Skip to main content
SpringerLink
Log in

Time-Resolved Energy Transfer and Conformational Distributions of Biopolymers

  • Chapter
Principles of Fluorescence Spectroscopy

Abstract

In the previous chapter we described the principles of resonance energy transfer (RET), and how the phenomenon could be used to measure distances between donor and acceptor sites on macromolecules or the association between donor-labeled and acceptor-labeled biomolecules. Energy transfer was described as a through-space interaction that occurred whenever the emission spectrum of the donor overlapped with the absorption spectrum of the acceptor. For a given donor—acceptor (D—A) pair, the efficiency of energy transfer decreases as r −6, where r is the D—A distance. Each D—A pair has a characteristic distance: the Förster distance (R 0) at which RET is 50% efficient. The extent of energy transfer, as seen from the steady-state data, can be used to measure the distance, to study protein folding, to determine the extent of association based on proximity, or to create images of associated intracellular proteins.

In this chapter we describe more advanced applications of RET, particularly those that rely on time-resolved measurements of covalently linked D—A pairs. For such pairs the time-resolved data can be used to recover the conformation-al distribution or distance distribution between the donor and acceptor. Donor-to-acceptor motions also influence the extent of energy transfer, which can be used to recover the mutual diffusion coefficient. In Chapter 15 we will consider RET between donors and acceptors that are not covalent-ly linked. In this case the extent of RET depends on the dimensional geometry of the molecules, such as planar distributions in membranes and one-dimensional distributions in double-helical DNA.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
eBook
USD 16.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 99.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 129.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Haas E, Wilchek M, Katchalski-Katzir E, Steinberg IA. 1975. Distribution of end-to-end distances of oligopeptides in solution as estimated by energy transfer. Proc Natl Acad Sci USA 72:1807–1811.

    Article  CAS  Google Scholar 

  2. Grinvald A, Haas E, Steinberg IZ. 1972. Evaluation of the distribution of distances between energy donors and acceptors by fluorescence decay. Proc Natl Acad Sci USA 69:2273–2277.

    Article  CAS  Google Scholar 

  3. Haas E, Katchalski-Katzir E, Steinberg IZ. 1978. Brownian motion of the ends of oligopeptide chains in solution as estimated by energy transfer between chain ends. Biopolymers 17:11–31.

    Article  CAS  Google Scholar 

  4. Wu P, Brand L. 1994. Conformational flexibility in a staphylococcal nuclease mutant K45C from time-resolved resonance energy transfer measurements. Biochemistry 33:10457–10462.

    Article  CAS  Google Scholar 

  5. Amir D, Krausz S, Haas E. 1992. Detection of local structures in reduced unfolded bovine pancreatic trypsin inhibitor. Proteins 13:162–173.

    Article  CAS  Google Scholar 

  6. Amir D, Haas E. 1986. Determination of intramolecular distance distributions in a globular protein by nonradiative excitation energy transfer measurements. Biopolymers 25:235–240.

    Article  CAS  Google Scholar 

  7. Lakowicz JR, Wiczk W, Gryczynski I, Johnson ML. 1990. Influence of oligopeptide flexibility on donor–acceptor distance distribution by frequency-domain fluorescence spectroscopy. Proc SPIE 1204:192– 205.

    Article  CAS  Google Scholar 

  8. She M, Xing J, Dong WJ, Umeda PK, Cheung HC. 1998. Calcium binding to the regulatory domain of skeletal muscle troponin C induces a highly constrained open conformation. J Mol Biol 281:445–452.

    Article  CAS  Google Scholar 

  9. Dong W-J, Chandra M, Xing J, She M, Solaro RJ, Cheung HC. 1997. Phosphorylation induced distance change in a cardiac muscle tro-ponin I mutant. Biochemistry 36:6754–6761.

    Article  CAS  Google Scholar 

  10. Maliwal BP, Lakowicz JR, Kupryszewski G, Rekowski P. 1993. Fluorescence study of conformational flexibility of RNase S-peptide: distance-distribution, end-to-end diffusion, and anisotropy decays. Biochemistry 32:12337–12345.

    Article  CAS  Google Scholar 

  11. Cheung HC, Gryczynski I, Malak H, Wiczk W, Johnson ML, Lakowicz JR. 1991. Conformational flexibility of the Cys 697–Cys 707 segment of myosin subfragment, 1: distance distributions by frequency-domain fluorometry. Biophys Chem 40:1–17.

