Skip to main content

Mechanisms of Signal Transduction

  • Chapter
Introduction to Fluorescence Sensing

Abstract

In previous chapters we discussed two essential functional components of every fluorescence sensor – the binding-recognition units (binders or receptors) and the units providing the response signal (reporters). Here we focus on the coupling between these functionalities. Such coupling must involve signal transduction resulting in changes on target biding of the reporter emission. The coupling mechanisms can be based on the excited-state reactions, such as electron transfer (intramolecular or intermolecular), intramolecular charge transfer, proton transfer or excited-state energy transfer. Conformational changes in receptor unit coupled with target binding may generate the reporter signal if they influence these reactions. In the case of several binding sites coupled with response functionality, nonlinear response functions can be obtained and simple logical operations realized.

How to couple the recognition and reporting functionalities? This is the theme of general discussion at the end of this Chapter with questions and problems addressed to the reader.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.99
Price excludes VAT (USA)
  • Compact, lightweight 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

References

  • Abe R, Ohashi H, Iijima I, Ihara M, Takagi H, Hohsaka T, Ueda H (2011) “Quenchbodies”: quench-based antibody probes that show antigen-dependent fluorescence. J Am Chem Soc 133(43):17386–17394

    Article  CAS  PubMed  Google Scholar 

  • Andréasson J, Pischel U (2010) Smart molecules at work—mimicking advanced logic operations. Chem Soc Rev 39(1):174–188

    Article  PubMed  Google Scholar 

  • Aneja A, Mathur N, Bhatnagar PK, Mathur PC (2008) Triple-FRET technique for energy transfer between conjugated polymer and TAMRA dye with possible applications in medical diagnostics. J Biol Phys 34(5):487–493

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Arnaut LG, Formosinho SJ (1993) Excited-state proton-transfer reactions. 1. Fundamentals and intermolecular reactions. J Photochem Photobiol A Chem 75(1):1–20

    Article  CAS  Google Scholar 

  • Aslan K, Lakowicz JR, Geddes CD (2004) Tunable plasmonic glucose sensing based on the dissociation of Con A-aggregated dextran-coated gold colloids. Anal Chim Acta 517(1–2):139–144

    Article  CAS  Google Scholar 

  • Baek MG, Stevens RC, Charych DH (2000) Design and synthesis of novel glycopolythiophene assemblies for colorimetric detection of influenza virus and E. coli. Bioconjug Chem 11(6):777–788

    Article  CAS  PubMed  Google Scholar 

  • Barbara PF, Gesquiere AJ, Park SJ, Lee YJ (2005) Single-molecule spectroscopy of conjugated polymers. Acc Chem Res 38(7):602–610

    Article  CAS  PubMed  Google Scholar 

  • Beutler M, Makrogianneli K, Vermeij RJ, Keppler M, Ng T, Jovin TM, Heintzmann R (2008) satFRET: estimation of Forster resonance energy transfer by acceptor saturation. Eur Biophys J 38(1):69–82

    Google Scholar 

  • Bhattacharyya K, Chowdhury M (1993) Environmental and magnetic field effects on exciplex and twisted charge transfer emission. Chem Rev 93:507–535

    Article  CAS  Google Scholar 

  • Blough NV, Simpson DJ (1988) Chemically mediated fluorescence yield switching in nitroxide-fluorophore adducts: optical sensors of radical/redox reactions. J Am Chem Soc 110:1915–1917

    Article  CAS  Google Scholar 

  • Bognar B, Osz E, Hideg K, Kalai T (2006) Synthesis of new double (spin and fluorescence) sensor reagents and labels. J Heterocycl Chem 43(1):81–86

    Article  CAS  Google Scholar 

  • Boudier C, Klymchenko AS, Mely Y, Follenius-Wund A (2009) Local environment perturbations in alpha1-antitrypsin monitored by a ratiometric fluorescent label. Photochem Photobiol Sci 8(6):814–821. doi:10.1039/b902309g

    Article  CAS  PubMed  Google Scholar 

  • Bourgeois D, Adam V (2012) Reversible photoswitching in fluorescent proteins: a mechanistic view. IUBMB Life 64(6):482–491. doi:10.1002/iub.1023

    Article  CAS  PubMed  Google Scholar 

  • Bourson J, Pouget J, Valeur B (1993) Ion-responsive fluorescent compounds. 4. Effect of cation binding on the photophysical properties of a coumarin linked to monoaza- and diaza-crown esters. J Phys Chem 97:4552–4557

    Article  CAS  Google Scholar 

  • Brandt O, Hoheisel JD (2004) Peptide nucleic acids on microarrays and other biosensors. Trends Biotechnol 22(12):617–622

    Article  CAS  PubMed  Google Scholar 

  • Bublitz GU, Boxer SG (1997) Stark spectroscopy: applications in chemistry, biology, and materials science. Annu Rev Phys Chem 48:213–242

    Article  CAS  PubMed  Google Scholar 

  • Burda C, Chen XB, Narayanan R, El-Sayed MA (2005) Chemistry and properties of nanocrystals of different shapes. Chem Rev 105(4):1025–1102

