References

ASRN+05

Wajih Al-Soufi, Belén Reija, Mercedes Novo, Suren Felekyan, Ralf Kühnemuth, and Claus AM Seidel. Fluorescence correlation spectroscopy, a tool to investigate supramolecular dynamics: inclusion complexes of pyronines with cyclodextrin. Journal of the American Chemical Society, 127(24):8775–8784, 2005.

AFGS06a

Matthew Antonik, Suren Felekyan, Alexander Gaiduk, and Claus A. M. Seidel. Separating structural heterogeneities from stochastic variations in fluorescence resonance energy transfer distributions via photon distribution analysis. The Journal of Physical Chemistry B, 110(13):6970–6978, 2006.

AFGS06b

Matthew Antonik, Suren Felekyan, Alexander Gaiduk, and Claus AM Seidel. Separating structural heterogeneities from stochastic variations in fluorescence resonance energy transfer distributions via photon distribution analysis. The Journal of Physical Chemistry B, 110(13):6970–6978, 2006.

Bec05

Wolfgang Becker. Advanced Time-Correlated Single Photon Counting Techniques. Springer Science & Business Media, December 2005. ISBN 978-3-540-28882-4. Google-Books-ID: fLP0PB9CZ94C.

BWR+02

Martin Bohmer, Michaek Wahl, Hans-Jurgen Rahn, Rainer Erdmann, and Jorg Enderlein. Time-resolved fluorescence correlation spectroscopy. Chemical Physics Letters, 353:439–445, 2002.

BSV+11

Axel T Brunger, Pavel Strop, Marija Vrljic, Steven Chu, and Keith R Weninger. Three-dimensional molecular modeling with single molecule fret. Journal of structural biology, 173(3):497–505, 2011.

CGM+11

Hoi Sung Chung, Irina V Gopich, Kevin McHale, Troy Cellmer, John M Louis, and William A Eaton. Extracting rate coefficients from single-molecule photon trajectories and fret efficiency histograms for a fast-folding protein. The journal of physical chemistry A, 115(16):3642–3656, 2011.

Cle92

Robert M Clegg. [18] fluorescence resonance energy transfer and nucleic acids. Methods in enzymology, 211:353–388, 1992.

Coa68

P B Coates. The correction for photon `pile-up' in the measurement of radiative lifetimes. Journal of Physics E: Scientific Instruments, 1(8):878–879, August 1968. URL: http://stacks.iop.org/0022-3735/1/i=8/a=437?key=crossref.19c54cc94064528a5003e3e0a645afc3 (visited on 2020-03-23), doi:10.1088/0022-3735/1/8/437.

DBS+05

Michelle A. Digman, Claire M. Brown, Parijat Sengupta, Paul W. Wiseman, Alan R. Horwitz, and Enrico Gratton. Measuring Fast Dynamics in Solutions and Cells with a Laser Scanning Microscope. Biophysical Journal, 89(2):1317–1327, August 2005. URL: http://www.sciencedirect.com/science/article/pii/S000634950572779X (visited on 2020-05-18), doi:10.1529/biophysj.105.062836.

DCZG08

Michelle A. Digman, Valeria R. Caiolfa, Moreno Zamai, and Enrico Gratton. The phasor approach to fluorescence lifetime imaging analysis. Biophysical Journal, 94(2):L14–L16, 2008. URL: https://www.sciencedirect.com/science/article/pii/S0006349508707112, doi:https://doi.org/10.1529/biophysj.107.120154.

DSW+05

Michelle A. Digman, Parijat Sengupta, Paul W. Wiseman, Claire M. Brown, Alan R. Horwitz, and Enrico Gratton. Fluctuation Correlation Spectroscopy with a Laser-Scanning Microscope: Exploiting the Hidden Time Structure. Biophysical Journal, 88(5):L33–L36, May 2005. URL: http://www.sciencedirect.com/science/article/pii/S0006349505733580 (visited on 2020-05-18), doi:10.1529/biophysj.105.061788.

