Abstract
Recognition units are the key functional units of molecular sensors that are responsible for selective target recognition in the proper range of target concentrations. Multi-point non-covalent interactions with the target with desired affinity allow providing selective target binding from a mixture of different and sometimes closely related compounds. In this Chapter we discuss different binding units and the principles of their design, construction and performance. They range from small coordination compounds targeting small molecules and ions to macromolecules such as enzyme substrates, proteins, nucleic acids, macromolecular assemblies or even the living cells. Most versatile and efficient of them are the antibodies and their short fragments and nucleic acid aptamers. Different ligand binding proteins are efficient addressing specific targets, and peptide nucleic acids became the basis of new technologies of DNA detection. The readier is requested to perform several tasks and respond to several questions at the end of this Chapter.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Al Attar HA, Norden J, O‘Brien S, Monkman AP (2008) Improved single nucleotide polymorphisms detection using conjugated polymer/surfactant system and peptide nucleic acid. Biosens Bioelectron 23(10):1466–1472
Alexander C, Andersson HS, Andersson LI, Ansell RJ, Kirsch N, Nicholls IA, O‘Mahony J, Whitcombe MJ (2006) Molecular imprinting science and technology: a survey of the literature for the years up to and including 2003. J Mol Recognit 19(2):106–180
Al-Hassan KA, Khanfer MF (1998) Fluorescence probes for cyclodextrin interiors. J Fluoresc 8(2):139–152
Azzazy HM, Highsmith WE Jr (2002) Phage display technology: clinical applications and recent innovations. Clin Biochem 35(6):425–445
Badjic JD, Nelson A, Cantrill SJ, Turnbull WB, Stoddart JF (2005) Multivalency and cooperativity in supramolecular chemistry. Acc Chem Res 38(9):723–732
Baker ES, Hong JW, Gaylord BS, Bazan GC, Bowers MT (2006) PNA/dsDNA complexes: site specific binding and dsDNA biosensor applications. J Am Chem Soc 128(26):8484–8492
Balabai N, Linton B, Napper A, Priyadarshy S, Sukharevsky AP, Waldeck DH (1998) Orientational dynamics of beta-cyclodextrin inclusion complexes. J Phys Chem B 102(48):9617–9624
Barthe P, Cohen-Gonsaud M, Aldrian-Herrada G, Chavanieu A, Labesse G, Roumestand C (2004) Design of an amphipathic alpha-helical hairpin peptide. C R Chim 7(3–4):249–252
Benhar I (2007) Design of synthetic antibody libraries. Expert Opin Biol Ther 7(5):763–779
Bethge L, Jarikote DV, Seitz O (2008) New cyanine dyes as base surrogates in PNA: forced intercalation probes (FIT-probes) for homogeneous SNP detection. Bioorg Med Chem 16(1):114–125
Biedermann F, Elmalem E, Ghosh I, Nau WM, Scherman OA (2012) Strongly fluorescent, switchable perylene bis(diimide) host-guest complexes with cucurbit[8]uril in water. Angew Chem Int Ed Engl. doi:10.1002/anie.201205393
Binz HK, Pluckthun A (2005) Engineered proteins as specific binding reagents. Curr Opin Biotechnol 16(4):459–469
Binz HK, Amstutz P, Pluckthun A (2005) Engineering novel binding proteins from nonimmunoglobulin domains. Nat Biotechnol 23(10):1257–1268
Bishop KJ, Wilmer CE, Soh S, Grzybowski BA (2009) Nanoscale forces and their uses in self‐assembly. Small 5(14):1600–1630
Boersma YL, Plückthun A (2011) DARPins and other repeat protein scaffolds: advances in engineering and applications. Curr Opin Biotechnol 22(6):849–857
Breslow R, Dong SD (1998) Biomimetic reactions catalyzed by cyclodextrins and their derivatives. Chem Rev 98(5):1997–2011
Brune M, Hunter JL, Corrie JET, Webb MR (1994) Direct, real-time measurement of rapid inorganic phosphate release using a novel fluorescent probe and its application to actomyosin subfragment 1 ATPase. Biochemistry 33:8262–8271
