1
|
Hamdi S, Coillet A, Cluzel B, Grelu P, Colman P. Superlocalization Reveals Long-Range Synchronization of Vibrating Soliton Molecules. PHYSICAL REVIEW LETTERS 2022; 128:213902. [PMID: 35687457 DOI: 10.1103/physrevlett.128.213902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
We implement a superlocalization method in the time domain that allows the observation of the external motion of soliton molecules in a fiber ring cavity laser with unprecedented accuracy. In particular, we demonstrate the synchronization of two oscillating soliton molecules separated by several nanoseconds, with intermolecular oscillations following the same pattern as the intramolecular motion of the individual molecules. These experimental findings indicate an interplay between the different interaction mechanisms that coexist inside the laser cavity, despite their very different characteristic ranges, timescales, strengths, and physical origins.
Collapse
Affiliation(s)
- Said Hamdi
- Laboratoire Interdisciplinaire Carnot de Bourgogne UMR CNRS 6303, Université Bourgogne-Franche-Comté, 9 avenue Savary, 21000 Dijon, France
| | - Aurélien Coillet
- Laboratoire Interdisciplinaire Carnot de Bourgogne UMR CNRS 6303, Université Bourgogne-Franche-Comté, 9 avenue Savary, 21000 Dijon, France
| | - Benoit Cluzel
- Laboratoire Interdisciplinaire Carnot de Bourgogne UMR CNRS 6303, Université Bourgogne-Franche-Comté, 9 avenue Savary, 21000 Dijon, France
| | - Philippe Grelu
- Laboratoire Interdisciplinaire Carnot de Bourgogne UMR CNRS 6303, Université Bourgogne-Franche-Comté, 9 avenue Savary, 21000 Dijon, France
| | - Pierre Colman
- Laboratoire Interdisciplinaire Carnot de Bourgogne UMR CNRS 6303, Université Bourgogne-Franche-Comté, 9 avenue Savary, 21000 Dijon, France
| |
Collapse
|
2
|
Perdomo-Pérez R, Martínez-Rivera J, Palmero-Cruz NC, Sandoval-Puentes MA, Gallegos JAS, Lázaro-Lázaro E, Valadez-Pérez NE, Torres-Carbajal A, Castañeda-Priego R. Thermodynamics, static properties and transport behaviour of fluids with competing interactions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:144005. [PMID: 35026739 DOI: 10.1088/1361-648x/ac4b29] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Competing interaction fluids have become ideal model systems to study a large number of phenomena, for example, the formation of intermediate range order structures, condensed phases not seen in fluids driven by purely attractive or repulsive forces, the onset of particle aggregation under in- and out-of-equilibrium conditions, which results in the birth of reversible and irreversible aggregates or clusters whose topology and morphology depend additionally on the thermodynamic constrictions, and a particle dynamics that has a strong influence on the transport behaviour and rheological properties of the fluid. In this contribution, we study a system of particles interacting through a potential composed by a continuous succession of a short-ranged square-well (SW), an intermediate-ranged square-shoulder and a long-ranged SW. This potential model is chosen to systematically analyse the contribution of every component of the interaction potential on the phase behaviour, the microstructure, the morphology of the resulting aggregates and the transport phenomena of fluids described by competing interactions. Our results indicate that the inclusion of a barrier and a second well leads to new and interesting effects, which in addition result in variations of the physical properties associated to the competition among interactions.
Collapse
Affiliation(s)
- Román Perdomo-Pérez
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Mexico
| | - Jaime Martínez-Rivera
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Mexico
| | - Norma C Palmero-Cruz
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Mexico
| | - Miguel A Sandoval-Puentes
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Mexico
| | - Javier A S Gallegos
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Mexico
| | - Edilio Lázaro-Lázaro
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Mexico
| | - Néstor E Valadez-Pérez
- Facultad de Ciencias en Física y Matemáticas, Universidad Autónoma de Chiapas, Carretera Emiliano Zapata km 8, 29050 Tuxtla Gutiérrez, Mexico
| | - Alexis Torres-Carbajal
- Unidad Profesional Interdisciplinaria de Ingeniería, Campus Tlaxcala, Instituto Politécnico Nacional. Plaza Bicentenario, Guillermo Valle 11, Centro, 9000 Tlaxcala de Xicohténcatl, Tlaxcala, México
| | - Ramón Castañeda-Priego
- Departamento de Ingeniería Física, División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Mexico
| |
Collapse
|
3
|
Huang D, Haddad L, Rahman F, Palma M, Sapelkin A. Engineering a DNA origami mediated multicolour quantum dot platform for sub-diffraction spectral separation imaging. RSC Adv 2022; 12:23778-23785. [PMID: 36093241 PMCID: PMC9394590 DOI: 10.1039/d2ra04316e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/04/2022] [Indexed: 12/04/2022] Open
Abstract
The validation of super-resolution optical imaging techniques requires well-defined reference samples that can be used repeatedly and reliably as model standards. Here, we engineer a DNA origami scaffold-mediated multicolour quantum dot hybrid nanostructure and test it using a recently proposed Quantum Dot-based spectral separation technique. We show that multivalent DNA structures offer a robust and precise nanoscale quantum dot placement scaffold, while the spectral resolution method provides relatively simple and fast image acquisition capabilities using any standard confocal or fluorescence microscope capable of spectral signal separation and a single excitation laser wavelength. The validation of super-resolution optical imaging techniques requires well-defined reference samples that can be used repeatedly and reliably as model standards.![]()
Collapse
Affiliation(s)
- Da Huang
- Department of Chemistry, Queen Mary University of London, London E1 4NS, UK
| | - Lucy Haddad
- Department of Physics and Astronomy, Queen Mary University of London, London E1 4NS, UK
| | - Fahmida Rahman
- Department of Physics and Astronomy, Queen Mary University of London, London E1 4NS, UK
| | - Matteo Palma
- Department of Chemistry, Queen Mary University of London, London E1 4NS, UK
| | - Andrei Sapelkin
- Department of Physics and Astronomy, Queen Mary University of London, London E1 4NS, UK
| |
Collapse
|
4
|
Tao G, Lai T, Xu X, Ma Y, Wu X, Pei X, Liu F, Li N. Colocalized Particle Counting Platform for Zeptomole Level Multiplexed Quantification. Anal Chem 2020; 92:3697-3706. [PMID: 32037812 DOI: 10.1021/acs.analchem.9b04823] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
For multiplexed detection, it is important yet challenging to simultaneously meet the requirement of sensitivity, throughput, and implementation convenience for practical applications. Using the detection of DNAs and miRNAs for illustration, we present a colocalized particle counting platform that can realize the separation-free multiplexed detection of 6 nucleic acid targets with a zeptomole sensitivity and a dynamic range of up to 5 orders of magnitude. The presence of target induces the formation of a sandwich nanostructure via hybridization; thus, there is an occurrence of colocalization of two microbeads with two different colors. The sequence specific coding is realized by an arbitrary combination of two fluorescence channels with different emitting colors. The platform presents robustness in detecting multiple nucleic acid targets with a minimal cross talk and matrix effect as well as the ability to distinguish the specific miRNA from members of the same family. The results of simultaneous detection of 3 miRNAs in 3 different cell lines present straight consistency with that of the standard qRT-PCR. This platform can be adapted to other multiplexing designs such as the "turn-off" mode, in which the proportion of colocalized microbeads is decreased due to the strand-displacement reaction initiated by the specific target. This separation-free platform offers the possibility to achieve the on-site multiplexed detection with compatibility to different experimental designs and extensibility to other signal sources for enumeration.
