1
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Foote A, Ishii K, Cullinane B, Tahara T, Goldsmith RH. Quantifying Microsecond Solution-Phase Conformational Dynamics of a DNA Hairpin at the Single-Molecule Level. ACS PHYSICAL CHEMISTRY AU 2024; 4:408-419. [PMID: 39069982 PMCID: PMC11274281 DOI: 10.1021/acsphyschemau.3c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 07/30/2024]
Abstract
Quantifying the rapid conformational dynamics of biological systems is fundamental to understanding the mechanism. However, biomolecules are complex, often containing static and dynamic heterogeneity, thus motivating the use of single-molecule methods, particularly those that can operate in solution. In this study, we measure microsecond conformational dynamics of solution-phase DNA hairpins at the single-molecule level using an anti-Brownian electrokinetic (ABEL) trap. Different conformational states were distinguished by their fluorescence lifetimes, and kinetic parameters describing transitions between these states were determined using two-dimensional fluorescence lifetime correlation (2DFLCS) analysis. Rather than combining fluorescence signals from the entire data set ensemble, long observation times of individual molecules allowed ABEL-2DFLCS to be performed on each molecule independently, yielding the underlying distribution of the system's kinetic parameters. ABEL-2DFLCS on the DNA hairpins resolved an underlying heterogeneity of fluorescence lifetimes and provided signatures of two-state exponential dynamics with rapid (
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Affiliation(s)
- Alexander
K. Foote
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Kunihiko Ishii
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center
for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Brendan Cullinane
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Tahei Tahara
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center
for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Randall H. Goldsmith
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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2
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Tan X, Hou S, Niver A, Zhang C, Johnson A, Welsher KD. Active-Feedback 3D Single-Molecule Tracking Using a Fast-Responding Galvo Scanning Mirror. J Phys Chem A 2023; 127:6320-6328. [PMID: 37477600 PMCID: PMC11025461 DOI: 10.1021/acs.jpca.3c02090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Real-time three-dimensional single-particle tracking (RT-3D-SPT) allows continuous detection of individual freely diffusing objects with high spatiotemporal precision by applying closed-loop active feedback in an optical microscope. However, the current tracking speed in RT-3D-SPT is primarily limited by the response time of the control actuators, impeding long-term observation of fast diffusive objects such as single molecules. Here, we present an RT-3D-SPT system with improved tracking performance by replacing the XY piezoelectric stage with a galvo scanning mirror with an approximately 5 times faster response rate (∼5 kHz). Based on the previously developed 3D single-molecule active real-time tracking (3D-SMART), this new implementation with a fast-responding galvo mirror eliminates the mechanical movement of the sample and allows a more rapid response to particle motion. The improved tracking performance of the galvo mirror-based implementation is verified through simulation and proof-of-principle experiments. Fluorescent nanoparticles and ∼1 kB double-stranded DNA molecules were tracked via both the original piezoelectric stage and new galvo mirror implementations. With the new galvo-based implementation, notable increases in tracking duration, localization precision, and the degree to which the objects are locked to the center of the detection volume were observed. These results suggest that faster control response elements can expand RT-3D-SPT to a broader range of chemical and biological systems.
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Affiliation(s)
- Xiaochen Tan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Shangguo Hou
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Anastasia Niver
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Chen Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Alexis Johnson
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Kevin D Welsher
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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3
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Pérez I, Heitkamp T, Börsch M. Mechanism of ADP-Inhibited ATP Hydrolysis in Single Proton-Pumping F oF 1-ATP Synthase Trapped in Solution. Int J Mol Sci 2023; 24:ijms24098442. [PMID: 37176150 PMCID: PMC10178918 DOI: 10.3390/ijms24098442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
FoF1-ATP synthases in mitochondria, in chloroplasts, and in most bacteria are proton-driven membrane enzymes that supply the cells with ATP made from ADP and phosphate. Different control mechanisms exist to monitor and prevent the enzymes' reverse chemical reaction of fast wasteful ATP hydrolysis, including mechanical or redox-based blockade of catalysis and ADP inhibition. In general, product inhibition is expected to slow down the mean catalytic turnover. Biochemical assays are ensemble measurements and cannot discriminate between a mechanism affecting all enzymes equally or individually. For example, all enzymes could work more slowly at a decreasing substrate/product ratio, or an increasing number of individual enzymes could be completely blocked. Here, we examined the effect of increasing amounts of ADP on ATP hydrolysis of single Escherichia coli FoF1-ATP synthases in liposomes. We observed the individual catalytic turnover of the enzymes one after another by monitoring the internal subunit rotation using single-molecule Förster resonance energy transfer (smFRET). Observation times of single FRET-labeled FoF1-ATP synthases in solution were extended up to several seconds using a confocal anti-Brownian electrokinetic trap (ABEL trap). By counting active versus inhibited enzymes, we revealed that ADP inhibition did not decrease the catalytic turnover of all FoF1-ATP synthases equally. Instead, increasing ADP in the ADP/ATP mixture reduced the number of remaining active enzymes that operated at similar catalytic rates for varying substrate/product ratios.
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Affiliation(s)
- Iván Pérez
- Single-Molecule Microscopy Group, Jena University Hospital, 07743 Jena, Germany
| | - Thomas Heitkamp
- Single-Molecule Microscopy Group, Jena University Hospital, 07743 Jena, Germany
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, 07743 Jena, Germany
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4
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Lavania A, Carpenter WB, Oltrogge LM, Perez D, Turnšek JB, Savage DF, Moerner WE. Exploring Masses and Internal Mass Distributions of Single Carboxysomes in Free Solution Using Fluorescence and Interferometric Scattering in an Anti-Brownian Trap. J Phys Chem B 2022; 126:8747-8759. [PMID: 36282790 PMCID: PMC9639131 DOI: 10.1021/acs.jpcb.2c05939] [Citation(s) in RCA: 1] [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: 08/18/2022] [Revised: 10/10/2022] [Indexed: 01/11/2023]
Abstract
Carboxysomes are self-assembled bacterial microcompartments that facilitate carbon assimilation by colocalizing the enzymes of CO2 fixation within a protein shell. These microcompartments can be highly heterogeneous in their composition and filling, so measuring the mass and loading of an individual carboxysome would allow for better characterization of its assembly and function. To enable detailed and extended characterizations of single nanoparticles in solution, we recently demonstrated an improved interferometric scattering anti-Brownian electrokinetic (ISABEL) trap, which tracks the position of a single nanoparticle via its scattering of a near-infrared beam and applies feedback to counteract its Brownian motion. Importantly, the scattering signal can be related to the mass of nanoscale proteinaceous objects, whose refractive indices are well-characterized. We calibrate single-particle scattering cross-section measurements in the ISABEL trap and determine individual carboxysome masses in the 50-400 MDa range by analyzing their scattering cross sections with a core-shell model. We further investigate carboxysome loading by combining mass measurements with simultaneous fluorescence reporting from labeled internal components. This method may be extended to other biological objects, such as viruses or extracellular vesicles, and can be combined with orthogonal fluorescence reporters to achieve precise physical and chemical characterization of individual nanoscale biological objects.
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Affiliation(s)
- Abhijit
A. Lavania
- Department
of Chemistry, Stanford University, Stanford, California94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California94305, United States
| | - William B. Carpenter
- Department
of Chemistry, Stanford University, Stanford, California94305, United States
| | - Luke M. Oltrogge
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California94720, United States
| | - Davis Perez
- Department
of Chemistry, Stanford University, Stanford, California94305, United States
| | - Julia B. Turnšek
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California94720, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California94720, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California94305, United States
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5
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van Heerden B, Vickers NA, Krüger TPJ, Andersson SB. Real-Time Feedback-Driven Single-Particle Tracking: A Survey and Perspective. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107024. [PMID: 35758534 PMCID: PMC9308725 DOI: 10.1002/smll.202107024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 04/07/2022] [Indexed: 05/14/2023]
Abstract
Real-time feedback-driven single-particle tracking (RT-FD-SPT) is a class of techniques in the field of single-particle tracking that uses feedback control to keep a particle of interest in a detection volume. These methods provide high spatiotemporal resolution on particle dynamics and allow for concurrent spectroscopic measurements. This review article begins with a survey of existing techniques and of applications where RT-FD-SPT has played an important role. Each of the core components of RT-FD-SPT are systematically discussed in order to develop an understanding of the trade-offs that must be made in algorithm design and to create a clear picture of the important differences, advantages, and drawbacks of existing approaches. These components are feedback tracking and control, ranging from simple proportional-integral-derivative control to advanced nonlinear techniques, estimation to determine particle location from the measured data, including both online and offline algorithms, and techniques for calibrating and characterizing different RT-FD-SPT methods. Then a collection of metrics for RT-FD-SPT is introduced to help guide experimentalists in selecting a method for their particular application and to help reveal where there are gaps in the techniques that represent opportunities for further development. Finally, this review is concluded with a discussion on future perspectives in the field.