Butler RS, Myers AK, Bellarmine P, Abboud KA, Castellano RK (2007) Highly fluorescent donor-acceptor purines. J Mater Chem 17(19):1863–1865
Casadei J, Powell MJ, Kenten JH (1990) Expression and secretion of aequorin as a chimeric antibody by means of a mammalian expression vector. Proc Natl Acad Sci U S A 87(6):2047–2051
Chen CT, Huang WP (2002) A highly selective fluorescent chemosensor for lead ions. J Am Chem Soc 124(22):6246–6247
Chmielewski MJ, Buhler E, Candau J, Lehn JM (2014) Multivalency by self‐assembly: binding of concanavalin A to metallosupramolecular architectures decorated with Multiple Carbohydrate Groups. Chemistry 20(23):6960–6977
Choulier L, Enander K (2010) Environmentally sensitive fluorescent sensors based on synthetic peptides. Sensors 10(4):3126–3144
Choulier L, Shvadchak VV, Naidoo A, Klymchenko AS, Mely Y, Altschuh D (2010) A peptide-based fluorescent ratiometric sensor for quantitative detection of proteins. Anal Biochem 401(2):188–195
Collett JR, Cho EJ, Ellington AD (2005) Production and processing of aptamer microarrays. Methods 37(1):4–15
Cox WG, Singer VL (2004) Fluorescent DNA hybridization probe preparation using amine modification and reactive dye coupling. Biotechniques 36(1):114–122
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
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
Demchenko AP (2001a) Concepts and misconcepts in the analysis of simple kinetics of protein folding. Curr Protein Pept Sci 2(1):73–98
Demchenko AP (2001b) Recognition between flexible protein molecules: induced and assisted folding. J Mol Recognit 14(1):42–61
Demchenko AP, Chinarov VA (1999) Tolerance of protein structures to the changes of amino acid sequences and their interactions. The nature of the folding code. Protein Pept Lett 6(3):115–129
Descalzo AB, Somoza C, Moreno-Bondi MC, Orellana G (2013) Luminescent core–shell imprinted nanoparticles engineered for targeted förster resonance energy transfer-based sensing. Anal Chem 85(11):5316–5320
Douhal A (2004) Ultrafast guest dynamics in cyclodextrin nanocavities. Chem Rev 104(4):1955–1976
Dsouza RN, Pischel U, Nau WM (2011) Fluorescent dyes and their supramolecular host/guest complexes with macrocycles in aqueous solution. Chem Rev 111(12):7941–7980
Dwyer MA, Hellinga HW (2004) Periplasmic binding proteins: a versatile superfamily for protein engineering. Curr Opin Struct Biol 14(4):495–504
Edwards BM, Barash SC, Main SH, Choi GH, Minter R, Ullrich S, Williams E, Du Fou L, Wilton J, Albert VR, Ruben SM, Vaughan TJ (2003) The remarkable flexibility of the human antibody repertoire; isolation of over one thousand different antibodies to a single protein, BLyS. J Mol Biol 334(1):103–118
Eklund M, Axelsson L, Uhlen M, Nygren PA (2002) Anti-idiotypic protein domains selected from protein A-based affibody libraries. Proteins Struct Funct Genet 48(3):454–462
Enander K, Dolphin GT, Andersson LK, Liedberg B, Lundstrom I, Baltzer L (2002) Designed, folded polypeptide scaffolds that combine key biosensing events of recognition and reporting. J Org Chem 67(9):3120–3123
Enander K, Dolphin GT, Baltzer L (2004a) Designed, functionalized helix-loop-helix motifs that bind human carbonic anhydrase II: a new class of synthetic receptor molecules. J Am Chem Soc 126(14):4464–4465
Enander K, Dolphin GT, Liedberg B, Lundstrom I, Baltzer L (2004b) A versatile polypeptide platform for integrated recognition and reporting: affinity arrays for protein-ligand interaction analysis. Chemistry 10(10):2375–2385
Enander K, Choulier L, Olsson AL, Yushchenko DA, Kanmert D, Klymchenko AS, Demchenko AP, Mely Y, Altschuh D (2008) A peptide-based, ratiometric biosensor construct for direct fluorescence detection of a protein analyte. Bioconjug Chem 19(9):1864–1870
Engfeldt T, Renberg B, Brumer H, Nygren PA, Karlstrom AE (2005) Chemical synthesis of triple-labelled three-helix bundle binding proteins for specific fluorescent detection of unlabelled protein. Chembiochem 6(6):1043–1050
