Modulated excitation fluorescence analysis

Weiss, Shimon; Kapanidis, Achillefs; Laurence, Ted A.; Lee, Nam K.

Title: Modulated excitation fluorescence analysis

Abstract

Fluorescence, spectroscopy is used to analyze small numbers of molecules that are present in a relatively small detection volume or zone. Information regarding physical and chemical properties of these molecules is determined by rapidly modulating the wavelength, intensity and/or polarization of laser energy to excite fluorophores that are attached either to the molecule of interest or a molecule that interacts with the molecule of interest. The emission profile of the fluorophores is used to determine useful information about the labeled and/or non-labeled molecules including molecular interactions between the molecules.

Inventors:: Weiss, Shimon; Kapanidis, Achillefs; Laurence, Ted A.; Lee, Nam K.

Issue Date:: 2008-11-25

Research Org.:: Univ. of California, Oakland, CA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1531572

Patent Number(s):: 7456954

Application Number:: 10/561,448

Assignee:: The Regents of the University of California (Oakland, CA)

Patent Classifications (CPCs):: G - PHYSICS G01 - MEASURING G01J - MEASUREMENT OF INTENSITY, VELOCITY, SPECTRAL CONTENT, POLARISATION, PHASE OR PULSE CHARACTERISTICS OF INFRA-RED, VISIBLE OR ULTRA-VIOLET LIGHT

G - PHYSICS G01 - MEASURING G01N - INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES

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G - PHYSICS G01 - MEASURING G01J - MEASUREMENT OF INTENSITY, VELOCITY, SPECTRAL CONTENT, POLARISATION, PHASE OR PULSE CHARACTERISTICS OF INFRA-RED, VISIBLE OR ULTRA-VIOLET LIGHT
G01J3/4338 - {Frequency modulated spectrometry}
G01J3/4406 - {Fluorescence spectrometry}

G - PHYSICS G01 - MEASURING G01N - INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
G01N2021/6419 - {Excitation at two or more wavelengths}
G01N2021/6421 - {Measuring at two or more wavelengths}
G01N2021/6441 - {with two or more labels}
G01N21/6408 - {with measurement of decay time, time resolved fluorescence}
G01N21/6428 - {Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes"
G01N21/6445 - {Measuring fluorescence polarisation}
G01N21/6458 - {Fluorescence microscopy
G01N21/648 - {using evanescent coupling or surface plasmon coupling for the excitation of fluorescence}

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DOE Contract Number:: FG03-02ER63339

Resource Type:: Patent

Resource Relation:: Patent File Date: 2004-06-17

Country of Publication:: United States

Language:: English

Subject:: 71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; 42 ENGINEERING

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                    Weiss, Shimon, Kapanidis, Achillefs, Laurence, Ted A., and Lee, Nam K. Modulated excitation fluorescence analysis.  United States: N. p., 2008. 
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                    Weiss, Shimon, Kapanidis, Achillefs, Laurence, Ted A., & Lee, Nam K. Modulated excitation fluorescence analysis.  United States.

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                    Weiss, Shimon, Kapanidis, Achillefs, Laurence, Ted A., and Lee, Nam K. Tue .  
        "Modulated excitation fluorescence analysis".  United States.  https://www.osti.gov/servlets/purl/1531572.

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@article{osti_1531572,

  title        = {Modulated excitation fluorescence analysis},

  author       = {Weiss, Shimon and Kapanidis, Achillefs and Laurence, Ted A. and Lee, Nam K.},

  abstractNote = {Fluorescence, spectroscopy is used to analyze small numbers of molecules that are present in a relatively small detection volume or zone. Information regarding physical and chemical properties of these molecules is determined by rapidly modulating the wavelength, intensity and/or polarization of laser energy to excite fluorophores that are attached either to the molecule of interest or a molecule that interacts with the molecule of interest. The emission profile of the fluorophores is used to determine useful information about the labeled and/or non-labeled molecules including molecular interactions between the molecules.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {2008},

  month        = {11}

}

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Methods and apparatus for single molecule sequencing using energy transfer detection
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US Patent Document 10,093,974
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Similar Records