Collapse
Affiliation(s)
- Guangyu Tao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Tiancheng Lai
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiao Xu
- Environmental Metrology Center, National Institute of Metrology, Beijing 100029, China
| | - Yurou Ma
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xi Wu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaojing Pei
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Feng Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Na Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| |
Collapse
|
5
|
Lee M, Shin S, Uhm H, Hong H, Kirk J, Hyun K, Kulikowicz T, Kim J, Ahn B, Bohr VA, Hohng S. Multiple RPAs make WRN syndrome protein a superhelicase. Nucleic Acids Res 2019; 46:4689-4698. [PMID: 29668972 PMCID: PMC5961295 DOI: 10.1093/nar/gky272] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/11/2018] [Indexed: 02/01/2023] Open
Abstract
RPA is known to stimulate the helicase activity of Werner syndrome protein (WRN), but the exact stimulation mechanism is not understood. We use single-molecule FRET and magnetic tweezers to investigate the helicase activity of WRN and its stimulation by RPA. We show that WRN alone is a weak helicase which repetitively unwind just a few tens of base pairs, but that binding of multiple RPAs to the enzyme converts WRN into a superhelicase that unidirectionally unwinds double-stranded DNA more than 1 kb. Our study provides a good case in which the activity and biological functions of the enzyme may be fundamentally altered by the binding of cofactors.
Collapse
Affiliation(s)
- Mina Lee
- Center for Nano-Bio Measurement, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Soochul Shin
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
| | - Heesoo Uhm
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
| | - Heesun Hong
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
| | - Jaewon Kirk
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
| | - Kwangbeom Hyun
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Tomasz Kulikowicz
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Byungchan Ahn
- Department of Life Sciences, University of Ulsan, Ulsan, Republic of Korea
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Sungchul Hohng
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
| |
Collapse
|
6
|
Measuring Nanometer Distances Between Fluorescent Labels Step-by-Step. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1663:189-203. [PMID: 28924669 DOI: 10.1007/978-1-4939-7265-4_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Super-resolution fluorescence microscopy methods are increasingly applied to study the structure of biological molecules within their natural context or at biomaterial interfaces. We here provide a protocol for Single-molecule High-Resolution Imaging with Photobleaching (SHRImP) that can be used to obtain information about the conformation of large proteins or other macromolecules at the single-molecule level. This procedure requires site-specific protein labeling with fluorescent dyes, immobilization and sample preparation, optimization of imaging buffer composition and microscope settings, and acquisition of short time-lapse movies that capture the stepwise bleaching behavior of individual molecules. We then describe a method for reliably determining the relative positions of labels from bleaching movies using the free image processing package Fiji (ImageJ) with the help of auxiliary macros that are provided as Supplementary Material. The presented approach allows for measuring intramolecular distance distributions in the range of a few to hundreds of nanometers and can be applied to a wide variety of biological systems.
Collapse
|
7
|
Yu F, Gao M, Li M, Chen L. A dual response near-infrared fluorescent probe for hydrogen polysulfides and superoxide anion detection in cells and in vivo. Biomaterials 2015; 63:93-101. [DOI: 10.1016/j.biomaterials.2015.06.007] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/04/2015] [Accepted: 06/06/2015] [Indexed: 01/10/2023]
|
8
|
Jing X, Yu F, Chen L. Visualization of nitroxyl (HNO) in vivo via a lysosome-targetable near-infrared fluorescent probe. Chem Commun (Camb) 2015; 50:14253-6. [PMID: 25283380 DOI: 10.1039/c4cc07561g] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We have presented a near-infrared fluorescent probe Lyso-JN for the detection of nitroxyl (HNO) in cells and in vivo. Lyso-JN is comprised of three moieties: an Aza-BODIPY fluorophore, a HNO-response modulator, diphenylphosphino-benzoyl, and a lysosomal locator, alkylmorpholine. The detection mechanism is based on aza-ylide intramolecular ester aminolysis reaction with HNO. The probe holds the ability to capture lysosomal HNO in RAW 264.7 cells, and it is also successfully employed to visualize HNO in mice.
Collapse
Affiliation(s)
- Xiaotong Jing
- The Key Laboratory of Life-Organic Analysis, College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, China
| | | | | |
Collapse
|
9
|
Liu J, Yang X, Wang K, Wang Q, Liu W, Wang D. Solid-phase single molecule biosensing using dual-color colocalization of fluorescent quantum dot nanoprobes. NANOSCALE 2013; 5:11257-11264. [PMID: 24089289 DOI: 10.1039/c3nr03291d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The development of solid-phase surface-based single molecule imaging technology has attracted significant interest during the past decades. Here we demonstrate a sandwich hybridization method for highly sensitive detection of a single thrombin protein at a solid-phase surface based on the use of dual-color colocalization of fluorescent quantum dot (QD) nanoprobes. Green QD560-modified thrombin binding aptamer I (QD560-TBA I) were deposited on a positive poly(l-lysine) assembled layer, followed by bovine serum albumin blocking. It allowed the thrombin protein to mediate the binding of the easily detectable red QD650-modified thrombin binding aptamer II (QD650-TBA II) to the QD560-TBA I substrate. Thus, the presence of the target thrombin can be determined based on fluorescent colocalization measurements of the nanoassemblies, without target amplification or probe separation. The detection limit of this assay reached 0.8 pM. This fluorescent colocalization assay has enabled single molecule recognition in a separation-free detection format, and can serve as a sensitive biosensing platform that greatly suppresses the nonspecific adsorption false-positive signal. This method can be extended to other areas such as multiplexed immunoassay, single cell analysis, and real time biomolecule interaction studies.
Collapse
Affiliation(s)
- Jianbo Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China.
| | | | | | | | | | | |
Collapse
|
10
|
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.
Collapse
Affiliation(s)
- X Michalet
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095-1547, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Shuang B, Byers CP, Kisley L, Wang LY, Zhao J, Morimura H, Link S, Landes CF. Improved analysis for determining diffusion coefficients from short, single-molecule trajectories with photoblinking. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:228-34. [PMID: 23215347 PMCID: PMC3648847 DOI: 10.1021/la304063j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Two maximum likelihood estimation (MLE) methods were developed for optimizing the analysis of single-molecule trajectories that include phenomena such as experimental noise, photoblinking, photobleaching, and translation or rotation out of the collection plane. In particular, short, single-molecule trajectories with photoblinking were studied, and our method was compared to existing analytical techniques applied to simulated data. The optimal method for various experimental cases was established, and the optimized MLE method was applied to a real experimental system: single-molecule diffusion of fluorescent molecular machines known as nanocars.
