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Liu C, Rastogi A, Yeh HC. Quantification of Rare Single-Molecule Species Based on Fluorescence Lifetime. Anal Chem 2017; 89:4772-4775. [PMID: 28397491 DOI: 10.1021/acs.analchem.7b00397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single-molecule tracking combined with fluorescence lifetime analysis can be a powerful tool for direct molecular quantification in solution. However, it is not clear what molecular identification accuracy and how many single-molecule tracks are required to achieve an accurate quantification of rare molecular species. Here we carry out calculations to answer these questions, based on experimentally obtained single-molecule lifetime data and an unbiased ratio estimator. Our results indicate that even at the molecular identification accuracy of 0.99999, 1.8 million tracks are still required in order to achieve 95% confidence level in rare-species quantification with relative error less than ±5%. Our work highlights the fundamental challenges that we are facing in accurate single-molecule identification and quantification without amplification.
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Affiliation(s)
- Cong Liu
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Ajay Rastogi
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
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2
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Li Z, Guo Z, Ruan W, Song W, Wang X, Wang H, Zhao B. Surface-enhanced fluorescent immunoassay on 2D silver nanotriangles array. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 124:655-662. [PMID: 24513713 DOI: 10.1016/j.saa.2014.01.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/04/2014] [Accepted: 01/07/2014] [Indexed: 06/03/2023]
Abstract
Long range ordered silver nanotriangles array was fabricated for surface-enhanced fluorescent immunoassay in this paper. By polystyrene (PS) microspheres based LB template method, the silver nanotriangle array with about 100 nm in height was constructed on the surface of glass slide. On the surface of Ag nanotriangles array, the immune reaction of antigens and labeled antibodies was carried out. Based on the interaction of fluorophores from antibodies with the plasmon resonance from Ag nanotriangles and the enrichment effect of this patterned array, 3.11 times enhancement of the fluorescent intensity of the target antibodies was obtained. According to the fitting curve of fluorescent intensities and logarithmic concentrations of labeled antibodies from 100 pg/mL to 10 μg/mL, it concludes that the limit of detection by this Ag nanotriangles array for immune complex is 100 pg/mL. Due to the advantages of high sensitivity, good reproducibility, and convenient fabrication, the 2D silver nanotriangles array could be an exciting platform for bioassays in proteomics, drug discovery and diagnostics.
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Affiliation(s)
- Zhishi Li
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, China; State Key Lab of Marine Coatings, 4 Jinhu Road, Qingdao 266071, China; Marine Chemical Research Institute, 4 Jinhu Road, Qingdao 266071, China
| | - Zhinan Guo
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, China
| | - Weidong Ruan
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, China
| | - Wei Song
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, China
| | - Xu Wang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, China
| | - Huajin Wang
- State Key Lab of Marine Coatings, 4 Jinhu Road, Qingdao 266071, China; Marine Chemical Research Institute, 4 Jinhu Road, Qingdao 266071, China
| | - Bing Zhao
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, China.
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3
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Dutta Choudhury S, Badugu R, Ray K, Lakowicz JR. Steering Fluorescence Emission with Metal-Dielectric-Metal Structures of Au, Ag and Al. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2013; 117:15798-15807. [PMID: 25126154 PMCID: PMC4128489 DOI: 10.1021/jp4051066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Directional control over fluorescence emission is important for improving the sensitivity of fluorescence based techniques. In recent years, plasmonic and photonic structures have shown great promise in shaping the spectral and spatial distribution of fluorescence, which otherwise is typically isotropic in nature and independent of the observation direction. In this work we have explored the potential of metal-dielectric-metal (MDM) structures composed of Au, Ag or Al in steering the fluorescence emission from various probes emitting in the NIR, Visible or UV/blue region. We show that depending on the optical properties of the metal and the thickness of the dielectric layer, the emission from randomly oriented fluorophores embedded within the MDM substrate is transformed into beaming emission normal to the substrate. Agreement of the observed angular emission patterns with reflectivity calculations reveals that the directional emission is due to the coupling of the fluorescence with the electromagnetic modes supported by the MDM structure.
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Affiliation(s)
- Sharmistha Dutta Choudhury
- Radiation & Photochemistry Division, Bhabha Atomic Research Center, Mumbai 400085, India
- Corresponding authors. ,
| | - Ramachandram Badugu
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 725 West Lombard Street, Baltimore, Maryland 21201, United States
| | - Krishanu Ray
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 725 West Lombard Street, Baltimore, Maryland 21201, United States
| | - Joseph R. Lakowicz
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 725 West Lombard Street, Baltimore, Maryland 21201, United States
- Corresponding authors. ,
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4
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Cheng LC, Chang CY, Lin CY, Cho KC, Yen WC, Chang NS, Xu C, Dong CY, Chen SJ. Spatiotemporal focusing-based widefield multiphoton microscopy for fast optical sectioning. OPTICS EXPRESS 2012; 20:8939-48. [PMID: 22513605 DOI: 10.1364/oe.20.008939] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In this study, a microscope based on spatiotemporal focusing offering widefield multiphoton excitation has been developed to provide fast optical sectioning images. Key features of this microscope are the integrations of a 10 kHz repetition rate ultrafast amplifier featuring high instantaneous peak power (maximum 400 μJ/pulse at a 90 fs pulse width) and a TE-cooled, ultra-sensitive photon detecting, electron multiplying charge-coupled camera into a spatiotemporal focusing microscope. This configuration can produce multiphoton images with an excitation area larger than 200 × 100 μm² at a frame rate greater than 100 Hz (current maximum of 200 Hz). Brownian motions of fluorescent microbeads as small as 0.5 μm were observed in real-time with a lateral spatial resolution of less than 0.5 μm and an axial resolution of approximately 3.5 μm. Furthermore, second harmonic images of chicken tendons demonstrate that the developed widefield multiphoton microscope can provide high resolution z-sectioning for bioimaging.
