1
|
Johnson A, Welsher KD. Single-nanoparticle electrophoretic mobility determination and trapping using active-feedback 3D tracking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602591. [PMID: 39131346 PMCID: PMC11312477 DOI: 10.1101/2024.07.08.602591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Nanoparticles (NP) are versatile materials with widespread applications across medicine and engineering. Despite rapid incorporation into drug delivery, therapeutics, and many more areas of research and development, there is a lack of robust characterization methods. Light scattering techniques such as dynamic light scattering (DLS) and electrophoretic light scattering (ELS) use an ensemble-averaged approach to the characterization of nanoparticle size and electrophoretic mobility (EM), leading to inaccuracies when applied to polydisperse or heterogeneous populations. To address this lack of single-nanoparticle characterization, this work applies 3D Single-Molecule Active Real-time Tracking (3D-SMART) to simultaneously determine NP size and EM on a per-particle basis. Single-nanoparticle EM is determined by using active feedback to "lock on" to a single particle and apply an oscillating electric field along one axis. A maximum likelihood approach is applied to extract the single-particle EM from the oscillating nanoparticle position along the field-actuated axis, while mean squared displacement is used along the non-actuated axes to determine size. Unfunctionalized and carboxyl-functionalized polystyrene NPs are found to have unique EM based on their individual size and surface characteristics, and it is demonstrated that single-nanoparticle EM is a more precise tool for distinguishing unique NP preparations than diffusion alone, able to determine the charge number of individual NPs to an uncertainty of less than 30. This method also explored individual nanoparticle EM in various ionic strengths (0.25-5 mM) and found decreased EM as a function of increasing ionic strength, in agreement with results determined via bulk characterization methods. Finally, it is demonstrated that the electric field can be manipulated in real time in response to particle position, resulting in one-dimensional electrokinetic trapping. Critically, this new single-nanoparticle EM determination and trapping method does not require microfluidics, opening the possibility for the exploration of single-nanoparticle EM in live tissue and more comprehensive characterization of nanoparticles in biologically relevant environments.
Collapse
Affiliation(s)
- Alexis Johnson
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Kevin D Welsher
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Nguyen TD, Chen YI, Chen LH, Yeh HC. Recent Advances in Single-Molecule Tracking and Imaging Techniques. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:253-284. [PMID: 37314878 DOI: 10.1146/annurev-anchem-091922-073057] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Since the early 1990s, single-molecule detection in solution at room temperature has enabled direct observation of single biomolecules at work in real time and under physiological conditions, providing insights into complex biological systems that the traditional ensemble methods cannot offer. In particular, recent advances in single-molecule tracking techniques allow researchers to follow individual biomolecules in their native environments for a timescale of seconds to minutes, revealing not only the distinct pathways these biomolecules take for downstream signaling but also their roles in supporting life. In this review, we discuss various single-molecule tracking and imaging techniques developed to date, with an emphasis on advanced three-dimensional (3D) tracking systems that not only achieve ultrahigh spatiotemporal resolution but also provide sufficient working depths suitable for tracking single molecules in 3D tissue models. We then summarize the observables that can be extracted from the trajectory data. Methods to perform single-molecule clustering analysis and future directions are also discussed.
Collapse
Affiliation(s)
- Trung Duc Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Yuan-I Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Limin H Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
- Texas Materials Institute, University of Texas at Austin, Austin, Texas, USA
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization. Nat Commun 2023; 14:1336. [PMID: 36906676 PMCID: PMC10008558 DOI: 10.1038/s41467-023-36879-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/17/2023] [Indexed: 03/13/2023] Open
Abstract
Reaching sub-millisecond 3D tracking of individual molecules in living cells would enable direct measurements of diffusion-limited macromolecular interactions under physiological conditions. Here, we present a 3D tracking principle that approaches the relevant regime. The method is based on the true excitation point spread function and cross-entropy minimization for position localization of moving fluorescent reporters. Tests on beads moving on a stage reaches 67 nm lateral and 109 nm axial precision with a time resolution of 0.84 ms at a photon count rate of 60 kHz; the measurements agree with the theoretical and simulated predictions. Our implementation also features a method for microsecond 3D PSF positioning and an estimator for diffusion analysis of tracking data. Finally, we successfully apply these methods to track the Trigger Factor protein in living bacterial cells. Overall, our results show that while it is possible to reach sub-millisecond live-cell single-molecule tracking, it is still hard to resolve state transitions based on diffusivity at this time scale.
