At the heart of any chemosensor or biosensor is its recognition unit (receptor). It is constructed for providing selective target binding from a mixture of different and sometimes closely related compounds. The high specificity and affinity of this unit is achieved by its appropriate structures allowing multi-point non-covalent interactions with the target. Such highly selective binding is called molecular recognition. In this chapter we discuss different binding units and the principles of their design and construction.

Some targets are small molecules and ions and for their recognition various coordination compounds can be used. Many of the targets, however, are larger molecules such as enzyme substrates, proteins, nucleic acids, macromolecular assemblies or even living cells. Their immense number requires a great variety of means for specific detection. All of these receptors or recognition units must be transformed into sensors by coupling a dye or nanoparticle to respond to the presence of the target without affecting the binding affinity. Therefore our goal is to achieve optimal binding and efficient labeling of the binder but to still maintain the target binding properties intact while adding the reporter function.


American Chemical Society Molecular Recognition Phage Display Peptide Nucleic Acid Imprint Polymer 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 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. Biosensors & Bioelectronics 23:1466–1472Google Scholar
  2. 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. Journal of Molecular Recognition 19:106–180PubMedGoogle Scholar
  3. Al-Hassan KA, Khanfer MF (1998) Fluorescence probes for cyclodextrin interiors. Journal of Fluorescence 8:139–152Google Scholar
  4. Al-Jamal KT, Ruenraroengsak P, Hartell N, Florence AT (2006) An intrinsically fluorescent den- drimer as a nanoprobe of cell transport. Journal of Drug Targeting 14:405–412PubMedGoogle Scholar
  5. Antoni P, Nystrom D, Hawker CJ, Hult A, Malkoch M (2007) A chemoselective approach for the accelerated synthesis of well-defined dendritic architectures. Chemical Communications:2249–2251Google Scholar
  6. Azzazy HM, Highsmith WE, Jr. (2002) Phage display technology: clinical applications and recent innovations. Clinical Biochemistry 35:425–445PubMedGoogle Scholar
  7. Baker ES, Hong JW, Gaylord BS, Bazan GC, Bowers MT (2006) PNA/dsDNA complexes: site specific binding and dsDNA biosensor applications. Journal of the American Chemical Society 128:8484–8492PubMedGoogle Scholar
  8. Balabai N, Linton B, Napper A, Priyadarshy S, Sukharevsky AP, Waldeck DH (1998) Orientational dynamics of beta-cyclodextrin inclusion complexes. Journal of Physical Chemistry B 102:9617–9624Google Scholar
  9. Barthe P, Cohen-Gonsaud M, Aldrian-Herrada G, Chavanieu A, Labesse G, Roumestand C (2004) Design of an amphipatic alpha-helical hairpin peptide. Comptes Rendus Chimie 7:249–252Google Scholar
  10. Benhar I (2007) Design of synthetic antibody libraries. Expert Opinion on Biological Therapy 7:763–779PubMedGoogle Scholar
  11. Bethge L, Jarikote DV, Seitz O (2008) New cyanine dyes as base surrogates in PNA: forced intercalation probes (FIT-probes) for homogeneous SNP detection. Bioorganic & Medicinal Chemistry 16:114–125Google Scholar
  12. Binz HK, Pluckthun A (2005) Engineered proteins as specific binding reagents. Current Opinion in Biotechnology 16:459–469PubMedGoogle Scholar
  13. Binz HK, Amstutz P, Pluckthun A (2005) Engineering novel binding proteins from nonimmu- noglobulin domains. Nature Biotechnology 23:1257–1268PubMedGoogle Scholar
  14. Breslow R, Dong SD (1998) Biomimetic reactions catalyzed by cyclodextrins and their derivatives. Chemical Reviews 98:1997–2011PubMedGoogle Scholar
  15. 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 sub-fragment 1 ATPase. Biochemistry 33:8262–8271PubMedGoogle Scholar
  16. Butler RS, Myers AK, Bellarmine P, Abboud KA, Castellano RK (2007) Highly fluorescent donor-acceptor purines. Journal of Materials Chemistry 17:1863–1865Google Scholar