    Article  CAS  Google Scholar 

  12. Cheung HC, Wang C-K, Gryczynski I, Wiczk W, Laczko G, Johnson ML, Lakowicz JR. 1991. Distance distributions and anisotropy decays of troponin C and its complex with troponin I. Biochemistry 30:5238–5247.

    Article  CAS  Google Scholar 

  13. Lakowicz JR, Gryczynski I, Cheung HC, Wang C-K, Johnson ML, Joshi N. 1988. Distance distributions in proteins recovered by using frequency-domain fluorometry: applications to troponin I and its complex with troponin C. Biochemistry 27:9149–9160.

    Article  CAS  Google Scholar 

  14. Zhao X, Kobayashi T, Malak H, Gryczynski I, Lakowicz JR, Wade R, Collins JH. 1995. Calcium-induced troponin flexibility revealed by distance distribution measurements between engineered sites. J Biol Chem 270(26):15507–15514.

    Article  CAS  Google Scholar 

  15. Eis PS, Kusba J, Johnson ML, Lakowicz JR. 1993. Distance distributions and dynamics of a zinc finger peptide from fluorescence resonance energy transfer measurements. J Fluoresc 3(1):23–31.

    Article  CAS  Google Scholar 

  16. 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.

    Article  CAS  Google Scholar 

  17. Bacchiocchi C, Graceffa P, Lehrer SS. 2004. Mysoin-induced movement of αα, αβ, and ββ smooth muscle tropomyosin on actin observed by multisite FRET. Biophys J 86:2295–2307.

    Article  CAS  Google Scholar 

  18. Miki M, Kouyama T. 1994. Domain motion in action observed by fluorescence resonance energy transfer. Biochemistry 33:10171– 10177.

    Article  CAS  Google Scholar 

  19. Dong WJ, Chandra M, Xing J, She M, Solaro RJ, Cheung HC. 1997. Phosphorylation-induced distance change in a cardiac muscle tro-ponin I mutant. Biochemistry 36:6754–6761.

    Article  CAS  Google Scholar 

  20. Navon A, Ittah V, Landsman P, Scheraga HA, Haas E. 2001. Distributions of intramolecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A: folding initiation structures in the C-terminal portions of the reduced protein. Biochemistry 40:105–118.

    Article  CAS  Google Scholar 

  21. Szmacinski H, Wiczk W, Fishman MN, Eis PS, Lakowicz JR, Johnson ML. 1996. Distance distributions from the tyrosyl to disul-fide residues in the oxytocin and [Arg8]-vasopressin measured using frequency-domain fluorescence resonance energy transfer. Eur Biophys J 24:185–193.

    Article  CAS  Google Scholar 

  22. Cheung HC. 1991. Resonance energy transfer. In Topics in fluorescence spectroscopy, Vol. 2: Principles, pp. 127–176. Ed JR Lakowicz. Plenum Press, New York.

    Google Scholar 

  23. Lakowicz JR, Gryczynski I, Wiczk W, Laczko G, Prendergast FC, Johnson ML. 1990. Conformational distributions of melittin in water/methanol mixtures from frequency-domain measurements of nonradiative energy transfer. Biophys Chem 36:99–115.

    Article  CAS  Google Scholar 

  24. Lakowicz JR, Gryczynski I, Laczko G, Wiczk W, Johnson ML. 1994. Distribution of distances between the tryptophan and the N-terminal residue of melittin in its complex with calmodulin, troponin C, and phospholipids. Protein Sci 3:628–637.

    Article  CAS  Google Scholar 

  25. Albaugh S, Steiner RF. 1989. Determination of distance distribution from time domain fluorometry. J Phys Chem 93:8013–8016.

    Article  CAS  Google Scholar 

  26. Katchalski-Katzir E, Haas E, Steinberg IA. 1981. Study of conformation and intramolecular motility of polypeptides in solution by a novel fluorescence method. Ann NY Acad Sci 36:44–61.

    Article  Google Scholar 

  27. Lakowicz JR, Johnson ML, Wiczk W, Bhat A, Steiner RF. 1987. Resolution of a distribution of distances by fluorescence energy transfer and frequency-domain fluorometry. Chem Phys Letts 138(6):587–593.