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Affiliation(s)
- Li-Chung Cheng
- Department of Photonics, National Cheng Kung University, Tainan 701, Taiwan
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5
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Swierczewska M, Lee S, Chen X. The design and application of fluorophore-gold nanoparticle activatable probes. Phys Chem Chem Phys 2011; 13:9929-41. [PMID: 21380462 PMCID: PMC3632443 DOI: 10.1039/c0cp02967j] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescence-based assays and detection techniques are among the most highly sensitive and popular biological tests for researchers. To match the needs of research and the clinic, detection limits and specificities need to improve, however. One mechanism is to decrease non-specific background signals, which is most efficiently done by increasing fluorescence quenching abilities. Reports in the literature of theoretical and experimental work have shown that metallic gold surfaces and nanoparticles are ultra-efficient fluorescence quenchers. Based on these findings, subsequent reports have described gold nanoparticle fluorescence-based activatable probes that were designed to increase fluorescence intensity based on a range of stimuli. In this way, these probes can detect and signify assorted biomarkers and changes in environmental conditions. In this review, we explore the various factors and theoretical models that affect gold nanoparticle fluorescence quenching, explore current uses of activatable probes, and propose an engineering approach for future development of fluorescence based gold nanoparticle activatable probes.
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Affiliation(s)
- Magdalena Swierczewska
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD 20892, USA
- Department of Biomedical Engineering, Stony Brook University, Bioengineering Building, Stony Brook, NY 11794-2580, USA
| | - Seulki Lee
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD 20892, USA
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6
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Hui-Ling W, Wen-You L, Xi-Wen H, Peng-Yuan Y, Hong L. Interactions of Night Blue with Nucleic Acids and Determination of Nucleic Acids Using Resonance Light Scattering Technique. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.20030210318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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7
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Fu Y, Zhang J, Lakowicz JR. Highly efficient detection of single fluorophores in blood serum samples with high autofluorescence. Photochem Photobiol 2009; 85:646-51. [PMID: 19192209 PMCID: PMC2755222 DOI: 10.1111/j.1751-1097.2008.00500.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single molecule detection (SMD) is usually performed on surface-immobilized molecules with diffraction-limited observation volumes, typically with confocal optics to suppress background from the sample and instrument. In this paper we consider the more difficult task of detecting single fluorophores in the presence of a substantial fluorescence background. We determined that for a readily accessible macroscopic observation volume of 1 pL that the background from undiluted blood serum was approximately equal to 2700 Cy5 molecules, and the background from whole blood equal to about 14 000 Cy5 molecules in whole blood. These high backgrounds appear to preclude the possibility of SMD of Cy5 molecules. However, we show that the signal-to-noise ratio (SNR) in high background samples can be increased dramatically by reduction of the observed volume. We were able to detect single surface-bound Cy5-labeled DNA (Cy5-DNA) oligomers in diluted blood serum with an SNR near 40. We also examined freely diffusing Cy5-DNA in blood serum. The data showed that single Cy5-DNA molecules could be detected even in the undiluted serum. We further investigated the SNR on silver island films. We found that the fluorescence signal was greatly enhanced in the presence of metallic nanostructures showing a larger SNR in the application tested. These results suggest the possibility of clinical assays based on SMD in blood serum and possibly whole blood. Increased SNR near metallic nanostructure could probably overcome the need for diffraction-limited volumes and enhance our ability to do in situ SMD.
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Affiliation(s)
- Yi Fu
- Department of Biochemistry and Molecular Biology, Center for Fluorescence Spectroscopy, University of Maryland School of Medicine, Baltimore, MD
| | - Jian Zhang
- Department of Biochemistry and Molecular Biology, Center for Fluorescence Spectroscopy, University of Maryland School of Medicine, Baltimore, MD
| | - Joseph R. Lakowicz
- Department of Biochemistry and Molecular Biology, Center for Fluorescence Spectroscopy, University of Maryland School of Medicine, Baltimore, MD
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8
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Irawan R, Tjin SC. Detection of fluorescence generated in microfluidic channel using in-fiber grooves and in-fiber microchannel sensors. Methods Mol Biol 2009; 503:403-422. [PMID: 19151955 DOI: 10.1007/978-1-60327-567-5_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In life sciences, the problem of very small volume of sample, analytes, and reagents is often faced. Micro-fluidic technology is ideal for handling costly and difficult-to-obtain samples, analytes, and reagents, because it requires very small volume of samples, in order of microL or even nL. Among many types of optical techniques commonly used for biosensing in microfluidic chip, fluorescence detection technique is the most common. The standard free-space detection techniques used to detect fluorescence emission from microfluidic channel often suffer issues like scattering noise, crosstalks, misalignment, autofluorescence of substrate, and low collection efficiency. This chapter describes two fluorescence detection methods, based on in-fiber microchannels and in-fiber grooves, which can solve those problems, as the techniques integrate the excitation and emission light paths, and the sensing part. Utilizing an optical fiber as a sensing component makes these detection techniques suitable for lab-on-a-chip or microTAS applications.
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Affiliation(s)
- Rudi Irawan
- BioMedical Engineering Research Centre, Singapore-University of Washington Alliance, Nanyang Technological University, Singapore
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9
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Irawan R, Chuan TS, Meng TC, Ming TK. Rapid constructions of microstructures for optical fiber sensors using a commercial CO2 laser system. Open Biomed Eng J 2008; 2:28-35. [PMID: 19662114 PMCID: PMC2701072 DOI: 10.2174/1874120700802010028] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 05/26/2008] [Accepted: 05/28/2008] [Indexed: 11/22/2022] Open
Abstract
Exposing an optical fiber core to the measurand surrounding the fiber is often used to enhance the sensitivity of an optical fiber sensor. This paper reports on the rapid fabrication of microstructures in an optical fiber using a CO₂ laser system which help exposing the optical fiber core to the measurand. The direct-write CO₂ laser system used is originally designed for engraving the polymeric material. Fabrications of microstructures such as in-fiber microhole, D-shaped fiber, in-fiber microchannel, side-sliced fiber and tapered fiber were attempted. The microstructures in the fibers were examined using a SEM and an optical microscope. Quality of microstructures shown by the SEM images and promising results from fluorescence sensor tests using in-fiber microchannels of 100μm width, 210μm depth and 10mm length show the prospect of this method for use in optical fiber sensor development. The direct-write CO₂ laser system is a flexible and fast machining tool for fabricating microstructures in an optical fiber, and can possibly be a replacement of the time consuming chemical etching and polishing methods used for microstructure fabrications of optical the fiber sensors reported in other literatures.