Title: Modulated excitation fluorescence analysis

Abstract

Citation Formats

Dual-color fluorescence cross-correlation spectroscopy for multicomponent diffusional analysis in solution journal, April 1997

Homogeneous Fluorescence Assay for Cyclic AMP journal, June 2003

Oligomerization of NTRC at the glnA enhancer is required for transcriptional activation. journal, November 1993

Molecular beacons for detecting DNA binding proteins journal, February 2002

On the analysis of high order moments of fluorescence fluctuations journal, February 1990

A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae journal, February 2000

System for distinguishing fluorescent molecule groups by time resolved fluorescence measurement patent, October 2000

A comprehensive two-hybrid analysis to explore the yeast protein interactome journal, March 2001

Correlating Structural Dynamics and Function in Single Ribozyme Molecules journal, May 2002

ANALYTICAL CHEMISTRY: How to Detect Weak Pairs journal, January 2003

Fluorescence correlation spectrometry of the interaction kinetics of tetramethylrhodamin α-bungarotoxin with Torpedo californica acetylcholine receptor journal, January 1996

Simultaneous photometering method and assembly for multi-dimensional measurements concerning biologically related materials patent, July 1979

Towards a truly integrative biology through the functional genomics of yeast journal, February 2001

Simultaneous two-photon excitation of distinct labels for dual-color fluorescence crosscorrelation analysis journal, September 2000

The Transcription Initiation Pathway of Sigma 54 Mutants That Bypass the Enhancer Protein Requirement: IMPLICATIONS FOR THE MECHANISM OF ACTIVATION journal, December 1996

Quantitative Identification of Different Single Molecules by Selective Time-Resolved Confocal Fluorescence Spectroscopy journal, August 1998

Unusual Oligomerization Required for Activity of NtrC, a Bacterial Enhancer-Binding Protein journal, March 1997

New Biarsenical Ligands and Tetracysteine Motifs for Protein Labeling in Vitro and in Vivo: Synthesis and Biological Applications journal, May 2002

Monitoring conformational dynamics of a single molecule by selective fluorescence spectroscopy journal, February 1998

Simultaneous Binding of Two DNA Duplexes to the NtrC−Enhancer Complex Studied by Two-Color Fluorescence Cross-Correlation Spectroscopy † journal, March 2000

Ultrahigh-resolution multicolor colocalization of single fluorescent probes journal, August 2000

Fluorescence-aided molecule sorting: Analysis of structure and interactions by alternating-laser excitation of single molecules journal, June 2004

MgATP Binding and Hydrolysis Determinants of NtrC, a Bacterial Enhancer-Binding Protein journal, August 1999

Method for differentiating or detecting particles in a sample by identifying signal segments of time-resolved, optical raw signals from the sample on the basis of single photon detection patent, March 2001

Photobleaching of Fluorescent Dyes under Conditions Used for Single-Molecule Detection: Evidence of Two-Step Photolysis journal, July 1998

Effect of A(n) tracts within the UP element proximal subsite of a model promoter on kinetics of open complex formation by Escherichia coli RNA polymerase. journal, September 2002

Specific Labeling of Polypeptides at Amino-Terminal Cysteine Residues Using Cy5-benzyl Thioester journal, September 2002

Determination of the diffusion coefficient of dye in solution at single molecule level journal, April 1997

Proteome, transcriptome and genome: top down or bottom up analysis? journal, November 2001

New energy transfer dyes for DNA sequencing journal, July 1997

Single-channel multicolored correlation analysis patent, May 2007

Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase journal, October 2002

Method for detecting reactions by means of coincidence analysis patent, March 2001

Ligand-induced conformational changes observed in single RNA molecules journal, August 1999

PROTEIN BIOCHEMISTRY:Protein Interaction Methods-Toward an Endgame journal, June 1999

FRET Study of a Trifluorophore-Labeled DNAzyme journal, December 2002

Ultrasensitive hybridization analysis using fluorescence correlation spectroscopy journal, May 1995

Methods of screening for ligands of target molecules patent-application, March 2003

