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Biospecific Interaction Analysis

A Tool for Drug Discovery and Development

  • Technology
  • Published:
American Journal of Pharmacogenomics

Abstract

The recent development of surface plasmon resonance (SPR)-based biosensor technologies for biospecific interaction analysis (BIA) enables the monitoring of a variety of molecular reactions in real-time. The biomolecular interactions occur at the surface of a flow cell of a sensor chip between a ligand immobilized on the surface and an injected analyte. SPR-based BIA offers many advantages over most of the other methodologies available for the study of biomolecular interactions, including full automation, no requirement for labeling, and the availability of a large variety of activated sensor chips that allow immobilization of DNA, RNA, proteins, peptides and cells. The assay is rapid and requires only small quanitities of both ligand and analyte in order to obtain informative results. In addition, the sensor chip can be re-used many times, leading to low running costs. Aside from the analysis of all possible combinations of peptide, protein, DNA and RNA interactions, this technology can also be used for screening of monoclonal antibodies and epitope mapping, analysis of interactions between low molecular weight compounds and proteins or nucleic acids, interactions between cells and ligands, and real-time monitoring of gene expression. Applications of SPR-based BIA in medicine include the molecular diagnosis of viral infections and genetic diseases caused by point mutations. Future perspectives include the combinations of SPR-based BIA with mass spectrometry, the use of biosensors in proteomics, and the application of this technology to design and develop efficient drug delivery systems.

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References

  1. Reen DJ. Enzyme-linked immunosorbent assay (ELISA). Methods Mol Biol 1994; 32: 461–6

    PubMed  CAS  Google Scholar 

  2. Padget K, Pearson AD, Austin CA. Quantitation of DNA topoisomerase II alpha and beta in human leukaemia cells by immunoblotting. Leukemia 2000; 14(11): 1997–2005

    Article  PubMed  CAS  Google Scholar 

  3. Carey J. Gel retardation. Methods Enzymology 1991; 208: 103–17

    Article  CAS  Google Scholar 

  4. Feriotto G, Ciucci A, Mischiati C, et al. Binding of Epstein-Barr virus nuclear antigen 1 to DNA: inhibition by distamycin and two novel distamycin analogues. Eur J Pharmacol 1994; 267: 143–9

    Article  PubMed  CAS  Google Scholar 

  5. Feriotto G, Mischiati C, Gambari R. Sequence-specific recognition of the HIV-1 long terminal repeat by distamycin: a DNase I footprinting study. Biochem J 1994; 299: 451–8

    PubMed  CAS  Google Scholar 

  6. Mischiati C, Borgatti M, Bianchi N, et al. Interaction of the human NF-kappaB p52 transcription factor with DNA-PNA hybrids mimicking the NF-kappaB binding sites of the human immunodeficiency virus type 1 promoter. J Biol Chem 1999; 274(46): 33114–22

    Article  PubMed  CAS  Google Scholar 

  7. Byfield MP, Abuknesha RA. Biochemical aspects of biosensors. Biosensors Electronics 1994; 9; 373–400

    Article  CAS  Google Scholar 

  8. Evtugyn GA, Budnikov HC, Kolskaya N. Sensitivity and selectivity of electrochemical enzyme sensors for inhibitor determination. Talanta 1998; 46: 465–84

    Article  PubMed  CAS  Google Scholar 

  9. Marko-Varga G, Emneus J, Gorton L. Development of enzyme-based amperometric sensors for the determination of phenolic compounds. Trends Anal Chem 1995; 14: 319–28

    CAS  Google Scholar 

  10. VanEmon JM, Lopez-Avila V. Immunochemical methods for environmental analysis. Anal Chem 1992; 64: 79–88

    Article  Google Scholar 

  11. Karube I. Microbial sensor. J Biotechnol 1990; 15: 255–66

    Article  PubMed  CAS  Google Scholar 

  12. Davies J. Surface Plasmon resonance — the technique and its applications to biomaterial processes. Nanobiology 1994; 3: 5–16

    CAS  Google Scholar 

  13. Jonsson U, Fagerstam L, Ivarsson B, et al. Real-time biospecific interaction analysis using surface plasmon resonance and a sensor chip technology. Bio-Techniques 1991; 11: 620–7