  17. Casadei J, Powell MJ, Kenten JH (1990) Expression and secretion of aequorin as a chimeric antibody by means of a mammalian expression vector. Proceedings of the National Academy of Sciences of the United States of America 87:2047–2051PubMedGoogle Scholar
  18. Chen CT, Huang WP (2002) A highly selective fluorescent chemosensor for lead ions. Journal of the American Chemical Society 124:6246–6247PubMedGoogle Scholar
  19. Collett JR, Cho EJ, Ellington AD (2005) Production and processing of aptamer microarrays. Methods 37:4–15PubMedGoogle Scholar
  20. Cox WG, Singer VL (2004) Fluorescent DNA hybridization probe preparation using amine modification and reactive dye coupling. Biotechniques 36:114–122PubMedGoogle Scholar
  21. 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 Science 11:2655–2675PubMedGoogle Scholar
  22. Demchenko AP (2001a) Concepts and misconcepts in the analysis of simple kinetics of protein folding. Current Protein & Peptide Science 2:73–98Google Scholar
  23. Demchenko AP (2001b) Recognition between flexible protein molecules: induced and assisted folding. Journal of Molecular Recognition 14:42–61Google Scholar
  24. 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 and Peptide Letters 6:115–129Google Scholar
  25. de Silva AP, Gunaratne HQN, Gunnaugsson T, Huxley AJM, McRoy CP, Rademacher JT, Rice TE (1997) Signaling recognition events with fluorescent sensors and switches. Chemical Reviews 97:1515–1566PubMedGoogle Scholar
  26. Douhal A (2004) Ultrafast guest dynamics in cyclodextrin nanocavities. Chemical Reviews 104:1955–1976PubMedGoogle Scholar
  27. Dwyer MA, Hellinga HW (2004) Periplasmic binding proteins: a versatile superfamily for protein engineering. Current Opinion in Structural Biology 14:495–504PubMedGoogle Scholar
  28. 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. Journal of Molecular Biology 334:103–118PubMedGoogle Scholar
  29. Eklund M, Axelsson L, Uhlen M, Nygren PA (2002) Anti-idiotypic protein domains selected from protein A-based affibody libraries. Proteins-Structure Function and Genetics 48:454–462Google Scholar
  30. 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. Journal of Organic Chemistry 67:3120–3123PubMedGoogle Scholar
  31. 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. Journal of the American Chemical Society 126:4464–4465Google Scholar
  32. 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-A European Journal 10:2375–2385Google Scholar
  33. Enander K, Choulier L, Olsson AL, Yushchenko DA, Kanmert D, Klymchenko AS, Demchenko AP, Mély Y, Altschuh DA (2008) Peptide-Based, Ratiometric Biosensor Construct for Direct Fluorescence Detection of a Protein Analyte. Bioconjugate Chemistry 19:1864–1870PubMedGoogle Scholar
  34. 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 6:1043–1050PubMedGoogle Scholar
  35. Fletcher S, Hamilton AD (2007) Protein-protein interaction inhibitors: small molecules from screening techniques. Current Topics in Medicinal Chemistry 7:922–927PubMedGoogle Scholar
  36. 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 Research 34:D296–D301PubMedGoogle Scholar
  37. Flower DR, North ACT, Sansom CE (2000) The lipocalin protein family: structural and sequence overview. Biochimica Et Biophysica Acta-Protein Structure and Molecular Enzymology 1482:9–24Google Scholar
  38. Gellman SH, Woolfson DN (2002) Mini-proteins Trp the light fantastic. Nature Structural Biology 9:408–410PubMedGoogle Scholar
  39. Gilardi G, Zhou LQ, Hibbert L, Cass AEG (1994) Engineering the maltose-binding protein for reagentless fluorescence sensing. Analytical Chemistry 66:3840–3847PubMedGoogle Scholar
  40. Glasner ME, Gerlt JA, Babbitt PC (2007) Mechanisms of protein evolution and their application to protein engineering. Advances in Enzymology and Related Areas in Molecular Biology 75:193–239,xii–xiiiGoogle Scholar
  41. Gomara MJ, Haro I (2007) Synthetic peptides for the immunodiagnosis of human diseases. Current Medicinal Chemistry 14:531–546PubMedGoogle Scholar