Collapse
Affiliation(s)
- Bo Shuang
- Department of Chemistry and Rice Quantum Institute, Rice University, Houston, Texas 77251-1892, United States
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Fuller CJ, Straight AF. Imaging nanometre-scale structure in cells using in situ aberration correction. J Microsc 2012; 248:90-101. [PMID: 22906048 DOI: 10.1111/j.1365-2818.2012.03654.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accurate distance measurements of cellular structures on a length scale relevant to single macromolecules or macromolecular complexes present a major challenge for biological microscopy. In addition to the inherent challenges of overcoming the limits imposed by the diffraction of light, cells themselves are a complex and poorly understood optical environment. We present an extension of the high-resolution colocalization method to measure three dimensional distances between diffraction-limited objects using standard widefield fluorescence microscopy. We use this method to demonstrate that in three dimensions, cells intrinsically introduce a large and variable amount of chromatic aberration into optical measurements. We present a means of correcting this aberration in situ [termed 'Colocalization and In-situ Correction of Aberration for Distance Analysis' (CICADA)] by exploiting the fact that there is a linear relationship between the degree of aberration between different wavelengths. By labelling a cellular structure with redundantly multi-colour labelled antibodies, we can create an intracellular fiducial marker for correcting the individual aberrations between two different wavelengths in the same cells. Our observations demonstrate that with suitable corrections, nanometre scale three-dimensional distance measurements can be used to probe the substructure of macromolecular complexes within cells.
Collapse
Affiliation(s)
- C J Fuller
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | | |
Collapse
|
13
|
Michalet X, Berglund AJ. Optimal diffusion coefficient estimation in single-particle tracking. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:061916. [PMID: 23005136 PMCID: PMC4917385 DOI: 10.1103/physreve.85.061916] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 05/03/2012] [Indexed: 05/03/2023]
Abstract
Single-particle tracking is increasingly used to extract quantitative parameters on single molecules and their environment, while advances in spatial and temporal resolution of tracking techniques inspire new questions and avenues of investigation. Correspondingly, sophisticated analytical methods are constantly developed to obtain more refined information from measured trajectories. Here we point out some fundamental limitations of these approaches due to the finite length of trajectories, the presence of localization error, and motion blur, focusing on the simplest motion regime of free diffusion in an isotropic medium (Brownian motion). We show that two recently proposed algorithms approach the theoretical limit of diffusion coefficient uncertainty. We discuss the practical performance of the algorithms as well as some important implications of these results for single-particle tracking.
Collapse
Affiliation(s)
- Xavier Michalet
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, California 90095, USA.
| | | |
Collapse
|
14
|
Churchman LS, Spudich JA. Colocalization of fluorescent probes: accurate and precise registration with nanometer resolution. Cold Spring Harb Protoc 2012; 2012:141-9. [PMID: 22301660 DOI: 10.1101/pdb.top067918] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Colocalization of fluorescent probes is commonly used in cell biology to discern the proximity of two proteins in the cell. Considering that the resolution limit of optical microscopy is on the order of 250 nm, there has not been a need for high-resolution colocalization techniques. However, with the advent of higher resolution techniques for cell biology and single-molecule biophysics, colocalization must also improve. For diffraction-limited applications, a geometric transformation (i.e., translation, scaling, and rotation) is typically applied to one color channel to align it with the other; however, to achieve high-resolution colocalization, this is not sufficient. Single-molecule high-resolution colocalization (SHREC) of single probes uses the local weighted mean transformation to achieve a colocalization resolution of at least 10 nm. This article describes the process of collecting a calibration data set of fiducials and the appropriate analysis to determine the transformation for colocalization.
Collapse
|
15
|
Targeting and imaging single biomolecules in living cells by complementation-activated light microscopy with split-fluorescent proteins. Proc Natl Acad Sci U S A 2011; 108:E201-10. [PMID: 21606345 DOI: 10.1073/pnas.1101929108] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-molecule (SM) microscopy allows outstanding insight into biomolecular mechanisms in cells. However, selective detection of single biomolecules in their native environment remains particularly challenging. Here, we introduce an easy methodology that combines specific targeting and nanometer accuracy imaging of individual biomolecules in living cells. In this method, named complementation-activated light microscopy (CALM), proteins are fused to dark split-fluorescent proteins (split-FPs), which are activated into bright FPs by complementation with synthetic peptides. Using CALM, the diffusion dynamics of a controlled subset of extracellular and intracellular proteins are imaged with nanometer precision, and SM tracking can additionally be performed with fluorophores and quantum dots. In cells, site-specific labeling of these probes is verified by coincidence SM detection with the complemented split-FP fusion proteins or intramolecular single-pair Förster resonance energy transfer. CALM is simple and combines advantages from genetically encoded and synthetic fluorescent probes to allow high-accuracy imaging of single biomolecules in living cells, independently of their expression level and at very high probe concentrations.
Collapse
|
16
|
Colyer RA, Scalia G, Rech I, Gulinatti A, Ghioni M, Cova S, Weiss S, Michalet X. High-throughput FCS using an LCOS spatial light modulator and an 8 × 1 SPAD array. BIOMEDICAL OPTICS EXPRESS 2010; 1:1408-1431. [PMID: 21258559 PMCID: PMC3018120 DOI: 10.1364/boe.1.001408] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 10/14/2010] [Accepted: 11/08/2010] [Indexed: 05/05/2023]
Abstract
We present a novel approach to high-throughput Fluorescence Correlation Spectroscopy (FCS) which enables us to obtain one order of magnitude improvement in acquisition time. Our approach utilizes a liquid crystal on silicon spatial light modulator to generate dynamically adjustable focal spots, and uses an eight-pixel monolithic single-photon avalanche photodiode array. We demonstrate the capabilities of this system by showing FCS of Rhodamine 6G under various viscosities, and by showing that, with proper calibration of each detection channel, one order of magnitude improvement in acquisition speed is obtained. More generally, our approach will allow higher throughput single-molecule studies to be performed.
Collapse
Affiliation(s)
- Ryan A. Colyer
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA
| | - Giuseppe Scalia
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA
| | - Ivan Rech
- Dipartimento di Elettronica ed Informazione, Politecnico di Milano, Milano, Italy
| | - Angelo Gulinatti
- Dipartimento di Elettronica ed Informazione, Politecnico di Milano, Milano, Italy
| | - Massimo Ghioni
- Dipartimento di Elettronica ed Informazione, Politecnico di Milano, Milano, Italy
| | - Sergio Cova
- Dipartimento di Elettronica ed Informazione, Politecnico di Milano, Milano, Italy
| | - Shimon Weiss
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA
| | - Xavier Michalet
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA
| |
Collapse
|
17
|
Michalet X. Mean square displacement analysis of single-particle trajectories with localization error: Brownian motion in an isotropic medium. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:041914. [PMID: 21230320 PMCID: PMC3055791 DOI: 10.1103/physreve.82.041914] [Citation(s) in RCA: 378] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 09/01/2010] [Indexed: 05/03/2023]
Abstract
We examine the capability of mean square displacement (MSD) analysis to extract reliable values of the diffusion coefficient D of a single particle undergoing Brownian motion in an isotropic medium in the presence of localization uncertainty. The theoretical results, supported by simulations, show that a simple unweighted least-squares fit of the MSD curve can provide the best estimate of D provided an optimal number of MSD points are used for the fit. We discuss the practical implications of these results for data analysis in single-particle tracking experiments.