DWHG09

Michelle A. Digman, Paul W. Wiseman, Alan R. Horwitz, and Enrico Gratton. Detecting Protein Complexes in Living Cells from Laser Scanning Confocal Image Sequences by the Cross Correlation Raster Image Spectroscopy Method. Biophysical Journal, 96(2):707–716, January 2009. URL: http://www.sciencedirect.com/science/article/pii/S0006349508000799 (visited on 2020-05-18), doi:10.1016/j.bpj.2008.09.051.

DPH+16

Mykola Dimura, Thomas O Peulen, Christian A Hanke, Aiswaria Prakash, Holger Gohlke, and Claus AM Seidel. Quantitative fret studies and integrative modeling unravel the structure and dynamics of biomolecular systems. Current opinion in structural biology, 40:163–185, 2016.

EBB+01

C Eggeling, S Berger, L Brand, JR Fries, J Schaffer, A Volkmer, and CAM Seidel. Data registration and selective single-molecule analysis using multi-parameter fluorescence detection. Journal of biotechnology, 86(3):163–180, 2001.

Els13

Elliot L Elson. 40 years of fcs: how it all began. Methods in enzymology, 518:1–10, 2013.

EM74

Elliot L Elson and Douglas Magde. Fluorescence correlation spectroscopy. i. conceptual basis and theory. Biopolymers: Original Research on Biomolecules, 13(1):1–27, 1974.

EE97

Jorg Enderlein and Rainer Erdmann. Fast fitting of multi-exponential decay curves. Optics Communications, 134:371–378, 1997.

End12

Jöerg Enderlein. Polymer dynamics, fluorescence correlation spectroscopy, and the limits of optical resolution. Phys Rev Lett., 2012. arXiv:1203.3204v1, doi:10.1103/PhysRevLett.108.108101.

FSK+13

Suren Felekyan, Hugo Sanabria, Stanislav Kalinin, Ralf Kühnemuth, and Claus AM Seidel. Analyzing förster resonance energy transfer with fluctuation algorithms. Methods in enzymology, 519:39–85, 2013.

FBE+98

Joachim R Fries, Leif Brand, Christian Eggeling, Malte Köllner, and Claus AM Seidel. Quantitative identification of different single molecules by selective time-resolved confocal fluorescence spectroscopy. The Journal of Physical Chemistry A, 102(33):6601–6613, 1998.

GS05

Irina Gopich and Attila Szabo. Theory of photon statistics in single-molecule förster resonance energy transfer. The Journal of chemical physics, 122(1):014707, 2005.

GS03

Irina V Gopich and Attila Szabo. Single-macromolecule fluorescence resonance energy transfer and free-energy profiles. The Journal of Physical Chemistry B, 107(21):5058–5063, 2003.

GS07

Irina V Gopich and Attila Szabo. Single-molecule fret with diffusion and conformational dynamics. The Journal of Physical Chemistry B, 111(44):12925–12932, 2007.

GS09

Irina V Gopich and Attila Szabo. Decoding the pattern of photon colors in single-molecule fret. The Journal of Physical Chemistry B, 113(31):10965–10973, 2009.

GS10

Irina V Gopich and Attila Szabo. Fret efficiency distributions of multistate single molecules. The Journal of Physical Chemistry B, 114(46):15221–15226, 2010.

GL10

Kaushik Gurunathan and Marcia Levitus. Fret fluctuation spectroscopy of diffusing biopolymers: contributions of conformational dynamics and translational diffusion. The Journal of Physical Chemistry B, 114(2):980–986, 2010.

HDSL16

Jelle Hendrix, Tomas Dekens, Waldemar Schrimpf, and Don C. Lamb. Arbitrary-Region Raster Image Correlation Spectroscopy. Biophysical Journal, 111(8):1785–1796, October 2016. URL: http://www.sciencedirect.com/science/article/pii/S0006349516308104 (visited on 2020-05-18), doi:10.1016/j.bpj.2016.09.012.