    Article  CAS  PubMed  Google Scholar 

  • Castellano FN, Dattelbaum JD, Lakowicz JR (1998) Long-lifetime Ru(II) complexes as labeling reagents for sulfhydryl groups. Anal Biochem 255(2):165–170

    Article  CAS  PubMed  Google Scholar 

  • Chattopadhyay A, London E (1987) Parallax method for direct measurement of membrane penetration depth utilizing fluorescence quenching by spin-labeled phospholipids. Biochemistry 26(1):39–45

    Article  CAS  PubMed  Google Scholar 

  • Cheah IK, Langford SJ, Latter MJ (2005) Concept transfer – from genetic instruction to molecular logic. Supramol Chem 17(1–2):121–128

    Article  CAS  Google Scholar 

  • Chen LH, McBranch DW, Wang HL, Helgeson R, Wudl F, Whitten DG (1999) Highly sensitive biological and chemical sensors based on reversible fluorescence quenching in a conjugated polymer. Proc Natl Acad Sci U S A 96(22):12287–12292

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Chen CY, Cheng CT, Lai CW, Wu PW, Wu KC, Chou PT, Chou YH, Chiu HT (2006) Potassium ion recognition by 15-crown-5 functionalized CdSe/ZnS quantum dots in H2O. Chem Commun 3:263–265

    Article  Google Scholar 

  • Cho YS, Kim KM, Lee D, Kim WJ, Ahn KH (2013) Turn‐on fluorescence detection of apoptotic cells using a zinc (II)‐dipicolylamine‐functionalized poly (diacetylene) liposome. Chem Asian J 8(4):755–759

    Article  CAS  PubMed  Google Scholar 

  • Choi K, Hamilton AD (2001) A dual channel fluorescence chemosensor for anions involving intermolecular excited state proton transfer. Angew Chem Int Ed 40(20):3912–3915

    Article  CAS  Google Scholar 

  • Choi SU, Ryu SY, Yoon SK, Jung NP, Park SH, Kim KH, Choi EJ, Lee CO (1999) Effects of flavonoids on the growth and cell cycle of cancer cells. Anticancer Res 19(6B):5229–5233

    CAS  PubMed  Google Scholar 

  • Claussen JC, Algar WR, Hildebrandt N, Susumu K, Ancona MG, Medintz IL (2013a) Biophotonic logic devices based on quantum dots and temporally-staggered Förster energy transfer relays. Nanoscale 5(24):12156–12170

    Article  CAS  PubMed  Google Scholar 

  • Claussen JC, Hildebrandt N, Susumu K, Ancona MG, Medintz IL (2013b) Complex logic functions implemented with quantum dot bionanophotonic circuits. ACS Appl Mater Interfaces 6(6):3771–3778

    Article  PubMed  CAS  Google Scholar 

  • Cooley LA, Martin VV, Gee KR (2013) Development and in vitro characterization of ratiometric and intensity-based fluorescent ion sensors. In: Chemical neurobiology. Meth Mol Biol v. 995 Springer New York, pp 133–145

    Google Scholar 

  • Daly B, Ling J, de Silva AP (2014) Information gathering and processing with fluorescent molecules. Front Chem Sci Eng 8(2):240–251

    Article  CAS  Google Scholar 

  • Davenport LD, Knutson JR, Brand L (1986) Excited-state proton transfer of equilenin and dihydro equilenin: inreractions with bilayer vesicles. Biochemistry 25:1186–1195

    Article  CAS  PubMed  Google Scholar 

  • de Lorimier RM, Smith JJ, Dwyer MA, Looger LL, Sali KM, Paavola CD, Rizk SS, Sadigov S, Conrad DW, Loew L, Hellinga HW (2002) Construction of a fluorescent biosensor family. Protein Sci 11(11):2655–2675

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • De Schryver FC, Vosch T, Cotlet M, Van der Auweraer M, Mullen K, Hofkens J (2005) Energy dissipation in multichromophoric single dendrimers. Acc Chem Res 38(7):514–522

    Article  PubMed  CAS  Google Scholar 

  • de Silva AP, Uchiyama S (2011) Molecular logic gates and luminescent sensors based on photoinduced electron transfer. In: Luminescence applied in sensor science. Springer Berlin-Heidelberg, pp 1–28

    Google Scholar 

  • de Silva AP, Gunaratne HQN, Gunnaugsson T, Huxley AJM, McRoy CP, Rademacher JT, Rice TE (1997) Signaling recognition events with fluorescent sensors and switches. Chem Rev 97:1515–1566

    Article  PubMed  Google Scholar 

  • de Silva AP, Fox DB, Moody TS, Weir SM (2001) The development of molecular fluorescent switches. Trends Biotechnol 19(1):29–34

    Article  PubMed  Google Scholar 

  • Demchenko AP (2001) Recognition between flexible protein molecules: induced and assisted folding. J Mol Recognit 14(1):42–61

    Article  CAS  PubMed  Google Scholar 

  • Demchenko AP (2006) Visualization and sensing of intermolecular interactions with two-color fluorescent probes. FEBS Lett 580(12):2951–2957

