Theoretical Aspects

  • Alexander P. Demchenko

Abstract

Quantitative measures are highly needed in fluorescence sensing. In this Chapter the reader finds discussion on parameters that have to be optimized in every sensor, such as selectivity, sensitivity and limit of detection. Concentrating on reversible binding, in which the mass action law is observed, the methods of determining the binding constants and modeling the ligand binding isotherms are presented. Kinetics of target binding and its influence on the results of analyte determination are discussed. Focusing on fluorescence sensing, linear and intensity-weighted formats are distinguished and analyzed. At the end of this Chapter the reader finds the Section “Sensing and thinking” with the list of questions and problems. It addresses the issue, how to provide the optimal quantitative measure of target binding.

Keywords

Sensor sensitivity and limit of detection Reversible/irreversible binding Mass action law Binding constants Binding isotherms Binding kinetics Fluorescence Linear/weighted response 

References

  1. Baker GA, Pandey S, Bright FV (2000) Extending the reach of immunoassays to optically dense specimens by using two-photon excited fluorescence polarization. Anal Chem 72(22):5748–5752CrossRefPubMedGoogle Scholar
  2. Bobrovnik SA (2003) Ligand–receptor interactions: a new method for determining the binding parameters. J Biochem Biophys Methods 55(1):71–86Google Scholar
  3. Bobrovnik SA (2005) New capabilities in determining the binding parameters for ligand-receptor interaction. J Biochem Biophys Methods 65(1):30–44Google Scholar
  4. Bobrovnik SA (2007) The influence of rigid or flexible linkage between two ligands on the effective affinity and avidity for reversible interactions with bivalent receptors. J Mol Recognit 20(4):253–262CrossRefPubMedGoogle Scholar
  5. Bobrovnik SA (2008) A simple and convenient approach for evaluation of the parameters of ligand–receptor interaction. Receptor blocking index and its application. J Mol Recognit 21(2):96–102Google Scholar
  6. Bobrovnik SA (2014) Avidity of polyreactive immunoglobulins. Ukr Biochem J 86(6):183–189CrossRefPubMedGoogle Scholar
  7. Boens N, Leen V, Dehaen W (2012) Fluorescent indicators based on BODIPY. Chem Soc Rev 41(3):1130–1172CrossRefPubMedGoogle Scholar
  8. Carletti E, Guerra E, Alberti S (2006) The forgotten variables of DNA array hybridization. Trends Biotechnol 24(10):443–448CrossRefPubMedGoogle Scholar
  9. Demchenko AP (2010) The concept of lambda-ratiometry in fluorescence sensing and imaging. J Fluoresc 20(5):1099–1128CrossRefPubMedGoogle Scholar
  10. Demchenko AP (2014) Practical aspects of wavelength ratiometry in the studies of intermolecular interactions. J Mol Struct 1077:51–67CrossRefGoogle Scholar
  11. Demidov VV, Frank-Kamenetskii MD (2004) Two sides of the coin: affinity and specificity of nucleic acid interactions. Trends Biochem Sci 29(2):62–71CrossRefPubMedGoogle Scholar
  12. Eaton BE, Gold L, Zichi DA (1995) Let’s get specific: the relationship between specificity and affinity. Chem Biol 2(10):633–638CrossRefPubMedGoogle Scholar
  13. Gaugain B, Barbet J, Capelle N, Roques BP, Le Pecq JB (1978) DNA Bifunctional intercalators. 2. Fluorescence properties and DNA binding interaction of an ethidium homodimer and an acridine ethidium heterodimer. Biochemistry 17(24):5078–5088CrossRefPubMedGoogle Scholar
  14. Hong S, Leroueil PR, Majoros IJ, Orr BG, Baker JR Jr, Banaszak Holl MM (2007) The binding avidity of a nanoparticle-based multivalent targeted drug delivery platform. Chem Biol 14(1):107–115CrossRefPubMedGoogle Scholar