    Article  CAS  Google Scholar 

  28. Kulinski T, Wennerberg ABA, Rigler R, Provencher SW, Pooga M, Langel U, Bartfai T. 1997. Conformational analysis of glanin using end to end distance distribution observed by Förster resonance energy transfer. Eur Biophys J 26:145–154.

    Article  CAS  Google Scholar 

  29. Lakowicz JR, Gryczynski I, Wiczk W, Kusba J, Johnson ML. 1991. Correction for incomplete labeling in the measurement of distance distributions by frequency-domain fluorometry. Anal Biochem 195:243–254.

    Article  CAS  Google Scholar 

  30. Yang M, Millar DP. 1996. Conformational flexibility of three-way DNA junctions containing unpaired nucleotides. Biochemistry 35:7959–7967.

    Article  CAS  Google Scholar 

  31. Englert A, Leclerc M. 1978. Intramolecular energy transfer in molecules with a large number of conformations. Proc Natl Acad Sci USA 75(3):1050–1051.

    Article  CAS  Google Scholar 

  32. Wu P, Brand L. 1992. Orientation factor in steady-state and time-resolved resonance energy transfer measurements. Biochemistry 31:7939–7947.

    Article  CAS  Google Scholar 

  33. Dos Remedios CG, Moens PDJ. 1995. Fluorescence resonance energy transfer spectroscopy is a reliable “ruler” for measuring structural changes in proteins. J Struc Biol 115:175–185.

    Article  Google Scholar 

  34. Beecham JM, Haas E. 1989. Simulations determination of intramolecular distance distributions and conformational dynamics by global analysis of energy transfer measurements. Biophys J 55:1225–1236.

    Article  Google Scholar 

  35. Ohmine I, Silbey R, Deutch JM. 1997. Energy transfer in labeled polymer chains in semidilute solutions. Macromolecules 10:862– 864.

    Article  Google Scholar 

  36. Walter NG, Burke JM, Millar DP. 1999. Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction. Nature Struct Biol 6(6):544–549.

    Article  CAS  Google Scholar 

  37. Walter NG, Harris DA, Pereira MJB, Rueda D. 2002. In the fluorescent spotlight: global and local conformational changes of small catalytic RNAs. Biopolymers 61:224–241.

    Article  CAS  Google Scholar 

  38. Yang M, Millar DP. 1997. Fluorescence resonance energy transfer as a probe of DNA structure and function. Methods Enzymol 278:417–444.

    Article  CAS  Google Scholar 

  39. Eis PS, Millar D P. 1993. Conformational distributions of a four-way DNA junction revealed by time-resolved fluorescence resonance energy transfer. Biochemistry 32:13852–13860.

    Article  CAS  Google Scholar 

  40. Clegg RM, Murchie AIH, Lilley DM. 1994. The solution structure of the four-way DNA junction at low-salt conditions: a fluorescence resonance energy transfer analysis. Biophys J 66:99–109.

    Article  CAS  Google Scholar 

  41. Yang M, Millar DP. 1996. Conformational flexibility of three-way DNA junctions containing unpaired nucleotides. Biochemistry 35:7959–7967.

    Article  CAS  Google Scholar 

  42. Lillo MP, Szpikowska BK, Mas MT, Sutin JD, Beechem JM. 1997. Real-time measurement of multiple intramolecular distances during protein folding reactions: a multisite stopped-flow fluorescence energy-transfer study of yeast phosphoglycerate kinase. Biochemistry 36:11273–11281.

    Article  CAS  Google Scholar 

  43. Lillo MP, Beechem JM, Szpikowska BK, Sherman MA, Mas MT. 1997. Design and characterization of a multisite fluorescence energy-transfer system for protein folding studies: a steady-state and time-resolved study of yeast phosphoglycerate kinase. Biochemistry 36:11261–11272.

    Article  CAS  Google Scholar 

  44. Ratner V, Kahana E, Eichler M, Haas E. 2002. A general strategy for site-specific double labeling of globular proteins for kinetic FRET studies. Bioconjugate Chem 13:1163–1170.

    Article  CAS  Google Scholar 

  45. Rice KG, Wu P, Brand L, Lee YC. 1991. Interterminal distance and flexibility of a triantennary glycopeptide as measured by resonance energy transfer. Biochemistry 30:6646–6655.