Luminescence assay using cyclical excitation wavelength sequence patent, September 2002

Ratiometric measurement and identification of single diffusing molecules journal, August 1999

Quantitative Hybridization Kinetics of DNA Probes to RNA in Solution Followed by Diffusional Fluorescence Correlation Analysis † journal, January 1996

Two-Dimensional Fluorescence Intensity Distribution Analysis: Theory and Applications journal, April 2000

Scanning force microscopy of Escherichia coli RNA polymerase·σ 54 holoenzyme complexes with DNA in buffer and in air 1 1Edited by W. Baumeister journal, November 1998

Role of integration host factor in stimulating transcription from the σ54-dependent nifH promoter journal, October 1992

Confocal microscope for optical determination of an observation volume patent, September 2000

Transcriptional activation via DNA-looping: visualization of intermediates in the activation pathway of E. coli RNA polymerase·σ54 holoenzyme by scanning force microscopy journal, July 1997

Method of characterizing fluorescent molecules or other particles using generating functions patent, April 2002

Method for characterizing samples by determination of a function of at least one specific property of particles in a sample patent, April 2003

Transcription therapy for cancer journal, May 2001

Flow-cytometric isolation of human antibodies from a nonimmune Saccharomyces cerevisiae surface display library journal, January 2003

Method and device for determining predetermined properties of target particles of a sample medium patent, October 2000

Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. journal, June 1996

Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy journal, October 2002

Fluorescence-intensity distribution analysis and its application in biomolecular detection technology journal, November 1999

Guilt-by-association goes global journal, February 2000

Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations journal, January 2003

High speed digital imaging microscope patent, August 1993

MINOR GROOVE-BINDING ARCHITECTURAL PROTEINS: Structure, Function, and DNA Recognition journal, June 1998

Multiparameter single-molecule fluorescence spectroscopy reveals heterogeneity of HIV-1 reverse transcriptase:primer/template complexes journal, February 2003

Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism journal, February 1999

Single-pair fluorescence resonance energy transfer on freely diffusing molecules: Observation of Forster distance dependence and subpopulations journal, March 1999

Association states of the transcription activator protein NtrC from E. coli determined by analytical ultracentrifugation 1 1Edited by K. Yamamoto journal, May 1998

Gene and Protein Expression Profiles of Shewanella oneidensis during Anaerobic Growth with Different Electron Acceptors journal, January 2002

Phosphorylation-Induced Signal Propagation in the Response Regulator NtrC journal, September 2000

DNA-looping and enhancer activity: association between DNA-bound NtrC activator and RNA polymerase at the bacterial glnA promoter. journal, July 1990

Networking proteins in yeast journal, April 2001

Fluorescence Intensity Multiple Distributions Analysis: Concurrent Determination of Diffusion Times and Molecular Brightness journal, December 2000

Method for characterizing samples on the basis of intermediate statistical data patent, February 2003

Abortive Cycling and the Release of Polymerase for Elongation at the σ54-dependent glnAp2 Promoter journal, October 1995

Fluorescent probes and bioconjugation chemistries for single-molecule fluorescence analysis of biomolecules journal, December 2002

Confocal microscope for optical determination of an observation volume patent, June 2002

Molecular beacons for detecting DNA binding proteins: mechanism of action journal, May 2003

Site-Specific Incorporation of Fluorescent Probes into Protein: Hexahistidine-Tag-Mediated Fluorescent Labeling with (Ni 2+ :Nitrilotriacetic Acid) n −Fluorochrome Conjugates journal, December 2001

Method for measuring the association of substructures of pathological protein depositions patent, December 2002

Thermodynamic Fluctuations in a Reacting System—Measurement by Fluorescence Correlation Spectroscopy journal, September 1972

Semiconductor Nanocrystals as Fluorescent Biological Labels patent, September 1998

Genome-wide protein interaction maps using two-hybrid systems journal, August 2000

Dual-color fluorescence cross-correlation spectroscopy for multicomponent diffusional analysis in solution
journal, April 1997

