A close look at fluorescence quenching of organic dyes by tryptophan

Doose S, Neuweiler H, Sauer M (2005)
CHEMPHYSCHEM 6(11): 2277-2285.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
Understanding fluorescence quenching processes of organic dyes by biomolecular compounds is of fundamental importance for in-vitro and in-vivo fluorescence studies. It has been reported that the excited singlet state of some oxazine and rhodamine derivatives is efficiently and almost exclusively quenched by the amino acid tryptophan (Trp) and the DNA base guanine via photoinduced electron transfer (PET). We present a detailed analysis of the quenching interactions between the oxazine dye MR121 and Trp in aqueous buffer. Steady-state and time-resolved fluorescence spectroscopy, together with fluorescence correlation spectroscopy (FCS), reveal three contributing quenching mechanisms: 1) diffusion-limited dynamic quenching with a bimolecular quenching rate constant k(d) of 4.0 x 10(9) s(-1) M-1, 2) static quenching with a bimolecular association constant K-s of 61 M-1, and 3) a sphere-of-action contribution to static quenching described by an exponential factor with a quenching constant lambda of 22 M-1. The latter two are characterized as nonfluorescent complexes, formed with approximate to 30% efficiency upon encounter, that are stable for tens of nanoseconds. The measured binding energy of 2030 kJmol(-1) is consistent with previous estimates from molecular dynamics simulations that proposed stacked complexes due to hydrophobic forces. We further evaluate the influence of glycerol and denaturant (guanidine hydrochloride) on the formation and stability of quenched complexes. Comparative measurements performed with two other dyes, ATTO 655 and Rhodamine 6G show similar results and thus demonstrate the general applicability of utilizing PET between organic dyes and Trp for the study of conformational dynamics of biopolymers on sub-nanometer length and nanosecond time-scales.
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CHEMPHYSCHEM
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6
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11
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2277-2285
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Doose S, Neuweiler H, Sauer M. A close look at fluorescence quenching of organic dyes by tryptophan. CHEMPHYSCHEM. 2005;6(11):2277-2285.
Doose, S., Neuweiler, H., & Sauer, M. (2005). A close look at fluorescence quenching of organic dyes by tryptophan. CHEMPHYSCHEM, 6(11), 2277-2285. doi:10.1002/cphc.200500191
Doose, S., Neuweiler, H., and Sauer, M. (2005). A close look at fluorescence quenching of organic dyes by tryptophan. CHEMPHYSCHEM 6, 2277-2285.
Doose, S., Neuweiler, H., & Sauer, M., 2005. A close look at fluorescence quenching of organic dyes by tryptophan. CHEMPHYSCHEM, 6(11), p 2277-2285.
S. Doose, H. Neuweiler, and M. Sauer, “A close look at fluorescence quenching of organic dyes by tryptophan”, CHEMPHYSCHEM, vol. 6, 2005, pp. 2277-2285.
Doose, S., Neuweiler, H., Sauer, M.: A close look at fluorescence quenching of organic dyes by tryptophan. CHEMPHYSCHEM. 6, 2277-2285 (2005).
Doose, S, Neuweiler, H, and Sauer, Markus. “A close look at fluorescence quenching of organic dyes by tryptophan”. CHEMPHYSCHEM 6.11 (2005): 2277-2285.