    Article  CAS  Google Scholar 

  46. Brown MP, Toptygin D, Lee KB, Animashaun T, Hughes RC, Lee YC, Brand L. 1998. The tryptophan fluorescence of tetracarbidium conophorum agglutinin II and a solution-based assay for the binding of a biantennary glycopeptide. J Protein Chem 17(2):149–159.

    Article  CAS  Google Scholar 

  47. Rice KG. 2001. Application of fluorescence resonance energy transfer to analyze carbohydrates. Anal Biochem 297:117–122.

    Article  CAS  Google Scholar 

  48. Wu P, Lee KB, Lee YC, Brand L. 1996. Solution conformations of a biantennary glycopeptide and a series of its exoglycosidase products from sequential trimming of sugar residues. J Biol Chem 271(3):1470–1474.

    Article  CAS  Google Scholar 

  49. Deniz AA, Laurence TA, Beligere GS, Dahan M, Martin AB, Chemla DS, Dawson PE, Schultz PG, Weiss S. 2000. Single-molecule protein folding: diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2. Proc Natl Acad Sci USA 97:5179–5184.

    Article  CAS  Google Scholar 

  50. Elangovan M, Day RN, Periasamy A. 2002. Nanosecond fluorescence resonance energy transfer-fluorescence lifetime imaging microscopy to localize the protein interactions in a single living cell. J Microsc 205:3–14.

    Article  CAS  Google Scholar 

  51. Wouters FS, Bastiaens PIH. 1999. Fluorescence lifetime imaging of receptor tyrosine kinase activity in cells. Curr Biol 9:1127–1130.

    Article  CAS  Google Scholar 

  52. Wallrabe H, Stanley M, Periasamy A, Barroso M. 2003. One- and two-photon fluorescence resonance energy transfer microscopy to establish a clustered distribution of receptor–ligand complexes in endocytic membranes. J Biomed Opt 8(3):339–346.

    Article  CAS  Google Scholar 

  53. Krishnan RV, Masuda A, Centonze VE, Herman B. 2003. Quantitative imaging of protein-protein interactions by multiphoton fluorescence lifetime imaging microscopy using a streak camera. J Biomed Opt 8(3):362–367.

    Article  CAS  Google Scholar 

  54. Mills JD, Stone JR, Rubin DG, Melon DE, Okonkwo DO, Periasamy A, Helm GA. 2003. Illuminating protein interactions in tissue using confocal and two-photon excitation fluorescent resonance energy transfer microscopy. J Biomed Opt 8(3):347–356.

    Article  CAS  Google Scholar 

  55. Tramier M, Gautier I, Piolot T, Ravalet S, Kemnitz K, Coppey J, Durieux C, Mignotte V, Coppey-Moisan M. 2002. Picosecond-het-ero-FRET microscopy to probe protein-protein interactions in live cells. Biophys J 83:3570–3577.

    Article  CAS  Google Scholar 

  56. Bacskai BJ, Skoch J, Hickey GA, Allen R, Hyman BT. 2003. Fluorescence resonance energy transfer determinations using multiphoton fluorescence lifetime imaging microscopy to characterize amyloid-beta plaques. J Biomed Opt 8(3):368–375.

    Article  CAS  Google Scholar 

  57. Lakowicz JR, Kusba J, Wiczk W, Gryczynski I, Johnson ML. 1990. End-to-end diffusion of a flexible bichromophoric molecule observed by intramolecular energy transfer and frequency domain fluorometry. Chem Phys Lett 173:319–326.

    Article  CAS  Google Scholar 

  58. Lakowicz JR, Gryczynski I, Kusba J, Wiczk W, Szmacinski H, Johnson ML. 1994. Site-to-site diffusion in proteins as observed by energy transfer and frequency domain fluorometry. Photochem Photobiol 59:16–29.

    Article  CAS  Google Scholar 

  59. Kusba J, Lakowicz JR. 1994. Diffusion-modulated energy transfer and quenching: analysis by numerical integration of diffusion equation in Laplace space. Methods Enzymol 240:216–262.

    Article  CAS  Google Scholar 

  60. Lakowicz JR, Kusba J, Wiczk W, Gryczynski I, Szmacinski H, Johnson ML. 1991. Resolution of the conformational distribution and dynamics of a flexible molecule using frequency domain fluo-rometry. Biophys Chem 39:79–84.