Collapse
Affiliation(s)
- Xavier Michalet
- Department of Chemistry & Biochemistry, University of California at Los Angeles, 607 Charles E. Young Drive E., Los Angeles, California 90095, USA.
| |
Collapse
|
18
|
Morgner F, Geißler D, Stufler S, Butlin NG, Löhmannsröben HG, Hildebrandt N. Ein Quantenpunkt-basiertes molekulares Lineal zur optischen Multiplexanalyse. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201002943] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
19
|
Morgner F, Geißler D, Stufler S, Butlin NG, Löhmannsröben HG, Hildebrandt N. A Quantum-Dot-Based Molecular Ruler for Multiplexed Optical Analysis. Angew Chem Int Ed Engl 2010; 49:7570-4. [DOI: 10.1002/anie.201002943] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
20
|
Pantoja R, Rodriguez EA, Dibas MI, Dougherty DA, Lester HA. Single-molecule imaging of a fluorescent unnatural amino acid incorporated into nicotinic receptors. Biophys J 2010; 96:226-37. [PMID: 19134478 DOI: 10.1016/j.bpj.2008.09.034] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Accepted: 09/29/2008] [Indexed: 10/21/2022] Open
Abstract
We report on the first, to our knowledge, successful detection of a fluorescent unnatural amino acid (fUAA), Lys(BODIPYFL), incorporated into a membrane protein (the muscle nicotinic acetylcholine receptor, nAChR) in a living cell. Xenopus oocytes were injected with a frameshift-suppressor tRNA, amino-acylated with Lys(BODIPYFL) and nAChR (alpha/beta19'GGGU/gamma/delta) mRNAs. We measured fluorescence from oocytes expressing nAChR beta19'Lys(BODIPYFL), using time-resolved total internal reflection fluorescence microscopy. Under conditions of relatively low receptor density (<0.1 receptors/microm(2)), we observed puncta with diffraction-limited profiles that were consistent with the point-spread function of our microscope. Furthermore, diffraction-limited puncta displayed step decreases in fluorescence intensity, consistent with single-molecule photobleaching. The puncta densities agreed with macroscopic ACh-induced current densities, showing that the fUAA was incorporated, and that receptors were functional. Dose-response relations for the nAChR beta19'Lys(BODIPYFL) receptors were similar to those for wild-type receptors. We also studied nAChR beta19'Lys(BODIPYFL) receptors labeled with alpha-bungarotoxin monoconjugated with Alexa488 (alphaBtxAlexa488). The nAChR has two alphaBtx binding sites, and puncta containing the Lys(BODIPYFL) labeled with alphaBtxAlexa488 yielded the expected three discrete photobleaching steps. We also performed positive control experiments with a nAChR containing enhanced green fluorescent protein in the gamma-subunit M3-M4 loop, which confirmed our nAChR beta19'Lys(BODIPYFL) measurements. Thus, we report on the cell-based single-molecule detection of nAChR beta19'Lys(BODIPYFL).
Collapse
Affiliation(s)
- Rigo Pantoja
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | | | | | | | | |
Collapse
|
21
|
|
22
|
Michalet X, Colyer RA, Antelman J, Siegmund OHW, Tremsin A, Vallerga JV, Weiss S. Single-quantum dot imaging with a photon counting camera. Curr Pharm Biotechnol 2009; 10:543-58. [PMID: 19689323 PMCID: PMC2830710 DOI: 10.2174/138920109788922100] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The expanding spectrum of applications of single-molecule fluorescence imaging ranges from fundamental in vitro studies of biomolecular activity to tracking of receptors in live cells. The success of these assays has relied on progress in organic and non-organic fluorescent probe developments as well as improvements in the sensitivity of light detectors. We describe a new type of detector developed with the specific goal of ultra-sensitive single-molecule imaging. It is a wide-field, photon-counting detector providing high temporal and high spatial resolution information for each incoming photon. It can be used as a standard low-light level camera, but also allows access to a lot more information, such as fluorescence lifetime and spatio-temporal correlations. We illustrate the single-molecule imaging performance of our current prototype using quantum dots and discuss on-going and future developments of this detector.
Collapse
Affiliation(s)
- X Michalet
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA, USA.
| | | | | | | | | | | | | |
Collapse
|
23
|
Antelman J, Wilking-Chang C, Weiss S, Michalet X. Nanometer distance measurements between multicolor quantum dots. NANO LETTERS 2009; 9:2199-205. [PMID: 19374434 PMCID: PMC2748936 DOI: 10.1021/nl901163k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Quantum dot dimers made of short double-stranded DNA molecules labeled with different color quantum dots at each end were imaged using multicolor stage-scanning confocal microscopy. This approach eliminates chromatic aberration and color registration issues usually encountered in other multicolor imaging techniques. We demonstrate nanometer accuracy in individual distance measurement by suppression of quantum dot blinking and thoroughly characterize the contribution of different effects to the variability observed between measurements. Our analysis opens the way to accurate structural studies of biomolecules and biomolecular complexes using multicolor quantum labeling.
Collapse
Affiliation(s)
| | | | | | - Xavier Michalet
- CORRESPONDING AUTHOR FOOTNOTE. Correspondence should be address to XM (, Ph: 310 794-6693, Fax: 310 267-4672)
| |
Collapse
|
24
|
Ebenstein Y, Gassman N, Kim S, Antelman J, Kim Y, Ho S, Samuel R, Michalet X, Weiss S. Lighting up individual DNA binding proteins with quantum dots. NANO LETTERS 2009; 9:1598-603. [PMID: 19290670 PMCID: PMC3084662 DOI: 10.1021/nl803820b] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The ability to determine the precise loci and occupancy of DNA-binding proteins is instrumental to our understanding of cellular processes like gene expression and regulation. We propose a single-molecule approach for the direct visualization of proteins bound to their template DNA. Fluorescent quantum dots (QD) are used to label proteins bound to DNA, allowing multicolor, nanometer-resolution localization. Protein-DNA complexes are linearly extended and imaged to determine the precise location of the protein binding sites. The method is demonstrated by detecting individual QD-labeled T7-RNA polymerases on the T7 bacteriophage genome. This work demonstrates the potential of this approach to precisely read protein binding position or, alternatively, "write" such information on extended DNA with QDs via sequence-specific molecular recognition.
Collapse
Affiliation(s)
- Yuval Ebenstein
- Department of Chemistry and Biochemistry, DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Antelman J, Ebenstein Y, Dertinger T, Michalet X, Weiss S. Suppression of quantum dot blinking in DTT-doped polymer films. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2009; 113:11541-11545. [PMID: 20161096 PMCID: PMC2745152 DOI: 10.1021/jp811078e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this report we evaluate the emission properties of single quantum dots embedded in a thin, thiol containing polymer film. We report the suppression of quantum dot blinking leading to a continuous photon flux from both organic and water soluble quantum dots and demonstrate their application as robust fluorescent point sources for ultrahigh resolution localization. In addition, we apply the polymer coating to cell samples immunostained with antibody conjugated QDs and show that fluorescence intensity from the polymer embedded cells shows no sign of degradation after 67 hours of continuous excitation. The reported thin polymer film coating may prove advantageous for immuno-cyto/histo-chemistry as well as for the fabrication of quantum dot containing devices requiring a reliable and stable photon source (including a single photon source) or stable charge characteristics while maintaining intimate contact between the quantum dot and the surrounding matrix.