Fasting C, Schalley CA, Weber M, Seitz O, Hecht S, Koksch B, Dernedde J, Graf C, Knapp EW, Haag R (2012) Multivalency as a chemical organization and action principle. Angew Chem Int Ed 51(42):10472–10498
Flores S, Echols N, Milburn D, Hespenheide B, Keating K, Lu J, Wells S, Yu EZ, Thorpe M, Gerstein M (2006) The database of macromolecular motions: new features added at the decade mark. Nucleic Acids Res 34:D296–D301
Flower DR, North ACT, Sansom CE (2000) The lipocalin protein family: structural and sequence overview. Biochim Biophys Acta Protein Struct Mol Enzymol 1482(1–2):9–24
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
Gellman SH, Woolfson DN (2002) Mini-proteins Trp the light fantastic. Nat Struct Biol 9(6):408–410
Gilardi G, Zhou LQ, Hibbert L, Cass AEG (1994) Engineering the maltose-binding protein for reagentless fluorescence sensing. Anal Chem 66(21):3840–3847
Glasner ME, Gerlt JA, Babbitt PC (2007) Mechanisms of protein evolution and their application to protein engineering. Adv Enzymol Relat Areas Mol Biol 75:193–239, xii–xiii
Gomara MJ, Haro I (2007) Synthetic peptides for the immunodiagnosis of human diseases. Curr Med Chem 14(5):531–546
Goodchild S, Love T, Hopkins N, Mayers C (2006) Engineering antibodies for biosensor technologies. Adv Appl Microbiol 58:185–226
Gopinath SCB (2007) Methods developed for SELEX. Anal Bioanal Chem 387(1):171–182
Gopinath SC, Tang T-H, Citartan M, Chen Y, Lakshmipriya T (2014) Current aspects in immunosensors. Biosens Bioelectron 57:292–302
Guntas G, Ostermeier M (2004) Creation of an allosteric enzyme by domain insertion. J Mol Biol 336(1):263–273
Guthrie JW, Hamula CLA, Zhang HQ, Le XC (2006) Assays for cytokines using aptamers. Methods 38(4):324–330
Hamada H, Kameshima N, Szymanska A, Wegner K, Lankiewicz L, Shinohara H, Taki M, Sisido M (2005) Position-specific incorporation of a highly photodurable and blue-laser excitable fluorescent amino acid into proteins for fluorescence sensing. Bioorg Med Chem 13(10):3379–3384
Hamula CLA, Guthrie JW, Zhang HQ, Li XF, Le XC (2006) Selection and analytical applications of aptamers. TrAC Trends Anal Chem 25(7):681–691
Haupt K, Mosbach K (1999) Molecularly imprinted polymers in chemical and biological sensing. Biochem Soc Trans 27(2):344–350
Haupt K, Mosbach K (2000) Molecularly imprinted polymers and their use in biomimetic sensors. Chem Rev 100(7):2495–2504
Hazra P, Chakrabarty D, Chakraborty A, Sarkar N (2004) Intramolecular charge transfer and solvation dynamics of Nile Red in the nanocavity of cyclodextrins. Chem Phys Lett 388(1–3):150–157
Hermann T, Patel DJ (2000) Biochemistry – adaptive recognition by nucleic acid aptamers. Science 287(5454):820–825
Hesselberth JR, Miller D, Robertus J, Ellington AD (2000) In vitro selection of RNA molecules that inhibit the activity of ricin A-chain. J Biol Chem 275(7):4937–4942
Heyduk E, Heyduk T (2005) Nucleic acid-based fluorescence sensors for detecting proteins. Anal Chem 77(4):1147–1156
Hicke BJ, Marion C, Chang YF, Gould T, Lynott CK, Parma D, Schmidt PG, Warren S (2001) Tenascin-C aptamers are generated using tumor cells and purified protein. J Biol Chem 276(52):48644–48654
Hillberg AL, Brain KR, Allender CJ (2005) Molecular imprinted polymer sensors: implications for therapeutics. Adv Drug Deliv Rev 57(12):1875–1889
Hossain MA, Mihara H, Ueno A (2003) Fluorescence resonance energy transfer in a novel cyclodextrin-peptide conjugate for detecting steroid molecules. Bioorg Med Chem Lett 13(24):4305–4308
Hosse RJ, Rothe A, Power BE (2006) A new generation of protein display scaffolds for molecular recognition. Protein Sci 15(1):14–27
Hunt CE, Ansell RJ (2006) Use of fluorescence shift and fluorescence anisotropy to evaluate the re-binding of template to (S)-propranolol imprinted polymers. Analyst 131(5):678–683
Hust M, Dubel S (2004) Mating antibody phage display with proteomics. Trends Biotechnol 22(1):8–14
