing new insights into their inner workings of operation not accessible by ensemble assays. In this chapter, we describe two of the most widely used single-molecule manipulation techniques for the study of DNA replication, optical and magnetic tweezers, and their application in the study of the activities of proteins involved in viral DNA replication.
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Affiliation(s)
- Rebeca Bocanegra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain
| | - Ismael Plaza G A
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain.
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34
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Abstract
This paper provides a perspective on potential applications of a new single-molecule technique, viz., the nanopore electro-osmotic trap (NEOtrap). This solid-state nanopore-based method uses locally induced electro-osmosis to form a hydrodynamic trap for single molecules. Ionic current recordings allow one to study an unlabeled protein or nanoparticle of arbitrary charge that can be held in the nanopore's most sensitive region for very long times. After motivating the need for improved single-molecule technologies, we sketch various possible technical extensions and combinations of the NEOtrap. We lay out diverse applications in biosensing, enzymology, protein folding, protein dynamics, fingerprinting of proteins, detecting post-translational modifications, and all that at the level of single proteins - illustrating the unique versatility and potential of the NEOtrap.
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Affiliation(s)
- Sonja Schmid
- Nanodynamics Lab, Laboratory of Biophysics, Wageningen University, Stippeneng 4, 6708WE Wageningen, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
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35
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Unsupervised selection of optimal single-molecule time series idealization criterion. Biophys J 2021; 120:4472-4483. [PMID: 34487708 PMCID: PMC8553667 DOI: 10.1016/j.bpj.2021.08.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/22/2021] [Accepted: 08/31/2021] [Indexed: 11/30/2022] Open
Abstract
Single-molecule (SM) approaches have provided valuable mechanistic information on many biophysical systems. As technological advances lead to ever-larger data sets, tools for rapid analysis and identification of molecules exhibiting the behavior of interest are increasingly important. In many cases the underlying mechanism is unknown, making unsupervised techniques desirable. The divisive segmentation and clustering (DISC) algorithm is one such unsupervised method that idealizes noisy SM time series much faster than computationally intensive approaches without sacrificing accuracy. However, DISC relies on a user-selected objective criterion (OC) to guide its estimation of the ideal time series. Here, we explore how different OCs affect DISC’s performance for data typical of SM fluorescence imaging experiments. We find that OCs differing in their penalty for model complexity each optimize DISC’s performance for time series with different properties such as signal/noise and number of sample points. Using a machine learning approach, we generate a decision boundary that allows unsupervised selection of OCs based on the input time series to maximize performance for different types of data. This is particularly relevant for SM fluorescence data sets, which often have signal/noise near the derived decision boundary and include time series of nonuniform length because of stochastic bleaching. Our approach, AutoDISC, allows unsupervised per-molecule optimization of DISC, which will substantially assist in the rapid analysis of high-throughput SM data sets with noisy samples and nonuniform time windows.
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36
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Chen X, Liu T, Qin X, Nguyen QQ, Lee SK, Lee C, Ren Y, Chu J, Zhu G, Yoon TY, Park CY, Park H. Simultaneous Real-Time Three-Dimensional Localization and FRET Measurement of Two Distinct Particles. NANO LETTERS 2021; 21:7479-7485. [PMID: 34491760 DOI: 10.1021/acs.nanolett.1c01328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Many biological processes employ mechanisms involving the locations and interactions of multiple components. Given that most biological processes occur in three dimensions, the simultaneous measurement of three-dimensional locations and interactions is necessary. However, the simultaneous three-dimensional precise localization and measurement of interactions in real time remains challenging. Here, we report a new microscopy technique to localize two spectrally distinct particles in three dimensions with an accuracy (2.35σ) of tens of nanometers with an exposure time of 100 ms and to measure their real-time interactions using fluorescence resonance energy transfer (FRET) simultaneously. Using this microscope, we tracked two distinct vesicles containing t-SNAREs or v-SNARE in three dimensions and observed FRET simultaneously during single-vesicle fusion in real time, revealing the nanoscale motion and interactions of single vesicles in vesicle fusion. Thus, this study demonstrates that our microscope can provide detailed information about real-time three-dimensional nanoscale locations, motion, and interactions in biological processes.