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Affiliation(s)
- Bertus van Heerden
- Department of Physics, University of Pretoria, Pretoria, 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Nicholas A Vickers
- Department of Mechanical Engineering, Boston University, Boston, MA, 02215, USA
| | - Tjaart P J Krüger
- Department of Physics, University of Pretoria, Pretoria, 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Sean B Andersson
- Department of Mechanical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Systems Engineering, Boston University, Boston, MA, 02215, USA
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6
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Masullo LA, Lopez LF, Stefani FD. A common framework for single-molecule localization using sequential structured illumination. BIOPHYSICAL REPORTS 2022; 2:100036. [PMID: 36425082 PMCID: PMC9680809 DOI: 10.1016/j.bpr.2021.100036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/22/2021] [Indexed: 06/16/2023]
Abstract
Localization of single fluorescent molecules is key for physicochemical and biophysical measurements, such as single-molecule tracking and super-resolution imaging by single-molecule localization microscopy. Over the last two decades, several methods have been developed in which the position of a single emitter is interrogated with a sequence of spatially modulated patterns of light. Among them, the recent MINFLUX technique outstands for achieving a ∼10-fold improvement compared with wide-field camera-based single-molecule localization, reaching ∼1-2 nm localization precision at moderate photon counts. Here, we present a common framework for this type of measurement. Using the Cramér-Rao bound as a limit for the achievable localization precision, we benchmark reported methods, including recent developments, such as MINFLUX and MINSTED, and long-established methods, such as orbital tracking. In addition, we characterize two new proposed schemes, orbital tracking and raster scanning, with a minimum of intensity. Overall, we found that approaches using an intensity minimum have a similar performance in the central region of the excitation pattern, independent of the geometry of the excitation pattern, and that they outperform methods featuring an intensity maximum.
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Affiliation(s)
- Luciano A. Masullo
- Centro de Investigaciones en Bionanociencias, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Lucía F. Lopez
- Centro de Investigaciones en Bionanociencias, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando D. Stefani
- Centro de Investigaciones en Bionanociencias, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
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7
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Heitkamp T, Börsch M. Fast ATP-Dependent Subunit Rotation in Reconstituted F oF 1-ATP Synthase Trapped in Solution. J Phys Chem B 2021; 125:7638-7650. [PMID: 34254808 DOI: 10.1021/acs.jpcb.1c02739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
FoF1-ATP synthases are ubiquitous membrane-bound, rotary motor enzymes that can catalyze ATP synthesis and hydrolysis. Their enzyme kinetics are controlled by internal subunit rotation, by substrate and product concentrations, and by mechanical inhibitory mechanisms but also by the electrochemical potential of protons across the membrane. Single-molecule Förster resonance energy transfer (smFRET) has been used to detect subunit rotation within FoF1-ATP synthases embedded in freely diffusing liposomes. We now report that kinetic monitoring of functional rotation can be prolonged from milliseconds to seconds by utilizing an anti-Brownian electrokinetic trap (ABEL trap). These extended observation times allowed us to observe fluctuating rates of functional rotation for individual FoF1-liposomes in solution. Broad distributions of ATP-dependent catalytic rates were revealed. The buildup of an electrochemical potential of protons was confirmed to limit the maximum rate of ATP hydrolysis. In the presence of ionophores or uncouplers, the fastest subunit rotation speeds measured in single reconstituted FoF1-ATP synthases were 180 full rounds per second. This was much faster than measured by biochemical ensemble averaging, but not as fast as the maximum rotational speed reported previously for isolated single F1 complexes uncoupled from the membrane-embedded Fo complex. Further application of ABEL trap measurements should help resolve the mechanistic causes of such fluctuating rates of subunit rotation.
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Affiliation(s)
- Thomas Heitkamp
- Single-Molecule Microscopy Group, Jena University Hospital, Nonnenplan 2-4, 07743 Jena, Germany
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Nonnenplan 2-4, 07743 Jena, Germany
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8
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Wang B, Davis LM. Diffusivity Measurement by Single-Molecule Recycling in a Capillary Microchannel. MICROMACHINES 2021; 12:800. [PMID: 34357210 PMCID: PMC8306395 DOI: 10.3390/mi12070800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/30/2021] [Accepted: 07/04/2021] [Indexed: 11/16/2022]
Abstract
Microfluidic devices have been extensively investigated in recent years in fields including ligand-binding analysis, chromatographic separation, molecular dynamics, and DNA sequencing. To prolong the observation of a single molecule in aqueous buffer, the solution in a sub-micron scale channel is driven by a electric field and reversed after a fixed delay following each passage, so that the molecule passes back and forth through the laser focus and the time before irreversible photobleaching is extended. However, this practice requires complex chemical treatment to the inner surface of the channel to prevent unexpected sticking to the surface and the confined space renders features, such as a higher viscosity and lower dielectric constant, which slow the Brownian motion of the molecule compared to the bulk solution. Additionally, electron beam lithography used for the fabrication of the nanochannel substantially increases the cost, and the sub-micron dimensions make the molecule difficult to locate. In this paper, we propose a method of single-molecule recycling in a capillary microchannel. A commercial fused-silica capillary with an inner diameter of 2 microns is chopped into a 1-inch piece and is fixed onto a cover slip. Two o-rings on the sides used as reservoirs and an o-ring in the middle used as observation window are glued over the capillary. The inner surface of the capillary is chemically processed to reduce the non-specific sticking and to improve capillary effect. The device does not require high-precision fabrication and thus is less costly and easier to prepare than the nanochannel. 40 nm Fluospheres® in 50% methanol are used as working solution. The capillary is translated by a piezo stage to recycle the molecule, which diffuses freely through the capillary, and a confocal microscope is used for fluorescence collection. The passing times of the molecule through the laser focus are calculated by a real-time control system based on an FPGA, and the commands of translation are given to the piezo stage through a feedback algorithm. The larger dimensions of the capillary overcomes the strong sticking, the reduced diffusivity, and the difficulty of localizing the molecule. We have achieved a maximum number of recycles of more than 200 and developed a maximum-likelihood estimation of the diffusivity of the molecule, which attains results of the same magnitude as the previous report. This technique simplifies the overall procedure of the single-molecule recycling and could be useful for the ligand-binding studies in high-throughput screening.
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Affiliation(s)
- Bo Wang
- Center for Laser Application, University of Tennessee Space Institute, 411 B H Goethert Pkwy, Tullahoma, TN 37388, USA
- Department of Physics and Astronomy, University of Tennessee Knoxville, 1408 Circle Dr, Knoxville, TN 37996, USA;
| | - Lloyd M. Davis
- Center for Laser Application, University of Tennessee Space Institute, 411 B H Goethert Pkwy, Tullahoma, TN 37388, USA
- Department of Physics and Astronomy, University of Tennessee Knoxville, 1408 Circle Dr, Knoxville, TN 37996, USA;
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9
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Wilson H, Wang Q. ABEL-FRET: tether-free single-molecule FRET with hydrodynamic profiling. Nat Methods 2021; 18:816-820. [PMID: 34127856 DOI: 10.1038/s41592-021-01173-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 05/04/2021] [Indexed: 02/03/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) has become a versatile and widespread method to probe nanoscale conformation and dynamics. However, current experimental modalities often resort to molecule immobilization for long observation times and do not always approach the resolution limit of FRET-based nanoscale metrology. Here we present ABEL-FRET, an immobilization-free platform for smFRET measurements with ultrahigh resolving power in FRET efficiency. Importantly, single-molecule diffusivity is used to provide additional size and shape information for hydrodynamic profiling of individual molecules, which, together with the concurrently measured intramolecular conformation through FRET, enables a holistic and dynamic view of biomolecules and their complexes.
