Two-photon excited fluorescence energy transfer: A study based on oligonucleotide rulers

Journal of Fluorescence

Volumn 16, Issue 3, 2006, Pages 379-386

  Wahlroos, Rina ^a   Toivonen, Juha ^a   Tirri, Marko ^a   Hänninen, Pekka ^a  

^a UNIVERSITY OF TURKU   (Finland)

Author keywords

DNA; Fluorescent labels; FRET; Hybridization; Oligonucleotide; Spectroscopy; Two photon excitation

Indexed keywords

FRET; HYBRIDIZATION; OLIGONUCLEOTIDE; TWO-PHOTON EXCITATION;

DNA; ENERGY TRANSFER; OLIGOMERS; QUENCHING; SPECTROSCOPIC ANALYSIS;

FLUORESCENCE;

OLIGONUCLEOTIDE; SINGLE STRANDED DNA;

ARTICLE; CHEMISTRY; COMPARATIVE STUDY; ENERGY TRANSFER; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; NUCLEIC ACID HYBRIDIZATION; PHOTON; SPECTROFLUOROMETRY;

DNA, SINGLE-STRANDED; ENERGY TRANSFER; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDES; PHOTONS; SPECTROMETRY, FLUORESCENCE;

EID: 33745473078     PISSN: 10530509     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10895-006-0084-x     Document Type: Article

References (44)

