Förster Resonance Energy Transfer Methods for Quantification of Protein–Protein Interactions on Microarrays

Methods in Molecular Biology

Volumn 723, Issue , 2011, Pages 303-320

  Schäferling, Michael ^a   Nagl, Stefan ^b  

^a UNIVERSITY OF REGENSBURG   (Germany)

^b UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

Biomolecular interaction; FRET; Protein microarray; Screening; Time resolved fluorescence

Indexed keywords

DNA MICROARRAY; ENERGY TRANSFER; ENZYME ACTIVITY; FLUORESCENCE MICROSCOPY; HIGH THROUGHPUT SCREENING; IMMUNOASSAY; MICROARRAY ANALYSIS; MOLECULAR BIOLOGY; PROTEIN MICROARRAY; PROTEIN PROTEIN INTERACTION; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; ANIMAL; FLUORESCENCE RESONANCE ENERGY TRANSFER; HUMAN; METHODOLOGY; PROTEIN ANALYSIS; REVIEW; TIME;

ANIMALS; FLUORESCENCE RESONANCE ENERGY TRANSFER; HUMANS; PROTEIN ARRAY ANALYSIS; PROTEIN INTERACTION MAPPING; TIME FACTORS;

EID: 79958279918     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-043-0_19     Document Type: Chapter

References (74)