  42. Goodchild S, Love T, Hopkins N, Mayers C (2006) Engineering antibodies for biosensor technologies. Advances in Applied Microbiology 58:185–226PubMedGoogle Scholar
  43. Gopinath SCB (2007) Methods developed for SELEX. Analytical and Bioanalytical Chemistry 387:171–182PubMedGoogle Scholar
  44. Guntas G, Ostermeier M (2004) Creation of an allosteric enzyme by domain insertion. Journal of Molecular Biology 336:263–273PubMedGoogle Scholar
  45. Guthrie JW, Hamula CLA, Zhang HQ, Le XC (2006) Assays for cytokines using aptamers.Methods 38:324–330PubMedGoogle Scholar
  46. 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. Bioorganic & Medicinal Chemistry 13:3379–3384Google Scholar
  47. Hamula CLA, Guthrie JW, Zhang HQ, Li XF, Le XC (2006) Selection and analytical applications of aptamers. Trac-Trends in Analytical Chemistry 25:681–691Google Scholar
  48. Haupt K, Mosbach K (1999) Molecularly imprinted polymers in chemical and biological sensing. Biochemical Society Transactions 27:344–350PubMedGoogle Scholar
  49. Haupt K, Mosbach K (2000) Molecularly imprinted polymers and their use in biomimetic sensors. Chemical Reviews 100:2495–2504PubMedGoogle Scholar
  50. Hazra P, Chakrabarty D, Chakraborty A, Sarkar N (2004) Intramolecular charge transfer and solvation dynamics of Nile Red in the nanocavity of cyclodextrins. Chemical Physics Letters 388:150–157Google Scholar
  51. Hermann T, Patel DJ (2000) Biochemistry - adaptive recognition by nucleic acid aptamers. Science 287:820–825PubMedGoogle Scholar
  52. Hesselberth JR, Miller D, Robertus J, Ellington AD (2000) In vitro selection of RNA molecules that inhibit the activity of ricin A-chain. Journal of Biological Chemistry 275:4937–4942PubMedGoogle Scholar
  53. Heyduk E, Heyduk T (2005) Nucleic acid-based fluorescence sensors for detecting proteins. Analytical Chemistry 77:1147–1156PubMedGoogle Scholar
  54. 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. Journal of Biological Chemistry 276:48644–48654PubMedGoogle Scholar
  55. Hillberg AL, Brain KR, Allender CJ (2005) Molecular imprinted polymer sensors: implications for therapeutics. Advanced Drug Delivery Reviews 57:1875–1889PubMedGoogle Scholar
  56. Hossain MA, Mihara H, Ueno A (2003) Fluorescence resonance energy transfer in a novel cyclo-dextrin-peptide conjugate for detecting steroid molecules. Bioorganic & Medicinal Chemistry Letters 13:4305–4308Google Scholar
  57. Hosse RJ, Rothe A, Power BE (2006) A new generation of protein display scaffolds for molecular recognition. Protein Science 15:14–27PubMedGoogle Scholar
  58. 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 131:678–683PubMedGoogle Scholar
  59. Hust M, Dubel S (2004) Mating antibody phage display with proteomics. Trends in Biotechnology 22:8–14PubMedGoogle Scholar
  60. Jennings K, Diamond D (2001) Enantioselective molecular sensing of aromatic amines using tetra-(S)-di-2-naphthylprolinol calix[4]arene. Analyst 126:1063–1067PubMedGoogle Scholar
  61. Jespers L, Bonnert TP, Winter G (2004) Selection of optical biosensors from chemisynthetic antibody libraries. Protein Engineering Design & Selection 17:709–713Google Scholar
  62. Jhaveri S, Rajendran M, Ellington AD (2000) In vitro selection of signaling aptamers. Nature Biotechnology 18:1293–1297PubMedGoogle Scholar
  63. Jiang Y, Fang X, Bai C (2004) Signaling aptamer/protein binding by a molecular light switch complex. Analytical Chemistry 76:5230–5235PubMedGoogle Scholar
  64. 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. Journal of the American Chemical Society 128:9288–9289PubMedGoogle Scholar
  65. Kachkovskiy GO, Shandura MP, Drapaylo AB, Slominskii JL, Tolmachev OI, Kalchenko VI (2006) New calix[4]arene based hydroxystyryl cyanine dyes. Journal of Inclusion Phenomena and Macrocyclic Chemistry 56:315–321Google Scholar
  66. Katilius E, Katiliene Z, Woodbury NW (2006) Signaling aptamers created using fluorescent nucleotide analogues. Analytical Chemistry 78:6484–6489PubMedGoogle Scholar