Collapse
|
6
|
Johnson C, Exell J, Lin Y, Aguilar J, Welsher KD. Capturing the start point of the virus-cell interaction with high-speed 3D single-virus tracking. Nat Methods 2022; 19:1642-1652. [PMID: 36357694 PMCID: PMC10154077 DOI: 10.1038/s41592-022-01672-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 09/30/2022] [Indexed: 11/12/2022]
Abstract
The early stages of the virus-cell interaction have long evaded observation by existing microscopy methods due to the rapid diffusion of virions in the extracellular space and the large three-dimensional cellular structures involved. Here we present an active-feedback single-particle tracking method with simultaneous volumetric imaging of the live cell environment called 3D-TrIm to address this knowledge gap. 3D-TrIm captures the extracellular phase of the infectious cycle in what we believe is unprecedented detail. We report what are, to our knowledge, previously unobserved phenomena in the early stages of the virus-cell interaction, including skimming contact events at the millisecond timescale, orders of magnitude change in diffusion coefficient upon binding and cylindrical and linear diffusion modes along cellular protrusions. Finally, we demonstrate how this method can move single-particle tracking from simple monolayer culture toward more tissue-like conditions by tracking single virions in tightly packed epithelial cells. This multiresolution method presents opportunities for capturing fast, three-dimensional processes in biological systems.
Collapse
Affiliation(s)
| | - Jack Exell
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Yuxin Lin
- Department of Chemistry, Duke University, Durham, NC, USA
| | | | | |
Collapse
|
7
|
Niver AJ, Welsher KD. Combined online Bayesian and windowed estimation of background and signal localization facilitates active-feedback particle tracking in complex environments. J Chem Phys 2022; 157:184108. [PMID: 36379789 PMCID: PMC9652022 DOI: 10.1063/5.0118317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/21/2022] [Indexed: 11/14/2022] Open
Abstract
Despite successes in tracking single molecules in vitro, the extension of active-feedback single-particle methods to tracking rapidly diffusing and unconfined proteins in live cells has not been realized. Since the existing active-feedback localization methods localize particles in real time assuming zero background, they are ill-suited to track in the inhomogeneous background environment of a live cell. Here, we develop a windowed estimation of signal and background levels using recent data to estimate the current particle brightness and background intensity. These estimates facilitate recursive Bayesian position estimation, improving upon current Kalman-based localization methods. Combined, online Bayesian and windowed estimation of background and signal (COBWEBS) surpasses existing 2D localization methods. Simulations demonstrate improved localization accuracy and responsivity in a homogeneous background for selected particle and background intensity combinations. Improved or similar performance of COBWEBS tracking extends to the majority of signal and background combinations explored. Furthermore, improved tracking durations are demonstrated in the presence of heterogeneous backgrounds for multiple particle intensities, diffusive speeds, and background patterns. COBWEBS can accurately track particles in the presence of high and nonuniform backgrounds, including intensity changes of up to three times the particle's intensity, making it a prime candidate for advancing active-feedback single fluorophore tracking to the cellular interior.