IDH73

Irvin Isenberg, Robert D. Dyson, and Richard Hanson. Studies on the Analysis of Fluorescence Decay Data by the Method of Moments. Biophysical Journal, 13(10):1090–1115, October 1973. URL: https://linkinghub.elsevier.com/retrieve/pii/S0006349573860473 (visited on 2020-04-30), doi:10.1016/S0006-3495(73)86047-3.

Joh06

Carey K Johnson. Calmodulin, conformational states, and calcium signaling. a single-molecule perspective. Biochemistry, 45(48):14233–14246, 2006.

KFAS07a

Stanislav Kalinin, Suren Felekyan, Matthew Antonik, and Claus A. M. Seidel. Probability distribution analysis of single-molecule fluorescence anisotropy and resonance energy transfer. The Journal of Physical Chemistry B, 111(34):10253–10262, 2007.

KFAS07b

Stanislav Kalinin, Suren Felekyan, Matthew Antonik, and Claus AM Seidel. Probability distribution analysis of single-molecule fluorescence anisotropy and resonance energy transfer. The Journal of Physical Chemistry B, 111(34):10253–10262, 2007.

KFVS08

Stanislav Kalinin, Suren Felekyan, Alessandro Valeri, and Claus AM Seidel. Characterizing multiple molecular states in single-molecule multiparameter fluorescence detection by probability distribution analysis. The Journal of Physical Chemistry B, 112(28):8361–8374, 2008.

KPS+12

Stanislav Kalinin, Thomas Peulen, Simon Sindbert, Paul J Rothwell, Sylvia Berger, Tobias Restle, Roger S Goody, Holger Gohlke, and Claus AM Seidel. A toolkit and benchmark study for fret-restrained high-precision structural modeling. Nature methods, 9(12):1218–1225, 2012.

KSM+10

Stanislav Kalinin, Evangelos Sisamakis, Steven W Magennis, Suren Felekyan, and Claus AM Seidel. On the origin of broadening of single-molecule fret efficiency distributions beyond shot noise limits. The journal of physical chemistry B, 114(18):6197–6206, 2010.

KVA+10

Stanislav Kalinin, Alessandro Valeri, Matthew Antonik, Suren Felekyan, and Claus AM Seidel. Detection of structural dynamics by fret: a photon distribution and fluorescence lifetime analysis of systems with multiple states. The Journal of Physical Chemistry B, 114(23):7983–7995, 2010.

KWB+07

Peter Kapusta, Michael Wahl, Ales Benda, Martin Hof, and Jorg Enderlein. Fluorescence lifetime correlation spectroscopy. Journal of Fluorescence, 17:43–48, 2007.

KHB+05

Sally A Kim, Katrin G Heinze, Kirsten Bacia, M Neal Waxham, and Petra Schwille. Two-photon cross-correlation analysis of intracellular reactions with variable stoichiometry. Biophysical Journal, 88(6):4319–4336, 2005.

KSM95

Masanori Koshioka, Keiji Sasaki, and Hiroshi Masuhara. Time-dependent fluorescence depolarization analysis in three-dimensional microspectroscopy. Applied spectroscopy, 49(2):224–228, 1995.

KSK+12

Volodymyr Kudryavtsev, Martin Sikor, Stanislav Kalinin, Dejana Mokranjac, Claus AM Seidel, and Don C Lamb. Combining mfd and pie for accurate single-pair förster resonance energy transfer measurements. ChemPhysChem, 13(4):1060–1078, 2012.

KuhnemuthS01

Ralf Kühnemuth and Claus A. M. Seidel. Principles of single molecule multiparameter fluorescence spectroscopy. Single Molecules, 2:251–254, 2001.

LFH06

Ted A. Laurence, Samantha Fore, and Thomas Huser. Fast, flexible algorithm for calculating photon correlations. Optics express, 31:829, 2006.