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Affiliation(s)
- Xingxiang Chen
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Teng Liu
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xianan Qin
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Quang Quan Nguyen
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Sang Kwon Lee
- Department of Biological Sciences, School of Life Sciences, UNIST, 44919, Ulsan, Republic of Korea
| | - Chanwoo Lee
- School of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Yaguang Ren
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jun Chu
- Research Lab for Biomedical Optics and Molecular Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Tae-Young Yoon
- School of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Chan Young Park
- Department of Biological Sciences, School of Life Sciences, UNIST, 44919, Ulsan, Republic of Korea
| | - Hyokeun Park
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- State Key Laboratory of Molecular Neuroscience The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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37
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Spinks RR, Spenkelink LM, Dixon NE, van Oijen AM. Single-Molecule Insights Into the Dynamics of Replicative Helicases. Front Mol Biosci 2021; 8:741718. [PMID: 34513934 PMCID: PMC8426354 DOI: 10.3389/fmolb.2021.741718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Helicases are molecular motors that translocate along single-stranded DNA and unwind duplex DNA. They rely on the consumption of chemical energy from nucleotide hydrolysis to drive their translocation. Specialized helicases play a critically important role in DNA replication by unwinding DNA at the front of the replication fork. The replicative helicases of the model systems bacteriophages T4 and T7, Escherichia coli and Saccharomyces cerevisiae have been extensively studied and characterized using biochemical methods. While powerful, their averaging over ensembles of molecules and reactions makes it challenging to uncover information related to intermediate states in the unwinding process and the dynamic helicase interactions within the replisome. Here, we describe single-molecule methods that have been developed in the last few decades and discuss the new details that these methods have revealed about replicative helicases. Applying methods such as FRET and optical and magnetic tweezers to individual helicases have made it possible to access the mechanistic aspects of unwinding. It is from these methods that we understand that the replicative helicases studied so far actively translocate and then passively unwind DNA, and that these hexameric enzymes must efficiently coordinate the stepping action of their subunits to achieve unwinding, where the size of each step is prone to variation. Single-molecule fluorescence microscopy methods have made it possible to visualize replicative helicases acting at replication forks and quantify their dynamics using multi-color colocalization, FRAP and FLIP. These fluorescence methods have made it possible to visualize helicases in replication initiation and dissect this intricate protein-assembly process. In a similar manner, single-molecule visualization of fluorescent replicative helicases acting in replication identified that, in contrast to the replicative polymerases, the helicase does not exchange. Instead, the replicative helicase acts as the stable component that serves to anchor the other replication factors to the replisome.
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Affiliation(s)
- Richard R Spinks
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
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38
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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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39
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Wolfbeis OS. Fluorescent chameleon labels for bioconjugation and imaging of proteins, nucleic acids, biogenic amines and surface amino groups. a review. Methods Appl Fluoresc 2021; 9. [PMID: 34340216 DOI: 10.1088/2050-6120/ac1a0a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/02/2021] [Indexed: 12/14/2022]
Abstract
Chameleon labels (ChLs) possess the unique property of changing (visible) color and fluorescence on binding to amino groups of biomolecules. MostChLs react with primary aliphatic amino groups such as those in lysine or with amino groups artificially introduced into polynucleic acids or saccharides, but someothers also react with secondary amino groups. Under controlled circumstances, the reactions are fairly specific. The review is subdivided into the following sections: (1) An introduction and classification of fluorescent labels; (2) pyrylium labels that undergo shortwave color changes upon labelling, typically from blue to red; (3) polymethine type of labels (that also undergo shortwave color changes, typically from green to blue; (4) various other (less common) chromogenic and fluorogenic systems; (5) hemicyanine labels that undergolongwavecolor changes, typically from yellow to purple; (6) the application of ChLs to labeling of proteins and oligonucleotides; (7) applications to fluorometric assays and sensing; (8) applications to fluorescence imaging of biomolecules; (9) applications in studies on affinity interactions (receptor-ligand binding); (10) applications in surface and interface chemistry; and (11) applications in chromatography, electrophoresis and isotachophoresis of biomolecules.