Homogeneous Fluorescence Assay for Cyclic AMP
journal, June 2003

Oligomerization of NTRC at the glnA enhancer is required for transcriptional activation.
journal, November 1993

Molecular beacons for detecting DNA binding proteins
journal, February 2002

On the analysis of high order moments of fluorescence fluctuations
journal, February 1990

A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
journal, February 2000

System for distinguishing fluorescent molecule groups by time resolved fluorescence measurement
patent, October 2000

A comprehensive two-hybrid analysis to explore the yeast protein interactome
journal, March 2001

Correlating Structural Dynamics and Function in Single Ribozyme Molecules
journal, May 2002

ANALYTICAL CHEMISTRY: How to Detect Weak Pairs
journal, January 2003

Fluorescence correlation spectrometry of the interaction kinetics of tetramethylrhodamin α-bungarotoxin with Torpedo californica acetylcholine receptor
journal, January 1996

Simultaneous photometering method and assembly for multi-dimensional measurements concerning biologically related materials
patent, July 1979

Towards a truly integrative biology through the functional genomics of yeast
journal, February 2001

Simultaneous two-photon excitation of distinct labels for dual-color fluorescence crosscorrelation analysis
journal, September 2000

The Transcription Initiation Pathway of Sigma 54 Mutants That Bypass the Enhancer Protein Requirement: IMPLICATIONS FOR THE MECHANISM OF ACTIVATION
journal, December 1996

Quantitative Identification of Different Single Molecules by Selective Time-Resolved Confocal Fluorescence Spectroscopy
journal, August 1998

Unusual Oligomerization Required for Activity of NtrC, a Bacterial Enhancer-Binding Protein
journal, March 1997

New Biarsenical Ligands and Tetracysteine Motifs for Protein Labeling in Vitro and in Vivo: Synthesis and Biological Applications
journal, May 2002

Monitoring conformational dynamics of a single molecule by selective fluorescence spectroscopy
journal, February 1998

Simultaneous Binding of Two DNA Duplexes to the NtrC−Enhancer Complex Studied by Two-Color Fluorescence Cross-Correlation Spectroscopy ^†
journal, March 2000

Ultrahigh-resolution multicolor colocalization of single fluorescent probes
journal, August 2000

Fluorescence-aided molecule sorting: Analysis of structure and interactions by alternating-laser excitation of single molecules
journal, June 2004

MgATP Binding and Hydrolysis Determinants of NtrC, a Bacterial Enhancer-Binding Protein
journal, August 1999

Method for differentiating or detecting particles in a sample by identifying signal segments of time-resolved, optical raw signals from the sample on the basis of single photon detection
patent, March 2001

Photobleaching of Fluorescent Dyes under Conditions Used for Single-Molecule Detection: Evidence of Two-Step Photolysis
journal, July 1998

Effect of A(n) tracts within the UP element proximal subsite of a model promoter on kinetics of open complex formation by Escherichia coli RNA polymerase.
journal, September 2002

Specific Labeling of Polypeptides at Amino-Terminal Cysteine Residues Using Cy5-benzyl Thioester
journal, September 2002

Determination of the diffusion coefficient of dye in solution at single molecule level
journal, April 1997

Proteome, transcriptome and genome: top down or bottom up analysis?
journal, November 2001

New energy transfer dyes for DNA sequencing
journal, July 1997

Single-channel multicolored correlation analysis
patent, May 2007

Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase
journal, October 2002

Method for detecting reactions by means of coincidence analysis
patent, March 2001

Ligand-induced conformational changes observed in single RNA molecules
journal, August 1999

PROTEIN BIOCHEMISTRY:Protein Interaction Methods-Toward an Endgame
journal, June 1999

FRET Study of a Trifluorophore-Labeled DNAzyme
journal, December 2002

Ultrasensitive hybridization analysis using fluorescence correlation spectroscopy
journal, May 1995

Methods of screening for ligands of target molecules
patent-application, March 2003

Luminescence assay using cyclical excitation wavelength sequence
patent, September 2002

Ratiometric measurement and identification of single diffusing molecules
journal, August 1999