Jennings K, Diamond D (2001) Enantioselective molecular sensing of aromatic amines using tetra-(S)-di-2-naphthylprolinol calix[4]arene. Analyst 126(7):1063–1067
Jespers L, Bonnert TP, Winter G (2004) Selection of optical biosensors from chemisynthetic antibody libraries. Protein Eng Des Sel 17(10):709–713
Jhaveri S, Rajendran M, Ellington AD (2000) In vitro selection of signaling aptamers. Nat Biotechnol 18(12):1293–1297
Jin T, Fujii F, Yamada E, Nodasaka Y, Kinjo M (2006) Control of the optical properties of quantum dots by surface coating with calix n arene carboxylic acids. J Am Chem Soc 128(29):9288–9289
Joseph R, Rao CP (2011) Ion and molecular recognition by lower rim 1, 3-di-conjugates of calix [4] arene as receptors. Chem Rev 111(8):4658–4702
Kachkovskiy GO, Shandura MP, Drapaylo AB, Slominskii JL, Tolmachev OI, Kalchenko VI (2006) New calix[4]arene based hydroxystyryl cyanine dyes. J Inclusion Phenom Macrocyclic Chem 56(3–4):315–321
Katilius E, Katiliene Z, Woodbury NW (2006) Signaling aptamers created using fluorescent nucleotide analogues. Anal Chem 78(18):6484–6489
Khan F, Pickup JC (2013) Near-infrared fluorescence glucose sensing based on glucose/galactose-binding protein coupled to 651-Blue Oxazine. Biochem Biophys Res Commun 438(3):488–492
Kodadek T (2002) Development of protein-detecting microarrays and related devices. Trends Biochem Sci 27(6):295–300
Korndorfer IP, Schlehuber S, Skerra A (2003) Structural mechanism of specific ligand recognition by a lipocalin tailored for the complexation of digoxigenin. J Mol Biol 330(2):385–396
Kubinyi M, Vidoczy T, Varga O, Nagy K, Bitter I (2005) Absorption and fluorescence spectroscopic study on complexation of oxazine 1 dye by calix 8 arenesulfonate. Appl Spectrosc 59(1):134–139
Kulagina NV, Shaffer KM, Anderson GP, Ligler FS, Taitt CR (2006) Antimicrobial peptide-based array for Escherichia coli and Salmonella screening. Anal Chim Acta 575(1):9–15
Lakowicz JR (2006) Principles of fluorescence spectroscopy, 3rd edn. Springer, New York
Leray I, Lefevre JP, Delouis JF, Delaire J, Valeur B (2001) Synthesis and photophysical and cation-binding properties of mono- and tetranaphthylcalix 4 arenes as highly sensitive and selective fluorescent sensors for sodium. Chemistry 7(21):4590–4598
Levin AM, Weiss GA (2006) Optimizing the affinity and specificity of proteins with molecular display. Mol Biosyst 2(1):49–57
Li JJ, Fang X, Tan W (2002) Molecular aptamer beacons for real-time protein recognition. Biochem Biophys Res Commun 292(1):31–40
Li J, Kendig CE, Nesterov EE (2007) Chemosensory performance of molecularly imprinted fluorescent conjugated polymer materials. J Am Chem Soc 129(51):15911–15918
Liu B, Bazan GC (2005) Methods for strand-specific DNA detection with cationic conjugated polymers suitable for incorporation into DNA chips and microarrays. Proc Natl Acad Sci U S A 102(3):589–593
Liu Y, Song Y, Chen Y, Li XQ, Ding F, Zhong RQ (2004) Biquinolino-modified beta-cyclodextrin dimers and their metal complexes as efficient fluorescent sensors for the molecular recognition of steroids. Chemistry 10(15):3685–3696
Liu Y, Liang P, Chen Y, Zhao YL, Ding F, Yu A (2005) Spectrophotometric study of fluorescence sensing and selective binding of biochemical substrates by 2,2′-bridged biso(beta-cyclodextrin) and its water-soluble fullerene conjugate. J Phys Chem B 109(49):23739–23744
Looger LL, Dwyer MA, Smith JJ, Hellinga HW (2003) Computational design of receptor and sensor proteins with novel functions. Nature 423(6936):185–190
MacKay S, Wishart D, Xing JZ, Chen J (2014) Developing trends in aptamer-based biosensor devices and their applications. IEEE Trans Biomed Circuits Syst 8(1):4–14
Makabe A, Kinoshita K, Narita M, Hamada F (2002) Guest-responsive fluorescence variations of gamma-cyclodextrins labeled with hetero-functionalized pyrene and tosyl moieties. Anal Sci 18(2):119–124