Collapse
Affiliation(s)
- Josh Antelman
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095 USA
| | - Yuval Ebenstein
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095 USA
| | - Thomas Dertinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095 USA
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095 USA
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095 USA
- Department of Physiology, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095 USA
- DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095 USA
| |
Collapse
|
26
|
Pinaud F, Michalet X, Iyer G, Margeat E, Moore HP, Weiss S. Dynamic partitioning of a glycosyl-phosphatidylinositol-anchored protein in glycosphingolipid-rich microdomains imaged by single-quantum dot tracking. Traffic 2009; 10:691-712. [PMID: 19416475 DOI: 10.1111/j.1600-0854.2009.00902.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent experimental developments have led to a revision of the classical fluid mosaic model proposed by Singer and Nicholson more than 35 years ago. In particular, it is now well established that lipids and proteins diffuse heterogeneously in cell plasma membranes. Their complex motion patterns reflect the dynamic structure and composition of the membrane itself, as well as the presence of the underlying cytoskeleton scaffold and that of the extracellular matrix. How the structural organization of plasma membranes influences the diffusion of individual proteins remains a challenging, yet central, question for cell signaling and its regulation. Here we have developed a raft-associated glycosyl-phosphatidyl-inositol-anchored avidin test probe (Av-GPI), whose diffusion patterns indirectly report on the structure and dynamics of putative raft microdomains in the membrane of HeLa cells. Labeling with quantum dots (qdots) allowed high-resolution and long-term tracking of individual Av-GPI and the classification of their various diffusive behaviors. Using dual-color total internal reflection fluorescence (TIRF) microscopy, we studied the correlation between the diffusion of individual Av-GPI and the location of glycosphingolipid GM1-rich microdomains and caveolae. We show that Av-GPI exhibit a fast and a slow diffusion regime in different membrane regions, and that slowing down of their diffusion is correlated with entry in GM1-rich microdomains located in close proximity to, but distinct, from caveolae. We further show that Av-GPI dynamically partition in and out of these microdomains in a cholesterol-dependent manner. Our results provide direct evidence that cholesterol-/sphingolipid-rich microdomains can compartmentalize the diffusion of GPI-anchored proteins in living cells and that the dynamic partitioning raft model appropriately describes the diffusive behavior of some raft-associated proteins across the plasma membrane.
Collapse
Affiliation(s)
- Fabien Pinaud
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA, USA.
| | | | | | | | | | | |
Collapse
|
27
|
Abstract
Considerable efforts have been deployed towards measuring molecular range distances in fluorescence microscopy. In the 1-10 nm range, Förster energy transfer microscopy is difficult to beat. Above 300 nm, conventional diffraction limited microscopy is suitable. We introduce a simple experimental technique that allows bridging the gap between those two resolution scales in both 2D and 3D with a resolution of about 20 nm. The method relies on a computational approach to accurately correct optical aberrations over the whole field of view. The method is differential because the probes of interest are affected in exactly the same manner by aberrations as are the reference probes used to construct the aberration deformation field. We expect that this technique will have significant implications for investigating structural and functional questions in bio-molecular sciences.
Collapse
Affiliation(s)
- P Vallotton
- CSIRO, Mathematical and Information Sciences, Locked Bag 17, North Ryde, NSW 1670, Australia.
| |
Collapse
|
28
|
Iyer G, Michalet X, Chang YP, Pinaud FF, Matyas SE, Payne G, Weiss S. High affinity scFv-hapten pair as a tool for quantum dot labeling and tracking of single proteins in live cells. NANO LETTERS 2008; 8:4618-23. [PMID: 19053789 PMCID: PMC3084663 DOI: 10.1021/nl8032284] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We describe a general approach to label cell surface proteins using quantum dots (QD) for single-molecule tracking. QDs coated with small-hapten modified peptides are targeted to cell surface fusion proteins containing the corresponding single-chain fragment antibody (scFv). The approach is illustrated with the small hapten fluorescein (FL) and a high-affinity anti-FL scFv fused to two different proteins in yeast and murine neuronal cell line N2a.
Collapse
|
29
|
Hamadani KM, Weiss S. Nonequilibrium single molecule protein folding in a coaxial mixer. Biophys J 2008; 95:352-65. [PMID: 18339751 PMCID: PMC2426651 DOI: 10.1529/biophysj.107.127431] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Accepted: 02/14/2008] [Indexed: 11/18/2022] Open
Abstract
We have developed a continuous-flow mixing device suitable for monitoring bioconformational reactions at the single-molecule level with a response time of approximately 10 ms under single-molecule flow conditions. Its coaxial geometry allows three-dimensional hydrodynamic focusing of sample fluids to diffraction-limited dimensions where diffusional mixing is rapid and efficient. The capillary-based design enables rapid in-lab construction of mixers without the need for expensive lithography-based microfabrication facilities. In-line filtering of sample fluids using granulated silica particles virtually eliminates clogging and extends the lifetime of each device to many months. In this article, to determine both the distance-to-time transfer function and the instrument response function of the device we characterize its fluid flow and mixing properties using both fluorescence cross-correlation spectroscopy velocimetry and finite element fluid dynamics simulations. We then apply the mixer to single molecule FRET protein folding studies of Chymotrypsin Inhibitor protein 2. By transiently populating the unfolded state of Chymotrypsin Inhibitor Protein 2 (CI2) under nonequilibrium in vitro refolding conditions, we spatially and temporally resolve the denaturant-dependent nonspecific collapse of the unfolded state from the barrier-limited folding transition of CI2. Our results are consistent with previous CI2 mixing results that found evidence for a heterogeneous unfolded state consisting of cis- and trans-proline conformers.
Collapse
Affiliation(s)
- Kambiz M Hamadani
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, California, USA.
| | | |
Collapse
|
30
|
Yao DK, Shao JY. A Novel Technique of Quantifying Flexural Stiffness of Rod-Like Structures. Cell Mol Bioeng 2008; 1:75-83. [PMID: 20333317 DOI: 10.1007/s12195-008-0012-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
In cellular and molecular biomechanics, extensional stiffness of rod-like structures such as leukocyte microvilli can be easily measured with many techniques, but not many techniques are available for measuring their flexural stiffness. In this paper, we report a novel technique of measuring the flexural stiffness of rod-like structures. This technique is based on image deconvolution and, as an example, it was used for determining the flexural stiffness of neutrophil microvilli. The probes we used were 40-nm-diameter fluorescent beads, which were bound to the tips of neutrophil microvilli by anti-L-selectin antibody. The fluorescent images of the bead, which was positioned at the center of the cell bottom, were acquired with high magnification and long exposure time (3 s). Using a Gaussian function as the point spread function of our imaging system, we established a convolution equation based on Boltzmann's law, which yields an analytical expression that relates the bead image profile to the flexural stiffness of the microvillus. The flexural stiffness was then obtained by the least squares regression. On average, the flexural stiffness was determined to be 7 pN/mum for single neutrophil microvilli. With the resolution of our imaging system, this technique can be used for measuring any flexural stiffness smaller than 34 pN/mum and it has great potential in single molecule biomechanics.
Collapse
Affiliation(s)
- Da-Kang Yao
- Department of Biomedical Engineering, Washington University in Saint Louis Saint Louis, MO 63130
| | | |
Collapse
|
31
|
Michalet X, Cheng A, Antelman J, Suyama M, Arisaka K, Weiss S. Hybrid photodetector for single-molecule spectroscopy and microscopy. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2008; 6862:68620F_1. [PMID: 21822361 PMCID: PMC3150536 DOI: 10.1117/12.763449] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
We report benchmark tests of a new single-photon counting detector based on a GaAsP photocathode and an electron-bombarded avalanche photodiode developed by Hamamatsu Photonics. We compare its performance with those of standard Geiger-mode avalanche photodiodes. We show its advantages for FCS due to the absence of after-pulsing and for fluorescence lifetime measurements due to its excellent time resolution. Its large sensitive area also greatly simplifies setup alignment. Its spectral sensitivity being similar to that of recently introduced CMOS SPADs, this new detector could become a valuable tool for single-molecule fluorescence measurements, as well as for many other applications.