    Article  CAS  PubMed  Google Scholar 

  • Demchenko AP (2009) Introduction to fluorescence sensing. Springer, Amsterdam

    Book  Google Scholar 

  • Demchenko AP (2010) The concept of lambda-ratiometry in fluorescence sensing and imaging. J Fluoresc 20(5):1099–1128

    Article  PubMed  Google Scholar 

  • Demchenko AP (2013) Nanoparticles and nanocomposites for fluorescence sensing and imaging. Meth Appl Fluoresc 1(2):022001

    Article  CAS  Google Scholar 

  • Demchenko AP, Yesylevskyy SO (2009) Nanoscopic description of biomembrane electrostatics: results of molecular dynamics simulations and fluorescence probing. Chem Phys Lipids 160(2):63–84

    Article  CAS  PubMed  Google Scholar 

  • Demchenko AP, Mely Y, Duportail G, Klymchenko AS (2009) Monitoring biophysical properties of lipid membranes by environment-sensitive fluorescent probes. Biophys J 96(9):3461–3470

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Demchenko AP, Tang KC, Chou PT (2013) Excited-state proton coupled charge transfer modulated by molecular structure and media polarization. Chem Soc Rev 42(3):1379–1408. doi:10.1039/c2cs35195a

    Article  CAS  PubMed  Google Scholar 

  • Díaz SA, Giordano L, Jovin TM, Jares-Erijman EA (2012) Modulation of a photoswitchable dual-color quantum dot containing a photochromic FRET acceptor and an internal standard. Nano Lett 12(7):3537–3544. doi:10.1021/nl301093s

    Article  PubMed  CAS  Google Scholar 

  • Dore K, Leclerc M, Boudreau D (2006) Investigation of a fluorescence signal amplification mechanism used for the direct molecular detection of nucleic acids. J Fluoresc 16(2):259–265

    Article  CAS  PubMed  Google Scholar 

  • Dudley AM, Aach J, Steffen MA, Church GM (2002) Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc Natl Acad Sci U S A 99(11):7554–7559

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Elghanian R, Storhoff JJ, Mucic RC, Letsinger RL, Mirkin CA (1997) Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science 277(5329):1078–1081

    Article  CAS  PubMed  Google Scholar 

  • El-Kemary M, Rettig W (2003) Multiple emission in coumarins with heterocyclic substituents. Phys Chem Chem Phys 5:5221–5228

    Article  CAS  Google Scholar 

  • Erbas-Cakmak S, Bozdemir OA, Cakmak Y, Akkaya EU (2013) Proof of principle for a molecular 1: 2 demultiplexer to function as an autonomously switching theranostic device. Chem Sci 4(2):858–862. doi:10.1039/c2sc21499g

    Article  CAS  Google Scholar 

  • Fan J, Hu M, Zhan P, Peng X (2013) Energy transfer cassettes based on organic fluorophores: construction and applications in ratiometric sensing. Chem Soc Rev 42(1):29–43

    Article  CAS  PubMed  Google Scholar 

  • Fonin AV, Stepanenko OV, Povarova OI, Volova CA, Philippova EM, Bublikov GS, Kuznetsova IM, Demchenko AP, Turoverov KK (2014) Spectral characteristics of the mutant form GGBP/H152C of D-glucose/D-galactose-binding protein labeled with fluorescent dye BADAN: influence of external factors. PeerJ 2:e275

    Article  PubMed Central  PubMed  Google Scholar 

  • Formosinho SJ, Arnaut LG (1993) Excited-state proton-transfer reactions. 2. Intramolecular reactions. J Photochem Photobiol A Chem 75(1):21–48

    Article  CAS  Google Scholar 

  • Gilardi G, Zhou LQ, Hibbert L, Cass AE (1994) Engineering the maltose binding protein for reagentless fluorescence sensing. Anal Chem 66(21):3840–3847

    Article  CAS  PubMed  Google Scholar 

  • Giordano L, Jovin TM, Irie M, Jares-Erijman EA (2002) Diheteroarylethenes as thermally stable photoswitchable acceptors in photochromic fluorescence resonance energy transfer (pcFRET). J Am Chem Soc 124(25):7481–7489. doi:ja016969k [pii]

    Google Scholar 

  • Grabowski ZR, Rotkiewicz K, Rettig W (2003) Structural changes accompanying intramolecular charge transfer: focus on twisted intramolecular charge transfer states and structures. Chem Rev 103:3899–4031

    Article  PubMed  Google Scholar 

  • Granda-Valdes M, Badia R, Pina-Luis G, Diaz-Garcia ME (2000) Photoinduced electron transfer systems and their analytical application in chemical sensing. Quim Anal 19:38–53

    CAS  Google Scholar 

  • Grynkiewicz G, Poenie M, Tsien RY (1985) A new generation of Ca2+ indicators with greatly improved fluorescence properties. J Biol Chem 260(6):3440–3450