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Masureel M, Zou Y, Picard LP, van der Westhuizen E, Mahoney JP, Rodrigues JPGLM, Mildorf TJ, Dror RO, Shaw DE, Bouvier M, Pardon E, Steyaert J, Sunahara RK, Weis WI, Zhang C, Kobilka BK., Nat Chem Biol 14(11), 2018
PMID: 30327561
Harnessing photoinduced electron transfer to optically determine protein sub-nanoscale atomic distances.
Pantazis A, Westerberg K, Althoff T, Abramson J, Olcese R., Nat Commun 9(1), 2018
PMID: 30413716
Molecular Determinants of BK Channel Functional Diversity and Functioning.
Latorre R, Castillo K, Carrasquel-Ursulaez W, Sepulveda RV, Gonzalez-Nilo F, Gonzalez C, Alvarez O., Physiol Rev 97(1), 2017
PMID: 27807200
Integrated view of internal friction in unfolded proteins from single-molecule FRET, contact quenching, theory, and simulations.
Soranno A, Holla A, Dingfelder F, Nettels D, Makarov DE, Schuler B., Proc Natl Acad Sci U S A 114(10), 2017
PMID: 28223518
Molecule Counts in Localization Microscopy with Organic Fluorophores.
Karathanasis C, Fricke F, Hummer G, Heilemann M., Chemphyschem 18(8), 2017
PMID: 28196307
Activation pH and Gating Dynamics of Influenza A M2 Proton Channel Revealed by Single-Molecule Spectroscopy.
Lin CW, Mensa B, Barniol-Xicota M, DeGrado WF, Gai F., Angew Chem Int Ed Engl 56(19), 2017
PMID: 28374543
Interaction between triethanolamine and singlet or triplet excited state of xanthene dyes in aqueous solution.
Li S, Zhang H, Lu R, Yu A., Spectrochim Acta A Mol Biomol Spectrosc 184(), 2017
PMID: 28499174
The interaction of amino acids with macrocyclic pH probes of pseudopeptidic nature.
Izquierdo MA, Wadhavane PD, Vigara L, Burguete MI, Galindo F, Luis SV., Photochem Photobiol Sci 16(8), 2017
PMID: 28726954
Placing molecules with Bohr radius resolution using DNA origami.
Funke JJ, Dietz H., Nat Nanotechnol 11(1), 2016
PMID: 26479026
Diazaoxatriangulenium: synthesis of reactive derivatives and conjugation to bovine serum albumin.
Bora I, Bogh SA, Rosenberg M, Santella M, Sørensen TJ, Laursen BW., Org Biomol Chem 14(3), 2016
PMID: 26633730
Molecular motions that shape the cardiac action potential: Insights from voltage clamp fluorometry.
Zhu W, Varga Z, Silva JR., Prog Biophys Mol Biol 120(1-3), 2016
PMID: 26724572
A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization.
van der Velde JH, Oelerich J, Huang J, Smit JH, Aminian Jazi A, Galiani S, Kolmakov K, Guoridis G, Eggeling C, Herrmann A, Roelfes G, Cordes T., Nat Commun 7(), 2016
PMID: 26751640
Multi-target spectrally resolved fluorescence lifetime imaging microscopy.
Niehörster T, Löschberger A, Gregor I, Krämer B, Rahn HJ, Patting M, Koberling F, Enderlein J, Sauer M., Nat Methods 13(3), 2016
PMID: 26808668
Comparison of Silicon Nanocrystals Prepared by Two Fundamentally Different Methods.
Cibulka O, Vorkötter C, Purkrt A, Holovský J, Benedikt J, Herynková K., Nanoscale Res Lett 11(1), 2016
PMID: 27699716
Quantitative interpretation of FRET experiments via molecular simulation: force field and validation.
Best RB, Hofmann H, Nettels D, Schuler B., Biophys J 108(11), 2015
PMID: 26039173
Photophysical processes in single molecule organic fluorescent probes.
Stennett EM, Ciuba MA, Levitus M., Chem Soc Rev 43(4), 2014
PMID: 24141280
Single-molecule super-resolution imaging by tryptophan-quenching-induced photoswitching of phalloidin-fluorophore conjugates.
Nanguneri S, Flottmann B, Herrmannsdörfer F, Thomas K, Heilemann M., Microsc Res Tech 77(7), 2014
PMID: 24595992
Recognition of free tryptophan in water by synthetic pseudopeptides: fluorescence and thermodynamic studies.
Martí-Centelles V, Izquierdo MA, Burguete MI, Galindo F, Luis SV., Chemistry 20(24), 2014
PMID: 24788579
Studies of protein folding and dynamics using single molecule fluorescence spectroscopy.
Basak S, Chattopadhyay K., Phys Chem Chem Phys 16(23), 2014
PMID: 24805942
Fluorescence quenching of (dimethylamino)naphthalene dyes Badan and Prodan by tryptophan in cytochromes P450 and micelles.
Pospíšil P, Luxem KE, Ener M, Sýkora J, Kocábová J, Gray HB, Vlček A, Hof M., J Phys Chem B 118(34), 2014
PMID: 25079965
Mutational definition of binding requirements of an hnRNP-like protein in Arabidopsis using fluorescence correlation spectroscopy.