  15. Kellner R, Mermet J-M, Otto M, Valcarcei M, Widmer HM (2004) Analytical chemistry. Wiley-VCH, New YorkGoogle Scholar
  16. Kitov PI, Bundle DR (2003) On the nature of the multivalency effect: a thermodynamic model. J Am Chem Soc 125(52):16271–16284CrossRefPubMedGoogle Scholar
  17. Klenin KV, Kusnezow W, Langowski J (2005) Kinetics of protein binding in solid-phase immunoassays: theory. J Chem Phys 122(21):214715CrossRefPubMedGoogle Scholar
  18. Klotz IM (1983) Ligand-receptor interactions – what we can and cannot learn from binding measurements. Trends Pharmacol Sci 4(6):253–255CrossRefGoogle Scholar
  19. Klotz IM, Hunston DL (1971) Properties of graphical representations of multiple classes of binding sites. Biochemistry 10(16):3065–3069CrossRefPubMedGoogle Scholar
  20. Kusnezow W, Jacob A, Walijew A, Diehl F, Hoheisel JD (2003) Antibody microarrays: an evaluation of production parameters. Proteomics 3(3):254–264CrossRefPubMedGoogle Scholar
  21. Lakowicz JR (1999) Principles of fluorescence spectroscopy. Kluwer, New YorkCrossRefGoogle Scholar
  22. Lakowicz JR (2006) Principles of fluorescence spectroscopy, 3rd edn. Springer, New YorkGoogle Scholar
  23. Li CY, Zhang XB, Han ZX, Akermark B, Sun L, Shen GL, Yu RQ (2006) A wide pH range optical sensing system based on a sol–gel encapsulated amino-functionalized corrole. Analyst 131(3):388–393CrossRefPubMedGoogle Scholar
  24. MacDougall D, Crummett WB (1980) Guidelines for data acquisition and data quality evaluation in environmental chemistry. Anal Chem 52(14):2242–2249CrossRefGoogle Scholar
  25. 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):4366–4371PubMedCentralCrossRefPubMedGoogle Scholar
  26. 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):389–398CrossRefGoogle Scholar
  27. Sadana A, Madugula A (1993) Binding kinetics of antigen by immobilized antibody or of antibody by immobilized antigen: influence of lateral interactions and variable rate coefficients. Biotechnol Prog 9(3):259–266CrossRefPubMedGoogle Scholar
  28. Sanchez SA, Gratton E (2005) Lipid–protein interactions revealed by two-photon microscopy and fluorescence correlation spectroscopy. Acc Chem Res 38(6):469–477CrossRefPubMedGoogle Scholar
  29. Sandanaraj BS, Demont R, Thayumanavan S (2007) Generating patterns for sensing using a single receptor scaffold. J Am Chem Soc 129(12):3506–3507Google Scholar
  30. Sekar MM, Bloch W, St John PM (2005) Comparative study of sequence-dependent hybridization kinetics in solution and on microspheres. Nucleic Acids Res 33(1):366–375PubMedCentralCrossRefPubMedGoogle Scholar
  31. Tetin SY, Hazlett TL (2000) Optical spectroscopy in studies of antibody-hapten interactions. Methods 20(3):341–361CrossRefPubMedGoogle Scholar
  32. Vallée-Bélisle A, Ricci F, Plaxco KW (2012) Engineering biosensors with extended, narrowed, or arbitrarily edited dynamic range. J Am Chem Soc 134(6):2876–2879PubMedCentralCrossRefPubMedGoogle Scholar
  33. Winzor DJ (2011) Allowance for antibody bivalence in the characterization of interactions by ELISA. J Mol Recognit 24(2):139–148CrossRefPubMedGoogle Scholar
  34. Yang RH, Li KA, Wang KM, Zhao FL, Li N, Liu F (2003) 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):612–621CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Alexander P. Demchenko
    • 1
  1. 1.Laboratory of Nanobiotechnology Palladin Institute of BiochemistryNational Academy of Sciences of UkraineKievUkraine

Personalised recommendations