    Article  CAS  Google Scholar 

  61. Lakowicz JR, Wiczk W, Gryczynski I, Szmacinski H, Johnson ML. 1990. Influence of end-to-end diffusion on intramolecular energy transfer as observed by frequency-domain fluorometry. Biophys Chem 38:99–109.

    Article  CAS  Google Scholar 

  62. Somogyi B, Matko J, Papp S, Hevessy J, Welch GR, Damjanovich S. 1984. Förster-type energy transfer as a probe for changes in local fluctuations of the protein matrix. Biochemistry 23:3404–3411.

    Article  Google Scholar 

  63. Haran G, Haas E, Szpikowska BK, Mas MT. 1992. Domain motions in phosphoglycerate kinase: determination of interdomain distance distributions by site-specific labeling and time-resolved fluorescence energy transfer. Proc Natl Acad Sci USA 89:11764–11768.

    Article  CAS  Google Scholar 

  64. Gerstein M, Lesk AM, Chothia C. 1994. Structural mechanisms for domain movements in proteins. Biochemistry 33(22):6738–6749.

    Article  Google Scholar 

  65. Blackwell MF, Gounaris K, Zara SJ, Barber J. 1987. A method for estimating lateral diffusion coefficients in membranes from steady state fluorescence quenching studies. J Biophys Soc 51:735–744.

    Article  CAS  Google Scholar 

  66. Ollmann M, Schwarzmann G, Sandhoff K, Galla H-J. 1987. Pyrene-labeled gangliosides: micelle formation in aqueous solution, lateral diffusion, and thermotropic behavior in phosphatidylcholine bilay-ers. Biochemistry 26:5943–5952.

    Article  CAS  Google Scholar 

  67. Buckler DR, Haas E, Scheraga HA. 1995. Analysis of the structure of ribonuclease A in native and partially denatured states by time-resolved nonradiative dynamic excitation energy transfer between site-specific extrinsic probes. Biochemistry 34:15965–15978.

    Article  CAS  Google Scholar 

  68. Representative Publications On Measurement Of Distance Distributions

    Google Scholar 

Proteins—Distance Distributions

  • Amir D, Haas E. 1987. Estimation of intramolecular distance distributions in bovine pancreatic trypsin inhibitor by site-specific labeling and nonradiative excitation energy-transfer measurements. Biochemistry 26:2162–2175.

    Article  CAS  Google Scholar 

  • Amir D, Haas E. 1988. Reduced bovine pancreatic trypsin inhibitor has a compact structure. Biochemistry 27:8889–8893.

    Article  CAS  Google Scholar 

  • Amir D, Levy DP, Levin Y, Haas E. 1986. Selective fluorescent labeling of amino groups of bovine pancreatic trypsin inhibitor by reductive alkylation. Biopolymers 25:1645–1658.

    Article  CAS  Google Scholar 

  • Amir D, Varshavski L, Haas E. 1985. Selective fluorescent labeling at the α—amino group of bovine pancreatic trypsin inhibitor. Biopolymers 24:623–638.

    Article  CAS  Google Scholar 

  • Beals JM, Haas E, Krausz S, Scheraga HA. 1991. Conformational studies of a peptide corresponding to a region of the C-terminus of ribonu-clease A: implications as a potential chain-folding initiation site. Biochemistry 30:7680–7692.

    Article  CAS  Google Scholar 

  • Haas E, McWherter CA, Scheraga HA. 1988. Conformational unfolding in the N-terminal region of ribonuclease A detected by nonradiative energy transfer: distribution of interresidue distances in the native, denatured, and reduced—denatured states. Biopolymers 27:1–21.

    Article  CAS  Google Scholar 

  • Haran G, Haas E, Szpikowska BK, Mas MT. 1992. Domain motions in phosphoglycerate kinase: determination of interdomain distance distributions by site-specific labeling and time-resolved fluorescence energy transfer. Proc Natl Acad Sci USA 89:11764–11768.

    Article  CAS  Google Scholar 

DNA Structures

  • Clegg RM, Murchie AIH, Zechel A, Lilley DMJ. 1993. Observing the helical geometry of double-stranded DNA in solution by fluorescence resonance energy transfer. Proc Natl Acad Sci USA 90:2994–2998.

    Article  CAS  Google Scholar 

  • McKinney SA, Dèclais AC, Lilley DMJ, Ha T. 2003. Structural dynamics of individual Holliday junctions. Nature Struct Biol 10(2):93–97.