    CAS  Google Scholar 

  14. Johnsson B, Lofas S, Lindquist G. Immobilization of proteins to a carboxymethyldextran-modified gold surface for biospecific interaction analysis in surface plasmon resonance sensors. Anal Biochem 1991; 198(2): 268–77

    Article  PubMed  CAS  Google Scholar 

  15. Karlsson R, Roos H, Fagerstam L, et al. Kinetic and concentration analysis using BIA technology. Methods 1994; 6: 99–110

    Article  CAS  Google Scholar 

  16. Jonsson U, Fagerstam L, Lofas S, et al. Introducing a biosensor based technology for real-time biospecific interaction analysis. Ann Biol Clin (Paris) 1993; 51(1): 19–26

    CAS  Google Scholar 

  17. Malmqvist M. Biospecific interactions analysis using biosensor technology. Nature 1993; 361: 186–7

    Article  PubMed  CAS  Google Scholar 

  18. Nilsson P, Persson B, Uhlén M, et al. Real-time monitoring of DNA manipulations using biosensor technology. Anal Biochem 1995; 224: 400–8

    Article  PubMed  CAS  Google Scholar 

  19. Niemeyer CM, Boldt L, Ceyhan B, et al. DNA-Directed immobilization: efficient, reversible, and site-selective surface binding of proteins by means of covalent DNA-streptavidin conjugates. Anal Biochem 1999; 268(1): 54–63

    Article  PubMed  CAS  Google Scholar 

  20. Feriotto G, Lucci M, Bianchi N, et al. Detection of the ΔF (F508del) mutation of the cystic fibrosis gene by surface plasmon resonance and biosensor technology. Human Mutation 1999; 13: 390–400

    Article  PubMed  CAS  Google Scholar 

  21. Bianchi N, Rutigliano C, Passadore M, et al. Targeting of the HIV-1 long terminal repeat with chromomycin potentiates the inhibitory effects of a triplex-forming oligonucleotide on Sp1-DNA interactions and in vitro transcription. Biochem J 1997; 326: 919–27

    PubMed  CAS  Google Scholar 

  22. Malmqvist M. Epitope mapping by label-free biomolecular interaction analysis. Methods 1996; 9(3): 525–32

    Article  PubMed  CAS  Google Scholar 

  23. Alfthan K. Surface plasmon resonance biosensors as a tool in antibody engineering. Biosens Bioelectron 1998; 13(6): 653–63

    Article  PubMed  CAS  Google Scholar 

  24. Parsons ID, Persson B, Mekhalfia A, et al. Probing the molecular mechanism of action of co-repressor in the E. coli methionine repressor-operator complex using surface plasmon resonance (SPR). Nucleic Acids Res 1995; 23(2): 211–6

    Article  PubMed  CAS  Google Scholar 

  25. Raghavan M, Bjorkman PJ. BIAcore: a microchip-based system for analyzing the formation of macromolecular complexes. Structure 1995; 3(4): 331–3

    Article  PubMed  CAS  Google Scholar 

  26. Fivash M, Towler EM, Fisher RJ. BIAcore for macromolecular interaction. Curr Opin Biotechnol 1998; 9(1): 97–101

    Article  PubMed  CAS  Google Scholar 

  27. Malmqvist M. BIACORE: an affinity biosensor system for characterization of biomolecular interactions. Biochem Soc Trans 1999; 7(2): 335–40

    Google Scholar 

  28. Myszka DG, Rich RL. Implementating surface plasmon resonance biosensors in drug discovery. Pharmaceutical Sci Technol Today 2000; 9: 3310–7

    Google Scholar 

  29. de Mol NJ, Plomp E, Fischer MJ, et al. Kinetic analysis of the mass transport limited interaction between the tyrosine kinase lck SH2 domain and a phosphorylated peptide studied by a new cuvette-based surface plasmon resonance instrument. Anal Biochem 2000; 279(1): 61–70

    Article  PubMed  CAS  Google Scholar 

  30. Buckle PE, Davies RD, Kinning T, et al. The resonant mirror: a novel optical biosensor for direct sensing of biomolecular interactions part II: applications. Biosensors Bioelectronics 1993; 8: 365–70