    CAS  PubMed  Google Scholar 

  • Guliyev R, Coskun A, Akkaya EU (2009) Design strategies for ratiometric chemosensors: modulation of excitation energy transfer at the energy donor site. J Am Chem Soc 131(25):9007–9013

    Article  CAS  PubMed  Google Scholar 

  • Gust D, Moore TA, Moore AL (2006) Molecular switches controlled by light. Chem Commun 11:1169–1178

    Article  Google Scholar 

  • Ha JH, Loh SN (2012) Protein conformational switches: from nature to design. Chemistry A Eur J 18(26):7984–7999

    Article  CAS  Google Scholar 

  • Heinlein T, Knemeyer J-P, Piestert O, Sauer M (2003) Photoinduced electron transfer between fluorescent dyes and guanosine residues in DNA-hairpins. J Phys Chem B 107:7957–7964

    Article  CAS  Google Scholar 

  • Henary MM, Wu YG, Cody J, Sumalekshmy S, Li J, Mandal S, Fahrni CJ (2007) Excited-state intramolecular proton transfer in 2-(2'-arylsulfonamidophenyl)benzimidazole derivatives: the effect of donor and acceptor substituents. J Org Chem 72(13):4784–4797

    Article  CAS  PubMed  Google Scholar 

  • Herland A, Thomsson D, Mirzov O (2008) Decoration of amyloid fibrils with luminescent conjugated polymers. J Mater Chem 18:126–132

    Article  CAS  Google Scholar 

  • Hermann T, Patel DJ (2000) Biochemistry – adaptive recognition by nucleic acid aptamers. Science 287(5454):820–825

    Article  CAS  PubMed  Google Scholar 

  • Hettie KS, Klockow JL, Glass TE (2014) Three-input logic gates with potential applications for neuronal imaging. J Am Chem Soc 136(13):4877–4880

    Article  CAS  PubMed  Google Scholar 

  • Ho HA, Leclerc M (2004) Optical sensors based on hybrid aptamer/conjugated polymer complexes. J Am Chem Soc 126(5):1384–1387

    Article  CAS  PubMed  Google Scholar 

  • Hochreiner H, Sanchez-Barragan I, Costa-Fernandez JM, Sanz-Medel A (2005) Dual emission probe for luminescence oxygen sensing: a critical comparison between intensity, lifetime and ratiometric measurements. Talanta 66(3):611–618

    Article  CAS  PubMed  Google Scholar 

  • Huang J, Peng AD, Fu HB, Ma Y, Zhai TY, Yao JN (2006) Temperature-dependent ratiometric fluorescence from an organic aggregates system. J Phys Chem A 110(29):9079–9083

    Article  CAS  PubMed  Google Scholar 

  • Jans H, Huo Q (2012) Gold nanoparticle-enabled biological and chemical detection and analysis. Chem Soc Rev 41(7):2849–2866

    Article  CAS  PubMed  Google Scholar 

  • Jares-Erijman EA, Jovin TM (2003) FRET imaging. Nat Biotechnol 21(11):1387–1395

    Article  CAS  PubMed  Google Scholar 

  • Jeong H-J, Ueda H (2014) Strategy for making a superior Quenchbody to proteins: effect of the fluorophore position. Sensors 14(7):13285–13297

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Jiang H, Zhao XY, Schanze KS (2007) Effects of polymer aggregation and quencher size on amplified fluorescence quenching of conjugated polyelectrolytes. Langmuir 23(18):9481–9486

    Article  CAS  PubMed  Google Scholar 

  • Johansson MK, Cook RM (2003) Intramolecular dimers: a new design strategy for fluorescence-quenched probes. Chemistry 9(15):3466–3471. doi:10.1002/chem.200304941

    Article  CAS  PubMed  Google Scholar 

  • Jones RM, Bergstedt TS, Buscher CT, McBranch D, Whitten D (2001) Superquenching and its applications in J-aggregated cyanine polymers. Langmuir 17(9):2568–2571

    Article  CAS  Google Scholar 

  • Kasha M (1986) Proton-transfer spectroscopy – perturbation of the tautomerization potential. J Chem Soc Faraday Trans II 82:2379–2392

    Article  CAS  Google Scholar 

  • Kim S, Pudavar HE, Prasad PN (2006) Dye-concentrated organically modified silica nanoparticles as a ratiometric fluorescent pH probe by one- and two-photon excitation. Chem Commun (Camb) 19:2071–2073

    Article  CAS  Google Scholar 

  • Klymchenko AS, Demchenko AP (2002) Electrochromic modulation of excited-state intramolecular proton transfer: the new principle in design of fluorescence sensors. J Am Chem Soc 124(41):12372–12379

    Article  CAS  PubMed  Google Scholar 

  • Knemeyer JP, Marme N, Sauer M (2000) Probes for detection of specific DNA sequences at the single-molecule level. Anal Chem 72(16):3717–3724

    Article  CAS  PubMed  Google Scholar 

  • Kohn JE, Plaxco KW (2005) Engineering a signal transduction mechanism for protein-based biosensors. Proc Natl Acad Sci U S A 102(31):10841–10845