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Affiliation(s)
- Hugh Wilson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Quan Wang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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10
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11
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Thermophoretic Micron-Scale Devices: Practical Approach and Review. ENTROPY 2020; 22:e22090950. [PMID: 33286719 PMCID: PMC7597233 DOI: 10.3390/e22090950] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/18/2020] [Accepted: 08/25/2020] [Indexed: 12/15/2022]
Abstract
In recent years, there has been increasing interest in the development of micron-scale devices utilizing thermal gradients to manipulate molecules and colloids, and to measure their thermophoretic properties quantitatively. Various devices have been realized, such as on-chip implements, micro-thermogravitational columns and other micron-scale thermophoretic cells. The advantage of the miniaturized devices lies in the reduced sample volume. Often, a direct observation of particles using various microscopic techniques is possible. On the other hand, the small dimensions lead to some technical problems, such as a precise temperature measurement on small length scale with high spatial resolution. In this review, we will focus on the "state of the art" thermophoretic micron-scale devices, covering various aspects such as generating temperature gradients, temperature measurement, and the analysis of the current micron-scale devices. We want to give researchers an orientation for their development of thermophoretic micron-scale devices for biological, chemical, analytical, and medical applications.
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12
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Abstract
To date, single molecule studies have been reliant on tethering or confinement to achieve long duration and high temporal resolution measurements. Here, we present a 3D single-molecule active real-time tracking method (3D-SMART) which is capable of locking on to single fluorophores in solution for minutes at a time with photon limited temporal resolution. As a demonstration, 3D-SMART is applied to actively track single Atto 647 N fluorophores in 90% glycerol solution with an average duration of ~16 s at count rates of ~10 kHz. Active feedback tracking is further applied to single proteins and nucleic acids, directly measuring the diffusion of various lengths (99 to 1385 bp) of single DNA molecules at rates up to 10 µm2/s. In addition, 3D-SMART is able to quantify the occupancy of single Spinach2 RNA aptamers and capture active transcription on single freely diffusing DNA. 3D-SMART represents a critical step towards the untethering of single molecule spectroscopy. Single molecule observation has been limited to tethered molecules to ensure that the target remains in the field of view (FOV). Here, the authors develop a real-time tracking method that locks onto rapidly diffusing targets and tracks them in a 3D volume, enabling single molecules to remain in the FOV for minutes at a time.
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Stergar J, Osterman N. Thermophoretic tweezers for single nanoparticle manipulation. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2020; 11:1126-1133. [PMID: 32802715 PMCID: PMC7404219 DOI: 10.3762/bjnano.11.97] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/06/2020] [Indexed: 05/11/2023]
Abstract
We present the trapping and manipulation of a single nano-object in an aqueous medium by optically induced temporally varying temperature gradients. By real-time object tracking and control of the position of the heating laser focus, we can precisely employ thermophoretic drift to oppose the random diffusive motion. As a result, a nano-object is confined in a micrometer-sized trap. Numerical modeling gives a quantitative prediction of the effect. Traps can be dynamically created and relocated, which we demonstrate by the controlled independent manipulation of two nanoparticles.
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Affiliation(s)
- Jošt Stergar
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, Ljubljana, Slovenia
- J. Stefan Institute, Jamova 39, Ljubljana, Slovenia
| | - Natan Osterman
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, Ljubljana, Slovenia
- J. Stefan Institute, Jamova 39, Ljubljana, Slovenia
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14
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Abstract
Anti-Brownian electrokinetic trapping is a method for trapping single particles in liquid based on particle position measurements and the application of feedback voltages. To achieve trapping in the axial direction, information on the axial particle position is required. However, existing strategies for determining the axial position that are based on measuring the size of the first diffraction ring, theory fitting, advanced optical setups or pre-determined axial image stacks are impractical for anisotropic particles. In this work, axial electrokinetic trapping of anisotropic particles is realized in devices with planar, transparent electrodes. The trapping algorithm uses Fourier-Bessel decomposition of standard microscopy images and is learning from the correlation between applied voltages and changes in the particle appearance. No previous knowledge on the particle appearance, theory fitting or advanced optical setup is required. The particle motion in the trap and the influence of screening of the electric field on this motion are analyzed. The axial trapping method opens new possibilities for measuring properties of anisotropic or isotropic particles and forces acting on such particles.
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15
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Real-Time 3D Single Particle Tracking: Towards Active Feedback Single Molecule Spectroscopy in Live Cells. Molecules 2019; 24:molecules24152826. [PMID: 31382495 PMCID: PMC6695621 DOI: 10.3390/molecules24152826] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/27/2019] [Accepted: 08/01/2019] [Indexed: 01/25/2023] Open
Abstract
Single molecule fluorescence spectroscopy has been largely implemented using methods which require tethering of molecules to a substrate in order to make high temporal resolution measurements. However, the act of tethering a molecule requires that the molecule be removed from its environment. This is especially perturbative when measuring biomolecules such as enzymes, which may rely on the non-equilibrium and crowded cellular environment for normal function. A method which may be able to un-tether single molecule fluorescence spectroscopy is real-time 3D single particle tracking (RT-3D-SPT). RT-3D-SPT uses active feedback to effectively lock-on to freely diffusing particles so they can be measured continuously with up to photon-limited temporal resolution over large axial ranges. This review gives an overview of the various active feedback 3D single particle tracking methods, highlighting specialized detection and excitation schemes which enable high-speed real-time tracking. Furthermore, the combination of these active feedback methods with simultaneous live-cell imaging is discussed. Finally, the successes in real-time 3D single molecule tracking (RT-3D-SMT) thus far and the roadmap going forward for this promising family of techniques are discussed.
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16
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High-throughput smFRET analysis of freely diffusing nucleic acid molecules and associated proteins. Methods 2019; 169:21-45. [PMID: 31356875 DOI: 10.1016/j.ymeth.2019.07.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/24/2019] [Accepted: 07/22/2019] [Indexed: 11/21/2022] Open
Abstract
Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique for nanometer-scale studies of single molecules. Solution-based smFRET, in particular, can be used to study equilibrium intra- and intermolecular conformations, binding/unbinding events and conformational changes under biologically relevant conditions without ensemble averaging. However, single-spot smFRET measurements in solution are slow. Here, we detail a high-throughput smFRET approach that extends the traditional single-spot confocal geometry to a multispot one. The excitation spots are optically conjugated to two custom silicon single photon avalanche diode (SPAD) arrays. Two-color excitation is implemented using a periodic acceptor excitation (PAX), allowing distinguishing between singly- and doubly-labeled molecules. We demonstrate the ability of this setup to rapidly and accurately determine FRET efficiencies and population stoichiometries by pooling the data collected independently from the multiple spots. We also show how the high throughput of this approach can be used o increase the temporal resolution of single-molecule FRET population characterization from minutes to seconds. Combined with microfluidics, this high-throughput approach will enable simple real-time kinetic studies as well as powerful molecular screening applications.
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17
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Squires A, Lavania AA, Dahlberg PD, Moerner WE. Interferometric Scattering Enables Fluorescence-Free Electrokinetic Trapping of Single Nanoparticles in Free Solution. NANO LETTERS 2019; 19:4112-4117. [PMID: 31117762 PMCID: PMC6604838 DOI: 10.1021/acs.nanolett.9b01514] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/13/2019] [Indexed: 05/05/2023]
Abstract
Anti-Brownian traps confine single particles in free solution by closed-loop feedback forces that directly counteract Brownian motion. Extended-duration measurements on trapped objects allow detailed characterization of photophysical and transport properties as well as observation of infrequent or rare dynamics. However, this approach has been generally limited to particles that can be tracked by fluorescence emission. Here we present the Interferometric Scattering Anti-Brownian ELectrokinetic (ISABEL) trap, which uses interferometric scattering rather than fluorescence to monitor particle position. By decoupling the ability to track (and therefore trap) a particle from collection of its spectroscopic data, the ISABEL trap enables confinement and extended study of single particles that do not fluoresce, only weakly fluoresce, or exhibit intermittent fluorescence or photobleaching. This new technique significantly expands the range of nanoscale objects that may be investigated at the single-particle level in free solution.