Collapse
Affiliation(s)
- Anastasia J. Niver
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Kevin D. Welsher
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| |
Collapse
|
8
|
van Heerden B, Kruger T. Theoretical comparison of real-time feedback-driven single-particle tracking techniques. J Chem Phys 2022; 157:084111. [DOI: 10.1063/5.0096729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Real-time feedback-driven single-particle tracking is a technique that uses feedbackcontrol to enable single-molecule spectroscopy of freely diffusing particles in nativeor near-native environments. A number of different RT-FD-SPT approaches exist,and comparisons between methods based on experimental results are of limited usedue to differences in samples and setups. In this study, we used statistical calcu-lations and dynamical simulations to directly compare the performance of differentmethods. The methods considered were the orbital method, the Knight's Tour (gridscan) method and MINFLUX, and we considered both fluorescence-based and inter-ferometric scattering (iSCAT) approaches. There is a fundamental trade-off betweenprecision and speed, with the Knight's Tour method being able to track the fastestdiffusion but with low precision, and MINFLUX being the most precise but onlytracking slow diffusion. To compare iSCAT and fluorescence, different biologicalsamples were considered, including labeled and intrinsically fluorescent samples. Thesuccess of iSCAT as compared to fluorescence is strongly dependent on the particlesize and the density and photophysical properties of the fluorescent particles. Usinga wavelength for iSCAT that is negligibly absorbed by the tracked particle allowsan increased illumination intensity, which results in iSCAT providing better trackingfor most samples. This work highlights the fundamental aspects of performance inRT-FD-SPT and should assist with the selection of an appropriate method for a par-ticular application. The approach used can easily be extended to other RT-FD-SPTmethods.
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Carpenter W, Lavania AA, Borden JS, Oltrogge LM, Perez D, Dahlberg PD, Savage DF, Moerner WE. Ratiometric Sensing of Redox Environments Inside Individual Carboxysomes Trapped in Solution. J Phys Chem Lett 2022; 13:4455-4462. [PMID: 35549289 PMCID: PMC9150107 DOI: 10.1021/acs.jpclett.2c00782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Diffusion of biological nanoparticles in solution impedes our ability to continuously monitor individual particles and measure their physical and chemical properties. To overcome this, we previously developed the interferometric scattering anti-Brownian electrokinetic (ISABEL) trap, which uses scattering to localize a particle and applies electrokinetic forces that counteract Brownian motion, thus enabling extended observation. Here we present an improved ISABEL trap that incorporates a near-infrared scatter illumination beam and rapidly interleaves 405 and 488 nm fluorescence excitation reporter beams. With the ISABEL trap, we monitored the internal redox environment of individual carboxysomes labeled with the ratiometric redox reporter roGFP2. Carboxysomes widely vary in scattering contrast (reporting on size) and redox-dependent ratiometric fluorescence. Furthermore, we used redox sensing to explore the chemical kinetics within intact carboxysomes, where bulk measurements may contain unwanted contributions from aggregates or interfering fluorescent proteins. Overall, we demonstrate the ISABEL trap's ability to sensitively monitor nanoscale biological objects, enabling new experiments on these systems.
Collapse
Affiliation(s)
- William
B. Carpenter
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Abhijit A. Lavania
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
| | - Julia S. Borden
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California 94720, United States
| | - Luke M. Oltrogge
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California 94720, United States
| | - Davis Perez
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Peter D. Dahlberg
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Division
of CryoEM and Bioimaging, SSRL, SLAC National
Accelerator Laboratory, Menlo Park, California 94025, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California 94720, 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
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Probing DNA-protein interactions using single-molecule diffusivity contrast. BIOPHYSICAL REPORTS 2021; 1:100009. [PMID: 36425309 PMCID: PMC9680706 DOI: 10.1016/j.bpr.2021.100009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/20/2021] [Indexed: 11/28/2022]
Abstract
Single-molecule fluorescence investigations of protein-nucleic acid interactions require robust means to identify the binding state of individual substrate molecules in real time. Here, we show that diffusivity contrast, widely used in fluorescence correlation spectroscopy at the ensemble level and in single-particle tracking on individual (but slowly diffusing) species, can be used as a general readout to determine the binding state of single DNA molecules with unlabeled proteins in solution. We first describe the technical basis of drift-free single-molecule diffusivity measurements in an anti-Brownian electrokinetic trap. We then cross-validate our method with protein-induced fluorescence enhancement, a popular technique to detect protein binding on nucleic acid substrates with single-molecule sensitivity. We extend an existing hydrodynamic modeling framework to link measured diffusivity to particular DNA-protein structures and obtain good agreement between the measured and predicted diffusivity values. Finally, we show that combining diffusivity contrast with protein-induced fluorescence enhancement allows simultaneous mapping of binding stoichiometry and location on individual DNA-protein complexes, potentially enhancing single-molecule views of relevant biophysical processes.