Collapse
Affiliation(s)
- X. Michalet
- Dept. of Chemistry & Biochemistry, University of California at Los Angeles, 607 Charles E Young Drive E, Los Angeles, CA 90095
| | - Adrian Cheng
- Dept. of Physics & Astronomy, University of California at Los Angeles, 405 Hilgard Ave, Los Angeles, CA 90095
| | - Joshua Antelman
- Dept. of Chemistry & Biochemistry, University of California at Los Angeles, 607 Charles E Young Drive E, Los Angeles, CA 90095
| | - Motohiro Suyama
- Electron Tube Division, Hamamatsu Photonics K.K., 315-5 Toyooka village, Iwata-gun 438-0193, Japan
| | - Katsushi Arisaka
- Dept. of Physics & Astronomy, University of California at Los Angeles, 405 Hilgard Ave, Los Angeles, CA 90095
| | - Shimon Weiss
- Dept. of Chemistry & Biochemistry, University of California at Los Angeles, 607 Charles E Young Drive E, Los Angeles, CA 90095
| |
Collapse
|
32
|
Quantum Optics: Colloidal Fluorescent Semiconductor Nanocrystals (Quantum Dots) in Single-Molecule Detection and Imaging. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-3-540-73924-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
|
33
|
Egner A, Geisler C, von Middendorff C, Bock H, Wenzel D, Medda R, Andresen M, Stiel AC, Jakobs S, Eggeling C, Schönle A, Hell SW. Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters. Biophys J 2007; 93:3285-90. [PMID: 17660318 PMCID: PMC2025649 DOI: 10.1529/biophysj.107.112201] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We demonstrate nanoscale resolution in far-field fluorescence microscopy using reversible photoswitching and localization of individual fluorophores at comparatively fast recording speeds and from the interior of intact cells. These advancements have become possible by asynchronously recording the photon bursts of individual molecular switching cycles. We present images from the microtubular network of an intact mammalian cell with a resolution of 40 nm.
Collapse
Affiliation(s)
- Alexander Egner
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
|
35
|
Michalet X, Siegmund OHW, Vallerga JV, Jelinsky P, Millaud JE, Weiss S. Detectors for single-molecule fluorescence imaging and spectroscopy. JOURNAL OF MODERN OPTICS 2007; 54:239. [PMID: 20157633 PMCID: PMC2821066 DOI: 10.1080/09500340600769067] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Single-molecule observation, characterization and manipulation techniques have recently come to the forefront of several research domains spanning chemistry, biology and physics. Due to the exquisite sensitivity, specificity, and unmasking of ensemble averaging, single-molecule fluorescence imaging and spectroscopy have become, in a short period of time, important tools in cell biology, biochemistry and biophysics. These methods led to new ways of thinking about biological processes such as viral infection, receptor diffusion and oligomerization, cellular signaling, protein-protein or protein-nucleic acid interactions, and molecular machines. Such achievements require a combination of several factors to be met, among which detector sensitivity and bandwidth are crucial. We examine here the needed performance of photodetectors used in these types of experiments, the current state of the art for different categories of detectors, and actual and future developments of single-photon counting detectors for single-molecule imaging and spectroscopy.
Collapse
Affiliation(s)
- X Michalet
- Department of Chemistry & Biochemistry, University of California at Los Angeles, 607 Charles E. Young Drive E., Los Angeles, CA 90095, USA
| | | | | | | | | | | |
Collapse
|
36
|
Lagerholm BC, Averett L, Weinreb GE, Jacobson K, Thompson NL. Analysis method for measuring submicroscopic distances with blinking quantum dots. Biophys J 2006; 91:3050-60. [PMID: 16861265 PMCID: PMC1578492 DOI: 10.1529/biophysj.105.079178] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A method is described that takes advantage of the intermittency ("blinking") in the fluorescence of quantum dots (QDs) to measure absolute positions of closely spaced QDs. The concept is that even if two QDs are separated by only tens of nanometers, the position of each QD is resolvable if the point spread function of each can be imaged independently of the other. In the case of QDs, this is possible if each QD separately blinks completely on and off during a time-lapse sequence. To demonstrate the principle of this method, time-lapse sequences of single blinking QDs were acquired and the centroids of the point spread functions determined. Images of the blinking QDs were then overlapped in software, pixel by pixel, generating a range of submicroscopic distances between QD pairs. Methods were developed for analyzing the overlapped time sequences of the QD pairs so that the positions of the QDs and the distances between them could be determined without prior knowledge of the single QD positions. We subsequently used this method to measure the end-to-end length of a 122-basepair double-stranded DNA fragment.
Collapse
Affiliation(s)
- B Christoffer Lagerholm
- Department of Cell and Developmental Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA
| | | | | | | | | |
Collapse
|
37
|
Michalet X, Weiss S. Using photon statistics to boost microscopy resolution. Proc Natl Acad Sci U S A 2006; 103:4797-8. [PMID: 16549771 PMCID: PMC1458746 DOI: 10.1073/pnas.0600808103] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Xavier Michalet
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
| | | |
Collapse
|
38
|
Ohnuki T, Michalet X, Tripathi A, Weiss S, Arisaka K. Development of an ultrafast single photon counting imager for single molecule imaging. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2006; 6092:60920P. [PMID: 29479131 PMCID: PMC5824729 DOI: 10.1117/12.658191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
We have begun developing an innovative ultra-fast single-photon counting imager which comprises a mega-pixel CMOS array and a newly-designed Image Intensifier. It is expected to have single photon sensitivity with 100 psec time resolution, operational at a total counting rate exceeding 1MHz. The readout is based on dead-time-free flash ADC, running at 1-2GS/s, followed by a FPGA for real-time parallel data processing. Such a device has not been realized before and is expected to revolutionize time-resolved fluorescence imaging and spectroscopy from a single-molecule to whole animal level. To evaluate the design principle, an Image Intensifier with a GaAsP photocathode (>40% quantum efficiency at 400-600 nm) followed by double MCP was evaluated together with an existing CMOS camera. In our future design, the image from CMOS Camera will be combined with the MCP output, followed by a set of FPGA and CPU for real time data processing. This stream line method will allow ultra fast single-photon counting with 100 psec time resolution and 20 µm position resolution (1M pixel imaging). In this paper, we present the design principle and preliminary results on its performance. Our future plan and the design goals are also described.