LKK+04

Ted A. Laurence, Achillefs N. Kapanidis, Xiangxu Kong, Daniel S. Chemla, and Shimon Weiss. Photon arrival-time interval distribution (PAID): a novel tool for analyzing molecular interactions. The Journal of Physical Chemistry B, 108(9):3051–3067, 2004.

Lev10

Marcia Levitus. Relaxation kinetics by fluorescence correlation spectroscopy: determination of kinetic parameters in the presence of fluorescent impurities. The journal of physical chemistry letters, 1(9):1346–1350, 2010.

MEW72

Douglas Magde, Elliot Elson, and Watt W Webb. Thermodynamic fluctuations in a reacting system—measurement by fluorescence correlation spectroscopy. Physical Review Letters, 29(11):705, 1972.

MCH+01

Michael Maus, Mircea Cotlet, Johan Hofkens, Thomas Gensch, Frans C De Schryver, J Schaffer, and CAM Seidel. An experimental comparison of the maximum likelihood estimation and nonlinear least-squares fluorescence lifetime analysis of single molecules. Analytical chemistry, 73(9):2078–2086, 2001.

MCZ+10

James J McCann, Ucheor B Choi, Liqiang Zheng, Keith Weninger, and Mark E Bowen. Optimizing methods to recover absolute fret efficiency from immobilized single molecules. Biophysical journal, 99(3):961–970, 2010.

NMH+06

Eyal Nir, Xavier Michalet, Kambiz M Hamadani, Ted A Laurence, Daniel Neuhauser, Yevgeniy Kovchegov, and Shimon Weiss. Shot-noise limited single-molecule fret histograms: comparison between theory and experiments. The Journal of Physical Chemistry B, 110(44):22103–22124, 2006.

OConnor12a

Desmond O'Connor. Time-correlated single photon counting. Academic press, 2012.

OConnor12b

Desmond O'Connor. Time-correlated single photon counting. Academic Press, December 2012. ISBN 978-0-323-14144-4. Google-Books-ID: ELQ0Mz6Rq1EC.

PMLK06

Kaupo Palo, Ülo Mets, Vello Loorits, and Peet Kask. Calculation of photon-count number distributions via master equations. Biophysical journal, 90(6):2179–2191, 2006.

PHW+93

N. O. Petersen, P. L. Höddelius, P. W. Wiseman, O. Seger, and K. E. Magnusson. Quantitation of membrane receptor distributions by image correlation spectroscopy: concept and application. Biophysical Journal, 65(3):1135–1146, September 1993. URL: http://www.sciencedirect.com/science/article/pii/S0006349593811731 (visited on 2020-05-18), doi:10.1016/S0006-3495(93)81173-1.

POS17

Thomas-Otavio Peulen, Oleg Opanasyuk, and Claus AM Seidel. Combining graphical and analytical methods with molecular simulations to analyze time-resolved fret measurements of labeled macromolecules accurately. The Journal of Physical Chemistry B, 121(35):8211–8241, 2017.

PAJ11

E Shane Price, Marek Aleksiejew, and Carey K Johnson. Fret-fcs detection of intralobe dynamics in calmodulin. The Journal of Physical Chemistry B, 115(29):9320–9326, 2011.

PDJ10

E Shane Price, Matthew S DeVore, and Carey K Johnson. Detecting intramolecular dynamics and multiple forster resonance energy transfer states by fluorescence correlation spectroscopy. The Journal of Physical Chemistry B, 114(17):5895–5902, 2010.

Qia90

Hong Qian. On the statistics of fluorescence correlation spectroscopy. Biophysical Chemistry, 38(1):49–57, 1990.

RMJG18

Suman Ranjit, Leonel Malacrida, David M Jameson, and Enrico Gratton. Fit-free analysis of fluorescence lifetime imaging data using the phasor approach. Nature protocols, 13(9):1979–2004, 2018.