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
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.
Collapse
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.
| |
Collapse
|
15
|
Dienerowitz M, Howard JAL, Quinn SD, Dienerowitz F, Leake MC. Single-molecule FRET dynamics of molecular motors in an ABEL trap. Methods 2021; 193:96-106. [PMID: 33571667 DOI: 10.1016/j.ymeth.2021.01.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/22/2021] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
Single-molecule Förster resonance energy transfer (smFRET) of molecular motors provides transformative insights into their dynamics and conformational changes both at high temporal and spatial resolution simultaneously. However, a key challenge of such FRET investigations is to observe a molecule in action for long enough without restricting its natural function. The Anti-Brownian ELectrokinetic Trap (ABEL trap) sets out to combine smFRET with molecular confinement to enable observation times of up to several seconds while removing any requirement of tethered surface attachment of the molecule in question. In addition, the ABEL trap's inherent ability to selectively capture FRET active molecules accelerates the data acquisition process. In this work we exemplify the capabilities of the ABEL trap in performing extended timescale smFRET measurements on the molecular motor Rep, which is crucial for removing protein blocks ahead of the advancing DNA replication machinery and for restarting stalled DNA replication. We are able to monitor single Rep molecules up to 6 seconds with sub-millisecond time resolution capturing multiple conformational switching events during the observation time. Here we provide a step-by-step guide for the rational design, construction and implementation of the ABEL trap for smFRET detection of Rep in vitro. We include details of how to model the electric potential at the trap site and use Hidden Markov analysis of the smFRET trajectories.
Collapse
Affiliation(s)
- Maria Dienerowitz
- Single-Molecule Microscopy Group, Universitätsklinikum Jena, Nonnenplan 2 - 4, 07743 Jena, Germany.
| | - Jamieson A L Howard
- Department of Physics, University of York, Heslington, York YO10 5DD, UK; Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Steven D Quinn
- Department of Physics, University of York, Heslington, York YO10 5DD, UK; York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
| | - Frank Dienerowitz
- Ernst-Abbe-Hochschule Jena, University of Applied Sciences, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
| | - Mark C Leake
- Department of Physics, University of York, Heslington, York YO10 5DD, UK; Department of Biology, University of York, Heslington, York YO10 5DD, UK; York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
| |
Collapse
|
16
|
|
17
|
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.
Collapse
|
18
|
Hou S, Welsher K. An Adaptive Real-Time 3D Single Particle Tracking Method for Monitoring Viral First Contacts. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1903039. [PMID: 31529595 PMCID: PMC6824287 DOI: 10.1002/smll.201903039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/25/2019] [Indexed: 05/26/2023]
Abstract
Here, an adaptive real-time 3D single particle tracking method is proposed, which is capable of capturing heterogeneous dynamics. Using a real-time measurement of a rapidly diffusing particle's positional variance, the 3D precision adaptive real-time tracking (3D-PART) microscope adjusts active-feedback parameters to trade tracking speed for precision on demand. This technique is demonstrated first on immobilized fluorescent nanoparticles, with a greater than twofold increase in the lateral localization precision (≈25 to ≈11 nm at 1 ms sampling) as well as a smaller increase in the axial localization precision (≈ 68 to ≈45 nm). 3D-PART also shows a marked increase in the precision when tracking freely diffusing particles, with lateral precision increasing from ≈100 to ≈70 nm for particles diffusing at 4 µm2 s-1 , although with a sacrifice in the axial precision (≈250 to ≈350 nm). This adaptive microscope is then applied to monitoring the viral first contacts of virus-like particles to the surface of live cells, allowing direct and continuous measurement of the viral particle at initial contact with the cell surface.