Collapse
Affiliation(s)
- Tohru Ohnuki
- Department of Physics and Astronomy, 405 Hilgard Ave
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, 607 Charles E. Young Drive E. University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Arun Tripathi
- Department of Physics and Astronomy, 405 Hilgard Ave
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, 607 Charles E. Young Drive E. University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | |
Collapse
|
39
|
Ferrara DE, Weiss D, Carnell PH, Vito RP, Vega D, Gao X, Nie S, Taylor WR. Quantitative 3D fluorescence technique for the analysis of en face preparations of arterial walls using quantum dot nanocrystals and two-photon excitation laser scanning microscopy. Am J Physiol Regul Integr Comp Physiol 2005; 290:R114-23. [PMID: 16223849 DOI: 10.1152/ajpregu.00449.2005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Traditional imaging with one-photon confocal microscopy and organic fluorophores poses several challenges for the visualization of vascular tissue, including autofluorescence, fluorophore crosstalk, and photobleaching. We studied human coronary arteries (HCAs) and mouse aortas with a modified immunohistochemical (IHC) "en face" method using quantum dot (Qdot) bioconjugates and two-photon excitation laser scanning microscopy (TPELSM). We demonstrated the feasibility of multilabeling intimal structures by exciting multicolored Qdots with only one laser wavelength (750 nm). Detailed cell structures, such as the granular appearance of von Willebrand factor (VWF) and the subcellular distribution of endothelial nitric oxide synthase, were visualized using green dots (525 nm), even when the emission maximum of these Qdots overlapped that of tissue autofluorescence (510-520 nm). In addition, sensitive fluorescence quantification of vascular cell adhesion molecule 1 expression at areas of varying hemodynamics (intercostal branches vs. nonbranching areas) was performed in normal C57Bl/6 mice. Finally, we took advantage of the photostability of Qdots and the inherent three-dimensional (3D) resolution of TPELSM to obtain large z-stack series without photobleaching. This innovative en face method allowed simple multicolor profiling, highly sensitive fluorescence quantitation, and 3D visualization of the vascular endothelium with excellent spatial resolution. This is a promising technique to define the spatial and temporal interactions of endothelial inflammatory markers and quantify the effects of different interventions on the endothelium.
Collapse
Affiliation(s)
- Dardo E Ferrara
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Ho YP, Kung MC, Yang S, Wang TH. Multiplexed hybridization detection with multicolor colocalization of quantum dot nanoprobes. NANO LETTERS 2005; 5:1693-7. [PMID: 16159207 DOI: 10.1021/nl050888v] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We demonstrate a hybridization detection method using multicolor oligonucleotide-functionalized quantum dots as nanoprobes. In the presence of various target sequences, combinatorial self-assembly of the nanoprobes via independent hybridization reactions leads to the generation of discernible sequence-specific spectral codings. Detection of single-molecule hybridization is achieved by measuring colocalization of individual nanoprobes. Genetic analysis for anthrax pathogenicity through simultaneous detection of multiple relevant sequences is demonstrated using this novel biosensing method as proof-of-concept.
Collapse
Affiliation(s)
- Yi-Ping Ho
- Department of Mechanical Engineering, The Johns Hopkins University and School of Medicine, Baltimore, Maryland 21218, USA
| | | | | | | |
Collapse
|
41
|
Kapanidis AN, Laurence TA, Lee NK, Margeat E, Kong X, Weiss S. Alternating-laser excitation of single molecules. Acc Chem Res 2005; 38:523-33. [PMID: 16028886 DOI: 10.1021/ar0401348] [Citation(s) in RCA: 244] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Single-molecule fluorescence spectroscopy addresses biological mechanisms and enables ultrasensitive diagnostics. We describe a new family of single-molecule fluorescence methods that uses alternating-laser excitation (ALEX) of diffusing or immobilized biomolecules to study their structure, interactions, and dynamics. This is accomplished using ratios that report on the distance between and the stoichiometry of fluorophores attached to the molecules of interest. The principle of alternation is compatible with several time scales, allowing monitoring of fast dynamics or simultaneous monitoring of a large number of individual molecules.
Collapse
Affiliation(s)
- Achillefs N Kapanidis
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, USA.
| | | | | | | | | | | |
Collapse
|
42
|
Tinnefeld P, Sauer M. Branching Out of Single‐Molecule Fluorescence Spectroscopy: Challenges for Chemistry and Influence on Biology. Angew Chem Int Ed Engl 2005; 44:2642-2671. [PMID: 15849689 DOI: 10.1002/anie.200300647] [Citation(s) in RCA: 182] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the last decade emerging single-molecule fluorescence-spectroscopy tools have been developed and adapted to analyze individual molecules under various conditions. Single-molecule-sensitive optical techniques are now well established and help to increase our understanding of complex problems in different disciplines ranging from materials science to cell biology. Previous dreams, such as the monitoring of the motility and structural changes of single motor proteins in living cells or the detection of single-copy genes and the determination of their distance from polymerase molecules in transcription factories in the nucleus of a living cell, no longer constitute unsolvable problems. In this Review we demonstrate that single-molecule fluorescence spectroscopy has become an independent discipline capable of solving problems in molecular biology. We outline the challenges and future prospects for optical single-molecule techniques which can be used in combination with smart labeling strategies to yield quantitative three-dimensional information about the dynamic organization of living cells.
Collapse
Affiliation(s)
- Philip Tinnefeld
- Applied Laserphysics und Laserspectroscopy, Faculty of Physics, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany, Fax: (+49) 521-106-2958
| | - Markus Sauer
- Applied Laserphysics und Laserspectroscopy, Faculty of Physics, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany, Fax: (+49) 521-106-2958
| |
Collapse
|
43
|
Tinnefeld P, Sauer M. Neue Wege in der Einzelmolekül-Fluoreszenzspektroskopie: Herausforderungen für die Chemie und Einfluss auf die Biologie. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200300647] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
44
|
Heinlein T, Biebricher A, Schlüter P, Roth CM, Herten DP, Wolfrum J, Heilemann M, Müller C, Tinnefeld P, Sauer M. High-Resolution Colocalization of Single Molecules within the Resolution Gap of Far-Field Microscopy. Chemphyschem 2005; 6:949-55. [PMID: 15884081 DOI: 10.1002/cphc.200400622] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To obtain detailed information about the three-dimensional (3D) organization of small biomolecular assemblies with a size of less than 100 nanometers, advanced techniques are required that enable the determination of absolute 3D positions and distances between individual fluorophores well below the resolution limit of conventional light microscopy. We show how spectrally resolved fluorescence lifetime imaging microscopy (SFLIM) can provide significant contributions and allow us to determine distances between conventional individual fluorophores (Bodipy 630/650 and Cy5.5) that are less than 20 nm apart. We take advantage of fluorescent dyes (here Cy5.5 and Bodipy 630/650) that can be efficiently excited by a single pulsed diode laser emitting at 635 nm but differ in their fluorescence lifetime and emission maxima. The potential of the method for ultrahigh colocalization studies is demonstrated by measuring the end-to-end distance between single fluorophores separated by double-stranded DNA of various lengths. Combining SFLIM with polarization-modulated excitation allows us to obtain, simultaneously, information about the relative orientation of fluorophores. Furthermore, we show that the environment-dependent photophysics of conventional fluorophores, that is, photostability, blinking pattern, and the tendency to enter irreversible nonfluorescent states, sets certain limitations to their in vitro and in vivo applications.
Collapse
Affiliation(s)
- Thomas Heinlein
- Institute of Physical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Zorov DB, Kobrinsky E, Juhaszova M, Sollott SJ. Examining intracellular organelle function using fluorescent probes: from animalcules to quantum dots. Circ Res 2005; 95:239-52. [PMID: 15297386 DOI: 10.1161/01.res.0000137875.42385.8e] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fluorescence microscopy imaging has become one of the most useful techniques to assess the activity of individual cells, subcellular trafficking of signals to and between organelles, and to appreciate how organelle function is regulated. The past 2 decades have seen a tremendous advance in the rational design and development in the nature and selectivity of probes to serve as reporters of the intracellular environment in live cells. These probes range from small organic fluorescent molecules to fluorescent biomolecules and photoproteins ingeniously engineered to follow signaling traffic, sense ionic and nonionic second messengers, and report various kinase activities. These probes, together with recent advances in imaging technology, have enabled significantly enhanced spatial and temporal resolution. This review summarizes some of these developments and their applications to assess intracellular organelle function.