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Affiliation(s)
- Rudi Irawan
- SUWA, BioMedical Engineering Research Centre, Nanyang Technological University, Singapore 637553.
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10
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Li L, Tian X, Zou G, Shi Z, Zhang X, Jin W. Quantitative Counting of Single Fluorescent Molecules by Combined Electrochemical Adsorption Accumulation and Total Internal Reflection Fluorescence Microscopy. Anal Chem 2008; 80:3999-4006. [DOI: 10.1021/ac702534h] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lu Li
- School of Chemistry and Chemical Engineering and Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan 250100, China
| | - Xinzhe Tian
- School of Chemistry and Chemical Engineering and Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan 250100, China
| | - Guizheng Zou
- School of Chemistry and Chemical Engineering and Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan 250100, China
| | - Zhikun Shi
- School of Chemistry and Chemical Engineering and Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan 250100, China
| | - Xiaoli Zhang
- School of Chemistry and Chemical Engineering and Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan 250100, China
| | - Wenrui Jin
- School of Chemistry and Chemical Engineering and Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan 250100, China
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11
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Tunable blinking kinetics of cy5 for precise DNA quantification and single-nucleotide difference detection. Biophys J 2008; 95:729-37. [PMID: 18424494 DOI: 10.1529/biophysj.107.127530] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fluorescence correlation spectroscopy (FCS) can resolve the intrinsic fast-blinking kinetics (FBKs) of fluorescent molecules that occur on the order of microseconds. These FBKs can be heavily influenced by the microenvironments in which the fluorescent molecules are contained. In this work, FCS is used to monitor the dynamics of fluorescence emission from Cy5 labeled on DNA probes. We found that the FBKs of Cy5 can be tuned by having more or less unpaired guanines (upG) and thymines (upT) around the Cy5 dye. The observed FBKs of Cy5 are found to predominantly originate from the isomerization and back-isomerization processes of Cy5, and Cy5-nucleobase interactions are shown to slow down these processes. These findings lead to a more precise quantification of DNA hybridization using FCS analysis, in which the FBKs play a major role rather than the diffusion kinetics. We further show that the alterations of the FBKs of Cy5 on probe hybridization can be used to differentiate DNA targets with single-nucleotide differences. This discrimination relies on the design of a probe-target-probe DNA three-way-junction, whose basepairing configuration can be altered as a consequence of a single-nucleotide substitution on the target. Reconfiguration of the three-way-junction alters the Cy5-upG or Cy5-upT interactions, therefore resulting in a measurable change in Cy5 FBKs. Detection of single-nucleotide variations within a sequence selected from the Kras gene is carried out to validate the concept of this new method.
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12
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Jing N, Kameoka J, Su CB, Chou CK, Hung MC. Nanofluidic Devices for Single Molecule Identification. J PHOTOPOLYM SCI TEC 2008. [DOI: 10.2494/photopolymer.21.531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Eggeling C, Widengren J, Brand L, Schaffer J, Felekyan S, Seidel CAM. Analysis of photobleaching in single-molecule multicolor excitation and Förster resonance energy transfer measurements. J Phys Chem A 2007; 110:2979-95. [PMID: 16509620 DOI: 10.1021/jp054581w] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dye photobleaching is a major constraint of fluorescence readout within a range of applications. In this study, we investigated the influence of photobleaching in fluorescence experiments applying multicolor laser as well as Förster resonance energy transfer (FRET) mediated excitation using several red-emitting dyes frequently used in multicolor experiments or as FRET acceptors. The chosen dyes (cyanine 5 (Cy5), MR121, Alexa660, Alexa680, Atto647N, Atto655) have chemically distinct chromophore systems and can be excited at 650 nm. Several fluorescence analysis techniques have been applied to detect photobleaching and to disclose the underlying photophysics, all of which are based on single-molecule detection: (1) fluorescence correlation spectroscopy (FCS) of bulk solutions, (2) fluorescence cross-correlation of single-molecule trajectories, and (3) multiparameter fluorescence detection (MFD) of single-molecule events. The maximum achievable fluorescence signals as well as the survival times of the red dyes were markedly reduced under additional laser irradiation in the range of 500 nm. Particularly at excitation levels at or close to saturation, the 500 nm irradiation effectively induced transitions to higher excited electronic states on already excited dye molecules, leading to a pronounced bleaching reactivity. A theoretical model for the observed laser irradiance dependence of the fluorescence brightness of a Cy5 FRET acceptor dye has been developed introducing the full description of the underlying photophysics. The model takes into account acceptor as well as donor photobleaching from higher excited electronic states, population of triplet states, and energy transfer to both the ground and excited states of the acceptor dye. Also, photoinduced reverse intersystem crossing via higher excited triplet states is included, which was found to be very efficient for Cy5 attached to DNA. Comparing continuous wave (cw) and pulsed donor excitation, a strong enhancement of acceptor photobleaching by a factor of 5 was observed for the latter. Thus, in the case of fluorescence experiments utilizing multicolor pulsed laser excitation, the application of the appropriate timing of synchronized green and red laser pulses in an alternating excitation mode can circumvent excessive photobleaching. Moreover, important new single-molecule analysis diagnosis tools are presented: (1) For the case of excessive acceptor photobleaching, cross-correlation analysis of single-molecule trajectories of the fluorescence signal detected in the donor and acceptor detection channels and vice versa shows an anticorrelated exponential decay and growth, respectively. (2) The time difference, Tg - Tr, of the mean observation times of all photons detected for the donor and acceptor detection channels within a single-molecule fluorescence burst allows one to identify and exclude molecules with an event of acceptor photobleaching. The presented single-molecule analysis methods can be constrained to, for example, FRET-active subpopulations, reducing bias from FRET-inactive molecules. The observations made are of strong relevance for and demand a careful choice of laser action in multicolor and FRET experiments, in particular when performed at or close to saturation.