    Article  Google Scholar 

  31. Cush R, Cronin JM, Stewart WJ, et al. The resonant mirror: a novel optical biosensor for direct sensing of biomolecular interactions part I: principle of operation and associated instrumentation. Biosensors Bioelectronics 1993; 8: 347–64

    Article  CAS  Google Scholar 

  32. Watts HJ, Yeung D, Parkes H. Real-time detection and quantification of DNA hybridization by an optical biosensor. Anal Chem 1995; 67: 4283–9

    Article  PubMed  CAS  Google Scholar 

  33. Lowe PA, Clark TJH, Davies RJ, et al. New approaches for the analysis of molecular recognition using the IAsys evanescent wave biosensor. J Mol Recognit 1998; 11: 194–9

    Article  PubMed  CAS  Google Scholar 

  34. Edwards PR, Maule CH, Leatherbarrow RJ, et al. Second-order kinetic analysis of IAsys biosensor data: its use and applicability. Anal Biochem 1998; 263: 1–12

    Article  PubMed  CAS  Google Scholar 

  35. Newman DJ, Thakkar H, Tang LP, et al. The use of optical sensors to understand cellular interactions with renal cells. Ren Fail 1999; 21: 349–57

    Article  PubMed  CAS  Google Scholar 

  36. Koval VV, Gnedenko OV, Ivanov YD, et al. Real-time oligonucleotide hybridization kinetics monitored by resonant mirror technique. IUMBM Life 1999; 48: 317–20

    CAS  Google Scholar 

  37. Melendez J, Carr R, Bartholomew DU, et al. Development of a surface plasmon resonance sensor for commercial applications. Sensors Actuators-B 1997; 39: 375–9

    Article  Google Scholar 

  38. Elkind JL, Stimpson DI, Anita A, et al. Integrated analytical sensors: the use of the TISPR-1 as a biosensor. Sensors and Actuators-B 1999; 54: 182–90

    Article  Google Scholar 

  39. Woodbury RG, Wendin C, Clendenning J, et al. Construction of surface plasmon resonance biosensors using a gold-binding polypeptide and a miniature integrated sensor. Biosensors Bioelectronics 1998; 13: 1117–26

    Article  PubMed  CAS  Google Scholar 

  40. Senzaki K, Ogawa M, Yagi T. Proteins of the CNR family are Multiple receptors for reelin. Cell 1999; 99: 635–47

    Article  PubMed  CAS  Google Scholar 

  41. Hosono M, Ishikawam K, Mineki R, et al. Tandem repeat structure of rhamnose-binding lectin from catfish (Silurus asotus) eggs. Biochim Biophys Acta 1999; 1472: 668–65

    Article  PubMed  CAS  Google Scholar 

  42. Karlsson R, Stahlberg R. Surface plasmon resonance detection and multispot sensing for direct monitoring of interactions involving low-molecular-weight analytes and for determination of low affinities. Anal Biochem 1995; 228: 274–80

    Article  PubMed  CAS  Google Scholar 

  43. Goldstein B, Coombs D, He X, et al. The influence of transport on the kinetics of binding to surface receptors: application to cells and BIAcore. J Mol Recognit 1999; 12(5): 293–9

    Article  PubMed  CAS  Google Scholar 

  44. Karlsson R. Affinity analysis of non-steady-state data obtained under mass transport limited conditions using BIAcore technology. J Mol Recognit 1999; 12(5): 285–92

    Article  PubMed  CAS  Google Scholar 

  45. Ober RJ, Ward ES. The influence of signal noise on the accuracy of kinetic constants measured by surface plasmon resonance experiments. Anal Biochem 1999; 273(1): 49–59

    Article  PubMed  CAS  Google Scholar 

  46. Ober RJ, Ward ES. The choice of reference cell in the analysis of kinetic data using BIAcore. Anal Biochem 1999; 271(1): 70–80

    Article  PubMed  CAS  Google Scholar 

  47. Joss L, Morton TA, Doyle ML, et al. Interpreting kinetic rate constants from optical biosensor data recorded on a decaying surface. Anal Biochem 1998; 261(2): 203–10