Collapse
Affiliation(s)
- Dmitry B Zorov
- Laboratories of Cardiovascular Sciences, Gerontology Research Center, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, Md 21224-6825, USA
| | | | | | | |
Collapse
|
46
|
Lee NK, Kapanidis AN, Wang Y, Michalet X, Mukhopadhyay J, Ebright RH, Weiss S. Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. Biophys J 2005; 88:2939-53. [PMID: 15653725 PMCID: PMC1282518 DOI: 10.1529/biophysj.104.054114] [Citation(s) in RCA: 313] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Fluorescence resonance energy transfer (FRET) between a donor (D) and an acceptor (A) at the single-molecule level currently provides qualitative information about distance, and quantitative information about kinetics of distance changes. Here, we used the sorting ability of confocal microscopy equipped with alternating-laser excitation (ALEX) to measure accurate FRET efficiencies and distances from single molecules, using corrections that account for cross-talk terms that contaminate the FRET-induced signal, and for differences in the detection efficiency and quantum yield of the probes. ALEX yields accurate FRET independent of instrumental factors, such as excitation intensity or detector alignment. Using DNA fragments, we showed that ALEX-based distances agree well with predictions from a cylindrical model of DNA; ALEX-based distances fit better to theory than distances obtained at the ensemble level. Distance measurements within transcription complexes agreed well with ensemble-FRET measurements, and with structural models based on ensemble-FRET and x-ray crystallography. ALEX can benefit structural analysis of biomolecules, especially when such molecules are inaccessible to conventional structural methods due to heterogeneity or transient nature.
Collapse
Affiliation(s)
- Nam Ki Lee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, USA
| | | | | | | | | | | | | |
Collapse
|
47
|
Hubner CG, Ksenofontov V, Nolde F, Mullen K, Basche T. Three-dimensional orientational colocalization of individual donor–acceptor pairs. J Chem Phys 2004; 120:10867-70. [PMID: 15268115 DOI: 10.1063/1.1760492] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report on the determination of the three-dimensional orientation of the donor and acceptor transition dipoles in individual fluorescence resonance energy transfer (FRET) pairs by means of scanning optical microscopy with annular illumination. Knowledge of the mutual orientation of the donor and acceptor dipole is mandatory for reliable distance determination based on FRET efficiency measurements. In our model system perylenediimide as the donor and terryelenediimide as the acceptor are coupled via a stiff p-terphenyl linker. The absorption dipoles of the donor and acceptor are selectively addressed by the 488 nm and 647 line of an Ar/Kr mixed gas laser, respectively. A clear deviation from collinearity is observed with a distribution of misalignment angles peaked around 22 degrees.
Collapse
|
48
|
Morrison IEG, Karakikes I, Barber RE, Fernández N, Cherry RJ. Detecting and quantifying colocalization of cell surface molecules by single particle fluorescence imaging. Biophys J 2003; 85:4110-21. [PMID: 14645098 PMCID: PMC1303710 DOI: 10.1016/s0006-3495(03)74823-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2003] [Accepted: 08/15/2003] [Indexed: 01/14/2023] Open
Abstract
Single particle fluorescence imaging (SPFI) uses the high sensitivity of fluorescence to visualize individual molecules that have been selectively labeled with small fluorescent particles. The positions of particles are determined by fitting the intensity profile of their images to a 2-D Gaussian function. We have exploited the positional information obtained from SPFI to develop a method for detecting colocalization of cell surface molecules. This involves labeling two different molecules with different colored fluorophores and determining their positions separately by dual wavelength imaging. The images are analyzed to quantify the overlap of the particle images and hence determine the extent of colocalization of the labeled molecules. Simulated images and experiments with a model system are used to investigate the extent to which colocalization occurs from chance proximity of randomly distributed molecules. A method of correcting for positional shifts that result from chromatic aberration is presented. The technique provides quantification of the extent of colocalization and can detect whether colocalized molecules occur singly or in clusters. We have obtained preliminary data for colocalization of molecules on intact cells. Cells often exhibit particulate autofluorescence that can interfere with the measurements; a method for overcoming this problem by triple wavelength imaging is described.
Collapse
Affiliation(s)
- Ian E G Morrison
- Department of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | | | | | | | | |
Collapse
|
49
|
Michalet X, Kapanidis AN, Laurence T, Pinaud F, Doose S, Pflughoefft M, Weiss S. The power and prospects of fluorescence microscopies and spectroscopies. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2003; 32:161-82. [PMID: 12598370 DOI: 10.1146/annurev.biophys.32.110601.142525] [Citation(s) in RCA: 180] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent years have witnessed a renaissance of fluorescence microscopy techniques and applications, from live-animal multiphoton confocal microscopy to single-molecule fluorescence spectroscopy and imaging in living cells. These achievements have been made possible not so much because of improvements in microscope design, but rather because of development of new detectors, accessible continuous wave and pulsed laser sources, sophisticated multiparameter analysis on one hand, and the development of new probes and labeling chemistries on the other. This review tracks the lineage of ideas and the evolution of thinking that have led to the actual developments, and presents a comprehensive overview of the field, with emphasis put on our laboratory's interest in single-molecule microscopy and spectroscopy.
Collapse
Affiliation(s)
- Xavier Michalet
- Department of Chemistry and Biochemistry, UCLA, Young Hall, 607 Charles E. Young Drive East, Los Angeles, California 90095, USA.
| | | | | | | | | | | | | |
Collapse
|
50
|
Heilemann M, Herten DP, Heintzmann R, Cremer C, Muller C, Tinnefeld P, Weston KD, Wolfrum J, Sauer M. High-resolution colocalization of single dye molecules by fluorescence lifetime imaging microscopy. Anal Chem 2002; 74:3511-7. [PMID: 12139062 DOI: 10.1021/ac025576g] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conventional fluorescence microscopy can be used to determine the positions of objects in space when those objects are separated by distances greater than several hundred nanometers, as restricted by the diffraction limit of light. Fluorescence microscopy/spectroscopy based on fluorescence resonance energy-transfer techniques can be used to measure separation distances below approximately 10 nm. To fill the gap between these fundamental limits, we have developed an alternative technique for high-resolution colocalization of fluorescent dyes. The technique is based on fluorescence lifetime imaging. Under favorable conditions, the method can be used to distinguish, and to measure the distance between, two dye molecules that are less than 30 nm apart. To demonstrate the method, lifetime images of a mixture of Cy5 and JF9 (rhodamine derivative) molecules statistically adsorbed on a glass surface were acquired and analyzed. Since these two molecular species differ in fluorescence lifetime (for Cy5, tau(f) = 2.0 ns, and for JF9, tau(f) = 4.0 ns), it is possible to assign the contribution of fluorescence of the two dye types to each image pixel using a pattern recognition technique. Since both dye types can be excited using the same laser wavelength, the measurement is free of chromatic aberrations. The results presented demonstrate the first high-precision distance measurements between single conventional fluorescent dyes based solely on fluorescence lifetime.
Collapse
Affiliation(s)
- Mike Heilemann
- Physikalisch-Chemisches Institut, Universität Heidelberg, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|