Mammen M, Choi S-K, Whitesides GM (1998) Polyvalent interactions in biological systems: implications for design and use of multivalent ligands and inhibitors. Angew Chem Int Ed 37(20):2754–2794
Martinez-Veracoechea FJ, Frenkel D (2011) Designing super selectivity in multivalent nano-particle binding. Proc Natl Acad Sci 108(27):10963–10968
Marvin JS, Hellinga HW (1998) Engineering biosensors by introducing fluorescent allosteric signal transducers: construction of a novel glucose sensor. J Am Chem Soc 120(1):7–11
Marvin JS, Hellinga HW (2001a) Conversion of a maltose receptor into a zinc biosensor by computational design. Proc Natl Acad Sci U S A 98(9):4955–4960
Marvin JS, Hellinga HW (2001b) Manipulation of ligand binding affinity by exploitation of conformational coupling. Nat Struct Biol 8(9):795–798
Marvin JS, Corcoran EE, Hattangadi NA, Zhang JV, Gere SA, Hellinga HW (1997) The rational design of allosteric interactions in a monomeric protein and its applications to the construction of biosensors. Proc Natl Acad Sci U S A 94(9):4366–4371
McCauley TG, Hamaguchi N, Stanton M (2003) Aptamer-based biosensor arrays for detection and quantification of biological macromolecules. Anal Biochem 319(2):244–250
McQuade DT, Pullen AE, Swager TM (2000) Conjugated polymer-based chemical sensors. Chem Rev 100(7):2537–2574
Medintz IL, Deschamps JR (2006) Maltose-binding protein: a versatile platform for prototyping biosensing. Curr Opin Biotechnol 17(1):17–27
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
Meyer T, Knapp EW (2014) Database of protein complexes with multivalent binding ability: bival‐bind. Proteins Struct Funct Bioinf 82(5):744–751
Miao Z, Ren G, Liu H, Jiang L, Cheng Z (2010) Cy5.5-labeled Affibody molecule for near-infrared fluorescent optical imaging of epidermal growth factor receptor positive tumors. J Biomed Opt 15(3):036007
Mohanty J, Bhasikuttan AC, Nau WM, Pal H (2006) Host-guest complexation of neutral red with macrocyclic host molecules: contrasting pK(a) shifts and binding affinities for cucurbit 7 uril and beta-cyclodextrin. J Phys Chem B 110(10):5132–5138
Mondal SK, Sahu K, Ghosh S, Sen P, Bhattacharyya K (2006) Excited-state proton transfer from pyranine to acetate in gamma-cyclodextrin and hydroxypropyl gamma-cyclodextrin. J Phys Chem A 110(51):13646–13652
Mosbach K, Haupt K (1998) Some new developments and challenges in non-covalent molecular imprinting technology. J Mol Recognit 11(1–6):62–68
Mulder A, Huskens J, Reinhoudt DN (2004) Multivalency in supramolecular chemistry and nanofabrication. Org Biomol Chem 2(23):3409–3424
Muyldermans S (2001) Single domain camel antibodies: current status. J Biotechnol 74(4):277–302
Nanduri V, Kim G, Morgan MT, Ess D, Hahm BK, Kothapalli A, Valadez A, Geng T, Bhunia AK (2006) Antibody immobilization on waveguides using a flow-through system shows improved Listeria monocytogenes detection in an automated fiber optic biosensor: RAPTOR (TM). Sensors 6(8):808–822
Nau WM, Florea M, Assaf KI (2011) Deep inside cucurbiturils: physical properties and volumes of their inner cavity determine the hydrophobic driving force for host–guest complexation. Isr J Chem 51(5–6):559–577
Navarro-Villoslada F, Urraca JL, Moreno-Bondi MC, Orellana G (2007) Zearalenone sensing with molecularly imprinted polymers and tailored fluorescent probes. Sens Actuators B 121(1):67–73
Neuweiler H, Schulz A, Vaiana AC, Smith JC, Kaul S, Wolfrum J, Sauer M (2002) Detection of individual p53-autoantibodies by using quenched peptide-based molecular probes. Angew Chem Int Ed Engl 41(24):4769–4773
Ngundi MM, Kulagina NV, Anderson GP, Taitt CR (2006) Nonantibody-based recognition: alternative molecules for detection of pathogens. Expert Rev Proteomics 3(5):511–524
Nishiyabu R, Kubo Y, James TD, Fossey JS (2012) Boronic acid building blocks: tools for sensing and separation. Chem Commun 47(4):1106–1123