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Affiliation(s)
- Allison
H. Squires
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Abhijit A. Lavania
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
| | - Peter D. Dahlberg
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
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18
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Sielaff H, Yanagisawa S, Frasch WD, Junge W, Börsch M. Structural Asymmetry and Kinetic Limping of Single Rotary F-ATP Synthases. Molecules 2019; 24:E504. [PMID: 30704145 PMCID: PMC6384691 DOI: 10.3390/molecules24030504] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/12/2022] Open
Abstract
F-ATP synthases use proton flow through the FO domain to synthesize ATP in the F₁ domain. In Escherichia coli, the enzyme consists of rotor subunits γεc10 and stator subunits (αβ)₃δab₂. Subunits c10 or (αβ)₃ alone are rotationally symmetric. However, symmetry is broken by the b₂ homodimer, which together with subunit δa, forms a single eccentric stalk connecting the membrane embedded FO domain with the soluble F₁ domain, and the central rotating and curved stalk composed of subunit γε. Although each of the three catalytic binding sites in (αβ)₃ catalyzes the same set of partial reactions in the time average, they might not be fully equivalent at any moment, because the structural symmetry is broken by contact with b₂δ in F₁ and with b₂a in FO. We monitored the enzyme's rotary progression during ATP hydrolysis by three single-molecule techniques: fluorescence video-microscopy with attached actin filaments, Förster resonance energy transfer between pairs of fluorescence probes, and a polarization assay using gold nanorods. We found that one dwell in the three-stepped rotary progression lasting longer than the other two by a factor of up to 1.6. This effect of the structural asymmetry is small due to the internal elastic coupling.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany.
| | - Seiga Yanagisawa
- School of Life Sciences, Arizona State University, Tempe, Arizona, AZ 85287, USA.
| | - Wayne D Frasch
- School of Life Sciences, Arizona State University, Tempe, Arizona, AZ 85287, USA.
| | - Wolfgang Junge
- Department of Biology & Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany.
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19
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Lee TJ, Lewallen CF, Bumbarger DJ, Yunker PJ, Reid RC, Forest CR. Transport and trapping of nanosheets via hydrodynamic forces and curvature-induced capillary quadrupolar interactions. J Colloid Interface Sci 2018; 531:352-359. [PMID: 30041112 DOI: 10.1016/j.jcis.2018.07.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/17/2018] [Accepted: 07/17/2018] [Indexed: 01/25/2023]
Abstract
HYPOTHESIS The manipulation of nanosheets on a fluid-fluid interface remains a significant challenge. At this interface, hydrodynamic forces can be used for long-range transport (>1× capillary length) but are difficult to utilize for accurate and repeatable positioning. While capillary multipole interactions have been used for particle trapping, how these interactions manifest on large but thin objects, i.e., nanosheets, remains an open question. Hence, we posit hydrodynamic forces in conjunction with capillary multipole interactions can be used for nanosheet transport and trapping. EXPERIMENTS We designed and characterized a fluidic device for transporting and trapping nanosheets on the water-air interface. Analytical models were compared against optical measurements of the nanosheet behavior to investigate capillary multipole interactions. Energy-based modeling and dimensional analysis were used to study trapping stability. FINDINGS Hydrodynamic forces and capillary interactions successfully transported and trapped nanosheets at a designated trapping location with a repeatability of 10% of the nanosheet's length and 12% of its width (length = 1500 µm, width = 1000 µm) and an accuracy of 20% of their length and width. Additionally, this is the first report that surface tension forces acting upon nanoscale-thick objects manifest as capillary quadrupolar interactions and can be used for precision manipulation of nanosheets.
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Affiliation(s)
- Timothy J Lee
- Georgia Institute of Technology, G. W. Woodruff School of Mechanical Engineering, Atlanta, GA 30332, USA.
| | - Colby F Lewallen
- Georgia Institute of Technology, G. W. Woodruff School of Mechanical Engineering, Atlanta, GA 30332, USA.
| | | | - Peter J Yunker
- Georgia Institute of Technology, School of Physics, Atlanta, GA 30332, USA.
| | - R Clay Reid
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
| | - Craig R Forest
- Georgia Institute of Technology, G. W. Woodruff School of Mechanical Engineering, Atlanta, GA 30332, USA.
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20
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Sielaff H, Duncan TM, Börsch M. The regulatory subunit ε in Escherichia coli F OF 1-ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:775-788. [PMID: 29932911 DOI: 10.1016/j.bbabio.2018.06.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 11/16/2022]
Abstract
F-type ATP synthases are extraordinary multisubunit proteins that operate as nanomotors. The Escherichia coli (E. coli) enzyme uses the proton motive force (pmf) across the bacterial plasma membrane to drive rotation of the central rotor subunits within a stator subunit complex. Through this mechanical rotation, the rotor coordinates three nucleotide binding sites that sequentially catalyze the synthesis of ATP. Moreover, the enzyme can hydrolyze ATP to turn the rotor in the opposite direction and generate pmf. The direction of net catalysis, i.e. synthesis or hydrolysis of ATP, depends on the cell's bioenergetic conditions. Different control mechanisms have been found for ATP synthases in mitochondria, chloroplasts and bacteria. This review discusses the auto-inhibitory behavior of subunit ε found in FOF1-ATP synthases of many bacteria. We focus on E. coli FOF1-ATP synthase, with insights into the regulatory mechanism of subunit ε arising from structural and biochemical studies complemented by single-molecule microscopy experiments.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
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21
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Heitkamp T, Grisshammer R, Börsch M. Towards monitoring conformational changes of the GPCR neurotensin receptor 1 by single-molecule FRET. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2018; 10498. [PMID: 30013286 DOI: 10.1117/12.2286787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Neurotensin receptor 1 (NTSR1) is a G protein-coupled receptor that is important for signaling in the brain and the gut. Its agonist ligand neurotensin (NTS), a 13-amino-acid peptide, binds with nanomolar affinity from the extracellular side to NTSR1 and induces conformational changes that trigger intracellular signaling processes. Our goal is to monitor the conformational dynamics of single fluorescently labeled NTSR1. For this, we fused the fluorescent protein mNeonGreen to the C terminus of NTSR1, purified the receptor fusion protein from E. coli membranes, and reconstituted NTSR1 into liposomes with E. coli polar lipids. Using single-molecule anisotropy measurements, NTSR1 was found to be monomeric in liposomes, with a small fraction being dimeric and oligomeric, showing homoFRET. Similar results were obtained for NTSR1 in detergent solution. Furthermore, we demonstrated agonist binding to NTSR1 by time-resolved single-molecule Förster resonance energy transfer (smFRET), using neurotensin labeled with the fluorophore ATTO594.
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Affiliation(s)
- Thomas Heitkamp
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University Jena, Nonnenplan 2 - 4, 07743 Jena, Germany
| | - Reinhard Grisshammer
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, 50 South Drive, Bethesda, MD 20814, USA
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University Jena, Nonnenplan 2 - 4, 07743 Jena, Germany
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22
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Kim K, Yun J, Lee D, Kim D. An efficient fluorescent single-particle position tracking system for long-term pulsed measurements of nitrogen-vacancy centers in diamond. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:023702. [PMID: 29495875 DOI: 10.1063/1.5003707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A simple and convenient design enables real-time three-dimensional position tracking of nitrogen-vacancy (NV) centers in diamond. The system consists entirely of commercially available components (a single-photon counter, a high-speed digital-to-analog converter, a phase-sensitive detector-based feedback device, and a piezo stage), eliminating the need for custom programming or rigorous optimization processes. With a large input range of counters and trackers combined with high sensitivity of single-photon counting, high-speed position tracking (upper bound recovery time of 0.9 s upon 250 nm of step-like positional shift) not only of bright ensembles, but also of low-photon-collection-efficiency single to few NV centers (down to 103 s-1) is possible. The tracking requires position modulation of only 10 nm, which allows simultaneous position tracking and pulsed measurements in the long term. Therefore, this tracking system enables measuring a single-spin magnetic resonance and Rabi oscillations at a very high resolution even without photon collection optimization. The system is widely applicable to various fields related to NV center quantum manipulation research such as NV optical trapping, NV tracking in fluid dynamics, and biological sensing using NV centers inside a biological cell.