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Affiliation(s)
- Christian Eggeling
- Department of NanoBiophotonics, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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14
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Wang L, Xu G, Shi Z, Jiang W, Jin W. Quantification of protein based on single-molecule counting by total internal reflection fluorescence microscopy with adsorption equilibrium. Anal Chim Acta 2007; 590:104-9. [PMID: 17416229 DOI: 10.1016/j.aca.2007.03.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Revised: 03/03/2007] [Accepted: 03/08/2007] [Indexed: 11/17/2022]
Abstract
We developed a sensitive single-molecule imaging method for quantification of protein by total internal reflection fluorescence microscopy with adsorption equilibrium. In this method, the adsorption equilibrium of protein was achieved between solution and glass substrate. Then, fluorescence images of protein molecules in a evanescent wave field were taken by a highly sensitive electron multiplying charge coupled device. Finally, the number of fluorescent spots corresponding to the protein molecules in the images was counted. Alexa Fluor 488-labeled goat anti-rat IgG(H+L) was chosen as the model protein. The spot number showed an excellent linear relationship with protein concentration. The concentration linear range was 5.4 x 10(-11) to 8.1 x 10(-10) mol L(-1).
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Affiliation(s)
- Lei Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, PR China
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15
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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.
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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
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16
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Irawan R, Tay CM, Tjin SC, Fu CY. Compact fluorescence detection using in-fiber microchannels-its potential for lab-on-a-chip applications. LAB ON A CHIP 2006; 6:1095-8. [PMID: 16874385 DOI: 10.1039/b607834f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
This paper reports a compact and practical fluorescence sensor using an in-fiber microchannel. A blue LED, a multimode PMMA or silica fiber and a mini-PMT were used as an excitation source, a light guide and a fluorescence detector, respectively. Microfluidic channels of 100 microm width and 210 microm depth were fabricated in the optical fibers using a direct-write CO(2) laser system. The experimental results show that the sensor has high sensitivity, able to detect 0.005 microg L(-1) of fluorescein in the PBS solution, and the results are reproducible. The results also show that the silica fiber sensor has better sensitivity than that of the PMMA fiber sensor. This could be due to the fouling effect of the frosty layer formed at the microchannel made within the PMMA fiber. It is believed that this fiber sensor has the potential to be integrated into microfluidic chips for lab-on-a-chip applications.
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Affiliation(s)
- Rudi Irawan
- Singapore-University of Washington Alliance, Biomedical Engineering Research Centre, Nanyang Technological University, Singapore.
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17
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Fang F, Zheng H, Li L, Wu Y, Chen J, Zhuo S, Zhu C. Determination of nucleic acids with a near infrared cyanine dye using resonance light scattering technique. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2006; 64:698-702. [PMID: 16650797 DOI: 10.1016/j.saa.2005.07.071] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Accepted: 07/25/2005] [Indexed: 05/08/2023]
Abstract
A new method for the determination of nucleic acids has been developed based on the enhancement effect of resonance light scattering (RLS) with a cationic near infrared (NIR) cyanine dye. Under the optimal conditions, the enhanced RLS intensity at 823 nm is proportional to the concentration of nucleic acids in the range of 0-400 ng mL-1 for both calf thymus DNA (CT DNA) and fish sperm DNA (FS DNA), 0-600 ng mL-1 for snake ovum RNA (SO RNA). The detection limits are 3.5 ng mL-1, 3.4 ng mL-1 and 2.9 ng mL-1 for CT DNA, FS DNA and SO RNA, respectively. Owing to performing in near infrared region, this method not only has high sensitivity endowed by RLS technique but also avoids possible spectral interference from background. It has been applied to the determination of nucleic acids in synthetic and real samples and satisfactory results were obtained.
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Affiliation(s)
- Fang Fang
- Anhui Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China
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18
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Kostov Y, Smith DS, Tolosa L, Rao G, Gryczynski I, Gryczynski Z, Malicka J, Lakowicz JR. Directional surface plasmon-coupled emission from a 3 nm green fluorescent protein monolayer. Biotechnol Prog 2006; 21:1731-5. [PMID: 16321058 PMCID: PMC6949142 DOI: 10.1021/bp050114k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High-sensitivity detection schemes are of great interest for a number of applications. Unfortunately, such schemes are usually high-cost. We demonstrate a low-cost approach to a high-sensitivity detection scheme based on surface plasmon-coupled emission (SPCE). The SPCE of a monomolecular layer of green fluorescent protein (GFP) is reported here. The protein was electrostatically attached to a thin, SiO(2)-protected silver film deposited on a quartz substrate. The visible, directional emission of GFP was observed at a sharp, well-defined angle of 47.5 degrees from the normal to the coupling prism, and the spectrum corresponded to that of GFP. The SPCE resulting from the reverse Kretschmann configuration showed a 12-fold enhancement over the free space fluorescence. The directional emission was 97% p-polarized. The directionality and high polarization can be coupled with the intrinsic spectral resolution of SPCE to be used in the design miniaturized spectrofluorometers. The observation of SPCE in the visible region of the spectrum from a monolayer of protein opens up new possibilities in protein-based sensing.