Niu WZ, Jiang N, Hu YH (2007) Detection of proteins based on amino acid sequences by multiple aptamers against tripeptides. Anal Biochem 362(1):126–135
Nutiu R, Li YF (2004) Structure-switching signaling aptamers: transducing molecular recognition into fluorescence signaling. Chemistry 10(8):1868–1876
Nutiu R, Li YF (2005a) Aptamers with fluorescence-signaling properties. Methods 37(1):16–25
Nutiu R, Li YF (2005b) In vitro selection of structure-switching signaling aptamers. Angew Chem Int Ed 44(7):1061–1065
O’Sullivan PJ, Burke M, Soini AE, Papkovsky DB (2002) Synthesis and evaluation of phosphorescent oligonucleotide probes for hybridisation assays. Nucleic Acids Res 30(21):e114
Ogoshi T, Harada A (2008) Chemical sensors based on cyclodextrin derivatives. Sensors 8(8):4961–4982
Oh KJ, Cash KJ, Hugenberg V, Plaxco KW (2007) Peptide beacons: a new design for polypeptide-based optical biosensors. Bioconjug Chem 18(3):607–609
Organero JA, Tormo L, Sanz M, Roshal A, Douhal A (2007) Complexation effect of gamma-cyclodextrin on a hydroxyflavone derivative: formation of excluded and included anions. J Photochem Photobiol A 188(1):74–82
Oshovsky GV, Reinhoudt DN, Verboom W (2007) Supramolecular chemistry in water. Angew Chem Int Ed 46(14):2366–2393
Ozaki H, Nishihira A, Wakabayashi M, Kuwahara M, Sawai H (2006) Biomolecular sensor based on fluorescence-labeled aptamer. Bioorg Med Chem Lett 16(16):4381–4384
Pagliari S, Corradini R, Galaverna G, Sforza S, Dossena A, Montalti M, Prodi L, Zaccheroni N, Marchelli R (2004) Enantioselective fluorescence sensing of amino acids by modified cyclodextrins: role of the cavity and sensing mechanism. Chemistry 10(11):2749–2758
Peczuh MW, Hamilton AD (2000) Peptide and protein recognition by designed molecules. Chem Rev 100(7):2479–2493
Pflum MKH (2004) Grafting miniature DNA binding proteins. Chem Biol 11(1):3–4
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
Proske D, Blank M, Buhmann R, Resch A (2005) Aptamers – basic research, drug development, and clinical applications. Appl Microbiol Biotechnol 69(4):367–374
Pu K-Y, Shi J, Cai L, Li K, Liu B (2011) Affibody-attached hyperbranched conjugated polyelectrolyte for targeted fluorescence imaging of HER2-positive cancer cell. Biomacromolecules 12(8):2966–2974
Purrello R, Gurrieri S, Lauceri R (1999) Porphyrin assemblies as chemical sensors. Coord Chem Rev 192:683–706
Quiocho FA, Ledvina PS (1996) Atomic structure and specificity of bacterial periplasmic receptors for active transport and chemotaxis: variation of common themes. Mol Microbiol 20(1):17–25
Rathbone DL, Bains A (2005) Tools for fluorescent molecularly imprinted polymers. Biosens Bioelectron 20(7):1438–1442
Raymond FR, Ho HA, Peytavi R, Bissonnette L, Boissinot M, Picard FJ, Leclerc M, Bergeron MG (2005) Detection of target DNA using fluorescent cationic polymer and peptide nucleic acid probes on solid support. BMC Biotechnol 5:10
Renberg B, Shiroyama I, Engfeldt T, Nygren PA, Karlstrom AE (2005) Affibody protein capture microarrays: synthesis and evaluation of random and directed immobilization of affibody molecules. Anal Biochem 341(2):334–343
Renberg B, Nordin J, Merca A, Uhlen M, Feldwisch J, Nygren PA, Karlstrom AE (2007) Affibody molecules in protein capture microarrays: evaluation of multidomain ligands and different detection formats. J Proteome Res 6(1):171–179
Renard M, Belkadi L, Hugo N, England P, Altschuh D, Bedouelle H (2002) Knowledge-based design of reagentless fluorescent biosensors from recombinant antibodies. J Mol Biol 318:429–42
Richter A, Eggenstein E, Skerra A (2014) Anticalins: exploiting a non-Ig scaffold with hypervariable loops for the engineering of binding proteins. FEBS Lett 588(2):213–218
Rodi DJ, Agoston GE, Manon R, Lapcevich R, Green SJ, Makowski L (2001) Identification of small molecule binding sites within proteins using phage display technology. Comb Chem High Throughput Screen 4(7):553–572