  67. Kim JS, Noh KH, Lee SH, Kim SK, Kim SK, Yoon JY (2003) Molecular taekwondo. 2. A new calix[4]azacrown bearing two different binding sites as a new fluorescent ionophore. Journal of Organic Chemistry 68:597–600PubMedGoogle Scholar
  68. Kodadek T (2002) Development of protein-detecting microarrays and related devices. Trends in Biochemical Sciences 27:295–300PubMedGoogle Scholar
  69. Korndorfer IP, Schlehuber S, Skerra A (2003) Structural mechanism of specific ligand recognition by a lipocalin tailored for the complexation of digoxigenin. Journal of Molecular Biology 330:385–396PubMedGoogle Scholar
  70. Kubinyi M, Vidoczy T, Varga O, Nagy K, Bitter I (2005) Absorption and fluorescence spectro-scopic study on complexation of oxazine 1 dye by calix 8 arenesulfonate. Applied Spectroscopy 59:134–139PubMedGoogle Scholar
  71. Kulagina NV, Shaffer KM, Anderson GP, Ligler FS, Taitt CR (2006) Antimicrobial peptide-based array for Escherichia coli and Salmonella screening. Analytica Chimica Acta 575:9–15PubMedGoogle Scholar
  72. Lakowicz JR (2007) Principles of fluorescence spectroscopy. Springer, New YorkGoogle Scholar
  73. 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-A European Journal 7:4590–4598Google Scholar
  74. Levin AM, Weiss GA (2006) Optimizing the affinity and specificity of proteins with molecular display. Molecular Biosystems 2:49–57PubMedGoogle Scholar
  75. Li J, Kendig CE, Nesterov EE (2007) Chemosensory performance of molecularly imprinted fluo rescent conjugated polymer materials. Journal of the American Chemical Society 129:15911–15918PubMedGoogle Scholar
  76. Li JJ, Fang X, Tan W (2002) Molecular aptamer beacons for real-time protein recognition. Biochemical and Biophysical Research Communications 292:31–40PubMedGoogle Scholar
  77. Liu B, Bazan GC (2005) Methods for strand-specific DNA detection with cationic conjugated polymers suitable for incorporation into DNA chips and microarrays. Proceedings of the National Academy of Sciences of the United States of America 102:589–593PubMedGoogle Scholar
  78. 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 10:3685–3696PubMedGoogle Scholar
  79. 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. Journal of Physical Chemistry B 109:23739–23744Google Scholar
  80. Looger LL, Dwyer MA, Smith JJ, Hellinga HW (2003) Computational design of receptor and sensor proteins with novel functions. Nature 423:185–190PubMedGoogle Scholar
  81. Makabe A, Kinoshita K, Narita M, Hamada F (2002) Guest-responsive fluorescence variations of gamma-cyclodextrins labeled with hetero-functionalized pyrene and tosyl moieties. Analytical Sciences 18:119–124PubMedGoogle Scholar
  82. Marvin JS, Hellinga HW (1998) Engineering biosensors by introducing fluorescent allosteric signal transducers: construction of a novel glucose sensor. Journal of the American Chemical Society 120:7–11Google Scholar
  83. Marvin JS, Hellinga HW (2001a) Conversion of a maltose receptor into a zinc biosensor by computational design. Proceedings of the National Academy of Sciences of the United States of America 98:4955–4960Google Scholar
  84. Marvin JS, Hellinga HW (2001b) Manipulation of ligand binding affinity by exploitation of con-formational coupling. Nature Structural Biology 8:795–798Google Scholar
  85. 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. Proceedings of the National Academy of Sciences of the United States of America 94:4366–4371PubMedGoogle Scholar
  86. McCauley TG, Hamaguchi N, Stanton M (2003) Aptamer-based biosensor arrays for detection and quantification of biological macromolecules. Analytical Biochemistry 319:244–250PubMedGoogle Scholar
  87. McQuade DT, Pullen AE, Swager TM (2000) Conjugated polymer-based chemical sensors. Chemical Reviews 100:2537–2574PubMedGoogle Scholar
  88. Medintz IL, Deschamps JR (2006) Maltose-binding protein: a versatile platform for prototyping biosensing. Current Opinion in Biotechnology 17:17–27PubMedGoogle Scholar