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Affiliation(s)
- Kiho Kim
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 08826, South Korea
| | - Jiwon Yun
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 08826, South Korea
| | - Donghyuck Lee
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 08826, South Korea
| | - Dohun Kim
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 08826, South Korea
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23
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Peng S, Wang W, Chen C. Breaking the Concentration Barrier for Single-Molecule Fluorescence Measurements. Chemistry 2017; 24:1002-1009. [DOI: 10.1002/chem.201704065] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Sijia Peng
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, and Beijing Advanced Innovation Center for Structural Biology; Tsinghua University; Beijing, 100084 P.R. China
| | - Wenjuan Wang
- School of Life Sciences and Technology Center for Protein Sciences; Tsinghua University; Beijing, 100084 P.R. China
| | - Chunlai Chen
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, and Beijing Advanced Innovation Center for Structural Biology; Tsinghua University; Beijing, 100084 P.R. China
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24
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Hou S, Lang X, Welsher K. Robust real-time 3D single-particle tracking using a dynamically moving laser spot. OPTICS LETTERS 2017; 42:2390-2393. [PMID: 28614318 DOI: 10.1364/ol.42.002390] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Real-time three-dimensional (3D) single-particle tracking uses optical feedback to lock on to freely diffusing nanoscale fluorescent particles, permitting precise 3D localization and continuous spectroscopic interrogation. Here we describe a new method of real-time 3D single-particle tracking wherein a diffraction-limited laser spot is dynamically swept through the detection volume in three dimensions using a two-dimensional (2D) electro-optic deflector and a tunable acoustic gradient lens. This optimized method, called 3D dynamic photon localization tracking (3D-DyPLoT), enables high-speed real-time tracking of single silica-coated non-blinking quantum dots (∼30 nm diameter) with diffusive speeds exceeding 10 μm2/s at count rates as low as 10 kHz, as well as YFP-labeled virus-like particles. The large effective detection area (1 μm×1 μm×4 μm) allows the system to easily pick up fast-moving particles, while still demonstrating high localization precision (σx=6.6 nm, σy=8.7 nm, and σz=15.6 nm). Overall, 3D-DyPLoT provides a fast and robust method for real-time 3D tracking of fast and lowly emitting particles, based on a single excitation and detection pathway, paving the way to more widespread application to relevant biological problems.
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25
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Shen H, Tauzin LJ, Baiyasi R, Wang W, Moringo N, Shuang B, Landes CF. Single Particle Tracking: From Theory to Biophysical Applications. Chem Rev 2017; 117:7331-7376. [PMID: 28520419 DOI: 10.1021/acs.chemrev.6b00815] [Citation(s) in RCA: 273] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
After three decades of developments, single particle tracking (SPT) has become a powerful tool to interrogate dynamics in a range of materials including live cells and novel catalytic supports because of its ability to reveal dynamics in the structure-function relationships underlying the heterogeneous nature of such systems. In this review, we summarize the algorithms behind, and practical applications of, SPT. We first cover the theoretical background including particle identification, localization, and trajectory reconstruction. General instrumentation and recent developments to achieve two- and three-dimensional subdiffraction localization and SPT are discussed. We then highlight some applications of SPT to study various biological and synthetic materials systems. Finally, we provide our perspective regarding several directions for future advancements in the theory and application of SPT.
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Affiliation(s)
- Hao Shen
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Lawrence J Tauzin
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Rashad Baiyasi
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Wenxiao Wang
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Nicholas Moringo
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Bo Shuang
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Christy F Landes
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
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26
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Kondo T, Chen WJ, Schlau-Cohen GS. Single-Molecule Fluorescence Spectroscopy of Photosynthetic Systems. Chem Rev 2017; 117:860-898. [DOI: 10.1021/acs.chemrev.6b00195] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Toru Kondo
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge Massachusetts 02139, United States
| | - Wei Jia Chen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge Massachusetts 02139, United States
| | - Gabriela S. Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge Massachusetts 02139, United States
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27
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Lee JE, Han YR, Ham S, Jun CH, Kim D. A solution-based single-molecule study of surface-bound PBIs: solvent-mediated environmental effects on molecular flexibility. Phys Chem Chem Phys 2017; 19:29255-29262. [DOI: 10.1039/c7cp04756h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have investigated the fundamental photophysical properties of surface-bound perylene bisimide (PBI) molecules in solution at the single-molecule level.
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Affiliation(s)
- Ji-Eun Lee
- Department of Chemistry and Spectroscopy Laboratory for Functional π–Electronic Systems
- Yonsei University
- Seodaemun-gu
- Republic of Korea
| | - Ye Ri Han
- Department of Chemistry and OrganoTransition Metal Catalysis–Hybrid Materials Laboratory
- Yonsei University
- Seodaemun-gu
- Republic of Korea
| | - Sujin Ham
- Department of Chemistry and Spectroscopy Laboratory for Functional π–Electronic Systems
- Yonsei University
- Seodaemun-gu
- Republic of Korea
| | - Chul-Ho Jun
- Department of Chemistry and OrganoTransition Metal Catalysis–Hybrid Materials Laboratory
- Yonsei University
- Seodaemun-gu
- Republic of Korea
| | - Dongho Kim
- Department of Chemistry and Spectroscopy Laboratory for Functional π–Electronic Systems
- Yonsei University
- Seodaemun-gu
- Republic of Korea
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28
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Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers. Sci Rep 2016; 6:33257. [PMID: 27641327 PMCID: PMC5027553 DOI: 10.1038/srep33257] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 08/24/2016] [Indexed: 01/24/2023] Open
Abstract
Advanced microscopy methods allow obtaining information on (dynamic) conformational changes in biomolecules via measuring a single molecular distance in the structure. It is, however, extremely challenging to capture the full depth of a three-dimensional biochemical state, binding-related structural changes or conformational cross-talk in multi-protein complexes using one-dimensional assays. In this paper we address this fundamental problem by extending the standard molecular ruler based on Förster resonance energy transfer (FRET) into a two-dimensional assay via its combination with protein-induced fluorescence enhancement (PIFE). We show that donor brightness (via PIFE) and energy transfer efficiency (via FRET) can simultaneously report on e.g., the conformational state of double stranded DNA (dsDNA) following its interaction with unlabelled proteins (BamHI, EcoRV, and T7 DNA polymerase gp5/trx). The PIFE-FRET assay uses established labelling protocols and single molecule fluorescence detection schemes (alternating-laser excitation, ALEX). Besides quantitative studies of PIFE and FRET ruler characteristics, we outline possible applications of ALEX-based PIFE-FRET for single-molecule studies with diffusing and immobilized molecules. Finally, we study transcription initiation and scrunching of E. coli RNA-polymerase with PIFE-FRET and provide direct evidence for the physical presence and vicinity of the polymerase that causes structural changes and scrunching of the transcriptional DNA bubble.
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29
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Tian H, Fürstenberg A, Huber T. Labeling and Single-Molecule Methods To Monitor G Protein-Coupled Receptor Dynamics. Chem Rev 2016; 117:186-245. [DOI: 10.1021/acs.chemrev.6b00084] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Alexandre Fürstenberg
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
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30
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Banterle N, Lemke EA. Nanoscale devices for linkerless long-term single-molecule observation. Curr Opin Biotechnol 2016; 39:105-112. [PMID: 26990172 PMCID: PMC7611743 DOI: 10.1016/j.copbio.2016.02.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/11/2016] [Accepted: 02/15/2016] [Indexed: 01/07/2023]
Abstract
Total internal reflection fluorescence microscopy (TIRFM) can offer favorably high signal-to-noise observation of biological mechanisms. TIRFM can be used routinely to observe even single fluorescent molecules for a long duration (several seconds) at millisecond time resolution. However, to keep the investigated sample in the evanescent field, chemical surface immobilization techniques typically need to be implemented. In this review, we describe some of the recently developed novel nanodevices that overcome this limitation enabling long-term observation of free single molecules and outline their biological applications. The working concept of many devices is compatible with high-throughput strategies, which will further help to establish unbiased single molecule observation as a routine tool in biology to study the molecular underpinnings of even the most complex biological mechanisms.