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kollmannsberger M, Rurack K, Resch-Genger U, Daub J (1998) Ultrafast charge transfer in amino-substituted boron dipyrromethene dyes and its inhibition by cation complexation: a new design concept for highly sensitive fluorescent probes. J Phys Chem A 102(50):10211–10220

    Article  CAS  Google Scholar 

  • Koner AL, Schatz J, Nau WM, Pischel U (2007) Selective sensing of citrate by a supramolecular 1,8-naphthalimide/calix[4]arene assembly via complexation-modulated pK(a) shifts in a ternary complex. J Org Chem 72(10):3889–3895

    Article  CAS  PubMed  Google Scholar 

  • Kwon JE, Park SY (2011) Advanced organic optoelectronic materials: harnessing Excited‐State Intramolecular Proton Transfer (ESIPT) process. Adv Mater 23(32):3615–3642

    Article  CAS  PubMed  Google Scholar 

  • Laws WR, Brand L (1979) Analysis of two-state excited-state reactions. The fluorescence decay of 2-naphthol. J Phys Chem 83:795–802

    Google Scholar 

  • Li C, Numata M, Takeuchi M, Shinkai S (2005) A sensitive colorimetric and fluorescent probe based on a polythiophene derivative for the detection of ATP. Angew Chem Int Ed Engl 44(39):6371–6374

    Article  CAS  PubMed  Google Scholar 

  • Li Q, Zhang J, Sun W, Yu J, Wu C, Qin W, Chiu DT (2014) Europium-complex grafted polymer dots for amplified quenching and cellular imaging applications. Langmuir 30(28), 8607–8614

    Google Scholar 

  • Liu J, Lee JH, Lu Y (2007) Quantum dot encoding of aptamer-linked nanostructures for one-pot simultaneous detection of multiple analytes. Anal Chem 79(11):4120–4125

    Article  CAS  PubMed  Google Scholar 

  • Lozinsky E, Martin VV, Berezina TA, Shames AI, Weis AL, Likhtenshtein GI (1999) Dual fluorophore-nitroxide probes for analysis of vitamin C in biological liquids. J Biochem Biophys Methods 38(1):29–42

    Article  CAS  PubMed  Google Scholar 

  • Lu L, Helgeson R, Jones RM, McBranch D, Whitten D (2002) Superquenching in cyanine pendant poly(L-lysine) dyes: dependence on molecular weight, solvent, and aggregation. J Am Chem Soc 124(3):483–488

    Article  CAS  PubMed  Google Scholar 

  • Magri DC, Brown GJ, McClean GD, de Silva AP (2006) Communicating chemical congregation: a molecular AND logic gate with three chemical inputs as a “lab-on-a-molecule” prototype. J Am Chem Soc 128(15):4950–4951

    Article  CAS  PubMed  Google Scholar 

  • Magri DC, Vance TP, de Silva AP (2007) From complexation to computation: recent progress in molecular logic. Inorg Chim Acta 360(3):751–764

    Article  CAS  Google Scholar 

  • Margulies D, Felder CE, Melman G, Shanzer A (2007) A molecular keypad lock: a photochemical device capable of authorizing password entries. J Am Chem Soc 129(2):347–354

    Article  CAS  PubMed  Google Scholar 

  • Marme N, Knemeyer JP, Sauer M, Wolfrum J (2003) Inter- and intramolecular fluorescence quenching of organic dyes by tryptophan. Bioconjug Chem 14(6):1133–1139

    Article  CAS  PubMed  Google Scholar 

  • Marras SA (2006) Selection of fluorophore and quencher pairs for fluorescent nucleic acid hybridization probes. Methods Mol Biol 335:3–16

    CAS  PubMed  Google Scholar 

  • Matsushita M, Meijler MM, Wirsching P, Lerner RA, Janda KD (2005) A blue fluorescent anti body-cofactor sensor for mercury. Org Lett 7(22):4943–4946

    Article  CAS  PubMed  Google Scholar 

  • Medintz IL, Deschamps JR (2006) Maltose-binding protein: a versatile platform for prototyping biosensing. Curr Opin Biotechnol 17(1):17–27

    Article  CAS  PubMed  Google Scholar 

  • Medintz IL, Goldman ER, Lassman ME, Mauro JM (2003) A fluorescence resonance energy transfer sensor based on maltose binding protein. Bioconjug Chem 14(5):909–918

    Article  CAS  PubMed  Google Scholar 

  • Minta A, Kao JP, Tsien RY (1989) Fluorescent indicators for cytosolic calcium based on rhodamine and fluorescein chromophores. J Biol Chem 264(14):8171–8178

    CAS  PubMed  Google Scholar 

  • Miyawaki A, Llopis J, Heim R, McCaffery JM, Adams JA, Ikura M, Tsien RY (1997) Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin. Nature 388(6645):882–887

    Article  CAS  PubMed  Google Scholar 

  • Miyawaki A, Griesbeck O, Heim R, Tsien RY (1999) Dynamic and quantitative Ca2+ measurements using improved cameleons. Proc Natl Acad Sci U S A 96(5):2135–2140