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Affiliation(s)
- Otto S Wolfbeis
- University of Regensburg, Institute of Analytical Chemistry, Chemo- and Biosensors, 94040 Regensburg, Germany
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40
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VEGF Detection via Simplified FLISA Using a 3D Microfluidic Disk Platform. BIOSENSORS-BASEL 2021; 11:bios11080270. [PMID: 34436072 PMCID: PMC8393963 DOI: 10.3390/bios11080270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 12/03/2022]
Abstract
Fluorescence-linked immunosorbent assay (FLISA) is a commonly used, quantitative technique for detecting biochemical changes based on antigen–antibody binding reactions using a well-plate platform. As the manufacturing technology of microfluidic system evolves, FLISA can be implemented onto microfluidic disk platforms which allows the detection of trace biochemical reactions with high resolutions. Herein, we propose a novel microfluidic system comprising a disk with a three-dimensional incubation chamber, which can reduce the amount of the reagents to 1/10 and the required time for the entire process to less than an hour. The incubation process achieves an antigen–antibody binding reaction as well as the binding of fluorogenic substrates to target proteins. The FLISA protocol in the 3D incubation chamber necessitates performing the antibody-conjugated microbeads’ movement during each step in order to ensure sufficient binding reactions. Vascular endothelial growth factor as concentration with ng mL−1 is detected sequentially using a benchtop process employing this 3D microfluidic disk. The 3D microfluidic disk works without requiring manual intervention or additional procedures for liquid control. During the incubation process, microbead movement is controlled by centrifugal force from the rotating disk and the sedimentation by gravitational force at the tilted floor of the chamber.
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41
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Shepherd JW, Higgins EJ, Wollman AJ, Leake MC. PySTACHIO: Python Single-molecule TrAcking stoiCHiometry Intensity and simulatiOn, a flexible, extensible, beginner-friendly and optimized program for analysis of single-molecule microscopy data. Comput Struct Biotechnol J 2021; 19:4049-4058. [PMID: 34377369 PMCID: PMC8327484 DOI: 10.1016/j.csbj.2021.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 11/18/2022] Open
Abstract
As camera pixel arrays have grown larger and faster, and optical microscopy techniques ever more refined, there has been an explosion in the quantity of data acquired during routine light microscopy. At the single-molecule level, analysis involves multiple steps and can rapidly become computationally expensive, in some cases intractable on office workstations. Complex bespoke software can present high activation barriers to entry for new users. Here, we redevelop our quantitative single-molecule analysis routines into an optimized and extensible Python program, with GUI and command-line implementations to facilitate use on local machines and remote clusters, by beginners and advanced users alike. We demonstrate that its performance is on par with previous MATLAB implementations but runs an order of magnitude faster. We tested it against challenge data and demonstrate its performance is comparable to state-of-the-art analysis platforms. We show the code can extract fluorescence intensity values for single reporter dye molecules and, using these, estimate molecular stoichiometries and cellular copy numbers of fluorescently-labeled biomolecules. It can evaluate 2D diffusion coefficients for the characteristically short single-particle tracking data. To facilitate benchmarking we include data simulation routines to compare different analysis programs. Finally, we show that it works with 2-color data and enables colocalization analysis based on overlap integration, to infer interactions between differently labelled biomolecules. By making this freely available we aim to make complex light microscopy single-molecule analysis more democratized.
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Affiliation(s)
- Jack W. Shepherd
- Department of Physics, University of York, York YO10 5DD, United Kingdom
- Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Ed J. Higgins
- Department of Physics, University of York, York YO10 5DD, United Kingdom
- IT Services, University of York, York YO10 5DD, United Kingdom
| | - Adam J.M. Wollman
- Biosciences Institute, Newcastle University, Newcastle NE1 7RU, United Kingdom
| | - Mark C. Leake
- Department of Physics, University of York, York YO10 5DD, United Kingdom
- Department of Biology, University of York, York YO10 5DD, United Kingdom
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42
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Shepherd JW, Payne-Dwyer AL, Lee JE, Syeda A, Leake MC. Combining single-molecule super-resolved localization microscopy with fluorescence polarization imaging to study cellular processes. JPHYS PHOTONICS 2021. [DOI: 10.1088/2515-7647/ac015d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Super-resolution microscopy has catalyzed valuable insights into the sub-cellular, mechanistic details of many different biological processes across a wide range of cell types. Fluorescence polarization spectroscopy tools have also enabled important insights into cellular processes through identifying orientational changes of biological molecules typically at an ensemble level. Here, we combine these two biophysical methodologies in a single home-made instrument to enable the simultaneous detection of orthogonal fluorescence polarization signals from single fluorescent protein molecules used as common reporters on the localization of proteins in cellular processes. These enable measurement of spatial location to a super-resolved precision better than the diffraction-limited optical resolution, as well as estimation of molecular stoichiometry based on the brightness of individual fluorophores. In this innovation we have adapted a millisecond timescale microscope used for single-molecule detection to enable splitting of fluorescence polarization emissions into two separate imaging channels for s- and p-polarization signals, which are imaged onto separate halves of the same high sensitivity back-illuminated CMOS camera detector. We applied this fluorescence polarization super-resolved imaging modality to a range of test fluorescent samples relevant to the study of biological processes, including purified monomeric green fluorescent protein, single combed DNA molecules, and protein assemblies and complexes from live Escherichia coli and Saccharomyces cerevisiae cells. Our findings are qualitative but demonstrate promise in showing how fluorescence polarization and super-resolved localization microscopy can be combined on the same sample to enable simultaneous measurements of polarization and stoichiometry of tracked molecular complexes, as well as the translational diffusion coefficient.