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Affiliation(s)
- Niccolò Banterle
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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31
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Stokes trap for multiplexed particle manipulation and assembly using fluidics. Proc Natl Acad Sci U S A 2016; 113:3976-81. [PMID: 27035979 DOI: 10.1073/pnas.1525162113] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability to confine and manipulate single particles and molecules has revolutionized several fields of science. Hydrodynamic trapping offers an attractive method for particle manipulation in free solution without the need for optical, electric, acoustic, or magnetic fields. Here, we develop and demonstrate the Stokes trap, which is a new method for trapping multiple particles using only fluid flow. We demonstrate simultaneous manipulation of two particles in a simple microfluidic device using model predictive control. We further show that this approach can be used for fluidic-directed assembly of multiple particles in solution. Overall, this technique opens new vistas for fundamental studies of particle-particle interactions and provides a new method for the directed assembly of colloidal particles.
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32
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Abstract
As of 2015, it has been 26 years since the first optical detection and spectroscopy of single molecules in condensed matter. This area of science has expanded far beyond the early low temperature studies in crystals to include single molecules in cells, polymers, and in solution. The early steps relied upon high-resolution spectroscopy of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral fine structure arising directly from the position-dependent fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 1990s, a variety of fascinating physical effects were observed for individual molecules, including imaging of the light from single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency. In the room temperature regime, researchers showed that bursts of light from single molecules could be detected in solution, leading to imaging and microscopy by a variety of methods. Studies of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. All of these early steps provided important fundamentals underpinning the development of super-resolution microscopy based on single-molecule localization and active control of emitting concentration. Current thrust areas include extensions to three-dimensional imaging with high precision, orientational analysis of single molecules, and direct measurements of photodynamics and transport properties for single molecules trapped in solution by suppression of Brownian motion. Without question, a huge variety of studies of single molecules performed by many talented scientists all over the world have extended our knowledge of the nanoscale and many microscopic mechanisms previously hidden by ensemble averaging.
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Affiliation(s)
- W E Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
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33
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Schlau-Cohen GS, Yang HY, Krüger TPJ, Xu P, Gwizdala M, van Grondelle R, Croce R, Moerner WE. Single-Molecule Identification of Quenched and Unquenched States of LHCII. J Phys Chem Lett 2015; 6:860-7. [PMID: 26262664 DOI: 10.1021/acs.jpclett.5b00034] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In photosynthetic light harvesting, absorbed sunlight is converted to electron flow with near-unity quantum efficiency under low light conditions. Under high light conditions, plants avoid damage to their molecular machinery by activating a set of photoprotective mechanisms to harmlessly dissipate excess energy as heat. To investigate these mechanisms, we study the primary antenna complex in green plants, light-harvesting complex II (LHCII), at the single-complex level. We use a single-molecule technique, the Anti-Brownian Electrokinetic trap, which enables simultaneous measurements of fluorescence intensity, lifetime, and spectra in solution. With this approach, including the first measurements of fluorescence lifetime on single LHCII complexes, we access the intrinsic conformational dynamics. In addition to an unquenched state, we identify two partially quenched states of LHCII. Our results suggest that there are at least two distinct quenching sites with different molecular compositions, meaning multiple dissipative pathways in LHCII. Furthermore, one of the quenched conformations significantly increases in relative population under environmental conditions mimicking high light.
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Affiliation(s)
| | - Hsiang-Yu Yang
- †Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Tjaart P J Krüger
- ‡Department of Physics, University of Pretoria, Private bag X20, Hatfield 0028, South Africa
| | - Pengqi Xu
- §Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam and LaserLab Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Michal Gwizdala
- §Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam and LaserLab Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Rienk van Grondelle
- §Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam and LaserLab Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Roberta Croce
- §Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam and LaserLab Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - W E Moerner
- †Department of Chemistry, Stanford University, Stanford, California 94305, United States
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Tabares LC, Gupta A, Aartsma TJ, Canters GW. Tracking electrons in biological macromolecules: from ensemble to single molecule. Molecules 2014; 19:11660-78. [PMID: 25102116 PMCID: PMC6271485 DOI: 10.3390/molecules190811660] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 07/23/2014] [Accepted: 07/25/2014] [Indexed: 11/29/2022] Open
Abstract
Nature utilizes oxido-reductases to cater to the energy demands of most biochemical processes in respiratory species. Oxido-reductases are capable of meeting this challenge by utilizing redox active sites, often containing transition metal ions, which facilitate movement and relocation of electrons/protons to create a potential gradient that is used to energize redox reactions. There has been a consistent struggle by researchers to estimate the electron transfer rate constants in physiologically relevant processes. This review provides a brief background on the measurements of electron transfer rates in biological molecules, in particular Cu-containing enzymes, and highlights the recent advances in monitoring these electron transfer events at the single molecule level or better to say, at the individual event level.
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Affiliation(s)
- Leandro C Tabares
- Commissariat à l'Energie Atomique, Institut de Biologie et de Technologies de Saclay, Service de Bioénergétique, Biologie Structurale et Mécanismes (CNRS UMR-8221), Gif-sur-Yvette Cedex 91191, France
| | - Ankur Gupta
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, PO Box 9504, RA Leiden 2300, The Netherlands
| | - Thijs J Aartsma
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, PO Box 9504, RA Leiden 2300, The Netherlands
| | - Gerard W Canters
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, PO Box 9504, RA Leiden 2300, The Netherlands.
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35
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Bockenhauer SD, Duncan TM, Moerner WE, Börsch M. The regulatory switch of F 1-ATPase studied by single-molecule FRET in the ABEL Trap. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2014; 8950:89500H. [PMID: 25309100 DOI: 10.1117/12.2042688] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
F1-ATPase is the soluble portion of the membrane-embedded enzyme FoF1-ATP synthase that catalyzes the production of adenosine triphosphate in eukaryotic and eubacterial cells. In reverse, the F1 part can also hydrolyze ATP quickly at three catalytic binding sites. Therefore, catalysis of 'non-productive' ATP hydrolysis by F1 (or FoF1) must be minimized in the cell. In bacteria, the ε subunit is thought to control and block ATP hydrolysis by mechanically inserting its C-terminus into the rotary motor region of F1. We investigate this proposed mechanism by labeling F1 specifically with two fluorophores to monitor the C-terminus of the ε subunit by Förster resonance energy transfer. Single F1 molecules are trapped in solution by an Anti-Brownian electrokinetic trap which keeps the FRET-labeled F1 in place for extended observation times of several hundreds of milliseconds, limited by photobleaching. FRET changes in single F1 and FRET histograms for different biochemical conditions are compared to evaluate the proposed regulatory mechanism.
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Affiliation(s)
- Samuel D Bockenhauer
- Department of Chemistry, Stanford University, Stanford, CA, USA ; Department of Physics, Stanford University, Stanford, CA, USA
| | - Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
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36
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Single-molecule motions enable direct visualization of biomolecular interactions in solution. Nat Methods 2014; 11:555-8. [PMID: 24608179 DOI: 10.1038/nmeth.2882] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 01/25/2014] [Indexed: 11/08/2022]
Abstract
Biomolecular interactions are generally accompanied by modifications in size and charge of biomolecules at the nanometer scale. Here we describe a single-molecule method to sense these changes in real time based on statistical learning of diffusive and electric field-induced motion parameters of a trapped molecule in solution. We demonstrate the approach by resolving a monomer-trimer mixture along a protein dissociation pathway and visualizing the binding-unbinding kinetics of a single DNA molecule.
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37
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Duncan TM, Düser MG, Heitkamp T, McMillan DGG, Börsch M. Regulatory conformational changes of the ε subunit in single FRET-labeled F oF 1-ATP synthase. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2014; 8948:89481J. [PMID: 25076824 DOI: 10.1117/12.2040463] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Subunit ε is an intrinsic regulator of the bacterial FoF1-ATP synthase, the ubiquitous membrane-embedded enzyme that utilizes a proton motive force in most organisms to synthesize adenosine triphosphate (ATP). The C-terminal domain of ε can extend into the central cavity formed by the α and β subunits, as revealed by the recent X-ray structure of the F1 portion of the Escherichia coli enzyme. This insertion blocks the rotation of the central γ subunit and, thereby, prevents wasteful ATP hydrolysis. Here we aim to develop an experimental system that can reveal conditions under which ε inhibits the holoenzyme FoF1-ATP synthase in vitro. Labeling the C-terminal domain of ε and the γ subunit specifically with two different fluorophores for single-molecule Förster resonance energy transfer (smFRET) allowed monitoring of the conformation of ε in the reconstituted enzyme in real time. New mutants were made for future three-color smFRET experiments to unravel the details of regulatory conformational changes in ε.