Ronnmark J, Kampf C, Asplund A, Hoiden-Guthenberg I, Wester K, Ponten F, Uhlen M, Nygren PA (2003) Affibody-beta-galactosidase immunoconjugates produced as soluble fusion proteins in the Escherichia coli cytosol. J Immunol Methods 281(1–2):149–160
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 127(1–3):89–100
Sadhu KK, Bag B, Bharadwaj PK (2007) A multi-receptor fluorescence signaling system exhibiting enhancement selectively in presence of Na(I) and Tl(I) ions. J Photochem Photobiol A 185(2–3):231–238
Schulz GE, Schirmer RH (1979) Principles of protein structure. Springer, New York
Sellergren B, Andersson LI (2000) Application of imprinted synthetic polymers in binding assay development. Methods 22(1):92–106
Shakeel S, Karim S, Ali A (2006) Peptide nucleic acid (PNA) – a review. J Chem Technol Biotechnol 81(6):892–899
Shimizu KD, Stephenson CJ (2010) Molecularly imprinted polymer sensor arrays. Curr Opin Chem Biol 14(6):743–750
Sillerud LO, Larson RS (2005) Design and structure of peptide and peptidomimetic antagonists of protein-protein interaction. Curr Protein Pept Sci 6(2):151–169
Singh Y, Dolphin GT, Razkin J, Dumy P (2006) Synthetic peptide templates for molecular recognition: recent advances and applications. Chembiochem 7(9):1298–1314
Skerra A (2007) Alternative non-antibody scaffolds for molecular recognition. Curr Opin Biotechnol 18(4):295–304
Sliwa W, Deska M (2011) Functionalization reactions of calixarenes. Arkivoc 1:496–551
Socher E, Jarikote DV, Knoll A, Roglin L, Burmeister J, Seitz O (2008) FIT probes: peptide nucleic acid probes with a fluorescent base surrogate enable real-time DNA quantification and single nucleotide polymorphism discovery. Anal Biochem 375(2):318–330
Song S, Wang L, Li J, Fan C, Zhao J (2008) Aptamer-based biosensors. TrAC Trends Anal Chem 27(2):108–117
Srivatsan SG, Tor Y (2007) Fluorescent pyrimidine ribonucleotide: synthesis, enzymatic incorporation, and utilization. J Am Chem Soc 129(7):2044–2053
Stadtherr K, Wolf H, Lindner P (2005) An aptamer-based protein biochip. Anal Chem 77(11):3437–3443
Stephenson CJ, Shimizu KD (2007) Colorimetric and fluorometric molecularly imprinted polymer sensors and binding assays. Polym Int 56(4):482–488
Stojanovic MN, Kolpashchikov DM (2004) Modular aptameric sensors. J Am Chem Soc 126(30):9266–9270
Stojanovic MN, Landry DW (2002) Aptamer-based colorimetric probe for cocaine. J Am Chem Soc 124(33):9678–9679
Stojanovic MN, de Prada P, Landry DW (2001) Aptamer-based folding fluorescent sensor for cocaine. J Am Chem Soc 123(21):4928–4931
Szejtli J (1998) Introduction and general overview of cyclodextrin chemistry. Chem Rev 98(5):1743–1753
Thodima V, Pirooznia M, Deng YP (2006) RiboaptDB: a comprehensive database of ribozymes and aptamers. BMC Bioinf 7:S6
Timmerman P, Beld J, Puijk WC, Meloen RH (2005) Rapid and quantitative cyclization of multiple peptide loops onto synthetic scaffolds for structural mimicry of protein surfaces. Chembiochem 6(5):821–824
Tolosa L, Ge XD, Rao G (2003) Reagentless optical sensing of glutamine using a dual-emitting glutamine-binding protein. Anal Biochem 314(2):199–205
Tombelli S, Minunni A, Mascini A (2005) Analytical applications of aptamers. Biosens Bioelectron 20(12):2424–2434
Traviesa-Alvarez JM, Sanchez-Barragan I, Costa-Fernandez JM, Pereiro R, Sanz-Medel A (2007) Room temperature phosphorescence optosensing of benzo a pyrene in water using halogenated molecularly imprinted polymers. Analyst 132(3):218–223
Tsou LK, Jain RK, Hamilton AD (2004) Protein surface recognition by porphyrin-based receptors. J Porphyrins Phthalocyanines 8(1–3):141–147
Uchiyama F, Tanaka Y, Minari Y, Toku N (2005) Designing scaffolds of peptides for phage display libraries. J Biosci Bioeng 99(5):448–456
Ueda H, Dong J (2014) From fluorescence polarization to quenchbody: recent progress in fluorescent reagentless biosensors based on antibody and other binding proteins. Biochim Biophys Acta 1844(11):1951–1959