  89. Medintz IL, Goldman ER, Lassman ME, Mauro JM (2003) A fluorescence resonance energy transfer sensor based on maltose binding protein. Bioconjugate Chemistry 14:909–918PubMedGoogle Scholar
  90. Metivier R, Leray I, Valeur B (2004) Lead and mercury sensing by calixarene-based fluoroiono-phores bearing two or four dansyl fluorophores. Chemistry-A European Journal 10:4480–4490Google Scholar
  91. 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. Journal of Physical Chemistry B 110:5132–5138Google Scholar
  92. 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. Journal of Physical Chemistry A 110:13646–13652Google Scholar
  93. Mosbach K, Haupt K (1998) Some new developments and challenges in non-covalent molecular imprinting technology. Journal of Molecular Recognition 11:62–68PubMedGoogle Scholar
  94. Muyldermans S (2001) Single domain camel antibodies: current status. Journal of Biotechnology 74:277–302PubMedGoogle Scholar
  95. 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 6:808–822Google Scholar
  96. Navarro-Villoslada F, Urraca JL, Moreno-Bondi MC, Orellana G (2007) Zearalenone sensing with molecularly imprinted polymers and tailored fluorescent probes. Sensors and Actuators B-Chemical 121:67–73Google Scholar
  97. 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. Angewandte Chemie-International Edition in English 41:4769–4773Google Scholar
  98. Ngundi MM, Kulagina NV, Anderson GP, Taitt CR (2006) Nonantibody-based recognition: alternative molecules for detection of pathogens. Expert Review of Proteomics 3:511–524PubMedGoogle Scholar
  99. Niu WZ, Jiang N, Hu YH (2007) Detection of proteins based on amino acid sequences by multiple aptamers against tripeptides. Analytical Biochemistry 362:126–135PubMedGoogle Scholar
  100. Nutiu R, Li YF (2004) Structure-switching signaling aptamers: transducing molecular recognition into fluorescence signaling. Chemistry-A European Journal 10:1868–1876Google Scholar
  101. Nutiu R, Li YF (2005a) Aptamers with fluorescence-signaling properties. Methods 37:16–25Google Scholar
  102. Nutiu R, Li YF (2005b) In vitro selection of structure-switching signaling aptamers. Angewandte Chemie-International Edition 44:1061–1065Google Scholar
  103. Oh KJ, Cash KJ, Hugenberg V, Plaxco KW (2007) Peptide beacons: a new design for polypeptide- based optical biosensors. Bioconjugate Chemistry 18:607–609PubMedGoogle Scholar
  104. 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. Journal of Photochemistry and Photobiology A-Chemistry 188:74–82Google Scholar
  105. Oshovsky GV, Reinhoudt DN, Verboom W (2007) Supramolecular chemistry in water. Angewandte Chemie-International Edition 46:2366–2393Google Scholar
  106. O'Sullivan PJ, Burke M, Soini AE, Papkovsky DB (2002) Synthesis and evaluation of phosphorescent oligonucleotide probes for hybridisation assays. Nucleic Acids Research 30:e114PubMedGoogle Scholar
  107. Ozaki H, Nishihira A, Wakabayashi M, Kuwahara M, Sawai H (2006) Biomolecular sensor based on fluorescence-labeled aptamer. Bioorganic & Medicinal Chemistry Letters 16:4381–4384Google Scholar
  108. 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 cyclodex- trins: role of the cavity and sensing mechanism. Chemistry-A European Journal 10:2749–2758Google Scholar
  109. Peczuh MW, Hamilton AD (2000) Peptide and protein recognition by designed molecules. Chemical Reviews 100:2479–2493PubMedGoogle Scholar
  110. Pflum MKH (2004) Grafting miniature DNA binding proteins. Chemistry & Biology 11:3–4Google Scholar
  111. Proske D, Blank M, Buhmann R, Resch A (2005) Aptamers - basic research, drug development, and clinical applications. Applied Microbiology and Biotechnology 69:367–374PubMedGoogle Scholar
  112. Pugh VJ, Hu QS, Pu L (2000) The first dendrimer-based enantioselective fluorescent sensor for the recognition of chiral amino alcohols. Angewandte Chemie-International Edition 39:3638–3641Google Scholar
  113. Purrello R, Gurrieri S, Lauceri R (1999) Porphyrin assemblies as chemical sensors. Coordination Chemistry Reviews 192:683–706Google Scholar