Quantitative Hybridization Kinetics of DNA Probes to RNA in Solution Followed by Diffusional Fluorescence Correlation Analysis ^†
journal, January 1996

Two-Dimensional Fluorescence Intensity Distribution Analysis: Theory and Applications
journal, April 2000

Scanning force microscopy of Escherichia coli RNA polymerase·σ 54 holoenzyme complexes with DNA in buffer and in air 1 1Edited by W. Baumeister
journal, November 1998

Role of integration host factor in stimulating transcription from the σ54-dependent nifH promoter
journal, October 1992

Confocal microscope for optical determination of an observation volume
patent, September 2000

Transcriptional activation via DNA-looping: visualization of intermediates in the activation pathway of E. coli RNA polymerase·σ54 holoenzyme by scanning force microscopy
journal, July 1997

Method of characterizing fluorescent molecules or other particles using generating functions
patent, April 2002

Method for characterizing samples by determination of a function of at least one specific property of particles in a sample
patent, April 2003

Transcription therapy for cancer
journal, May 2001

Flow-cytometric isolation of human antibodies from a nonimmune Saccharomyces cerevisiae surface display library
journal, January 2003

Method and device for determining predetermined properties of target particles of a sample medium
patent, October 2000

Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor.
journal, June 1996

Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy
journal, October 2002

Fluorescence-intensity distribution analysis and its application in biomolecular detection technology
journal, November 1999

Guilt-by-association goes global
journal, February 2000

Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations
journal, January 2003

High speed digital imaging microscope
patent, August 1993

MINOR GROOVE-BINDING ARCHITECTURAL PROTEINS: Structure, Function, and DNA Recognition
journal, June 1998

Multiparameter single-molecule fluorescence spectroscopy reveals heterogeneity of HIV-1 reverse transcriptase:primer/template complexes
journal, February 2003

Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism
journal, February 1999

Single-pair fluorescence resonance energy transfer on freely diffusing molecules: Observation of Forster distance dependence and subpopulations
journal, March 1999

Association states of the transcription activator protein NtrC from E. coli determined by analytical ultracentrifugation 1 1Edited by K. Yamamoto
journal, May 1998

Gene and Protein Expression Profiles of Shewanella oneidensis during Anaerobic Growth with Different Electron Acceptors
journal, January 2002

Phosphorylation-Induced Signal Propagation in the Response Regulator NtrC
journal, September 2000

DNA-looping and enhancer activity: association between DNA-bound NtrC activator and RNA polymerase at the bacterial glnA promoter.
journal, July 1990

Networking proteins in yeast
journal, April 2001

Fluorescence Intensity Multiple Distributions Analysis: Concurrent Determination of Diffusion Times and Molecular Brightness
journal, December 2000

Method for characterizing samples on the basis of intermediate statistical data
patent, February 2003

Abortive Cycling and the Release of Polymerase for Elongation at the σ54-dependent glnAp2 Promoter
journal, October 1995

Fluorescent probes and bioconjugation chemistries for single-molecule fluorescence analysis of biomolecules
journal, December 2002

Confocal microscope for optical determination of an observation volume
patent, June 2002

Molecular beacons for detecting DNA binding proteins: mechanism of action
journal, May 2003

Site-Specific Incorporation of Fluorescent Probes into Protein: Hexahistidine-Tag-Mediated Fluorescent Labeling with (Ni ²⁺ :Nitrilotriacetic Acid) _n −Fluorochrome Conjugates
journal, December 2001

Method for measuring the association of substructures of pathological protein depositions
patent, December 2002

Thermodynamic Fluctuations in a Reacting System—Measurement by Fluorescence Correlation Spectroscopy
journal, September 1972

Semiconductor Nanocrystals as Fluorescent Biological Labels
patent, September 1998

Genome-wide protein interaction maps using two-hybrid systems
journal, August 2000

Two excitation wavelength video imaging microscope
patent, September 1992

Analysis of the Shewanella oneidensis proteome by two-dimensional gel electrophoresis under nondenaturing conditions
journal, May 2003

Method and apparatus for identifying fluorophores
patent, July 1998