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43
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Jarillo J, Ibarra B, Cao-García FJ. DNA replication: In vitro single-molecule manipulation data analysis and models. Comput Struct Biotechnol J 2021; 19:3765-3778. [PMID: 34285777 PMCID: PMC8267548 DOI: 10.1016/j.csbj.2021.06.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/05/2022] Open
Abstract
Data analysis allows to extract information from the noisy single-molecule data. Models provide insight in the underlying biochemical processes. Ligands can activate or inhibit DNA replication and DNA unwinding.
DNA replication is a key biochemical process of the cell cycle. In the last years, analysis of in vitro single-molecule DNA replication events has provided new information that cannot be obtained with ensembles studies. Here, we introduce crucial techniques for the proper analysis and modelling of DNA replication in vitro single-molecule manipulation data. Specifically, we review some of the main methods to analyze and model the real-time kinetics of the two main molecular motors of the replisome: DNA polymerase and DNA helicase. Our goal is to facilitate access to and understanding of these techniques to promotetheir use in the study of DNA replication at the single-molecule level. A proper analysis of single-molecule data is crucial to obtain a detailed picture of, among others, the kinetics rates, equilibrium contants and conformational changes of the system under study. The techniques presented here have been used or can be adapted to study the operation of other proteins involved in nucleic acids metabolism.
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Affiliation(s)
- Javier Jarillo
- University of Namur, Institute of Life-Earth-Environment, Namur Center for Complex Systems, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, C/ Faraday 9, 28049 Madrid, Spain
| | - Francisco Javier Cao-García
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, C/ Faraday 9, 28049 Madrid, Spain.,Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Pza. de Ciencias, 1, 28040 Madrid, Spain
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44
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Biochemistry: one molecule at a time. Essays Biochem 2021; 65:1-3. [PMID: 33860798 PMCID: PMC8056033 DOI: 10.1042/ebc20210015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 02/26/2021] [Accepted: 02/26/2021] [Indexed: 12/20/2022]
Abstract
Biological processes are orchestrated by complex networks of molecules. Conventional approaches for studying the action of biomolecules operate on a population level, averaging out any inhomogeneities within the ensemble. Investigating one biological macromolecule at a time allows researchers to directly probe individual behaviours, and thus characterise the intrinsic molecular heterogeneity of the system. Single-molecule methods have unravelled unexpected modes of action for many seemingly well-characterised biomolecules and often proved instrumental in understanding the intricate mechanistic basis of biological processes. This collection of reviews aims to showcase how single-molecule techniques can be used to address important biological questions and to inspire biochemists to ‘zoom in’ to the population and probe individual molecular behaviours, beyond the ensemble average. Furthermore, this issue of Essays in Biochemistry is the very first written and edited entirely by early career researchers, and so it also highlights the strength, diversity and excellence of the younger generation single-molecule scientists who drive this exciting field of research forward.