  114. Quiocho FA, Ledvina PS (1996) Atomic structure and specificity of bacterial periplasmic receptors for active transport and chemotaxis: variation of common themes. Molecular Microbiology 20:17–25PubMedGoogle Scholar
  115. Rathbone DL, Bains A (2005) Tools for fluorescent molecularly imprinted polymers. Biosensors & Bioelectronics 20:1438–1442Google Scholar
  116. 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 Biotechnology 5:10PubMedGoogle Scholar
  117. Renard M, Belkadi L, Hugo N, England P, Altschuh D, Bedouelle H (2002) Knowledge-based design of reagentless fluorescent biosensors from recombinant antibodies. Journal of Molecular Biology 318:429–442PubMedGoogle Scholar
  118. 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. Analytical Biochemistry 341:334–343PubMedGoogle Scholar
  119. 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. Journal of Proteome Research 6:171–179PubMedGoogle Scholar
  120. 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. Combinatorial Chemistry & High Throughput Screening 4:553–572Google Scholar
  121. 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. Journal of Immunological Methods 281:149–160PubMedGoogle Scholar
  122. 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. Journal of Photochemistry and Photobiology A-Chemistry 127:89–100Google Scholar
  123. 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. Journal of Photochemistry and Photobiology A-Chemistry 185:231–238Google Scholar
  124. Schulz GE, Schirmer RH (1979) Principles of protein structure. Springer, New YorkGoogle Scholar
  125. Sellergren B, Andersson LI (2000) Application of imprinted synthetic polymers in binding assay development. Methods 22:92–106PubMedGoogle Scholar
  126. Shakeel S, Karim S, Ali A (2006) Peptide nucleic acid (PNA) — a review. Journal of Chemical Technology and Biotechnology 81:892–899Google Scholar
  127. Sillerud LO, Larson RS (2005) Design and structure of peptide and peptidomimetic antagonists of protein-protein interaction. Current Protein & Peptide Science 6:151–169Google Scholar
  128. Singh Y, Dolphin GT, Razkin J, Dumy P (2006) Synthetic peptide templates for molecular recognition: recent advances and applications. Chembiochem 7:1298–1314PubMedGoogle Scholar
  129. 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. Analytical Biochemistry 375:318–330PubMedGoogle Scholar
  130. Srivatsan SG, Tor Y (2007) Fluorescent pyrimidine ribonucleotide: synthesis, enzymatic incorporation, and utilization. Journal of the American Chemical Society 129:2044–2053PubMedGoogle Scholar
  131. Stadtherr K, Wolf H, Lindner P (2005) An aptamer-based protein biochip. Analytical Chemistry 77:3437–3443PubMedGoogle Scholar
  132. Stephenson CJ, Shimizu KD (2007) Colorimetric and fluorometric molecularly imprinted polymer sensors and binding assays. Polymer International 56:482–488Google Scholar
  133. Stojanovic MN, Kolpashchikov DM (2004) Modular aptameric sensors. Journal of the American Chemical Society 126:9266–9270PubMedGoogle Scholar
  134. Stojanovic MN, Landry DW (2002) Aptamer-based colorimetric probe for cocaine. Journal of the American Chemical Society 124:9678–9679PubMedGoogle Scholar
  135. Stojanovic MN, de Prada P, Landry DW (2001) Aptamer-based folding fluorescent sensor for cocaine. Journal of the American Chemical Society 123:4928–4931PubMedGoogle Scholar
  136. Szejtli J (1998) Introduction and general overview of cyclodextrin chemistry. Chemical Reviews 98:1743–1753PubMedGoogle Scholar
  137. Thodima V, Pirooznia M, Deng YP (2006) RiboaptDB: a comprehensive database of ribozymes and aptamers. BMC Bioinformatics 7Google Scholar
  138. 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 6:821–824PubMedGoogle Scholar
  139. Tolosa L, Ge XD, Rao G (2003) Reagentless optical sensing of glutamine using a dual-emitting glutamine-binding protein. Analytical Biochemistry 314:199–205PubMedGoogle Scholar