Leder V, Lummer M, Tegeler K, Humpert F, Lewinski M, Schüttpelz M, Staiger D., Biochem Biophys Res Commun 453(1), 2014
PMID: 25251471
High-throughput development of a hybrid-type fluorescent glutamate sensor for analysis of synaptic transmission.
Takikawa K, Asanuma D, Namiki S, Sakamoto H, Ariyoshi T, Kimpara N, Hirose K., Angew Chem Int Ed Engl 53(49), 2014
PMID: 25297726
The pH probe CypHer™5E is effectively quenched by FM dyes.
Welzel O, Loy K, Tischbirek CH, Tabor A, Gmeiner P, Kornhuber J, Groemer TW., J Fluoresc 23(3), 2013
PMID: 23397486
Long-lived bright red emitting azaoxa-triangulenium fluorophores.
Maliwal BP, Fudala R, Raut S, Kokate R, Sørensen TJ, Laursen BW, Gryczynski Z, Gryczynski I., PLoS One 8(5), 2013
PMID: 23667570
Systematic evaluation of fluorescence correlation spectroscopy data analysis on the nanosecond time scale.
Steger K, Bollmann S, Noé F, Doose S., Phys Chem Chem Phys 15(25), 2013
PMID: 23685745
Conformational transitions during FtsK translocase activation of individual XerCD-dif recombination complexes.
Zawadzki P, May PF, Baker RA, Pinkney JN, Kapanidis AN, Sherratt DJ, Arciszewska LK., Proc Natl Acad Sci U S A 110(43), 2013
PMID: 24101525
Spectroscopic studies of protein folding: linear and nonlinear methods.
Serrano AL, Waegele MM, Gai F., Protein Sci 21(2), 2012
PMID: 22109973
Dimer formation of organic fluorophores reports on biomolecular dynamics under denaturing conditions.
Bollmann S, Löllmann M, Sauer M, Doose S., Phys Chem Chem Phys 13(28), 2011
PMID: 21687885
Conformational flexibility of glycosylated peptides.
Bollmann S, Burgert A, Plattner C, Nagel L, Sewald N, Löllmann M, Sauer M, Doose S., Chemphyschem 12(16), 2011
PMID: 21922630
Galectin-1-asialofetuin interaction is inhibited by peptides containing the tyr-xxx-tyr motif acting on the glycoprotein.
Wéber E, Hetényi A, Váczi B, Szolnoki E, Fajka-Boja R, Tubak V, Monostori E, Martinek TA., Chembiochem 11(2), 2010
PMID: 19938027
Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains.
Daidone I, Neuweiler H, Doose S, Sauer M, Smith JC., PLoS Comput Biol 6(1), 2010
PMID: 20098498
Light-mediated spatial control via photolabile fluorescently quenched peptide cassettes.
Lee HM, Priestman MA, Lawrence DS., J Am Chem Soc 132(5), 2010
PMID: 20073458
Simultaneous fluorescent monitoring of proteasomal subunit catalysis.
Wakata A, Lee HM, Rommel P, Toutchkine A, Schmidt M, Lawrence DS., J Am Chem Soc 132(5), 2010
PMID: 20078037
Suborganelle sensing of mitochondrial cAMP-dependent protein kinase activity.
Agnes RS, Jernigan F, Shell JR, Sharma V, Lawrence DS., J Am Chem Soc 132(17), 2010
PMID: 20380406
Multicolor photoswitching microscopy for subdiffraction-resolution fluorescence imaging.
van de Linde S, Endesfelder U, Mukherjee A, Schüttpelz M, Wiebusch G, Wolter S, Heilemann M, Sauer M., Photochem Photobiol Sci 8(4), 2009
PMID: 19337659
Observing proteins as single molecules encapsulated in surface-tethered polymeric nanocontainers.
Rosenkranz T, Katranidis A, Atta D, Gregor I, Enderlein J, Grzelakowski M, Rigler P, Meier W, Fitter J., Chembiochem 10(4), 2009
PMID: 19191249
Quantifying adsorbed protein on surfaces using confocal fluorescence microscopy.
Togashi DM, Ryder AG, Heiss G., Colloids Surf B Biointerfaces 72(2), 2009
PMID: 19423302
Confocal laser scanning microscopy as an analytical tool in chromatographic research.
Hubbuch J, Kula MR., Bioprocess Biosyst Eng 31(3), 2008
PMID: 18196281
Nonequilibrium single molecule protein folding in a coaxial mixer.
Hamadani KM, Weiss S., Biophys J 95(1), 2008
PMID: 18339751
The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy.
Kim J, Doose S, Neuweiler H, Sauer M., Nucleic Acids Res 34(9), 2006
PMID: 16687657
Molecular fluorescence, phosphorescence, and chemiluminescence spectrometry.
Fletcher KA, Fakayode SO, Lowry M, Tucker SA, Neal SL, Kimaru IW, McCarroll ME, Patonay G, Oldham PB, Rusin O, Strongin RM, Warner IM., Anal Chem 78(12), 2006
PMID: 16771540
A microscopic view of miniprotein folding: enhanced folding efficiency through formation of an intermediate.
Neuweiler H, Doose S, Sauer M., Proc Natl Acad Sci U S A 102(46), 2005
PMID: 16269542