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Affiliation(s)
| | | | | | - Govind Rao
- To whom correspondence should be addressed. (G.R.) Fax: 410-455-6500. . (Z.G.) Fax: 410-706-8408.
| | | | - Zygmunt Gryczynski
- To whom correspondence should be addressed. (G.R.) Fax: 410-455-6500. . (Z.G.) Fax: 410-706-8408.
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19
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Park M, Kim HH, Kim D, Song NW. Counting the Number of Fluorophores Labeled in Biomolecules by Observing the Fluorescence-Intensity Transient of a Single Molecule. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2005. [DOI: 10.1246/bcsj.78.1612] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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20
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Dittrich PS, Manz A. Single-molecule fluorescence detection in microfluidic channels—the Holy Grail in μTAS? Anal Bioanal Chem 2005; 382:1771-82. [PMID: 16075229 DOI: 10.1007/s00216-005-3335-9] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2005] [Revised: 05/12/2005] [Accepted: 05/19/2005] [Indexed: 10/25/2022]
Abstract
Both single-molecule detection (SMD) methods and miniaturization technologies have developed very rapidly over the last ten years. By merging these two techniques, it may be possible to achieve the optimal requirements for the analysis and manipulation of samples on a single molecule scale. While miniaturized structures and channels provide the interface required to handle small particles and molecules, SMD permits the discovery, localization, counting and identification of compounds. Widespread applications, across various bioscience/analytical science fields, such as DNA-analysis, cytometry and drug screening, are envisaged. In this review, the unique benefits of single fluorescent molecule detection in microfluidic channels are presented. Recent and possible future applications are discussed.
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Affiliation(s)
- Petra S Dittrich
- Department of Miniaturization, Institute for Analytical Sciences (ISAS), Bunsen-Kirchhoff-Str. 11, 44139 Dortmund, Germany.
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21
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Ferris MM, Habbersett RC, Wolinsky M, Jett JH, Yoshida TM, Keller RA. Statistics of single-molecule measurements: applications in flow-cytometry sizing of DNA fragments. Cytometry A 2005; 60:41-52. [PMID: 15229856 DOI: 10.1002/cyto.a.20000] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND The measurement of physical properties from single molecules has been demonstrated. However, the majority of single-molecule studies report values based on relatively large data sets (e.g., N > 50). While there are studies that report physical quantities based on small sample sets, there has not been a detailed statistical analysis relating sample size to the reliability of derived parameters. METHODS Monte Carlo simulations and multinomial analysis, dependent on quantifiable experimental parameters, were used to determine the minimum number of single-molecule measurements required to produce an accurate estimate of a population mean. Simulation results were applied to the fluorescence-based sizing of DNA fragments by ultrasensitive flow cytometry (FCM). RESULTS Our simulations show, for an analytical technique with a 10% CV, that the average of as few as five single-molecule measurements would provide a mean value within one SD of the population mean. Additional simulations determined the number of measurements required to obtain the desired number of replicates for each subpopulation within a mixture. Application of these results to flow cytometry data for lambda/HindIII and S. aureus Mu50/SmaI DNA digests produced accurate DNA fingerprints from as few as 98 single-molecule measurements. CONCLUSIONS A surprisingly small number of single-molecule measurements are required to obtain a mean measurement descriptive of a normally-distributed parent population.
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Affiliation(s)
- Matthew M Ferris
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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22
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Abstract
A new method of fluorescence detection that promises to increase sensitivity by 20- to 1000-fold is described. This method will also decrease the contribution of sample autofluorescence to the detected signal. The method depends on the coupling of excited fluorophores with the surface plasmon resonance present in thin metal films, typically silver and gold. The phenomenon of surface plasmon-coupled emission (SPCE) occurs for fluorophores 20-250 nm from the metal surface, allowing detection of fluorophores over substantial distances beyond the metal-sample interface. SPCE depends on interactions of the excited fluorophore with the metal surface. This interaction is independent of the mode of excitation; that is, it does not require evanescent wave or surface-plasmon excitation. In a sense, SPCE is the inverse process of the surface plasmon resonance absorption of thin metal films. Importantly, SPCE occurs over a narrow angular distribution, converting normally isotropic emission into easily collected directional emission. Up to 50% of the emission from unoriented samples can be collected, much larger than typical fluorescence collection efficiencies near 1% or less. SPCE is due only to fluorophores near the metal surface and may be regarded as emission from the induced surface plasmons. Autofluorescence from more distal parts of the sample is decreased due to decreased coupling. SPCE is highly polarized and autofluorescence can be further decreased by collecting only the polarized component or only the light propagating with the appropriate angle. Examples showing how simple optical configurations can be used in diagnostics, sensing, or biotechnology applications are presented. Surface plasmon-coupled emission is likely to find widespread applications throughout the biosciences.
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Affiliation(s)
- Joseph R Lakowicz
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland at Baltimore, 725 West Lombard Street, Baltimore, MD 21201, USA.
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23
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Zhu C, Zhuo S, Li Y, Wang L, Zhao D, Chen J, Wu Y. Determination of nucleic acids with tetra-(N-hexadecylpyridiniumyl) porphyrin sensitized by cetyltrimethylammonium bromide (CTMAB) using a Rayleigh light-scattering technique. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2004; 60:959-964. [PMID: 15036109 DOI: 10.1016/s1386-1425(03)00325-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2003] [Accepted: 07/11/2003] [Indexed: 05/24/2023]
Abstract
Using a common spectrofluorometer to measure the intensity of Rayleigh light-scattering (RLS), a method for determination of nucleic acids has been developed. At pH 10.24 and ionic strength 0.01 mol l-1 (NaCl), the Rayleigh light-scattering of the tetra-(N-hexadecylpyridiniumyl) porphyrin (TC16PyP) is greatly enhanced by nucleic acids in the presence of cetyltrimethylammonium bromide (CTMAB), with the scattering peak located at 311.8 nm. The enhanced RLS intensity is in proportion to the concentration of calf thymus DNA (ctDNA) in the range 0.2-6.0 microg ml-1 and to that of fish sperm DNA (fsDNA) in the range 0.05-3.0microg ml-1. The limits of detection are 0.016 microg ml-1 for calf thymus DNA and 0.023 microg ml-1 for fish sperm DNA when the concentration of TPP was chosen 2.0 x 10(-6) mol l-1. Four synthetic samples were determined satisfactorily.