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Affiliation(s)
- Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Monika G Düser
- 3 Institute of Physics, Stuttgart University, Stuttgart, Germany
| | - Thomas Heitkamp
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Duncan G G McMillan
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
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38
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Schlau-Cohen GS, Bockenhauer S, Wang Q, Moerner WE. Single-molecule spectroscopy of photosynthetic proteins in solution: exploration of structure–function relationships. Chem Sci 2014. [DOI: 10.1039/c4sc00582a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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39
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Cummins Z, Probst R, Shapiro B. Electrokinetic tweezing: three-dimensional manipulation of microparticles by real-time imaging and flow control. LAB ON A CHIP 2013; 13:4040-4046. [PMID: 23945777 DOI: 10.1039/c3lc50674f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Electrokinetic tweezing in three dimensions is achieved for the first time using a multi-layer microfluidic device, a model-based control algorithm, and a 3D imaging algorithm connected in a feedback loop. Here we demonstrate steering of microparticles along 3D trajectories and trapping in all three dimensions with accuracy as good as 1 μm.
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Affiliation(s)
- Zachary Cummins
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA.
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40
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Ropp C, Cummins Z, Nah S, Qin S, Seog JH, Lee SB, Fourkas JT, Shapiro B, Waks E. Fabrication of nanoassemblies using flow control. NANO LETTERS 2013; 13:3936-3941. [PMID: 23883172 DOI: 10.1021/nl402059u] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Synthetic nanostructures, such as nanoparticles and nanowires, can serve as modular building blocks for integrated nanoscale systems. We demonstrate a microfluidic approach for positioning, orienting, and assembling such nanostructures into nanoassemblies. We use flow control combined with a cross-linking photoresist to position and immobilize nanostructures in desired positions and orientations. Immobilized nanostructures can serve as pivots, barriers, and guides for precise placement of subsequent nanostructures.
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Affiliation(s)
- Chad Ropp
- Department of Electrical and Computer Engineering/IREAP, University of Maryland, College Park, Maryland 20742, United States
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41
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Zarrabi N, Ernst S, Verhalen B, Wilkens S, Börsch M. Analyzing conformational dynamics of single P-glycoprotein transporters by Förster resonance energy transfer using hidden Markov models. Methods 2013; 66:168-79. [PMID: 23891547 DOI: 10.1016/j.ymeth.2013.07.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 07/04/2013] [Accepted: 07/16/2013] [Indexed: 12/15/2022] Open
Abstract
Single-molecule Förster resonance energy (smFRET) transfer has become a powerful tool for observing conformational dynamics of biological macromolecules. Analyzing smFRET time trajectories allows to identify the state transitions occuring on reaction pathways of molecular machines. Previously, we have developed a smFRET approach to monitor movements of the two nucleotide binding domains (NBDs) of P-glycoprotein (Pgp) during ATP hydrolysis driven drug transport in solution. One limitation of this initial work was that single-molecule photon bursts were analyzed by visual inspection with manual assignment of individual FRET levels. Here a fully automated analysis of Pgp smFRET data using hidden Markov models (HMM) for transitions up to 9 conformational states is applied. We propose new estimators for HMMs to integrate the information of fluctuating intensities in confocal smFRET measurements of freely diffusing lipid bilayer bound membrane proteins in solution. HMM analysis strongly supports that under conditions of steady state turnover, conformational states with short NBD distances and short dwell times are more populated compared to conditions without nucleotide or transport substrate present.
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Affiliation(s)
- Nawid Zarrabi
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University Jena, 07743 Jena, Germany; 3rd Institute of Physics, University of Stuttgart, 70550 Stuttgart, Germany
| | - Stefan Ernst
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Brandy Verhalen
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Stephan Wilkens
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University Jena, 07743 Jena, Germany; 3rd Institute of Physics, University of Stuttgart, 70550 Stuttgart, Germany.
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42
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Single-molecule spectroscopy reveals photosynthetic LH2 complexes switch between emissive states. Proc Natl Acad Sci U S A 2013; 110:10899-903. [PMID: 23776245 DOI: 10.1073/pnas.1310222110] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Photosynthetic organisms flourish under low light intensities by converting photoenergy to chemical energy with near unity quantum efficiency and under high light intensities by safely dissipating excess photoenergy and deleterious photoproducts. The molecular mechanisms balancing these two functions remain incompletely described. One critical barrier to characterizing the mechanisms responsible for these processes is that they occur within proteins whose excited-state properties vary drastically among individual proteins and even within a single protein over time. In ensemble measurements, these excited-state properties appear only as the average value. To overcome this averaging, we investigate the purple bacterial antenna protein light harvesting complex 2 (LH2) from Rhodopseudomonas acidophila at the single-protein level. We use a room-temperature, single-molecule technique, the anti-Brownian electrokinetic trap, to study LH2 in a solution-phase (nonperturbative) environment. By performing simultaneous measurements of fluorescence intensity, lifetime, and spectra of single LH2 complexes, we identify three distinct states and observe transitions occurring among them on a timescale of seconds. Our results reveal that LH2 complexes undergo photoactivated switching to a quenched state, likely by a conformational change, and thermally revert to the ground state. This is a previously unobserved, reversible quenching pathway, and is one mechanism through which photosynthetic organisms can adapt to changes in light intensities.
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43
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Tanyeri M, Schroeder CM. Manipulation and confinement of single particles using fluid flow. NANO LETTERS 2013; 13:2357-64. [PMID: 23682823 PMCID: PMC3689313 DOI: 10.1021/nl4008437] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
High precision control of micro- and nanoscale objects in aqueous media is an essential technology for nanoscience and engineering. Existing methods for particle trapping primarily depend on optical, magnetic, electrokinetic, and acoustic fields. In this work, we report a new hydrodynamic flow based approach that allows for fine-scale manipulation and positioning of single micro- and nanoscale particles using automated fluid flow. As a proof-of-concept, we demonstrate trapping and two-dimensional (2D) manipulation of 500 nm and 2.2 μm diameter particles with a positioning precision as small as 180 nm during confinement. By adjusting a single flow parameter, we further show that the shape of the effective trap potential can be efficiently controlled. Finally, we demonstrate two distinct features of the flow-based trapping method, including isolation of a single particle from a crowded particle solution and active control over the surrounding medium of a trapped object. The 2D flow-based trapping method described here further expands the micro/nanomanipulation toolbox for small particles and holds strong promise for applications in biology, chemistry, and materials research.
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Affiliation(s)
- Melikhan Tanyeri
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Charles M. Schroeder
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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44
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Michalet X, Colyer RA, Scalia G, Ingargiola A, Lin R, Millaud JE, Weiss S, Siegmund OHW, Tremsin AS, Vallerga JV, Cheng A, Levi M, Aharoni D, Arisaka K, Villa F, Guerrieri F, Panzeri F, Rech I, Gulinatti A, Zappa F, Ghioni M, Cova S. Development of new photon-counting detectors for single-molecule fluorescence microscopy. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120035. [PMID: 23267185 PMCID: PMC3538434 DOI: 10.1098/rstb.2012.0035] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Two optical configurations are commonly used in single-molecule fluorescence microscopy: point-like excitation and detection to study freely diffusing molecules, and wide field illumination and detection to study surface immobilized or slowly diffusing molecules. Both approaches have common features, but also differ in significant aspects. In particular, they use different detectors, which share some requirements but also have major technical differences. Currently, two types of detectors best fulfil the needs of each approach: single-photon-counting avalanche diodes (SPADs) for point-like detection, and electron-multiplying charge-coupled devices (EMCCDs) for wide field detection. However, there is room for improvements in both cases. The first configuration suffers from low throughput owing to the analysis of data from a single location. The second, on the other hand, is limited to relatively low frame rates and loses the benefit of single-photon-counting approaches. During the past few years, new developments in point-like and wide field detectors have started addressing some of these issues. Here, we describe our recent progresses towards increasing the throughput of single-molecule fluorescence spectroscopy in solution using parallel arrays of SPADs. We also discuss our development of large area photon-counting cameras achieving subnanosecond resolution for fluorescence lifetime imaging applications at the single-molecule level.