52 References

Daten bereitgestellt von Europe PubMed Central.


Seidel, J. Phys. Chem. 100(), 1996
New fluorescent dyes in the red region for biodiagnostics.
Sauer M, Han KT, Muller R, Nord S, Schulz A, Seeger S, Wolfrum J, Arden-Jacob J, Deltau G, Marx NJ, Zander C, Drexhage KH., J Fluoresc 5(3), 1995
PMID: 24226792
Conformational transitions monitored for single molecules in solution.
Edman L, Mets U, Rigler R., Proc. Natl. Acad. Sci. U.S.A. 93(13), 1996
PMID: 8692883
Monitoring conformational dynamics of a single molecule by selective fluorescence spectroscopy.
Eggeling C, Fries JR, Brand L, Gunther R, Seidel CA., Proc. Natl. Acad. Sci. U.S.A. 95(4), 1998
PMID: 9465054
Probes for detection of specific DNA sequences at the single-molecule level.
Knemeyer JP, Marme N, Sauer M., Anal. Chem. 72(16), 2000
PMID: 10959954

Piestert, Nano Lett. 3(), 2003

Heinlein, J. Phys. Chem. B 107(), 2003

Neuweiler, Angew. Chem. 2002, 114 (), 0

AUTHOR UNKNOWN, Angew. Chem. Int. Ed. 41(), 2002
Measurement of submicrosecond intramolecular contact formation in peptides at the single-molecule level.
Neuweiler H, Schulz A, Bohmer M, Enderlein J, Sauer M., J. Am. Chem. Soc. 125(18), 2003
PMID: 12720444
Fluorescence quenching of dyes by tryptophan: interactions at atomic detail from combination of experiment and computer simulation.
Vaiana AC, Neuweiler H, Schulz A, Wolfrum J, Sauer M, Smith JC., J. Am. Chem. Soc. 125(47), 2003
PMID: 14624606
Inter- and intramolecular fluorescence quenching of organic dyes by tryptophan.
Marme N, Knemeyer JP, Sauer M, Wolfrum J., Bioconjug. Chem. 14(6), 2003
PMID: 14624626