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Affiliation(s)
- Changqing Zhu
- College of Chemistry and Materials Science, Anhui Normal Unversity, Wuhu 241000, PR China.
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24
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Böhmer M, Enderlein J. Fluorescence spectroscopy of single molecules under ambient conditions: methodology and technology. Chemphyschem 2003; 4:793-808. [PMID: 12961976 DOI: 10.1002/cphc.200200565] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
This review presents an overview of the fluorescence detection and spectroscopy of single molecules (SMS) in liquids and on surfaces under ambient conditions. The various techniques of SMS, such as confocal epifluorescence detection and wide-field imaging are presented and discussed, together with the different methods of data analysis such as fluorescence correlation spectroscopy and burst-by-burst analysis. Selected applications of the various techniques in physics, chemistry, and biology are described.
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Affiliation(s)
- Martin Böhmer
- IBI-1, Forschungszentrum Jülich 52425 Jülich, Germany
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25
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Lakowicz JR, Malicka J, Gryczynski I, Gryczynski Z. Directional surface plasmon-coupled emission: A new method for high sensitivity detection. Biochem Biophys Res Commun 2003; 307:435-9. [PMID: 12893239 PMCID: PMC2737392 DOI: 10.1016/s0006-291x(03)01214-2] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Fluorescence emission is nearly isotropic in space. With typical optical components the collection efficiency is 1% or less. In this preliminary report, we describe a novel approach to transforming the normally isotropic emission into directional emission with a collection efficiency near 50%. This can be accomplished for fluorophores located near a semi-transparent silver film on a glass substrate. The emission couples with the surface plasmon resonance on the silver surface and enters the transparent substrate at a sharply defined angle, the surface plasmon angle for the emission wavelength. We estimate that 40-70% of the total emission enters the substrate at the plasmon angle and can thus be directed towards a detector. Background emission from fluorophores distant from the silver does not couple with the plasmon and is not detected. Different emission wavelengths couple at different angles allowing spectral discrimination without additional optics. Surface plasmon-coupled emission represents a new technology which can be used for high detection efficiency with microfluidic and/or surface-bound assay formats.
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Affiliation(s)
- Joseph R Lakowicz
- University of Maryland at Baltimore, Department of Biochemistry and Molecular Biology, 725 West Lombard Street, Baltimore, MD 21201, USA.
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26
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Lakowicz JR, Malicka J, Gryczynski I, Gryczynski Z, Geddes CD. Radiative decay engineering: the role of photonic mode density in biotechnology. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2003; 36:R240-R249. [PMID: 19763236 PMCID: PMC2744994 DOI: 10.1088/0022-3727/36/14/203] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Fluorescence detection is a central technology in biological research and biotechnology. A vast array of fluorescent probes are available with diverse spectral properties. These properties were 'engineered' into fluorophores by modification of the chemical structures. Essentially, all present uses of fluorescence rely on the radiation of energy into optically transparent media, the free space which surrounds the fluorophores. In this paper, we summarize an opportunity for novel fluorescence technology based on modification of the photonic mode density around the fluorophore and thus control of its spectral properties. This modification can be accomplished by proximity of fluorophores to metallic particles of gold, silver and possibly others. By engineering the size and shape of the metal particles, and the location of the fluorophores relative to the surfaces, fluorophores can be quenched, display increases in quantum yield, and changes in lifetime. Fluorophore-metal surface combinations can even display directional rather than isotropic emission. We describe recent experimental results and suggest potential biomedical applications of fluorophore-metal particle interactions.
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Affiliation(s)
- Joseph R Lakowicz
- Department of Biochemistry and Molecular Biology, Centre for Fluorescence Spectroscopy, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
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27
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Geddes CD, Parfenov A, Lakowicz JR. Photodeposition of silver can result in metal-enhanced fluorescence. APPLIED SPECTROSCOPY 2003; 57:526-31. [PMID: 14658678 PMCID: PMC2737405 DOI: 10.1366/000370203321666542] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Chemically deposited silver particles are widely used for surface-enhanced Raman scattering (SERS) and more recently for surface-enhanced fluorescence (SEF), also known as metal-enhanced fluorescence (MEF). We now show that metallic silver deposited by laser illumination results in an approximately 7-fold increased intensity of locally bound indocyanine green. The increased intensity is accompanied by a decreased lifetime and increased photostability. These results demonstrate the possibility of photolithographic preparation of surfaces for enhanced fluorescence in microfluidics, medical diagnostics, and other applications.
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Affiliation(s)
- Chris D Geddes
- University Maryland Baltimore, Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, 725 West Lombard Street, Baltimore, Maryland 21201, USA
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28
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Werner JH, Cai H, Jett JH, Reha-Krantz L, Keller RA, Goodwin PM. Progress towards single-molecule DNA sequencing: a one color demonstration. J Biotechnol 2003; 102:1-14. [PMID: 12668309 DOI: 10.1016/s0168-1656(03)00006-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Single molecules of fluorescently labeled nucleotides were detected during the cleavage of individual DNA fragments by a processive exonuclease. In these experiments, multiple (10-100) strands of DNA with tetramethyl rhodamine labeled dUMP (TMR-dUMP) incorporated into the sequence were anchored in flow upstream of the detection region of an ultra sensitive flow cytometer. A dilute solution of Exonuclease I passed over the microspheres. When an exonuclease attached to a strand, processive digestion of that strand began. The liberated, labeled bases flowed through the detection region and were detected at high efficiency at the single-molecule level by laser-induced fluorescence. The digestion of a single strand of DNA by a single exonuclease was discernable in these experiments. This result demonstrates the feasibility of single-molecule DNA sequencing. In addition, these experiments point to a new and practical means of arriving at a consensus sequence by individually reading out identical sequences on multiple fragments.