    Article  CAS  Google Scholar 

  • Miick SM, Fee RS, Millar DP, Chazin WJ. 1997. Crossover isomer bias is the primary sequence-dependent property of immobilized Holliday junctions. Proc Natl Acad Sci USA 94:9080–9084.

    Article  CAS  Google Scholar 

  • Mizukoshi T, Kodama TS, Fujiwara Y, Furuno T, Nakanishi M, Iwai S. 2001. Structural study of DNA duplexes containing the (6–4) photo-product by fluorescence resonance energy transfer. Nucleic Acids Res 29(24):4948–4954.

    Article  CAS  Google Scholar 

  • Murchie AIH, Clegg RM, von Kitzing E, Duckett DR, Diekmann S, Lilley DMJ. 1989. Fluorescence energy transfer shows that the four-way DNA junction is a right-handed cross of antiparallel molecules. Nature 341:763–766.

    Article  CAS  Google Scholar 

  • Norman DG, Grainger RJ, Uhrín D, Lilley DMJ. 2000. Location of cya-nine-3 on double-stranded DNA: importance for fluorescence resonance energy transfer studies. Biochemistry 39:6317–6324.

    Article  CAS  Google Scholar 

  • Parkhurst KM, Parkhurst LJ. 1995. Donor–acceptor distributions in a double-labeled fluorescent oligonucleotide both as a single strand and in duplexes. Biochemistry 34:293–300.

    Article  CAS  Google Scholar 

  • Patel LR, Curran T, Kerppola TK. 1994. Energy transfer analysis of Fos-Jun dimerization and DNA binding. Proc Natl Acad Sci USA 91:7360–7364.

    Article  CAS  Google Scholar 

  • Ramirez-Carrozzi VR, Kerppola TK. 2001. Dynamics of Fos–Jun–NFAT1 complexes. Proc Natl Acad Sci USA 98(9):4893–4898.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

End-to-End Diffusion

  • Bandyopadhyay T, Ghosh SK. 2003. Diffusion assisted end-to-end relaxation of a flexible Rouse polymer chain: fluorescence quenching through a model energy transfer. J Chem Phys 119(1):572–584.

    Article  CAS  Google Scholar 

  • Duus JØ, Meldal M, Winkler JR. 1998. Fluorescence energy-transfer probes of conformation in peptides: the 2-aminobenzamide/nitroty-rosine pair. J Phys Chem B 102:6413–6418.

    Article  CAS  Google Scholar 

  • Gryczynski I, Lakowicz JR, Kusba J. 1995. End-to-end diffusion coefficients and distance distributions from fluorescence energy transfer measurements: enhanced resolution by using multiple donors with different lifetimes. J Fluoresc 5(2):195–203.

    Article  CAS  Google Scholar 

  • Lakowicz JR, Kusba J, Gryczynski I, Wiczk W, Szmacinski H, Johnson M. 1991. End-to-end diffusion and distance distributions of flexible donor–acceptor systems observed by intramolecular energy transfer and frequency-domain fluorometry; enhanced resolution by global analysis of externally quenched and nonquenched samples. J Phys Chem 95:9654–9660.

    Article  CAS  Google Scholar 

  • Lakowicz JR, Nair R, Piszczek G, Gryczynski I. 2000. End-to-end diffusion on the microsecond timescale measured with resonance energy transfer from a long-lifetime rhenium metal–ligand complex. Photochem Photobiol 71(2):157–161.

    Article  CAS  Google Scholar 

  • Maliwal BP, Lakowicz JR. 1993. Fluorescence study of conformational flexibility of RNAse S-peptide: distance-distribution, end-to-end diffusion and anisotropy decays. Biochemistry 32:12337–12345.

    Article  CAS  Google Scholar 

  • Maliwal BP, Kusba J, Wiczk W, Johnson M, Lakowicz JR. 1993. End-to-end diffusion coefficients and distance distributions from fluorescence energy transfer measurements: enhanced resolution by using multiple acceptors with different Förster distances. Biophys Chem 46:273–281.

    Article  CAS  Google Scholar 

  • Neuweiler H, Schulz A, Böhmer M, Enderlein J, Sauer M. 2003. Measurement of submicrosecond intramolecular contact formation in peptides at the single-molecule level. J Am Chem Soc 125:5324–5330.