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mordon S, Devoisselle JM, Soulie S (1995) Fluorescence spectroscopy of pH in vivo using a dual-emission fluorophore (C-SNAFL-1). J Photochem Photobiol B 28(1):19–23

    Article  CAS  PubMed  Google Scholar 

  • Nilsson KPR, Inganas O (2004) Optical emission of conjugated polyuelectrolite. Calcium-induced conformational changes in calmodulin and calmodulin-calcineurin interactions. Macromolecules 37:9109–9113

    Article  CAS  Google Scholar 

  • Nilsson KP, Rydberg J, Baltzer L, Inganas O (2003) Self-assembly of synthetic peptides control conformation and optical properties of a zwitterionic polythiophene derivative. Proc Natl Acad Sci U S A 100(18):10170–10174

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • O’Neal DP, Meledeo MA, Davis JR, Ibey BL, Gant VA, Pishko MV, Cote GL (2004) Oxygen sensor based on the fluorescence quenching of a ruthenium complex immobilized in a biocompatible poly(ethylene glycol) hydrogel. IEEE Sens J 4(6):728–734

    Article  CAS  Google Scholar 

  • Okamoto A, Tanaka K, Saito I (2004) DNA logic gates. J Am Chem Soc 126(30):9458–9463

    Article  CAS  PubMed  Google Scholar 

  • Papkovsky DB, O'Riordan TC (2005) Emerging applications of phosphorescent metalloporphyrins. J Fluoresc 15(4):569–584

    Article  CAS  PubMed  Google Scholar 

  • Pecher J, Mecking S (2010) Nanoparticles of conjugated polymers. Chem Rev 110(10):6260–6279

    Article  CAS  PubMed  Google Scholar 

  • Perez-Inestrosa E, Montenegro JM, Collado D, Suau R, Casado J (2007) Molecules with multiple light-emissive electronic excited states as a strategy toward molecular reversible logic gates. J Phys Chem C 111(18):6904–6909

    Article  CAS  Google Scholar 

  • Petitjean A, Lehn JM (2007) Conformational switching of the pyridine-pyrimidine-pyridine scaffold for ion-controlled FRET. Inorg Chim Acta 360(3):849–856

    Article  CAS  Google Scholar 

  • Pickup JC, Khan F, Zhi Z-L, Coulter J, Birch DJ (2013) Fluorescence intensity-and lifetime-based glucose sensing using glucose/galactose-binding protein. J Diabetes Sci Technol 7(1):62–71

    Article  PubMed Central  PubMed  Google Scholar 

  • Pivovarenko VG, Klueva AV, Doroshenko AO, Demchenko AP (2000) Bands separation in fluorescence spectra of ketocyanine dyes: evidence for their complex formation with monohydric alcohols. Chem Phys Lett 325(4):389–398

    Article  CAS  Google Scholar 

  • Plaxco KW, Soh HT (2011) Switch-based biosensors: a new approach towards real-time, in vivo molecular detection. Trends Biotechnol 29(1):1–5

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Povrozin YA, Markova LI, Tatarets AL, Sidorov VI, Terpetschnig EA, Patsenker LD (2009) Near-infrared, dual-ratiometric fluorescent label for measurement of pH. Anal Biochem 390(2):136–140

    Article  CAS  PubMed  Google Scholar 

  • Pu F, Ren J, Qu X (2014) “Plug and play” logic gates based on fluorescence switching regulated by self-assembly of nucleotide and lanthanide ions. ACS Appl Mater Interfaces 6(12):9557–9562

    Article  CAS  PubMed  Google Scholar 

  • Puleo CM, Liu K, Wang TH (2006) Pushing miRNA quantification to the limits: high-throughput miRNA gene expression analysis using single-molecule detection. Nanomedicine 1(1):123–127

    Article  CAS  PubMed  Google Scholar 

  • Raymo FM, Yildiz I (2007) Luminescent chemosensors based on semiconductor quantum dots. Phys Chem Chem Phys 9(17):2036–2043

    Article  CAS  PubMed  Google Scholar 

  • Roshal AD, Grigorovich AV, Doroshenko AO, Pivovarenko VG, Demchenko AP (1998) Flavonols and crown-flavonols as metal cation chelators. The different nature of Ba2+ and Mg2+ complexes. J Phys Chem A 102(29):5907–5914

    Article  CAS  Google Scholar 

  • Roshal AD, Grigorovich AV, Doroshenko AO, Pivovarenko VG, Demchenko AP (1999) Flavonols as metal-ion chelators: complex formation with Mg2+ and Ba2+ cations in the excited state. J Photochem Photobiol A Chem 127(1–3):89–100

    Article  CAS  Google Scholar 

  • Rurack K (2001) Flipping the light switch ‘on’ – the design of sensor molecules that show cation-induced fluorescence enhancement with heavy and transition metal ions. Spectrochim Acta A 57:2161–2195

    Article  CAS  Google Scholar 

  • Rurack K, Danel A, Rotkiewicz K, Grabka D, Spieles M, Rettig W (2002) 1,3-Diphenyl-1H-pyrazolo[3,4-b]quinoline: a versatile fluorophore for the design of brightly emissive molecular sensors. Org Lett 4(26):4647–4650