1. Lakowicz JR (2006) Principles of fluorescence spectroscopy, 3rd edn. Springer, Berlin
2. Valeur B (2002) Molecular fluorescence – principles and applications. Wiley-VCH, Weinheim
3. Sapsford KE, Berti L, Medintz IL (2006) Materials for fluorescence resonance energy transfer analysis: beyond traditional donor-acceptor combinations. Angew Chem Int Ed 45:4562–4588
4. Roda A, Guardigli M, Michelini E, Mirasoli M (2009) Nanobioanalytical luminescence: Förster-type energy transfer methods. Anal Bioanal Chem 393:109–123
5. Roda A, Guardigli M, Michelini E, Mirasoli M, Pasani P (2003) Analytical bioluminescence and chemiluminescence. Anal Chem 75:462A–470A
6. Clegg RM (1996) Fluorescence resonance energy transfer. In: Wang XF, Herman B (eds) Fluorescence imaging spectroscopy and microscopy. Wiley, New York, pp 179–252
7. Enderlein J (2003) Electrodynamics of fluorescence. http://www.joerg-enderlein.de/fileadmin/downloads/Tutorial.pdf. Accessed 22 July 2009
8. Selvin PR (2000) The renaissance of fluorescence resonance energy transfer. Nat Struct Biol 7:730–734
9. Szollosi J, Damjanovich S, Matyus L (1998) Application of fluorescence resonance energy transfer in the clinical laboratory: routine and research. Cytometry B 34:159–179
10. Williams C (2004) cAMP detection methods in HTS: selecting the best from the rest. Nat Rev Drug Discov 3:125–135
11. Bremer C, Tung CH, Weissleder R (2001) In vivo molecular target assessment of matrix metalloproteinase inhibition. Nat Med 7: 743–748
12. Kohl T, Heinze KG, Kuhlemann R, Koltermann A, Schwille P (2002) A protease assay for two-photon crosscorrelation and FRET analysis based solely on fluorescent proteins. Proc Natl Acad Sci U S A 99:12161–12166
13. Yang Y, Babiak P, Reymond JL (2006) Low background FRET-substrates for lipases and esterases suitable for high-throughput screening under basic (pH 11) conditions. Org Biomol Chem 4:1746–1754
14. Lyon E, Wittwer CT (2009) LightCycler technology in molecular diagnostics. J Mol Diagn 11:93–101
15. Smith CJ (2005) Quantitative real-time PCR. In: Osborn AM, Smith CJ (eds) Molecular microbial ecology. Taylor & Francis, New York, pp 151–166
16. Tapp I, Malmberg L, Rennel E, Wik M, Syvanen AC (2000) Homogeneous scoring of single-nucleotide polymorphisms: comparison of the 5¢-nuclease TaqMan assay and Molecular Beacon probes. Biotechniques 28:732–738
17. Goel G, Kumar A, Puniya AK, Chen W, Singh K (2005) Molecular beacon: a multitask probe. J Appl Microbiol 99:435–442
18. + channel organization. In: Lopatin A, Nichols CG (eds) Ion channel localization. Humana, Totowa, pp 261–274
19. Arun KHS, Kaul CL, Ramarao P (2005) Green fluorescent proteins in receptor research: an emerging tool for drug discovery. J Pharmacol Toxicol Methods 51:1–23
20. Takanishi CL, Bykova EA, Cheng W, Zheng J (2006) GFP-based FRET analysis in live cells. Brain Res 1091:132–139
21. Jares-Erijman EA, Jovin TM (2003) FRET imaging. Nat Biotechnol 21:1387–1395
22. Kokko T, Kokko L, Lövgren T, Soukka T (2007) Homogeneous noncompetitive immunoassay for 17beta-estradiol based on fluorescence resonance energy transfer. Anal Chem 79:5935–5940
23. Mathis G (1993) Rare earth cryptates and homogeneous fluoroimmunoassays with human sera. Clin Chem 39:1953–1959
24. Kim SH, Jeyakumar M, Katzenellenbogen JA (2007) Dual-mode fluorophore-doped nickel nitrilotriacetic acid-modified silica nanoparticles combine histidine-tagged protein purification with site-specific fluorophore labeling. J Am Chem Soc 129:13254–13264
25. Kürner JM, Wolfbeis OS, Klimant I (2002) Homogeneous luminescence decay time-based assay using energy transfer from nano-spheres. Anal Chem 74:2151–2156
26. Valanne A, Lindroos H, Lövgren T, Soukka T (2005) A novel homogeneous assay format utilising proximity dependent fluorescence energy transfer between particulate labels. Anal Chim Acta 539:251–256
27. Kuningas K, Ukonaho T, Päkkilä H, Rantanen T, Rosenberg J, Lövgren T, Soukka T (2006) Upconversion fluorescence resonance energy transfer in a homogeneous immunoassay for estradiol. Anal Chem 78:4690–4696
28. Shen Y, Wu BL (2009) Microarray-based genomic DNA profiling technologies in clinical molecular diagnostics. Clin Chem 55: 659–669
29. Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR (2005) Whole-genome patterns of common DNA variation in three human populations. Science 307:1072–1079
30. Uttamchandani M, Neo JL, Ong BNZ, Moochhala S (2008) Applications of microarrays in pathogen detection and biodefence. Trends Biotechnol 27:53–61
31. Ahmed FE (2004) DNA-based methods for GMO detection: historical developments and future prospects. In: Ahmed FE (ed) Testing of genetically modified organisms in foods. Haworth, Binghamton, pp 221–253
32. Hakes L, Pinney JW, Robertson DL, Lovell SC (2008) Protein-protein interaction networks and biology – what’s the connection? Nat Biotechnol 26:69–72
33. Caiazzo RJ Jr, Maher AJ, Drummond MP, Lander CI, Tassinari OW, Nelson BP, Liu BCS (2009) Protein microarrays as an application for disease biomarkers. Proteomics Clin Appl 3:138–147
34. Hartmann M, Roeraade J, Stoll D, Templin MF, Joos TO (2009) Protein microarrays for diagnostic assays. Anal Bioanal Chem 393: 1407–1416
35. Jonkheijm P, Weinrich D, Schroeder H, Niemeyer CM, Waldmann H (2008) Chemical strategies for generating protein biochips. Angew Chem Int Ed 47: 9618–9647
36. Seidel M, Niessner R (2008) Automated analytical microarrays: a critical review. Anal Bioanal Chem 391:1521–1544
37. Kersten B, Wanker EE, Hoheisel JD, Angenendt P (2005) Multiplex approaches in protein microarray technology. Expert Rev Proteomics 2:499–510
38. Schäferling M, Nagl S (2006) Optical technologies for the read out and quality control of DNA and protein microarrays. Anal Bioanal Chem 385:500–517