Collapse
Affiliation(s)
- Shangguo Hou
- Department of Chemistry, Duke University, 124 Science Dr., Durham, NC, 27708, USA
| | - Kevin Welsher
- Department of Chemistry, Duke University, 124 Science Dr., Durham, NC, 27708, USA
| |
Collapse
|
19
|
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.
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Yang HY, Moerner WE. Resolving Mixtures in Solution by Single-Molecule Rotational Diffusivity. NANO LETTERS 2018; 18:5279-5287. [PMID: 30001492 DOI: 10.1021/acs.nanolett.8b02280] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Sensing the size of individual molecules in an ensemble has proven to be a powerful tool to investigate biomolecular interactions and association-dissociation processes. In biologically relevant solution environments, molecular size is often sensed by translational or rotational diffusivity. The rotational diffusivity is more sensitive to the size and conformation of the molecules as it is inversely proportional to the cube of the hydrodynamic radius, as opposed to the inverse linear dependence of the translational diffusion coefficient. Single-molecule rotational diffusivity has been measured with time-resolved fluorescence anisotropy decay, but the ability to sense different sizes has been restricted by the limited number of photons available or has required surface attachment to observe each molecule longer, and the attachment may be perturbative. To address these limitations, we show how to measure and monitor single-molecule rotational diffusivity by combining the solution-phase Anti-Brownian ELectrokinetic (ABEL) trap and maximum likelihood analysis of time-resolved fluorescence anisotropy based on the information inherent in each detected photon. We demonstrate this approach by resolving a mixture of single- and double-stranded fluorescently labeled DNA molecules at equilibrium, freely rotating in a native solution environment. The rotational diffusivity, fluorescence brightness and lifetime, and initial and steady-state anisotropy are simultaneously determined for each trapped single DNA molecule. The time resolution and precision of this method are analyzed using statistical signal analysis and simulations. We present key parameters that define the usefulness of a particular fluorescent label for extracting molecular size information from single-molecule rotational diffusivity measurements.
Collapse
Affiliation(s)
- Hsiang-Yu Yang
- Department of Chemistry , Stanford University , Stanford , California 94305-4401 , United States
| | - W E Moerner
- Department of Chemistry , Stanford University , Stanford , California 94305-4401 , United States
| |
Collapse
|
22
|
Eilers Y, Ta H, Gwosch KC, Balzarotti F, Hell SW. MINFLUX monitors rapid molecular jumps with superior spatiotemporal resolution. Proc Natl Acad Sci U S A 2018; 115:6117-6122. [PMID: 29844182 PMCID: PMC6004438 DOI: 10.1073/pnas.1801672115] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Compared with localization schemes solely based on evaluating patterns of molecular emission, the recently introduced single-molecule localization concept called MINFLUX and the fluorescence nanoscopies derived from it require up to orders of magnitude fewer emissions to attain single-digit nanometer resolution. Here, we demonstrate that the lower number of required fluorescence photons enables MINFLUX to detect molecular movements of a few nanometers at a temporal sampling of well below 1 millisecond. Using fluorophores attached to thermally fluctuating DNA strands as model systems, we demonstrate that measurement times as short as 400 microseconds suffice to localize fluorescent molecules with ∼2-nm precision. Such performance is out of reach for popular camera-based localization by centroid calculation of emission diffraction patterns. Since theoretical limits have not been reached, our results show that emerging MINFLUX nanoscopy bears great potential for dissecting the motions of individual (macro)molecules at hitherto-unattained combinations of spatial and temporal resolution.