  140. Tombelli S, Minunni A, Mascini A (2005) Analytical applications of aptamers. Biosensors & Bioelectronics 20:2424–2434Google Scholar
  141. 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 132:218–223PubMedGoogle Scholar
  142. Tsou LK, Jain RK, Hamilton AD (2004) Protein surface recognition by porphyrin-based receptors. Journal of Porphyrins and Phthalocyanines 8:141–147Google Scholar
  143. Uchiyama F, Tanaka Y, Minari Y, Toku N (2005) Designing scaffolds of peptides for phage display libraries. Journal of Bioscience and Bioengineering 99:448–456PubMedGoogle Scholar
  144. Urraca JL, Moreno-Bondi MC, Orellana G, Sellergren B, Hall AJ (2007) Molecularly imprinted polymers as antibody mimics in automated on-line fluorescent competitive assays. Analytical Chemistry 79:4915–4923PubMedGoogle Scholar
  145. Valeur B (2002) Molecular fluorescence. Wiley-VCH, Weinheim Valeur B, Leray I (2007) Ion-responsive supramolecular fluorescent systems based on multi- chromophoric calixarenes: a review. Inorganica Chimica Acta 360:765–774Google Scholar
  146. Vogt M, Skerra A (2004) Construction of an artificial receptor protein (“anticalin”) based on the human apolipoprotein D. Chembiochem 5:191–199PubMedGoogle Scholar
  147. Weiss GA, Lowman HB (2000) Anticalins versus antibodies: made-to-order binding proteins for small molecules. Chemistry & Biology 7:R177–R184Google Scholar
  148. Wenz G, Han BH, Muller A (2006) Cyclodextrin rotaxanes and polyrotaxanes. Chemical Reviews 106:782–817PubMedGoogle Scholar
  149. Wiederstein M, Sippl MJ (2005) Protein sequence randomization: efficient estimation of protein stability using knowledge-based potentials. Journal of Molecular Biology 345:1199–1212PubMedGoogle Scholar
  150. Wosnick JH, Swager TM (2004) Enhanced fluorescence quenching in receptor-containing conjugated polymers: a calix 4 arene-containing poly(phenylene ethynylene). Chemical Communications:2744–2745Google Scholar
  151. Yang CJ, Jockusch S, Vicens M, Turro NJ, Tan W (2005) Light-switching excimer probes for rapid protein monitoring in complex biological fluids. Proceedings of the National Academy of Sciences of the United States of America 102:17278–17283PubMedGoogle Scholar
  152. 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. Journal of the American Chemical Society 125:2884–2885Google Scholar
  153. Yang RH, Li KA, Wang KM, Zhao FL, Li N, Liu F (2003b) Porphyrin assembly on beta-cyclo- dextrin for selective sensing and detection of a zinc ion based on the dual emission fluorescence ratio. Analytical Chemistry 75:612–621Google Scholar
  154. Yesylevskyy SO, Klymchenko AS, Demchenko AP (2005) Semi-empirical study of two-color fluorescent dyes based on 3-hydroxychromone. Journal of Molecular Structure-Theochem 755:229–239Google Scholar
  155. Yesylevskyy SO, Kharkyanen VN, Demchenko AP (2006) The change of protein intradomain mobility on ligand binding: is it a commonly observed phenomenon? Biophysical Journal 91:3002–3013PubMedGoogle Scholar
  156. 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. Analytica Chimica Acta 584:112–121PubMedGoogle Scholar
  157. Zahnd C, Amstutz P, Pluckthun A (2007) Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target. Nature Methods 4:269–279PubMedGoogle Scholar
  158. Zhang L, Feng W (2007) Dendritic conjugated polymers. Progress in Chemistry 19:337–349Google Scholar
  159. Zheng GX, Shao Y, Xu B (2006) Synthesis and characterization of polyaniline coated gold nano-particle and its primary application. Acta Chimica Sinica 64:733–737Google Scholar
  160. Zhou H, Baldini L, Hong J, Wilson AJ, Hamilton AD (2006) Pattern recognition of proteins based on an array of functionalized porphyrins. Journal of the American Chemical Society 128:2421–2425PubMedGoogle Scholar
  161. Zimmerman SC, Zharov I, Wendland MS, Rakow NA, Suslick KS (2003) Molecular imprinting inside dendrimers. Journal of the American Chemical Society 125:13504–13518PubMedGoogle Scholar

Copyright information

© Springer Science + Business Media B.V. 2009

Personalised recommendations