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Affiliation(s)
- James H Werner
- Bioscience Division, Los Alamos National Laboratory, Mail Stop J586, Los Alamos, NM 87545, USA.
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29
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Palo K, Brand L, Eggeling C, Jäger S, Kask P, Gall K. Fluorescence intensity and lifetime distribution analysis: toward higher accuracy in fluorescence fluctuation spectroscopy. Biophys J 2002; 83:605-18. [PMID: 12124251 PMCID: PMC1302173 DOI: 10.1016/s0006-3495(02)75195-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Fluorescence fluctuation methods such as fluorescence correlation spectroscopy and fluorescence intensity distribution analysis (FIDA) have proven to be versatile tools for studying molecular interactions with single molecule sensitivity. Another well-known fluorescence technique is the measurement of the fluorescence lifetime. Here, we introduce a method that combines the benefits of both FIDA and fluorescence lifetime analysis. It is based on fitting the two-dimensional histogram of the number of photons detected in counting time intervals of given width and the sum of excitation to detection delay times of these photons. Referred to as fluorescence intensity and lifetime distribution analysis (FILDA), the technique distinguishes fluorescence species on the basis of both their specific molecular brightness and the lifetime of the excited state and is also able to determine absolute fluorophore concentrations. The combined information yielded by FILDA results in significantly increased accuracy compared to that of FIDA or fluorescence lifetime analysis alone. In this paper, the theory of FILDA is elaborated and applied to both simulated and experimental data. The outstanding power of this technique in resolving different species is shown by quantifying the binding of calmodulin to a peptide ligand, thus indicating the potential for application of FILDA to similar problems in the life sciences.
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30
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Abstract
The Human Genome Project and other major genomic sequencing projects have pushed the development of sequencing technology. In the past six years alone, instrument throughput has increased 15-fold. New technologies are now on the horizon that could yield massive increases in our capacity for de novo DNA sequencing. This review presents a summary of state-of-the-art technologies for genomic sequencing and describes technologies that may be candidates for the next generation of DNA sequencing instruments.
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Affiliation(s)
- A Marziali
- Department of Physics and Astronomy, 6224 Agricultural Road, University of British Columbia, Vancouver, BC, Canada, V6T-1Z1.
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31
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Lakowicz JR, Shen Y, D'Auria S, Malicka J, Fang J, Gryczynski Z, Gryczynski I. Radiative decay engineering. 2. Effects of Silver Island films on fluorescence intensity, lifetimes, and resonance energy transfer. Anal Biochem 2002; 301:261-77. [PMID: 11814297 PMCID: PMC6909932 DOI: 10.1006/abio.2001.5503] [Citation(s) in RCA: 369] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Metallic surfaces can have unusual effects on fluorophores such as increasing or decreasing the rates of radiative decay and the rates of resonance energy transfer (RET). In the present article we describe the effects of metallic silver island films on the emission spectra, lifetimes, and energy transfer for several fluorophores. The fluorophores are not covalently coupled to the silver islands so that there are a range of fluorophore-to-metal distances. We show that proximity of fluorophores to the silver islands results in increased fluorescence intensity, with the largest enhancement for the lowest-quantum-yield fluorophores. Importantly, the metal-induced increases in intensity are accompanied by decreased lifetimes and increased photostability. These effects demonstrate that the silver islands have increased the radiative decay rates of the fluorophore. For solvent-sensitive fluorophores the emission spectra shifted to shorted wavelengths in the presence of the silver islands, which is consistent with a decrease of the apparent lifetime for fluorophores near the metal islands. We also observed an increased intensity and blue spectral shift for the protein human glyoxalase, which displays a low quantum yield for its intrinsic tryptophan emission. In this case the blue shift is thought to be due to increased emission from a buried low-quantum-yield tryptophan residue. Increased intensities were also observed for the intrinsic emission of the nucleic acid bases adenine and thymine and for single-stranded 15-mers poly(T) and poly(C). And finally, we observed increased RET for donors and acceptors in solution and when bound to double-helical DNA. These results demonstrate that metallic particles can be used to modify the emission from intrinsic and extrinsic fluorophores in biochemical systems.
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Affiliation(s)
- Joseph R Lakowicz
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 725 West Lombard Street, Baltimore, Maryland 21201, USA
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32
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Abstract
Fluorescence spectroscopy is a widely used research tool in biochemistry and molecular biology. Fluorescence has also become the dominant method enabling the revolution in medical diagnostics, DNA sequencing, and genomics. To date all the fluorescence observables, including spectral shifts, anisotropies, quantum yields, and lifetimes, have all been utilized in basic and applied uses of fluorescence. In this forward-looking article we describe a new opportunity in fluorescence, radiative decay engineering (RDE). By RDE we mean modifying the emission of fluorophores or chromophores by increasing or decreasing their radiative decay rates. In most fluorescence experiments the radiative rates are not changed because these rates depend on the extinction coefficient of the fluorophore. This intrinsic rate is not changed by quenching and is only weakly dependent on environmental effects. Spectral changes are usually caused by changes in the nonradiative rates resulting from quenching or resonance energy transfer. These processes affect the emission by providing additional routes for decay of the excited states without emission. In contrast to the relatively constant radiative rates in free solution, it is known that the radiative rates can be modified by placing the fluorophores at suitable distances from metallic surfaces and particles. This Review summarizes results from the physics literature which demonstrate the effects of metallic surfaces, colloids, or islands on increasing or decreasing emissive rates, increasing the quantum yields of low quantum yield chromophores, decreasing the lifetimes, and directing the typically isotropic emission in specific directions. These effects are not due to reflection of the emitted photons, but rather as the result of the fluorophore dipole interacting with free electrons in the metal. These interactions change the intensity and temporal and spatial distribution of the radiation. We describe the unusual effects expected from increases in the radiative rates with reference to intrinsic and extrinsic biochemical fluorophores. For instance, the decreased lifetime can result in an effective increase in photostability. Proximity to nearby metallic surfaces can also increase the local field and modify the rate of excitation. We predict that the appropriate localization of fluorophores near particles can result in usefully high emission from "nonfluorescent" molecules and million-fold increases in the number of photons observable from each fluorophore. We also describe how RDE can be applied to medical testing and biotechnology. As one example we predict that nearby metal surfaces can be used to increase the low intrinsic quantum yields of nucleic acids and make unlabeled DNA detectable using its intrinsic metal-enhanced fluorescence.