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Kopu̅stas A, Ivanovaitė Š, Rakickas T, Pocevičiu̅tė E, Paksaitė J, Karvelis T, Zaremba M, Manakova E, Tutkus M. Oriented Soft DNA Curtains for Single-Molecule Imaging. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3428-3437. [PMID: 33689355 PMCID: PMC8280724 DOI: 10.1021/acs.langmuir.1c00066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Over the past 20 years, single-molecule methods have become extremely important for biophysical studies. These methods, in combination with new nanotechnological platforms, can significantly facilitate experimental design and enable faster data acquisition. A nanotechnological platform, which utilizes a flow-stretch of immobilized DNA molecules, called DNA Curtains, is one of the best examples of such combinations. Here, we employed new strategies to fabricate a flow-stretch assay of stably immobilized and oriented DNA molecules using a protein template-directed assembly. In our assay, a protein template patterned on a glass coverslip served for directional assembly of biotinylated DNA molecules. In these arrays, DNA molecules were oriented to one another and maintained extended by either single- or both-end immobilization to the protein templates. For oriented both-end DNA immobilization, we employed heterologous DNA labeling and protein template coverage with the antidigoxigenin antibody. In contrast to single-end immobilization, both-end immobilization does not require constant buffer flow for keeping DNAs in an extended configuration, allowing us to study protein-DNA interactions at more controllable reaction conditions. Additionally, we increased the immobilization stability of the biotinylated DNA molecules using protein templates fabricated from traptavidin. Finally, we demonstrated that double-tethered Soft DNA Curtains can be used in nucleic acid-interacting protein (e.g., CRISPR-Cas9) binding assay that monitors the binding location and position of individual fluorescently labeled proteins on DNA.
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Affiliation(s)
- Aurimas Kopu̅stas
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Šaru̅nė Ivanovaitė
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
| | - Tomas Rakickas
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
| | - Ernesta Pocevičiu̅tė
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Justė Paksaitė
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Tautvydas Karvelis
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Mindaugas Zaremba
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Elena Manakova
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Marijonas Tutkus
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
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46
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Miranda A, Gómez-Varela AI, Stylianou A, Hirvonen LM, Sánchez H, De Beule PAA. How did correlative atomic force microscopy and super-resolution microscopy evolve in the quest for unravelling enigmas in biology? NANOSCALE 2021; 13:2082-2099. [PMID: 33346312 DOI: 10.1039/d0nr07203f] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With the invention of the Atomic Force Microscope (AFM) in 1986 and the subsequent developments in liquid imaging and cellular imaging it became possible to study the topography of cellular specimens under nearly physiological conditions with nanometric resolution. The application of AFM to biological research was further expanded with the technological advances in imaging modes where topographical data can be combined with nanomechanical measurements, offering the possibility to retrieve the biophysical properties of tissues, cells, fibrous components and biomolecules. Meanwhile, the quest for breaking the Abbe diffraction limit restricting microscopic resolution led to the development of super-resolution fluorescence microscopy techniques that brought the resolution of the light microscope comparable to the resolution obtained by AFM. The instrumental combination of AFM and optical microscopy techniques has evolved over the last decades from integration of AFM with bright-field and phase-contrast imaging techniques at first to correlative AFM and wide-field fluorescence systems and then further to the combination of AFM and fluorescence based super-resolution microscopy modalities. Motivated by the many developments made over the last decade, we provide here a review on AFM combined with super-resolution fluorescence microscopy techniques and how they can be applied for expanding our understanding of biological processes.
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Affiliation(s)
- Adelaide Miranda
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal.
| | - Ana I Gómez-Varela
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal. and Department of Applied Physics, University of Santiago de Compostela, E-15782, Santiago de Compostela, Spain.
| | - Andreas Stylianou
- Cancer Biophysics Laboratory, University of Cyprus, Nicosia, Cyprus and School of Sciences, European University Cyprus, Nicosia, Cyprus
| | - Liisa M Hirvonen
- Centre for Microscopy, Characterisation and Analysis (CMCA), The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Humberto Sánchez
- Faculty of Applied Sciences, Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Pieter A A De Beule
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal.
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47
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Grigolato F, Arosio P. The role of surfaces on amyloid formation. Biophys Chem 2021; 270:106533. [PMID: 33529995 DOI: 10.1016/j.bpc.2020.106533] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 01/02/2023]
Abstract
Interfaces can strongly accelerate or inhibit protein aggregation, destabilizing proteins that are stable in solution or, conversely, stabilizing proteins that are aggregation-prone. Although this behaviour is well-known, our understanding of the molecular mechanisms underlying surface-induced protein aggregation is still largely incomplete. A major challenge is represented by the high number of physico-chemical parameters involved, which are highly specific to the considered combination of protein, surface properties, and solution conditions. The key aspect determining the role of interfaces is the relative propensity of the protein to aggregate at the surface with respect to bulk. In this review, we discuss the multiple molecular determinants that regulate this balance. We summarize current experimental techniques aimed at characterizing protein aggregation at interfaces, and highlight the need to complement experimental analysis with theoretical modelling. In particular, we illustrate how chemical kinetic analysis can be combined with experimental methods to provide insights into the molecular mechanisms underlying surface-induced protein aggregation, under both stagnant and agitation conditions. We summarize recent progress in the study of important amyloids systems, focusing on selected relevant interfaces.