    Article  CAS  Google Scholar 

  • Nyitrai M, Hild G, Bódis E, Lukács A, Somogyi B. 2000. Flexibility of myosin-subfragment-1 in its complex with actin as revealed by fluorescence resonance energy transfer. Eur J Biochem 267:4334–4338.

    Article  CAS  Google Scholar 

  • Talaga DS, Lau WL, Roder H, Tang J, Jia Y, DeGrado WF, Hochstrasser RM. 2000. Dynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy. Proc Natl Acad Sci USA 97(24):13021–13026.

    Article  CAS  Google Scholar 

Reviews

  • Wemmer DA, Case DA, Millar DP. 2002. Fluorescence spectroscopy and nucleic acids. Biopolymers Nucleic Acid Sci 61(3):143–242.

    Google Scholar 

Ribozymes

  • Lafontaine DA, Norman DG, Lilley DMJ. 2002. The global structure of the VS ribozyme. EMBO J 21(10):2461–3471.

    Article  CAS  Google Scholar 

  • Tan E, Wilson TJ, Nahas MK, Clegg RM, Lilley DMJ, Ha T. 2003. A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate. Proc Natl Acad Sci USA 100(16):9308–9313.

    Article  CAS  Google Scholar 

  • Walter F, Murchie AIH, Duckett DR, Lilley DMJ. 1998. Global structure of four-way RNA junctions studied using fluorescence resonance energy transfer. RNA 4:719–728.

    Article  CAS  Google Scholar 

  • Walter F, Murchie AIH, Thomson JB, Lilley DMJ. 1998. Structure and activity of the hairpin ribozyme in its natural junction conformation: effect of metal ions. Biochemistry 37:14195–14203.

    Article  CAS  Google Scholar 

  • Wilson TJ, Lilley DMJ. 2002. Metal ion binding and the folding of the hairpin ribozyme. RNA 8:587–600.

    Article  CAS  Google Scholar 

Ribozomes

  • Klostermeier D, Sears P, Wong CH, Millar DP, Williamson JR. 2004. A three-fluorophore FRET assay for high-throughput screening of small-molecule inhibitors of ribosome assembly. Nucleic Acids Res 32(9):2707–2715.

    Article  CAS  Google Scholar 

  • Melcher SE, Wilson TJ, Lilley DMJ. 2003. The dynamic nature of the four-way junction of the hepatitis C virus IRES. RNA 9:809–820.

    Article  CAS  Google Scholar 

Theory

  • Farinha JPS, Spiro JG, Winnik MA. 2004. Dipole–dipole electronic energy transfer: fluorescence decay functions for arbitrary distributions of donors and acceptors in systems with cylindrical symmetry. J Phys Chem B 108:16392–16400.

    Article  CAS  Google Scholar 

  • Rolinski O, Birch DJS, McCartney LJ, Pickup JC. 2000. A method of determining donor acceptor distribution functions in Förster resonance energy transfer. Chem Phys Lett 324:95–100.

    Article  CAS  Google Scholar 

  • Rolinski O, Birch DJS, McCartney LJ, Pickup JC. 2001. Fluorescence nanotomography using resonance energy transfer: demonstration with a protein–sugar complex. Phys Med Biol 46:N221–N226.

    Article  CAS  Google Scholar 

  • Srinivas G, Yethiraj A, Bagchi B. 2001. FRET by FET and dynamics of polymer folding, 2001. J Phys Chem 105(13):2475–2478.

    CAS  Google Scholar 

  • Valeur B, Mugnier J, Pouget J, Bourson J, Santi F. 1989. Calculation of the distribution of donor–acceptor distances in flexible bichromophoric molecules: application to intramolecular transfer of excitation energy. J Phys Chem 93:6073–6079.

    Article  CAS  Google Scholar 

Download references

Editor information

Editors and Affiliations

  1. Center for Fluorescence Spectroscopy, University of Maryland School of Medicine, Baltimore, MD, 21201, USA

    Joseph R. Lakowicz

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

(2006). Time-Resolved Energy Transfer and Conformational Distributions of Biopolymers. In: Lakowicz, J.R. (eds) Principles of Fluorescence Spectroscopy. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-46312-4_14

Download citation

Publish with us

Policies and ethics

Search

Navigation