Abstract
Fluorescence correlation spectroscopy (FCS) provides a versatile tool to investigate molecular interaction under native conditions, approximating infinite dilution. One precondition for its application is a sufficient difference between the molecular weights of the fluorescence-labelled unbound and bound ligand. In previous studies, an 8-fold difference in molecular weights or correspondingly a 1.6-fold difference in diffusion coefficients was required to accurately distinguish between two diffusion species by FCS. In the presented work, the hybridization of two complementary equally sized RNA single strands was investigated at an excellent signal-to-noise ratio enabled by the highly photostable fluorophore Atto647N. The fractions of ssRNA and dsRNA were quantified by applying multicomponent model analysis of single autocorrelation functions and globally fitting several autocorrelation functions. By introducing a priori knowledge into the fitting procedure, 1.3- to 1.4-fold differences in diffusion coefficients of single- and double-stranded RNA of 26, 41, and 54 nucleotides could be accurately resolved. Global fits of autocorrelation functions of all titration steps enabled a highly accurate quantification of diffusion species fractions and mobilities. At a high signal-to-noise ratio, the median of individually fitted autocorrelation functions allowed a robust representation of heterogeneous data. These findings point out the possibility of studying molecular interaction of equally sized molecules based on their diffusional behavior, which significantly broadens the application spectrum of FCS.
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Abbreviations
- AF:
-
Autocorrelation function
- bp:
-
Base pair
- dsRNA:
-
Double-stranded RNA
- FCS:
-
Fluorescence correlation spectroscopy
- FCCS:
-
Fluorescence crosscorrelation spectroscopy
- GAPDH:
-
Glyceraldehyde-3-phosphate dehydrogenase
- K d :
-
Dissociation constant
- nt:
-
Nucleotide
- ssRNA:
-
Single-stranded RNA
References
Andersen ES, Contera SA, Knudsen B, Damgaard CK, Besenbacher F, Kjems J (2004) Role of the trans-activation response element in dimerization of HIV-1 RNA. J Biol Chem 279:22243–22249
Arnott S, Hukins DW, Dover SD, Fuller W, Hodgson AR (1973) Structures of synthetic polynucleotides in the A-RNA and A′-RNA conformations: X-ray diffraction analyses of the molecular conformations of polyadenylic acid polyuridylic acid and polyinosinic acid polycytidylic acid. J Mol Biol 81:107–122
Bacia K, Schwille P (2007) Practical guidelines for dual-color fluorescence cross-correlation spectroscopy. Nat Protoc 2:2842–2856
Batey RT, Rambo RP, Doudna JA (1999) Tertiary motifs in RNA structure and folding. Angew Chem Int Ed 38:2326–2343
Beechem JM, Gratton E, Ameloot M, Knutson J, Brand L (1991) The global analysis of fluorescence intensity and anisotropy decay data: second-generation theory and programs. In: Lakowicz J (ed) Topics in fluorescence spectroscopy, vol 2. Plenum, New York, pp 241–305
Chen Y, Müller JD, So PTC, Gratton E (1999) The photon counting histogram in fluorescence fluctuation spectroscopy. Biophys J 77:553–567
Dertinger T, Loman A, Ewers B, Muller CB, Kramer B, Enderlein J (2008) The optics and performance of dual-focus fluorescence correlation spectroscopy. Opt Express 16:14353–14368
Didier P, Godet J, Mely Y (2009) Two-photon two-focus fluorescence correlation spectroscopy with a tunable distance between the excitation volumes. J Fluoresc 19:561–565
Eggeling C, Widengren J, Brand L, Schaffer J, Felekyan S, Seidel CAM (2006) Analysis of photobleaching in single molecule multicolor excitation and Förster resonance energy transfer measurements. J Phys Chem A 110:2979–2995
Ehrenberg M, Rigler R (1974) Rotational Brownian motion and fluorescence intensity fluctuations. Chem Phys 4:390–401
Eigen M, Rigler R (1994) Sorting single molecules: application to diagnostics and evolutionary biotechnology. Proc Natl Acad Sci USA 91:5740–5747
Enderlein J, Gregor I, Patra D, Fitter J (2004) Art and artefacts of fluorescence correlation spectroscopy. Curr Pharm Biotech 5:155–161
Ennifar E, Bernacci S, Wolff P, Dumas P (2007) Influence of C-5 halogenation of uridines on hairpin versus duplex RNA folding. RNA 13:1445–1452
Farazi TA, Juranek SA, Tuschl T (2008) The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development 135:1201–1214
Fernandes MX, Ortega A, Lopez Martinez MC, García de la Torre J (2002) Calculation of hydrodynamic properties of small nucleic acids from their atomic structure. Nucleic Acids Res 30:1782–1788
Filipowicz W, Bhattacharyya SN, Sonenberg N (2008) Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9:102–114
Flory P (1989) Statistical mechanics of chain molecules. Hanser, Munich
Fradin C, Zbaida D, Elbaum M (2005) Dissociation of nuclear import cargo complexes by the protein Ran: a fluorescence correlation spectroscopy study. C R Biol 328:1073–1082
Heinicke LA, Wong CJ, Lary J, Nallagatla SR, Diegelman-Parente A, Zheng X, Cole JL, Bevilacqua PC (2009) RNA dimerization promotes PKR dimerization and activation. J Mol Biol 390:319–338