    Article  PubMed  CAS  Google Scholar 

  48. Kortt AA, Oddie GW, Iliades P, et al. Nonspecific amine immobilization of ligand can be a potential source of error in BIAcore binding experiments and may reduce binding affinities. Anal Biochem 1997; 253(1): 103–11

    Article  PubMed  CAS  Google Scholar 

  49. VanCott TC, Loomis LD, Redfield RR, et al. Real-time biospecific interaction analysis of antibody reactivity to peptides from the envelope glycoprotein, gp160, of HIV-1. J Immunol Methods 1992; 146(2): 163–76

    Article  Google Scholar 

  50. Altschuh D, Dubs MC, Weiss E, et al. Determination of kinetic constants for the interaction between a monoclonal antibody and peptides using surface plasmon resonance. Biochemistry 1992; 31(27): 6298–304

    Article  PubMed  CAS  Google Scholar 

  51. Mani JC, Marchi V, Cucurou C. Effect of HIV-1 peptide presentation on the affinity constants of two monoclonal antibodies determined by BIAcore technology. Mol Immunol 1994; 31(6): 439–44

    Article  PubMed  CAS  Google Scholar 

  52. Wohlhueter RM, Parekh K, Udhayakumar V, et al. Analysis of binding of monoclonal antibody to a malarial peptide by surface plasmon resonance biosensor and integrated rate equations. J Immunol 1994; 153(1): 181–9

    PubMed  CAS  Google Scholar 

  53. Hefta LJ, Neumaier M, Shively JE. Kinetic and affinity constants of epitope specific anti-carcinoembryonic antigen (CEA) monoclonal antibodies for CEA and engineered CEA domain constructs. Immunotechnology 1998; 4(1): 49–57

    Article  PubMed  CAS  Google Scholar 

  54. Dougan DA, Malby RL, Gruen LC, et al. Effects of substitutions in the binding surface of an antibody on antigen affinity. Protein Eng 1998; 11(1): 65–74

    Article  PubMed  CAS  Google Scholar 

  55. Osborne J, Harrison P, Butcher R, et al. Novel super-high affinity sheep monoclonal antibodies against CEA bind colon and lung adenocarcinoma. Hybridoma 1999; 18(2): 183–91

    Article  PubMed  CAS  Google Scholar 

  56. Mobini R, Fu M, Wallukat G, et al. A monoclonal antibody directed against an autoimmune epitope on the human beta1-adrenergic receptor recognized in idiopathic dilated cardiomyopathy. Hybridoma 2000; 19(2): 135–42

    Article  PubMed  CAS  Google Scholar 

  57. Johne B. Epitope mapping by surface plasmon resonance in the BIAcore. Mol Biotechnol 1998; 9(1): 65–71

    Article  PubMed  CAS  Google Scholar 

  58. Fisher RJ, Rein A, Fivash M, et al. Sequence-specific binding of human immunodeficiency virus type 1 nucleocapsid protein to short oligonucleotides. J Virol 1998; 72(3): 1902–9

    PubMed  CAS  Google Scholar 

  59. Malmqvist M. Epitope mapping by label-free biomolecular interaction analysis. Methods 1996; 9(3): 525–32

    Article  PubMed  CAS  Google Scholar 

  60. Johne B, Gadnell M, Hansen K. Epitope mapping and binding kinetics of monoclonal antibodies studied by real time biospecific interaction analysis using surface plasmon resonance. J Immunol Methods 1993; 160(2): 191–8

    Article  PubMed  CAS  Google Scholar 

  61. Bellanger L, Andres C, Seguin P. Epitope mapping of 53 antibodies against prostate-specific antigen. Tumour Biol 1999; 20: 18–23

    Article  PubMed  CAS  Google Scholar 

  62. Van Der Geld YM, Limburg PC, Kallenberg CG. Characterization of monoclonal antibodies to proteinase 3 (PR3) as candidate tools for epitope mapping of human anti-PR3 autoantibodies. Clin Exp Immunol 1999; 118(3): 487–96