Valeur B (2002) Molecular fluorescence. Wiley VCH, Weinheim
Valeur B, Leray I (2007) Ion-responsive supramolecular fluorescent systems based on multichromophoric calixarenes: a review. Inorg Chim Acta 360(3):765–774
Vogt M, Skerra A (2004) Construction of an artificial receptor protein (“anticalin”) based on the human apolipoprotein D. Chembiochem 5(2):191–199
Wang R, Bardelang D, Waite M, Udachin KA, Leek DM, Yu K, Ratcliffe CI, Ripmeester JA (2009) Inclusion complexes of coumarin in cucurbiturils. Org Biomol Chem 7(11):2435–2439
Weiss GA, Lowman HB (2000) Anticalins versus antibodies: made-to-order binding proteins for small molecules. Chem Biol 7(8):R177–R184
Wenz G, Han BH, Muller A (2006) Cyclodextrin rotaxanes and polyrotaxanes. Chem Rev 106(3):782–817
Wiederstein M, Sippl MJ (2005) Protein sequence randomization: efficient estimation of protein stability using knowledge-based potentials. J Mol Biol 345(5):1199–1212
Wosnick JH, Swager TM (2004) Enhanced fluorescence quenching in receptor-containing conjugated polymers: a calix 4 arene-containing poly(phenylene ethynylene). Chem Commun 23:2744–2745
Wu X, Li Z, Chen X-X, Fossey JS, James TD, Jiang Y-B (2013) Selective sensing of saccharides using simple boronic acids and their aggregates. Chem Soc Rev 42(20):8032–8048
Yang RH, Chan WH, Lee AWM, Xia PF, Zhang HK, Li KA (2003a) A ratiometric fluorescent sensor for Ag-1 with high selectivity and sensitivity. J Am Chem Soc 125(10):2884–2885
Yang RH, Li KA, Wang KM, Zhao FL, Li N, Liu F (2003b) Porphyrin assembly on beta-cyclodextrin for selective sensing and detection of a zinc ion based on the dual emission fluorescence ratio. Anal Chem 75(3):612–621
Yang W, Fan H, Gao X, Gao S, Karnati VVR, Ni W, Hooks WB, Carson J, Weston B, Wang B (2004) The first fluorescent diboronic acid sensor specific for hepatocellular carcinoma cells expressing sialyl Lewis X. Chem Biol 11(4):439–448
Yesylevskyy SO, Klymchenko AS, Demchenko AP (2005) Semi-empirical study of two-color fluorescent dyes based on 3-hydroxychromone. J Mol Struct THEOCHEM 755(1–3):229–239
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
Yoshimatsu K, Reimhult K, Krozer A, Mosbach K, Sode K, Ye L (2007) Uniform molecularly imprinted microspheres and nanoparticles prepared by precipitation polymerization: the control of particle size suitable for different analytical applications. Anal Chim Acta 584(1):112–121
Zahnd C, Amstutz P, Pluckthun A (2007) Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target. Nat Methods 4(3):269–279
Zeytun A, Jeromin A, Scalettar BA, Waldo GS, Bradbury AR (2003) Retraction: fluorobodies combine GFP fluorescence with the binding characteristics of antibodies. Nat Biotechnol 21(12):1473–1479
Zhang M, Yan X, Huang F, Niu Z, Gibson HW (2014) Stimuli-responsive host–guest systems based on the recognition of cryptands by organic guests. Acc Chem Res 47(14):1995–2005
Zhao Q, Cheng L (2013) Detection of thrombin using an excimer aptamer switch labeled with dual pyrene molecules. Anal Bioanal Chem 405(25):8233–8239
Zheng GX, Shao Y, Xu B (2006) Synthesis and characterization of polyaniline coated gold nanoparticle and its primary application. Acta Chim Sin 64(8):733–737
Zhou H, Baldini L, Hong J, Wilson AJ, Hamilton AD (2006) Pattern recognition of proteins based on an array of functionalized porphyrins. J Am Chem Soc 128(7):2421–2425
Author information
Authors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Demchenko, A.P. (2015). Recognition Units. In: Introduction to Fluorescence Sensing. Springer, Cham. https://doi.org/10.1007/978-3-319-20780-3_7
Download citation
DOI: https://doi.org/10.1007/978-3-319-20780-3_7
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-20779-7
Online ISBN: 978-3-319-20780-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)