39. Nagl S, Schaeferling M, Wolfbeis OS (2005) Fluorescence analysis in microarray technology. Microchim Acta 151:1–21
40. Templin MF, Stoll D, Schwenk JM, Pötz O, Kramer S, Joos TO (2003) Protein microarrays: promising tools for proteomic research. Proteomics 3:2155–2166
41. Schäferling M, Schiller S, Paul H, Kruschina M, Pavlickova P, Giammasi C, Kambhampati D (2002) Application of self-assembly techniques in the design of biocompatible protein microarray surfaces. Electrophoresis 23: 3097–3105
42. MacBeath G (2002) Protein microarrays and proteomics. Nat Genet 32:526–532
43. Schwartz DE, Gong P, Shepard KL (2008) Time-resolved Förster-resonance-energy-transfer DNA assay on an active CMOS microarray. Biosens Bioelectron 24:383–390
44. Frutos AG, Pal S, Quesada M, Lahiri J (2002) Method for detection of single-base mismatches using bimolecular beacons. J Am Chem Soc 124:2396–2397
45. Fang X, Liu X, Schuster S, Tan WJ (1999) Designing a novel molecular beacon for sur-face-immobilized DNA hybridization studies. J Am Chem Soc 121:2921–2922
46. Kim H, Kane MD, Kim S, Dominguez W, Applegate BM, Savikhin S (2007) A molecular beacon DNA microarray system for rapid detection of E. coli O157:H7 that eliminates the risk of a false negative signal. Biosens Bioelectron 22:1041–1047
47. Diaz-Mochon JJ, Bialy L, Bradley M (2006) Dual colour, microarray-based, analysis of 10,000 protease substrates. Chem Commun 38:3984–3986
48. Kong A, Leboucher P, Leek R, Calleja V, Winter S, Harris A, Parker PJ, Larijani B (2006) Prognostic value of an activation state marker for epidermal growth factor receptor in tissue microarrays of head and neck cancer. Cancer Res 66:2834–2843
49. Usui K, Takahashi M, Nokihara K, Mihara H (2004) Peptide arrays with designed a-helical structures for characterization of proteins from FRET fingerprint patterns. Mol Diver 8:209–218
50. Castellana ET, Cremer PS (2007) Imaging large arrays of supported lipid bilayers with a macroscope. Biointerphases 2:57–63
51. Vogel KW, Riddle SM, Horton RA, Robers MB, Michaud GA (2008) FRET-based kinase and ubiquitination assay using a fluorescent fusion protein substrate and a luminescent metal complex, and screening applications. PCT Int. Appl. WO 2008011601
52. Herman P, Lin HJ, Lakowicz JR (2003) Lifetime-based imaging. In: Vo-Dinh T (ed) Biomedical photonics handbook. CRC, Boca Raton, pp 9.1–9.30
53. Nagl S, Bauer R, Sauer U, Preininger C, Bogner U, Schäferling M (2008) Microarray analysis of protein-protein interactions based on FRET using subnanosecond-resolved fluorescence lifetime imaging. Biosens Bioelectron 24:397–402
54. Woods RJ, Scypinski S, Cline Love LJ, Ashworth HA (1984) Transient digitizer for the determination of microsecond luminescence lifetimes. Anal Chem 56:1395–1400
55. Hartmann M, Schrenk M, Doettinger A, Nagel S, Roeraade J, Joos TO, Templin MF (2008) Expanding assay dynamics: a combined competitive and direct assay system for the quantification of proteins in multiplexed immunoassays. Clin Chem 54:956–963
56. Cervino C, Sauceda JC, Niessner R, Knopp D (2008) Mycotoxin analysis by automated flow-through immunoassay with chemolumi-nescence readout. Luminescence 23:206–207
57. Roy R, Hohng S, Ha T (2008) A practical guide to single-molecule FRET. Nat Methods 5:507–516
58. Kokko T, Liljenbäck T, Peltola MT, Kokko L, Soukka T (2008) Homogeneous dual-param-eter assay for prostate-specific antigen based on fluorescence resonance energy transfer. Anal Chem 80:9763–9768
59. Kuningas K, Päkkilä H, Ukonaho T, Rantanen T, Lövgren T, Soukka T (2007) Upconversion fluorescence enables homogeneous immunoassay in whole blood. Clin Chem 53: 145–146
60. Campbell RE (2009) Fluorescent-protein-based biosensors: modulation of energy transfer as a design principle. Anal Chem 81:5972–5979
61. Malicka J, Gryczynski I, Fang J, Kusba J, Lakowicz JR (2003) Increased resonance energy transfer between fluorophores bound to DNA in proximity to metallic silver particles. Anal Biochem 315:160–169
62. Rosi NL, Mirkin CA (2005) Nanostructures in biodiagnostics. Chem Rev 105:1547–1562
63. Ray PC, Fortner A, Darbha GK (2006) Gold nanoparticle based FRET assay for the detection of DNA cleavage. J Phys Chem B 110:20745–20748
64. Haas E, Wilchek M, Katchalski-Katzir E, Steinberg IZ (1975) Distribution of end-to-end distances of oligopeptides in solution as estimated by energy transfer. Proc Natl Acad Sci U S A 72:1807–1811
65. Borochov-Neori H, Montal M (1989) Rhodopsin-G-protein interactions monitored by resonance energy transfer. Biochemistry 28:1711–1718
66. Kosk-Kosicka D, Bzdega T, Wawrzynow A (1989) Fluorescence energy transfer studies of purified erythrocyte calcium ATPase. Calcium regulated activation by oligomerization. J Biol Chem 264:19495–19499
67. Ha T, Rasnik I, Cheng W, Babcock HP, Gauss GH, Lohman TM, Chu S (2002) Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase. Nature 419: 638–641
68. Schuler B, Lipman EA, Eaton WA (2002) Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature 419:743–747
69. Kokko T, Kokko L, Soukka T (2009) Terbium(III) chelate as an efficient donor for multiple-wavelength fluorescent acceptors. J Fluoresc 19:159–164
70. Selvin PR (2002) Principles and biophysical applications of lanthanide-based probes. Annu Rev Biophys Biomol Struct 31:275–302
71. Patterson GH, Piston DW, Barisas BG (2000) Förster distances between green fluorescent protein pairs. Anal Biochem 284:438–440
72. Medintz IL, Clapp AR, Melinger JS, Deschamps JR, Mattoussi H (2005) A reagentless biosensing assembly based on quantum dot-donor Förster resonance energy transfer. Adv Mater 17:2450–2455
73. Kim JH, Morikis D, Ozkan M (2004) Adaptation of inorganic quantum dots for stable molecular beacons. Sens Actuators B 102:315–319
74. Selvin PR, Rana TM, Hearst JE (1994) Luminescence resonance energy transfer. J Am Chem Soc 116:6029–6030