Collapse
Affiliation(s)
- Yvan Eilers
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Haisen Ta
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Klaus C Gwosch
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Francisco Balzarotti
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Stefan W Hell
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| |
Collapse
|
23
|
Voith von Voithenberg L, Lamb DC. Single Pair Förster Resonance Energy Transfer: A Versatile Tool To Investigate Protein Conformational Dynamics. Bioessays 2018; 40. [DOI: 10.1002/bies.201700078] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 12/05/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Lena Voith von Voithenberg
- Department Chemie; Center for Nanoscience (CeNS); Center for Integrated Protein Science Munich (CIPSM); Nanosystem Initiative Munich (NIM); Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 München Germany
- BIOSS Centre for Signalling Studies; Schänzlestr. 18 79104 Freiburg Germany
| | - Don C. Lamb
- Department Chemie; Center for Nanoscience (CeNS); Center for Integrated Protein Science Munich (CIPSM); Nanosystem Initiative Munich (NIM); Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 München Germany
| |
Collapse
|
24
|
Abstract
Real-time three-dimensional single particle tracking (RT-3D-SPT) has the potential to shed light on fast, 3D processes in cellular systems. Although various RT-3D-SPT methods have been put forward in recent years, tracking high speed 3D diffusing particles at low photon count rates remains a challenge. Moreover, RT-3D-SPT setups are generally complex and difficult to implement, limiting their widespread application to biological problems. This protocol presents a RT-3D-SPT system named 3D Dynamic Photon Localization Tracking (3D-DyPLoT), which can track particles with high diffusive speed (up to 20 µm2/s) at low photon count rates (down to 10 kHz). 3D-DyPLoT employs a 2D electro-optic deflector (2D-EOD) and a tunable acoustic gradient (TAG) lens to drive a single focused laser spot dynamically in 3D. Combined with an optimized position estimation algorithm, 3D-DyPLoT can lock onto single particles with high tracking speed and high localization precision. Owing to the single excitation and single detection path layout, 3D-DyPLoT is robust and easy to set up. This protocol discusses how to build 3D-DyPLoT step by step. First, the optical layout is described. Next, the system is calibrated and optimized by raster scanning a 190 nm fluorescent bead with the piezoelectric nanopositioner. Finally, to demonstrate real-time 3D tracking ability, 110 nm fluorescent beads are tracked in water.
Collapse
|
25
|
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.
Collapse
|
26
|
Pandey H, Szafran SA, Underhill PT. Passive trapping of rigid rods due to conformation-dependent electrophoretic mobility. SOFT MATTER 2016; 12:3121-3126. [PMID: 26892384 DOI: 10.1039/c5sm02816g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present computer simulations of a rigid rod in a combination of an extensional fluid flow and extensional electric field. The electrophoretic mobility of the rod is different parallel or perpendicular to the rod. The dependence of the mobility on the conformation (orientation) leads to a new phenomenon where the rods can be passively trapped in all directions at the stagnation point. This contrasts with the behavior in either fluid flow or electric field alone, in which an object can be pushed towards the stagnation point along some directions but is pushed away in others. We have determined the state space where trapping occurs and have developed a model that describes the strength of trapping when it does occur. This new phenomenon could be used in the future to separate objects based on a coupling between their mobility and ability to be oriented.
Collapse
Affiliation(s)
- Harsh Pandey
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th St, Troy, New York 12180, USA.
| | - Sylvia A Szafran
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th St, Troy, New York 12180, USA.
| | - Patrick T Underhill
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th St, Troy, New York 12180, USA.
| |
Collapse
|
27
|
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.