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Affiliation(s)
- X Michalet
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095-1547, USA.
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45
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Sielaff H, Börsch M. Twisting and subunit rotation in single F(O)(F1)-ATP synthase. Philos Trans R Soc Lond B Biol Sci 2012; 368:20120024. [PMID: 23267178 DOI: 10.1098/rstb.2012.0024] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
F(O)F(1)-ATP synthases are ubiquitous proton- or ion-powered membrane enzymes providing ATP for all kinds of cellular processes. The mechanochemistry of catalysis is driven by two rotary nanomotors coupled within the enzyme. Their different step sizes have been observed by single-molecule microscopy including videomicroscopy of fluctuating nanobeads attached to single enzymes and single-molecule Förster resonance energy transfer. Here we review recent developments of approaches to monitor the step size of subunit rotation and the transient elastic energy storage mechanism in single F(O)F(1)-ATP synthases.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Nonnenplan 2-4, 07743 Jena, Germany
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46
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Wang Q, Moerner WE. Lifetime and Spectrally Resolved Characterization of the Photodynamics of Single Fluorophores in Solution Using the Anti-Brownian Electrokinetic Trap. J Phys Chem B 2012. [DOI: 10.1021/jp308949d] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Quan Wang
- Department
of Chemistry and ‡Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department
of Chemistry and ‡Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
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47
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Wang Q, Goldsmith RH, Jiang Y, Bockenhauer SD, Moerner W. Probing single biomolecules in solution using the anti-Brownian electrokinetic (ABEL) trap. Acc Chem Res 2012; 45:1955-64. [PMID: 22616716 DOI: 10.1021/ar200304t] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Single-molecule fluorescence measurements allow researchers to study asynchronous dynamics and expose molecule-to-molecule structural and behavioral diversity, which contributes to the understanding of biological macromolecules. To provide measurements that are most consistent with the native environment of biomolecules, researchers would like to conduct these measurements in the solution phase if possible. However, diffusion typically limits the observation time to approximately 1 ms in many solution-phase single-molecule assays. Although surface immobilization is widely used to address this problem, this process can perturb the system being studied and contribute to the observed heterogeneity. Combining the technical capabilities of high-sensitivity single-molecule fluorescence microscopy, real-time feedback control and electrokinetic flow in a microfluidic chamber, we have developed a device called the anti-Brownian electrokinetic (ABEL) trap to significantly prolong the observation time of single biomolecules in solution. We have applied the ABEL trap method to explore the photodynamics and enzymatic properties of a variety of biomolecules in aqueous solution and present four examples: the photosynthetic antenna allophycocyanin, the chaperonin enzyme TRiC, a G protein-coupled receptor protein, and the blue nitrite reductase redox enzyme. These examples illustrate the breadth and depth of information which we can extract in studies of single biomolecules with the ABEL trap. When confined in the ABEL trap, the photosynthetic antenna protein allophycocyanin exhibits rich dynamics both in its emission brightness and its excited state lifetime. As each molecule discontinuously converts from one emission/lifetime level to another in a primarily correlated way, it undergoes a series of state changes. We studied the ATP binding stoichiometry of the multi-subunit chaperonin enzyme TRiC in the ABEL trap by counting the number of hydrolyzed Cy3-ATP using stepwise photobleaching. Unlike ensemble measurements, the observed ATP number distributions depart from the standard cooperativity models. Single copies of detergent-stabilized G protein-coupled receptor proteins labeled with a reporter fluorophore also show discontinuous changes in emission brightness and lifetime, but the various states visited by the single molecules are broadly distributed. As an agonist binds, the distributions shift slightly toward a more rigid conformation of the protein. By recording the emission of a reporter fluorophore which is quenched by reduction of a nearby type I Cu center, we probed the enzymatic cycle of the redox enzyme nitrate reductase. We determined the rate constants of a model of the underlying kinetics through an analysis of the dwell times of the high/low intensity levels of the fluorophore versus nitrite concentration.
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Affiliation(s)
- Quan Wang
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
| | - Randall H. Goldsmith
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
| | - Yan Jiang
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
| | - Samuel D. Bockenhauer
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
| | - W.E. Moerner
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
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48
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Kamagata K, Kawaguchi T, Iwahashi Y, Baba A, Fujimoto K, Komatsuzaki T, Sambongi Y, Goto Y, Takahashi S. Long-Term Observation of Fluorescence of Free Single Molecules To Explore Protein-Folding Energy Landscapes. J Am Chem Soc 2012; 134:11525-32. [DOI: 10.1021/ja3020555] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Kiyoto Kamagata
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai
980-8577, Japan
| | - Toshifumi Kawaguchi
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai
980-8577, Japan
| | - Yoshitomo Iwahashi
- Optonica Corporation, 1-26-11, Matsuigaoka, Kyotanabe,
Kyoto 610-0353, Japan
| | - Akinori Baba
- RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi,
Chuo-ku, Kobe 650-0047, Japan
| | - Kazuya Fujimoto
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tamiki Komatsuzaki
- Molecule & Life Nonlinear Sciences Laboratory, Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo 001-0020, Japan
- Core Research for Evolutional Science and
Technology, Japan Science and Technology Agency, 4-1-8, Honmachi, Kawaguchi, Saitama 332-0012, Japan
| | - Yoshihiro Sambongi
- Core Research for Evolutional Science and
Technology, Japan Science and Technology Agency, 4-1-8, Honmachi, Kawaguchi, Saitama 332-0012, Japan
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4, Kagamiyama, Higashi-Hiroshima,
Hiroshima 739-8528, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Takahashi
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai
980-8577, Japan
- Core Research for Evolutional Science and
Technology, Japan Science and Technology Agency, 4-1-8, Honmachi, Kawaguchi, Saitama 332-0012, Japan
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49
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Lesoine JF, Venkataraman PA, Maloney PC, Dumont M, Novotny L. Nanochannel-based single molecule recycling. NANO LETTERS 2012; 12:3273-8. [PMID: 22662745 PMCID: PMC3377747 DOI: 10.1021/nl301341m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We present a method for measuring the fluorescence from a single molecule hundreds of times without surface immobilization. The approach is based on the use of electroosmosis to repeatedly drive a single target molecule in a fused silica nanochannel through a stationary laser focus. Single molecule fluorescence detected during the transit time through the laser focus is used to repeatedly reverse the electrical potential controlling the flow direction. Our method does not rely on continuous observation and therefore is less susceptible to fluorescence blinking than existing fluorescence-based trapping schemes. The variation in the turnaround times can be used to measure the diffusion coefficient on a single molecule level. We demonstrate the ability to recycle both proteins and DNA in nanochannels and show that the procedure can be combined with single-pair Förster energy transfer. Nanochannel-based single molecule recycling holds promise for studying conformational dynamics on the same single molecule in solution and without surface tethering.
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Affiliation(s)
- John F. Lesoine
- Institute of Optics, University of Rochester, Rochester NY 14627
| | - Prahnesh A. Venkataraman
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14627
| | - Peter C. Maloney
- Department of Physiology, Johns Hopkins Medical School, Baltimore, MD, USA
| | - Mark Dumont
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14627
| | - Lukas Novotny
- Institute of Optics, University of Rochester, Rochester NY 14627
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50
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Liu C, Qu Y, Luo Y, Fang N. Recent advances in single-molecule detection on micro- and nano-fluidic devices. Electrophoresis 2012; 32:3308-18. [PMID: 22134976 DOI: 10.1002/elps.201100159] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single-molecule detection (SMD) allows static and dynamic heterogeneities from seemingly equal molecules to be revealed in the studies of molecular structures and intra- and inter-molecular interactions. Micro- and nanometer-sized structures, including channels, chambers, droplets, etc., in microfluidic and nanofluidic devices allow diffusion-controlled reactions to be accelerated and provide high signal-to-noise ratio for optical signals. These two active research frontiers have been combined to provide unprecedented capabilities for chemical and biological studies. This review summarizes the advances of SMD performed on microfluidic and nanofluidic devices published in the past five years. The latest developments on optical SMD methods, microfluidic SMD platforms, and on-chip SMD applications are discussed herein and future development directions are also envisioned.
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Affiliation(s)
- Chang Liu
- Ames Laboratory, US Department of Energy, Ames, Iowa, USA
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