Marme, Angew. Chem. 116(), 2004

AUTHOR UNKNOWN, Angew. Chem. Int. Ed. 43(), 2004
Mechanism of quenching of fluorescein by anti-fluorescein IgG antibodies.
Watt RM, Voss EW Jr., Immunochemistry 14(7), 1977
PMID: 303233

Nazarenko, Nucleic Acids Res. 30(), 2002
Effect of primary and secondary structure of oligodeoxyribonucleotides on the fluorescent properties of conjugated dyes.
Nazarenko I, Pires R, Lowe B, Obaidy M, Rashtchian A., Nucleic Acids Res. 30(9), 2002
PMID: 11972350

Karolin, J. Am. Chem. Soc. 116(), 1994

Kurata, Nucleic Acids Res. 29(), 2001

Sauer, Angew. Chem. 115(), 2003

AUTHOR UNKNOWN, Angew. Chem. Int. Ed. 42(), 2003
Dynamics of photoinduced charge transfer and hole transport in synthetic DNA hairpins.
Lewis FD, Letsinger RL, Wasielewski MR., Acc. Chem. Res. 34(2), 2001
PMID: 11263874

Wagenknecht, J. Am. Chem. Soc. 122(), 2000
Protein conformational dynamics probed by single-molecule electron transfer.
Yang H, Luo G, Karnchanaphanurach P, Louie TM, Rech I, Cova S, Xun L, Xie XS., Science 302(5643), 2003
PMID: 14551431

Neuweiler, Anal. Chem. 77(), 2005
Fluorescence correlation spectroscopy. II. An experimental realization.
Magde D, Elson EL, Webb WW., Biopolymers 13(1), 1974
PMID: 4818131

Rigler, Eur. Biophys. J. 22(), 1993
Biological and chemical applications of fluorescence correlation spectroscopy: a review.
Hess ST, Huang S, Heikal AA, Webb WW., Biochemistry 41(3), 2002
PMID: 11790090

Krichevsky, Rep. Prog. Phys. 65(), 2002

Widengren, Chem. Phys. 216(), 1997

Widengren, J. Phys. Chem. 99(), 1995

Widengren, J. Phys. Chem. A 104(), 2000
Water-soluble quantum dots for multiphoton fluorescence imaging in vivo.
Larson DR, Zipfel WR, Williams RM, Clark SW, Bruchez MP, Wise FW, Webb WW., Science 300(5624), 2003
PMID: 12775841

Lakowicz, 1999
Spectroscopic study and evaluation of red-absorbing fluorescent dyes.
Buschmann V, Weston KD, Sauer M., Bioconjug. Chem. 14(1), 2003
PMID: 12526709

Cohen, J. Chem. Soc. 2(), 1962

Frank, Z. Phys. 69(), 1931

Adams, J. Phys. Chem. B 107(), 2003

Einstein, Ann. Phys. 17(), 1905

AUTHOR UNKNOWN, 0

Sheely, 1932
Viscosity and density of aqueous solutions of urea and guanidine hydrochloride.
Kawahara K, Tanford C., J. Biol. Chem. 241(13), 1966
PMID: 5912116
Measuring unfolding of proteins in the presence of denaturant using fluorescence correlation spectroscopy.
Chattopadhyay K, Saffarian S, Elson EL, Frieden C., Biophys. J. 88(2), 2004
PMID: 15556973

Hell, J. Microsc. 169(), 1993
Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules.
Kapanidis AN, Lee NK, Laurence TA, Doose S, Margeat E, Weiss S., Proc. Natl. Acad. Sci. U.S.A. 101(24), 2004
PMID: 15175430
Determination of ultrafast protein folding rates from loop formation dynamics.
Buscaglia M, Kubelka J, Eaton WA, Hofrichter J., J. Mol. Biol. 347(3), 2005
PMID: 15755457

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