    Article  CAS  PubMed  Google Scholar 

  • Saha K, Agasti SS, Kim C, Li X, Rotello VM (2012) Gold nanoparticles in chemical and biological sensing. Chem Rev 112(5):2739–2779

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Schazmann B, Alhashimy N, Diamond D (2006) Chloride selective calix[4]arene optical sensor combining urea functionality with pyrene excimer transduction. J Am Chem Soc 128(26):8607–8614

    Article  CAS  PubMed  Google Scholar 

  • Shynkar VV, Klymchenko AS, Piemont E, Demchenko AP, Mely Y (2004) Dynamics of intermolecular hydrogen bonds in the excited states of 4'-dialkylamino-3-hydroxyflavones. On the pathway to an ideal fluorescent hydrogen bonding sensor. J Phys Chem A 108(40):8151–8159

    Article  CAS  Google Scholar 

  • Simeonov A, Matsushita M, Juban EA, Thompson EHZ, Hoffman TZ, Beuscher AE, Taylor MJ, Wirsching P, Rettig W, McCusker JK, Stevens RC, Millar DP, Schultz PG, Lerner RA, Janda KD (2000) Blue-fluorescent antibodies. Science 290(5490):307–313

    Article  CAS  PubMed  Google Scholar 

  • Snee PT, Somers RC, Nair G, Zimmer JP, Bawendi MG, Nocera DG (2006) A ratiometric CdSe/ZnS nanocrystal pH sensor. J Am Chem Soc 128(41):13320–13321

    Article  CAS  PubMed  Google Scholar 

  • Stojanovic MN, Kolpashchikov DM (2004) Modular aptameric sensors. J Am Chem Soc 126(30):9266–9270

    Article  CAS  PubMed  Google Scholar 

  • Stojanovic MN, Stefanovic D (2003) Deoxyribozyme-based half-adder. J Am Chem Soc 125(22):6673–6676

    Article  CAS  PubMed  Google Scholar 

  • 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(7):883–887

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Straight SD, Liddell PA, Terazono Y, Moore TA, Moore AL, Gust D (2007) All-photonic molecular XOR and NOR logic gates based on photochemical control of fluorescence in a fulgimide-porphyrin-dithienylethene triad. Adv Funct Mater 17(5):777–785

    Article  CAS  Google Scholar 

  • Subach FV, Verkhusha VV (2012) Chromophore transformations in red fluorescent proteins. Chem Rev 112(7):4308–4327

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sumalekshmy S, Henary MM, Siegel N, Lawson PV, Wu Y, Schmidt K, Bredas JL, Perry JW, Fahrni CJ (2007) Design of emission ratiometric metal-ion sensors with enhanced two-photon cross section and brightness. J Am Chem Soc 129(39):11888

    Article  CAS  PubMed  Google Scholar 

  • Szacilowski K (2012) Infochemistry: information processing at the nanoscale. John Wiley & Sons., Chichester, West Sussex, UK

    Google Scholar 

  • Tainaka K, Sakaguchi R, Hayashi H, Nakano S, Liew FF, Morii T (2010) Design strategies of fluorescent biosensors based on biological macromolecular receptors. Sensors 10(2):1355–1376

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Takakusa H, Kikuchi K, Urano Y, Kojima H, Nagano T (2003) A novel design method of ratiometric fluorescent probes based on fluorescence resonance energy transfer switching by spectral overlap integral. Chemistry 9(7):1479–1485

    Article  CAS  PubMed  Google Scholar 

  • Thurley S, Roglin L, Seitz O (2007) Hairpin peptide beacon: dual-labeled PNA-peptide-hybrids for protein detection. J Am Chem Soc 129(42):12693

    Article  CAS  PubMed  Google Scholar 

  • Tomasulo M, Yildiz I, Kaanumalle SL, Raymo FM (2006) pH-sensitive ligand for luminescent quantum dots. Langmuir 22(24):10284–10290

    Article  CAS  PubMed  Google Scholar 

  • Tyagi S, Kramer FR (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 14(3):303–308

    Article  CAS  PubMed  Google Scholar 

  • Ueberfeld J, Walt DR (2004) Reversible ratiometric probe for quantitative DNA measurements. Anal Chem 76(4):947–952

    Article  CAS  PubMed  Google Scholar 

  • Valentini P, Pompa PP (2013) Gold nanoparticles for naked-eye DNA detection: smart designs for sensitive assays. RSC Adv 3(42):19181–19190

    Article  CAS  Google Scholar 

  • Valeur B (2002) Molecular fluorescence. Wiley VCH, Weinheim

    Google Scholar 

  • Valeur B, Leray I (2000) Design principles of fluorescent molecular sensors for cation recognition. Coord Chem Rev 205:3–40

    Article  CAS  Google Scholar 

  • Valeur B, Leray I (2007) Ion-responsive supramolecular fluorescent systems based on multichromophoric calixarenes: a review. Inorg Chim Acta 360(3):765–774