1. Xu C, Zipfel W, Shear JB, Williams RM, Webb WW (1996) Multiphoton fluorescence excitation: new spectral windows for biological nonlinear microscopy. Proc Natl Acad Sci USA 93:10763-10768
2. Stryer L, Haugland RP (1967) Energy transfer: A spectroscopic ruler. Proc Natl Acad Sci USA 58:719-726
3. Wu P, Brand L (1994) Resonance energy transfer: Methods and applications. Anal Biochem 218:1-13
4. Clegg RM (1995) Fluorescence resonance energy transfer. Curr Opin Biotechnol 6:103-110
5. Lakowicz Joseph R (1991) Topics in fluorescence spectroscopy. Principles 2
6. Kikuchi K, Takakusa H, Nagano T (2004) Recent advances in the design of small molecule-based FRET sensors for cell biology. TrAC Trends Anal Chem 23:407-415
7. Moens PD, Helms MK, Jameson DM (2004) Detection of tryptophan to tryptophan energy transfer in proteins. Protein J 23:79-83
8. Norman DG, Grainger RJ, Uhrin D, Lilley DM (2000) Location of cyanine-3 on double-stranded DNA: Importance for fluorescence resonance energy transfer studies. Biochemistry 39:6317-6324
9. Dietrich A, Buschmann V, Muller C, Sauer M (2002) Fluorescence resonance energy transfer (FRET) and competing processes in donor-acceptor substituted DNA strands: A comparative study of ensemble and single-molecule data. J Biotechnol 82:211-231
10. Salvatore AEM, Kramer FR, Tyagi S (2002). Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res 30:e122
11. Toth K, Sauermann V, Langowski J (1998) DNA curvature in solution measured by fluorescence resonance energy transfer. Biochemistry 37:8173-8179
12. Tsuji A, Koshimoto H, Sato Y, Hirano M, Sei-Iida Y, Kondo S, Ishibashi K (2000) Direct observation of specific messenger RNA in a single living cell under a fluorescence microscope. Biophys J 78:3260-3274
13. Tsuji A, Sato Y, Hirano M, Suga T, Koshimoto H, Taguchi T, Ohsuka S (2001). Development of a time-resolved fluorometric method for observing hybridization in living cells using fluorescence resonance energy transfer. Biophys J 81:501-515
14. Cooper JP, Hagerman PJ (1990) Analysis of fluorescence energy transfer in duplex and branched DNA molecules. Biochemistry 29:9261-9268
15. Laib S, Seeger S (2004) FRET studies of the interaction of dimeric cyanine dyes with DNA. J Fluoresc 14:187-191
16. Hill J, Heriot SY, Worsfold O, Richardson TH, Fox AM, Bradley DDC (2003) Dynamics of Forster transfer in polyfluorene-based polymer blends and Langmuir-Blodgettnanostructures. Synth Met 139:787-790
17. Heyduk E, Heyduk T, Claus P, Wisniewski JR (1997) Conformational changes of DNA induced by binding of Chironomus high mobility group protein la (cHMG1a). Regions flanking an HMG1 box domain do not influence the bend angle of the DNA. J Biol Chem 272:19763-19770
18. Mizukoshi T, Kodama TS, Fujiwara Y, Furuno T, Nakanishi M, Iwai S (2001) Structural study of DNA duplexes containing the (64) photoproduct by fluorescence resonance energy transfer. Nucleic Acids Res 29:4948-4954
19. Mergny JL, Boutorine AS, Garestier T et al (1994) Fluorescence energy transfer as a probe for nucleic acid structures and sequences. Nucleic Acids Res 22:920-928
20. Howell WM, Jobs M, Brookes AJ (2002) iFRET: An improved fluorescence system for DNA-melting analysis. Genome Res 12:1401-1407
21. Sei-Iida Y, Koshimoto H, Kondo S, Tsuji A (2000) Real-time monitoring of in vitro transcriptional RNA synthesis using fluorescence resonance energy transfer. Nucleic Acids Res 28:E59
22. Cardullo RA, Agrawal S, Flores C, Zamecnik PC, Wolf DE (1988) Detection of nucleic acid hybridization by nonradiative fluorescence resonance energy transfer. Proc Natl Acad Sci USA 85:8790-8794
23. Okamura Y, Kondo S, Sase I, Suga T, Mise K, Furusawa I, Kawakami S, Watanabe Y (2000) Double-labeled donor probe can enhance the signal of fluorescence resonance energy transfer (FRET) in detection of nucleic acid hybridization. Nucleic Acids Res 28:E107
24. Zal T, Gascoigne MR (2004) Using live FRET imaging to reveal early protein-protein interactions during T cell activation. Curr Opin Immunol 16:674-683
25. Bjornson KP, Modrich P (2003) Differential and simultaneous adenosine di- and triphosphate binding by MutS. J Biol Chem 278:18557-18562
26. Eis PS, Lakowicz JR (1993). Time-resolved energy transfer measurements of donor-acceptor distance distributions and intramolecular flexibility of a CCHH zinc finger peptide. Biochemistry 32:7981-7993
27. Rolinski OJ, Birch DJ, McCartney L, Pickup JC (2001) Molecular distribution sensing in a fluorescence resonance energy transfer based affinity assay for glucose. Spectrochim Acta A Mol Biomol Spectrosc 57:2245-2254
28. Grant SA, Xu J, Bergeron EJ, Mroz J (2001) Development of dual receptor biosensors: An analysis of FRET pairs. Biosens Bioelectron 16:231-237
29. Tolosa L, Malak H, Raob G, Lakowicz JR (1997) Optical assay for glucose based on the luminescence decay time of the long wavelength dye Cy5tm. Sens Actuators B: Chem B45:93-99
30. Mittoo S, Sundstrom LE, Bradley M (2003) Synthesis and evaluation of fluorescent probes for the detection of calpain activity. Anal Biochem 319:234-238
31. Lakowicz JR (1997) Topics in fluorescence spectroscopy. Nonlinear and two-photon induced fluorescence 5
32. LaMorte VJ, Zoumi A, Tromberg BJ (2003) Spectroscopic approach for monitoring two-photon excited fluorescence resonance energy transfer from homodimers at the subcellular level. J Biomed Opt 8:357-361
33. Soini JT, Soukka JM, Soini E, Hanninen PE (2002) Two-photon excitation microfluorometer for multiplexed single-step bioaffinity assays. Rev Sci Instrum 73:2680-2685
34. Brousmiche DW, Serin JM, Frechet JM, He GS, Lin TC, Chung SJ, Prasad PN (2003) Fluorescence resonance energy transfer in a novel two-photon absorbing system. J Am Chem Soc 125:1448-1449
35. Deniz AA, Dahan M, Grunwell JR, Ha T, Faulhaber AE, Chemla DS, Weiss S, Schultz PG (1999) Single-pair fluorescence resonance energy transfer on freely diffusing molecules: Observation of Forster distance dependence and subpopulations. Proc Natl Acad Sci USA 96:3670-3675
36. Lee NK, Kapanidis AN, Wang Y, Michalet X, Mukhopadhyay J, Ebright RH, Weiss S (2005) Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. Biophys J 88:2939-2953
37. Clegg RM, Murchie AI, Zechel A, Lilley DM (1993) Observing the helical geometry of double-stranded DNA in solution by fluorescence resonance energy transfer. Proc Natl Acad Sci USA 90:2994-2998
38. Masuko M, Ohuchi S, Sode K, Ohtani H, Shimadzu A (2000) Fluorescence resonance energy transfer from pyrene to perylene labels for nucleic acid hybridization assays under homogeneous solution conditions. Nucleic Acids Res 28:E34
39. Meltola NJ, Wahlroos R, Soini AE (2004) Hydrophilic labeling reagents of dipyrrylmethene-BF2 dyes for two-photon excited fluorometry: Syntheses and photophysical characterization. J Fluoresc 14:635-647
40. Meltola NJ, Vaarno J, Soini AE (2005) Dipyrrylmetheneboron difluorides as labels in two-photon excited fluorometry. Part II: Nucleic acid hybridisation assays. J Fluoresc 15:243-252
41. Ha T, Enderle T, Ogletree DF, Chemla DS, Selvin PR, Weiss S (1996) Probing the interaction between two single molecules: Fluorescence resonance energy transfer between a single donor and a single acceptor. Proc Natl Acad Sci USA 93:6264-6268
42. Hink MA, Visser NV, Borst JW, Hoek AV, Visser AJWG (2003) Practical use of corrected fluorescence excitation and emission spectra of fluorescent proteins in Förster resonance energy transfer (FRET) studies. J Fluoresc 13:185-188
43. Storhoff JJ, Lucas AD, Garimella V, Bao YP, Muller UR (2004) Homogeneous detection of unamplified genomic DNA sequences based on colorimetric scatter of gold nanoparticle probes. Nat Biotechnol 22:883-887
44. Ku WC, Lau WK, Tseng YT, Tzeng CM, Chiu SK (2004) Dextran sulfate provides a quantitative and quick microarray hybridization reaction. Biochem Biophys Res Commun 315:30-37