Holeman LA, Robinson SL, Szostak JW, Wilson C (1998) Isolation and characterization of fluorophore-binding RNA aptamers. Fold Des 3:423–431
Jinek M, Doudna JA (2009) A three-dimensional view of the molecular machinery of RNA interference. Nature 457:405–412
Kask P, Günther R, Axhausen P (1997) Statistical accuracy in fluorescence fluctuation experiments. Eur Biophys J 25:163–169
Kibbe W (2007) OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Res 35:W43–W46. doi: 10.1093/nar/gkm234
Kolb F, Zhang H, Jaronczyk K, Tahbaz N, Hobman T, Filipowicz W (2005) Human dicer: purification, properties, and interaction with PAZ PIWI domain proteins. Methods Enzym 392:316–336
Koppel DE (1974) Statistical accuracy in fluorescence correlation spectroscopy. Phys Rev A 10:1938–1945
Lemmon E, McLinden M, Friend D (2011) Thermophysical properties of fluid systems, vol 69. National Institute of Standards and Technology, Gaithersburg
Loman A, Dertinger T, Koberling F, Enderlein J (2008) Comparison of optical saturation effects in conventional and dual-focus fluorescence correlation spectroscopy. Chem Phys Lett 459:18–21
Magde D, Elson E, Webb WW (1972) Thermodynamic fluctuations in a reacting system—measurement by fluorescence correlation spectroscopy. Phys Rev Lett 29:705–708
Marquardt D (1963) An algorithm for least squares estimation of nonlinear parameters. J Soc Ind Appl Math 11:431–441
Meseth U, Wohland T, Rigler R, Vogel H (1999) Resolution of fluorescence correlation measurements. Biophys J 76:1619–1631
Nakano S, Kirihata T, Fujii S, Sakai H, Kuwahara M, Sawai H, Sugimoto N (2007) Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides. Nucleic Acids Res 35:486–494
Novikov E, van Hoek A, Visser A, Hofstraat J (1999) Linear algorithms for stretched exponential decay analysis. Opt Commun 166:189–199
Paillart J, Marquet R, Skripkin E, Ehresmann C, Ehresmann B (1996) Dimerization of retroviral genomic RNAs: structural and functional implications. Biochimie 78:639–653
Qian H (1990) On the statistics of fluorescence correlation spectroscopy. Biophys Chem 38:49–57
Qian H, Elson EL (1990) On the analysis of high order moments of fluorescence fluctuations. Biophys J 57:375–380
Rauer B, Neumann E, Widengren J, Rigler R (1996) Fluorescence correlation spectrometry of the interaction kinetics of tetramethylrhodamin a-bungarotoxin with Torpedo californica acetylcholine receptor. Biophys Chem 58:3–12
Riccelli PV, Vallone PM, Kashin I, Faldasz BD, Lane MJ, Benight AS (1999) Thermodynamic, spectroscopic, and equilibrium binding studies of DNA sequence context effects in six 22-base pair deoxyoligonucleotides. Biochemistry 38:11197–11208
Robertson RM, Laib S, Smith DE (2006) Diffusion of isolated DNA molecules: dependence on length and topology. Proc Natl Acad Sci USA 106:7310–7314
Saffarian S, Elson EL (2003) Statistical analysis of fluorescence correlation spectroscopy: the standard deviation and bias. Biophys J 84:2030–2042
Schwille P, Meyer-Almes F-J, Rigler R (1997) Dual-color fluorescence cross-correlation spectroscopy for multicomponent diffusional analysis in solution. Biophys J 72:1878–1886
Skakun VV, Hink MA, Digris AV, Engel R, Novikov EG, Apanasovich VV, Visser AJWG (2005) Global analysis of fluorescence fluctuation data. Eur Biophys J 34:323–334
Stombaugh J, Zirbel CL, Westhof E, Leontis NB (2009) Frequency and isostericity of RNA base pairs. Nucleic Acids Res 37:2294–2312
Tirado MM, Martinez CL, García de la Torre J (1984) Comparism of theories for the translational and rotational diffusion coefficients of rod-like macromolecules. Applications to short DNA fragments. J Chem Phys 81:2047–2052
van Holde KE, Johnson WE, Ho PS (1998) Principles of physical biochemistry. Prentice-Hall, New Jersey
Varshavsky A (2006) Discovering the RNA double helix and hybridization. Cell 127:1295–1297
Voss NR, Gerstein M (2005) Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly. J Mol Biol 346:477–492
Weisshart K, Jüngel V, Briddon SJ (2004) The LSM 510 META-ConfoCor 2 system: an integrated imaging and spectroscopic platform for single-molecule detection. Curr Pharm Biotech 5:135–154
Widengren J, Schwille P (2000) Characterization of photoinduced isomerization and back-isomerization of the cyanine dye Cy5 by fluorescence correlation spectroscopy. J Phys Chem 104:6416–6428
Wohland T, Rigler R, Vogel H (2001) The standard deviation in fluorescence correlation spectroscopy. Biophys J 80:2987–2999
Ye K, Malinina L, Patel DJ (2003) Recognition of small interfering RNA by a viral suppressor of RNA silencing. Nature 426:874–878
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We thank Johan Strömqvist for his advice in nonlinear regression analysis.
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Werner, A., Skakun, V.V., Meyer, C. et al. RNA dimerization monitored by fluorescence correlation spectroscopy. Eur Biophys J 40, 907–921 (2011). https://doi.org/10.1007/s00249-011-0701-8
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DOI: https://doi.org/10.1007/s00249-011-0701-8