    Article  CAS  Google Scholar 

  • Van Munster EB, Kremers GJ, Adjobo-Hermans MJ, Gadella TW Jr (2005) Fluorescence resonance energy transfer (FRET) measurement by gradual acceptor photobleaching. J Microsc 218(Pt 3):253–262

    Article  PubMed  Google Scholar 

  • Walkup GK, Imperiali B (1996) Design and evaluation of a peptidyl fluorescent chemosensor for divalent zinc. J Am Chem Soc 118:3053–3054

    Article  CAS  Google Scholar 

  • Wang S-L, Lee T-C, Ho T-I (2002) Excited state proton transfer and steric effect on the hydrogen bonding interaction of the styrylquinoline system. J Photochem Photobiol A Chem 151:21–26

    Article  CAS  Google Scholar 

  • Wang S, Gaylord BS, Bazan GC (2004) Fluorescein provides a resonance gate for FRET from conjugated polymers to DNA intercalated dyes. J Am Chem Soc 126(17):5446–5451

    Article  CAS  PubMed  Google Scholar 

  • Whitaker JE, Haugland RP, Prendergast FG (1991) Spectral and photophysical studies of benzo[c]xanthene dyes: dual emission pH sensors. Anal Biochem 194(2):330–344

    Article  CAS  PubMed  Google Scholar 

  • Wu J, Zou Y, Li C, Sicking W, Piantanida I, Yi T, Schmuck C (2012) A molecular peptide beacon for the ratiometric sensing of nucleic acids. J Am Chem Soc 134(4):1958–1961

    Article  CAS  PubMed  Google Scholar 

  • Yang RH, Chan WH, Lee AWM, Xia PF, Zhang HK, Li KA (2003) A ratiometric fluorescent sensor for Ag-1 with high selectivity and sensitivity. J Am Chem Soc 125(10):2884–2885

    Article  CAS  PubMed  Google Scholar 

  • Yao S, Schafer-Hales KJ, Belfield KD (2007) A new water-soluble near-neutral ratiometric fluorescent pH indicator. Org Lett 9(26):5645–5648

    Article  CAS  PubMed  Google Scholar 

  • Yashchuk VMN, Syromyatnikov VG, Ogul’chansky TY, Kolendo AY, Prot T, Blazejowski J, Kudrya VY (2000) Multifunctional macromolecules and structures as one-way exciton conductors. Mol Cryst Liq Cryst 353:287–300

    Article  CAS  Google Scholar 

  • Yashchuk V, Kudrya V, Losytskyy M, Suga H, Ohul'chanskyy T (2006) The nature of the electronic excitations capturing centres in the DNA. J Mol Liq 127(1–3):79–83

    Article  CAS  Google Scholar 

  • Yatsuhashi T, Nakajima Y, Shimada T, Tachibana H, Inoue H (1998) Molecular mechanism for the radationless deactivation of the interamolecular charge-transfer excited singlet state of aminofluorenones through hydrogen bonds with alcohols. J Phys Chem A 102:8657–8663

    Article  CAS  Google Scholar 

  • Yesylevskyy SO, Kharkyanen VN, Demchenko AP (2006) The change of protein intradomain mobility on ligand binding: is it a commonly observed phenomenon? Biophys J 91(8):3002–3013

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Yesylevskyy SO, Kharkyanen VN, Demchenko AP (2007) The blind search for the closed states of hinge-bending proteins. Proteins 71(2):831–843

    Article  CAS  Google Scholar 

  • Yguerabide J, Yguerabide EE (1998) Light-scattering submicroscopic particles as highly fluorescent analogs and their use as tracer labels in clinical and biological applications – II. Experimental characterization. Anal Biochem 262(2):157–176

    Article  CAS  PubMed  Google Scholar 

  • Yoshida W, Yokobayashi Y (2007) Photonic boolean logic gates based on DNA aptamers. Chem Commun 2:195–197

    Article  Google Scholar 

  • Yoshihara T, Galievsky VA, Druzhinin SI, Saha S, Zachariasse KA (2003) Singlet excited state dipole moments of dual fluorescent N-phenylpyrroles and 4-(dimethylamino)benzonitrile from solvatochromic and thermochromic spectral shifts. Photochem Photobiol Sci 2:342–353

    Article  CAS  PubMed  Google Scholar 

  • Yuan MS, Liu ZQ, Fang Q (2007) Donor-and-acceptor substituted truxenes as multifunctional fluorescent probes. J Org Chem 72(21):7915–7922

    Article  CAS  PubMed  Google Scholar 

  • Zhou YC, Zhang DQ, Zhang YZ, Tang YL, Zhu DB (2005) Tuning the CD spectrum and optical rotation value of a new binaphthalene molecule with two spiropyran units: mimicking the function of a molecular “AND” logic gate and a new chiral molecular switch. J Org Chem 70(16):6164–6170

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Demchenko, A.P. (2015). Mechanisms of Signal Transduction. In: Introduction to Fluorescence Sensing. Springer, Cham. https://doi.org/10.1007/978-3-319-20780-3_8

Download citation

Publish with us

Policies and ethics