RBC+10

J. Ries, M. Bayer, Csucs, G, Dirkx, R, M. Solimena, H. Ewers, and P. Schwille. Automated suppression of sample-related artifacts in fluorescence correlation spectroscopy. Optics express, 18(11):11073–11082, 2010.

SEM05

Chandran R Sabanayagam, John S Eid, and Amit Meller. Using fluorescence resonance energy transfer to measure distances along individual dna molecules: corrections due to nonideal transfer. The Journal of chemical physics, 122(6):061103, 2005.

STK10

Yusdi Santoso, Joseph P Torella, and Achillefs N Kapanidis. Characterizing single-molecule fret dynamics with probability distribution analysis. ChemPhysChem, 11(10):2209–2219, 2010.

SVK+10

Evangelos Sisamakis, Alessandro Valeri, Stanislav Kalinin, Paul J Rothwell, and Claus AM Seidel. Accurate single-molecule fret studies using multiparameter fluorescence detection. Methods in enzymology, 475:455–514, 2010.

SAU+04

Brian D Slaughter, Michael W Allen, Jay R Unruh, Ramona J Bieber Urbauer, and Carey K Johnson. Single-molecule resonance energy transfer and fluorescence correlation spectroscopy of calmodulin in solution. The Journal of Physical Chemistry B, 108(29):10388–10397, 2004.

SBUJ05

Brian D Slaughter, Ramona J Bieber-Urbauer, and Carey K Johnson. Single-molecule tracking of sub-millisecond domain motion in calmodulin. The Journal of Physical Chemistry B, 109(26):12658–12662, 2005.

SUA+05

Brian D Slaughter, Jay R Unruh, Michael W Allen, Ramona J Bieber Urbauer, and Carey K Johnson. Conformational substates of calmodulin revealed by single-pair fluorescence resonance energy transfer: influence of solution conditions and oxidative modification. Biochemistry, 44(10):3694–3707, 2005.

SRB01

Konstantin Starchev, Jaro Ricka, and Jacques Buffle. Noise on fluorescence correlation spectroscopy. Journal of Colloid and Interface Science, 2001.

SSSV99

George Striker, Vinod Subramaniam, Claus AM Seidel, and Andreas Volkmer. Photochromicity and fluorescence lifetimes of green fluorescent protein. The Journal of Physical Chemistry B, 103(40):8612–8617, 1999.

TTM+12

Toma E Tomov, Roman Tsukanov, Rula Masoud, Miran Liber, Noa Plavner, and Eyal Nir. Disentangling subpopulations in single-molecule fret and alex experiments with photon distribution analysis. Biophysical journal, 102(5):1163–1173, 2012.

TL07

Tedman Torres and Marcia Levitus. Measuring conformational dynamics: a new fcs-fret approach. The Journal of Physical Chemistry B, 111(25):7392–7400, 2007.

VopelHP+14

Tobias Vöpel, Carola S Hengstenberg, Thomas-Otavio Peulen, Yathrib Ajaj, Claus AM Seidel, Christian Herrmann, and Johann P Klare. Triphosphate induced dimerization of human guanylate binding protein 1 involves association of the c-terminal helices: a joint double electron–electron resonance and fret study. Biochemistry, 53(28):4590–4600, 2014.

WGPE03

Michael Wahl, Ingo Gregor, Matthias Patting, and Jörg Enderlein. Fast calculation of fluorescence correlation data with asynchronous time-correlated single-photon counting. Optics express, 11(26):3583–3591, 2003.

WRV01

Thorsten Wohland, Rudolf Rigler, and Horst Vogel. The standard deviation in fluorescence correlation spectroscopy. Biophysical Journal, 80(6):2987–2999, 2001.

ZY05

Kai Zhang and Haw Yang. Photon-by-photon determination of emission bursts from diffusing single chromophores. The Journal of Physical Chemistry B, 109(46):21930–21937, 2005.