Collapse
Affiliation(s)
- W E Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
| | | | | |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
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
|
32
|
Bockenhauer SD, Moerner WE. Photo-induced conformational flexibility in single solution-phase peridinin-chlorophyll-proteins. J Phys Chem A 2013; 117:8399-406. [PMID: 23919352 DOI: 10.1021/jp405790a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The peridinin-chlorophyll-protein (PCP) is an accessory light-harvesting complex found in red-tide dinoflagellates. PCP absorbs photons primarily in the blue-green spectral region via peridinin (Per) carotenoid pigments which then transfer excitations to chlorophyll (Chl) and ultimately downstream to photosystem II (PSII). Whereas the ultrafast dynamics of PCP are well-studied, much less is known about slower protein dynamics on time scales of milliseconds and seconds. Previous single-molecule studies of spectral emission and intensity have attached PCP to surfaces, but the native environment of PCP is in the lumen, meaning that a surface-attached environment could perturb its native conformations. To address this concern, we use the anti-Brownian electrokinetic (ABEL) trap to study single PCP monomers in solution for several seconds each. We measure, for the first time, simultaneous single-molecule intensity, lifetime, and spectral emission shifts for each trapped PCP monomer. The rate of reversible spectral redshifts depends linearly on irradiance over a factor of 30, indicating a light-induced mechanism which we attribute to a protein conformational change. Independent of these spectral shifts, our measurements of intensity and lifetime show reversible Chl quenching. In contrast to previous work, we show that this quenching cannot result from isolated photobleaching of Chl. These independent mechanisms arise from distinct conformational changes which maintain relatively stable fluorescence emission.
Collapse
|
33
|
Zhao Y, Chen D, Yue H, French JB, Rufo J, Benkovic SJ, Huang TJ. Lab-on-a-chip technologies for single-molecule studies. LAB ON A CHIP 2013; 13:2183-98. [PMID: 23670195 PMCID: PMC3955889 DOI: 10.1039/c3lc90042h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Recent developments on various lab-on-a-chip techniques allow miniaturized and integrated devices to perform on-chip single-molecule studies. Fluidic-based platforms that utilize unique microscale fluidic behavior are capable of conducting single-molecule experiments with high sensitivities and throughputs, while biomolecular systems can be studied on-chip using techniques such as DNA curtains, magnetic tweezers, and solid-state nanopores. The advances of these on-chip single-molecule techniques lead to next-generation lab-on-a-chip devices, such as DNA transistors, and single-molecule real-time (SMRT) technology for rapid and low-cost whole genome DNA sequencing. In this Focus article, we will discuss some recent successes in the development of lab-on-a-chip techniques for single-molecule studies and expound our thoughts on the near future of on-chip single-molecule studies.
Collapse
Affiliation(s)
- Yanhui Zhao
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802 USA
| | - Danqi Chen
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802 USA
| | - Hongjun Yue
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802 USA
| | - Jarrod B. French
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802 USA
| | - Joey Rufo
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802 USA
| | - Stephen J. Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802 USA
| | - Tony Jun Huang
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802 USA
| |
Collapse
|
34
|
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.
Collapse
|
35
|
Ernst D, Köhler J. Measuring a diffusion coefficient by single-particle tracking: statistical analysis of experimental mean squared displacement curves. Phys Chem Chem Phys 2013. [PMID: 23202416 DOI: 10.1039/c2cp43433d] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We provide experimental results on the accuracy of diffusion coefficients obtained by a mean squared displacement (MSD) analysis of single-particle trajectories. We have recorded very long trajectories comprising more than 1.5 × 10(5) data points and decomposed these long trajectories into shorter segments providing us with ensembles of trajectories of variable lengths. This enabled a statistical analysis of the resulting MSD curves as a function of the lengths of the segments. We find that the relative error of the diffusion coefficient can be minimized by taking an optimum number of points into account for fitting the MSD curves, and that this optimum does not depend on the segment length. Yet, the magnitude of the relative error for the diffusion coefficient does, and achieving an accuracy in the order of 10% requires the recording of trajectories with about 1000 data points. Finally, we compare our results with theoretical predictions and find very good qualitative and quantitative agreement between experiment and theory.
Collapse
Affiliation(s)
- Dominique Ernst
- Experimental Physics IV and Bayreuth Institute of Macromolecular Research (BIMF), University of Bayreuth, 95440 Bayreuth, Germany
| | | |
Collapse
|
36
|
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
| |
Collapse
|
37
|
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.