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Affiliation(s)
- Fulvio Grigolato
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland.
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48
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Lostao A, Medina M. Atomic Force Microscopy: Single-Molecule Imaging and Force Spectroscopy in the Study of Flavoproteins Ligand Binding and Reaction Mechanisms. Methods Mol Biol 2021; 2280:157-178. [PMID: 33751434 DOI: 10.1007/978-1-0716-1286-6_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Atomic force microscopy (AFM) is one of the most versatile tools currently used in nanoscience. AFM allows for performing nondestructive imaging of almost any sample in either air or liquid, regardless whether the specimen is insulating, conductive, transparent, or opaque. It also allows for measuring interaction forces between a sharp probe and a sample surface, therefore allowing to probe nanomechanical properties of the specimen by either applying a controlled force or pulling the sample. It can provide topography, mechanical, magnetic, and conductive maps for very different type of samples. Transferred to the field of biology, today, AFM is the only microscopy technique able to produce images from biomolecules to bacteria and cells with nanometric resolution in aqueous media. Here, we will focus on the biological applications of AFM to flavoproteins. Despite references in the literature are scarce in this particular field, here it is described how imaging with AFM can contribute to describe catalysis mechanisms of some flavoenzymes, how oxidation states or binding of relevant ligands influence the association state of molecules, the dynamics of functional quaternary assemblies, and even visualize structural differences of individual protein molecules. Furthermore, we will show how force spectroscopy can be used to obtain the kinetic parameters, the dissociation landscape and the mechanical forces that maintain flavoprotein complexes, including the possibility to specifically detect particular flavoproteins on a sample.
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Affiliation(s)
- Anabel Lostao
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza, Spain. .,Laboratorio de Microscopias Avanzadas, Universidad de Zaragoza, Zaragoza, Spain. .,Fundación ARAID, Zaragoza, Spain.
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, Zaragoza, Spain
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49
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Mass-sensitive particle tracking to elucidate the membrane-associated MinDE reaction cycle. Nat Methods 2021; 18:1239-1246. [PMID: 34608318 PMCID: PMC8490154 DOI: 10.1038/s41592-021-01260-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/03/2021] [Indexed: 02/08/2023]
Abstract
In spite of their great importance in biology, methods providing access to spontaneous molecular interactions with and on biological membranes have been sparse. The recent advent of mass photometry to quantify mass distributions of unlabeled biomolecules landing on surfaces raised hopes that this approach could be transferred to membranes. Here, by introducing a new interferometric scattering (iSCAT) image processing and analysis strategy adapted to diffusing particles, we enable mass-sensitive particle tracking (MSPT) of single unlabeled biomolecules on a supported lipid bilayer. We applied this approach to the highly nonlinear reaction cycles underlying MinDE protein self-organization. MSPT allowed us to determine the stoichiometry and turnover of individual membrane-bound MinD/MinDE protein complexes and to quantify their size-dependent diffusion. This study demonstrates the potential of MSPT to enhance our quantitative understanding of membrane-associated biological systems.
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50
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Bell NAW, Molloy JE. Microfluidic flow-cell with passive flow control for microscopy applications. PLoS One 2020; 15:e0244103. [PMID: 33320916 PMCID: PMC7737957 DOI: 10.1371/journal.pone.0244103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/02/2020] [Indexed: 11/19/2022] Open
Abstract
We present a fast, inexpensive and robust technique for constructing thin, optically transparent flow-cells with pump-free flow control. Using layers of glass, patterned adhesive tape and polydimethylsiloxane (PDMS) connections, we demonstrate the fabrication of planar devices with chamber height as low as 25 μm and with millimetre-scale (x,y) dimensions for wide-field microscope observation. The method relies on simple benchtop equipment and does not require microfabrication facilities, glass drilling or other workshop infrastructure. We also describe a gravity perfusion system that exploits the strong capillary action in the flow chamber as a passive limit-valve. Our approach allows simple sequential sample exchange with controlled flow rates, sub-5 μL sample chamber size and zero dead volume. We demonstrate the system in a single-molecule force spectroscopy experiment using magnetic tweezers.
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