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Affiliation(s)
- J R Lakowicz
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland at Baltimore, 725 W. Lombard Street, Baltimore, Maryland 21201, USA
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33
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Dörre K, Stephan J, Eigen M. Highly Efficient Single Molecule Detection in Different Micro and submicrometer Channels with cw-excitation. ACTA ACUST UNITED AC 2001. [DOI: 10.1002/1438-5171(200110)2:3<165::aid-simo165>3.0.co;2-g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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34
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Deniz AA, Laurence TA, Dahan M, Chemla DS, Schultz PG, Weiss S. Ratiometric single-molecule studies of freely diffusing biomolecules. Annu Rev Phys Chem 2001; 52:233-53. [PMID: 11326065 DOI: 10.1146/annurev.physchem.52.1.233] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We outline recent developments in biological single-molecule fluorescence detection with particular emphasis on observations by ratiometric fluorescence resonance energy transfer (FRET) of biomolecules freely diffusing in solution. Single-molecule-diffusion methodologies were developed to minimize perturbations introduced by interactions between molecules and surfaces. Confocal microscopy is used in combination with sensitive detectors to observe bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract ratiometric observables such as FRET efficiency and polarization anisotropy. We describe the development of single-molecule FRET methodology and its application to the observation of the Förster distance dependence and the study of protein folding and polymer physics problems. Finally, we discuss future advances in data acquisition and analysis techniques that can provide a more complete picture of the accessible molecular information.
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Affiliation(s)
- A A Deniz
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
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35
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Stephan J, Dörre K, Brakmann S, Winkler T, Wetzel T, Lapczyna M, Stuke M, Angerer B, Ankenbauer W, Földes-Papp Z, Rigler R, Eigen M. Towards a general procedure for sequencing single DNA molecules. J Biotechnol 2001; 86:255-67. [PMID: 11257535 DOI: 10.1016/s0168-1656(00)00417-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this paper we report on the latest technical advances towards single molecule sequencing, a useful method currently developed especially for fast and easy de novo sequencing. Different approaches for complete labeling of DNA with fluorescent dyes are described. In addition, the experimental set-up for the sequencing process is shown. We demonstrate the ability to purify the buffer and enzyme solutions. Inorganic buffers were purified down to at least 20 fM of remaining fluorescent impurities. The exonuclease buffer solution could be cleaned down to 0.8 pM whereby its full activity was kept. Finally, we show a selection procedure for beads and present the data of a model experiment, in which immobilized DNA is degraded by an exonuclease within a polymethylmethacrylate (PMMA) microstructure. Furthermore, the mathematical processing of the obtained raw data is described. A first complete experimental cycle is shown, combining all preparatory steps which are necessary for single molecule sequencing in microstructures.
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Affiliation(s)
- J Stephan
- Max-Planck-Institut für biophysikalische Chemie, Abteilung Biochemische Kinetik, Am Fassberg 2, D-37077 Göttingen, Germany.
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36
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Enderlein J, Sauer M. Optimal Algorithm for Single-Molecule Identification with Time-Correlated Single-Photon Counting. J Phys Chem A 2000. [DOI: 10.1021/jp002358n] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jörg Enderlein
- Institute of Physical Chemistry, University of Regensburg, PF 10 10 42, D-93040 Regensburg, Germany, and Institute of Physical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, D-69120 Heidelberg, Germany
| | - Markus Sauer
- Institute of Physical Chemistry, University of Regensburg, PF 10 10 42, D-93040 Regensburg, Germany, and Institute of Physical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, D-69120 Heidelberg, Germany
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38
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Oldham PB, McCarroll ME, McGown LB, Warner IM. Molecular fluorescence, phosphorescence, and chemiluminescence spectrometry. Anal Chem 2000; 72:197R-209R. [PMID: 10882209 DOI: 10.1021/a1000017p] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- P B Oldham
- Department of Chemistry, Mississippi State University 39762, USA
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39
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Gensch T, Hofkens J, Herrmann A, Tsuda K, Verheijen W, Vosch T, Christ T, Basché T, Müllen K, De Schryver F. Fluoreszenzuntersuchungen einzelner Dendrimermoleküle mit mehreren Chromophoren. Angew Chem Int Ed Engl 1999. [DOI: 10.1002/(sici)1521-3757(19991216)111:24<3970::aid-ange3970>3.0.co;2-i] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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Takano H, Kenseth JR, Wong SS, O'Brien JC, Porter MD. Chemical and biochemical analysis using scanning force microscopy. Chem Rev 1999; 99:2845-90. [PMID: 11749504 DOI: 10.1021/cr9801317] [Citation(s) in RCA: 226] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- H Takano
- Ames Laboratory-USDOE, Microanalytical Instrumentation Center, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
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41
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Chiu DT, Wilson CF, Karlsson A, Danielsson A, Lundqvist A, Strömberg A, Ryttsén F, Davidson M, Nordholm S, Orwar O, Zare RN. Manipulating the biochemical nanoenvironment around single molecules contained within vesicles. Chem Phys 1999. [DOI: 10.1016/s0301-0104(99)00154-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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