Collapse
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
| |
Collapse
|
38
|
Ernst D, Hain S, Köhler J. Setup for single-particle orbit tracking: artifacts and corrections. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2012; 29:1277-1287. [PMID: 22751393 DOI: 10.1364/josaa.29.001277] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We report on an experimental setup for single-particle orbit tracking, which allows following fluorescent nanoparticles for more than 10 min with a temporal resolution of 4 ms and a dynamic position accuracy of better than 10 nm. On a model sample--20 nm sized fluorescent polymer beads in glycerol--we will illustrate how artifacts caused by unavoidable experimental shortcomings (might) obscure the experimental result and how misinterpretations can be prevented.
Collapse
Affiliation(s)
- Dominique Ernst
- Experimental Physics IV and Bayreuth Institute of Macromolecular Research, University of Bayreuth, Bayreuth, Germany
| | | | | |
Collapse
|
39
|
Redox cycling and kinetic analysis of single molecules of solution-phase nitrite reductase. Proc Natl Acad Sci U S A 2011; 108:17269-74. [PMID: 21969548 DOI: 10.1073/pnas.1113572108] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-molecule measurements are a valuable tool for revealing details of enzyme mechanisms by enabling observation of unsynchronized behavior. However, this approach often requires immobilizing the enzyme on a substrate, a process which may alter enzyme behavior. We apply a microfluidic trapping device to allow, for the first time, prolonged solution-phase measurement of single enzymes in solution. Individual redox events are observed for single molecules of a blue nitrite reductase and are used to extract the microscopic kinetic parameters of the proposed catalytic cycle. Changes in parameters as a function of substrate concentration are consistent with a random sequential substrate binding mechanism.
Collapse
|
40
|
Wang Q, Moerner WE. An Adaptive Anti-Brownian ELectrokinetic trap with real-time information on single-molecule diffusivity and mobility. ACS NANO 2011; 5:5792-5799. [PMID: 21612271 DOI: 10.1021/nn2014968] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We present the design and implementation of an adaptive Anti-Brownian ELectrokinetic (ABEL) trap capable of extracting estimates of the diffusion coefficient and mobility of single trapped fluorescent nanoscale objects such as biomolecules in solution. The system features rapid acousto-optic scanning of a confocal excitation spot on a 2D square lattice to encode position information on the arrival time of each detected photon, and Kalman filter-based signal processing unit for refined position estimation. We demonstrate stable trapping of multisubunit proteins (D ≈ 22 μm(2)/s) with a count rate of 6 kHz for as long as 15 s and small single-stranded DNA molecules (D ≈ 118 μm(2)/s) at a 15 kHz count rate for seconds. Moreover, we demonstrate real-time measurement of diffusion coefficient and electrokinetic mobility of trapped objects, using adaptive tuning of the Kalman filter parameters.
Collapse
Affiliation(s)
- Quan Wang
- Department of Chemistry, Stanford University, Mail Code 5080, Stanford, California 94305-5080, USA
| | | |
Collapse
|
41
|
Abstract
Anti-Brownian electrokinetic traps have been used to trap and study the free-solution dynamics of large protein complexes and long chains of DNA. Small molecules in solution have thus far proved too mobile to trap by any means. Here we explore the ultimate limits on trapping single molecules. We developed a feedback-based anti-Brownian electrokinetic trap in which classical thermal noise is compensated to the maximal extent allowed by quantum measurement noise. We trapped single fluorophores with a molecular weight of < 1 kDa and a hydrodynamic radius of 6.7 Å for longer than one second, in aqueous buffer at room temperature. This achievement represents an 800-fold decrease in the mass of objects trapped in solution, and opens the possibility to trap and manipulate any soluble molecule that can be fluorescently labeled. To illustrate the use of this trap, we studied the binding of unlabeled RecA to fluorescently labeled single-stranded DNA. Binding of RecA induced changes in the DNA diffusion coefficient, electrophoretic mobility, and brightness, all of which were measured simultaneously and on a molecule-by-molecule basis. This device greatly extends the size range of molecules that can be studied by room temperature feedback trapping, and opens the door to further studies of the binding of unmodified proteins to DNA in free solution.
Collapse
|