    Article  Google Scholar 

  63. Zhang J, Kuvelkar R, Murgolo NJ, et al. Mapping and characterization of the epitope(s) of Sch 55700, a humanized mAb, that inhibits human IL-5. Int Immunol 1999; 11(12): 1935–44

    Article  PubMed  CAS  Google Scholar 

  64. Karim B, Beliard R, Huart JJ, et al. Four epitopes on tumor necrosis factor-alpha defined by murine anti-tumor necrosis factor-alpha monoclonal antibodies. Immunol Lett 1994; 41: 139–45

    Article  PubMed  CAS  Google Scholar 

  65. Stigbrand T, Andres C, Bellanger L, et al. Epitope specificity of 30 monoclonal antibodies against cytokeratin antigens: the ISOBM TD5-1 Workshop. Tumour Biol1998; 19: 132–152

    Article  PubMed  CAS  Google Scholar 

  66. Bjorquist P, Ehnebom J, Inghardt T, et al. Epitopes on plasminogen activator inhibitor type-1 important for binding to tissue plasminogen activator. Biochim Biophys Acta 1997; 1341(1): 87–98

    Article  PubMed  CAS  Google Scholar 

  67. Ota A, Ueda S. Evaluation of the affinity measurement of anti-HIV-1 p17 monoclonal antibody by BIAcore. Hybridoma 1998; 17: 471–7

    Article  PubMed  CAS  Google Scholar 

  68. Khalifa MB, Weidenhaupt M, Choulier L, et al. Effects on interaction kinetics of mutations at the VH-VL interface of Fabs depend on the structural context. J Mol Recognit 2000; 13(3): 127–39

    Article  PubMed  CAS  Google Scholar 

  69. Stenman U, Paus E, Allard WJ, et al. Summary report of the TD-3 workshop: characterization of 83 antibodies against prostate-specific antigen. Tumour Biol 1999; 20: 1–12

    Article  PubMed  CAS  Google Scholar 

  70. Liautard J, Gaillard JP, Mani JC, et al. Epitope analysis of human IL-6 receptor gp80 molecule with monoclonal antibodies. Eur Cytokine Netw 1994; 5(3): 293–300

    PubMed  CAS  Google Scholar 

  71. Robert B, Dorvillius M, Buchegger F, et al. Tumor targeting with newly designed biparatopic antibodies directed against two different epitopes of the carcinoembryonic antigen (CEA). Int J Cancer 1999; 81(2): 285–91

    Article  PubMed  CAS  Google Scholar 

  72. Thompson JE, Vaughan TJ, Williams AJ, et al. A fully human antibody neutralising biologically active human TGFbeta2 for use in therapy. J Immunol Methods 1999; 227: 17–29

    Article  PubMed  CAS  Google Scholar 

  73. Coomber DW, Hawkins NJ, Clark MA, et al. Generation of anti-p53 Fab fragments from individuals with colorectal cancer using phage display. J Immunol 1999; 163(4): 2276–83

    PubMed  CAS  Google Scholar 

  74. Vassilev TL, Kazatchkine MD, Van Huyen JP, et al. Inhibition of cell adhesion by antibodies to Arg-Gly-Asp (RGD) in normal immunoglobulin for therapeutic use (intravenous immunoglobulin, IVIg). Blood 1999; 93(11): 3624–31

    PubMed  CAS  Google Scholar 

  75. Allauzen S, Mani JC, Granier C, et al. Epitope mapping and binding analysis of insulin-specific monoclonal antibodies using a biosensor approach. J Immunol Methods 1995; 183(1): 27–32

    Article  PubMed  CAS  Google Scholar 

  76. Manes S, Kremer L, Albar JP, et al. Functional epitope mapping of insulin-like growth factor I (IGF-I) by anti-IGF-I monoclonal antibodies. Endocrinology 1997; 138(3): 905–15

    Article  PubMed  CAS  Google Scholar 

  77. Brigham-Burke M, Edwards JR, O’shannessy DJ. Detection of receptor-ligand interactions using surface plasmon resonance: model studies employing the HIV-1 gp120/CD4 interaction. Anal Biochem 1992; 205(1): 125–31

    Article  PubMed  CAS  Google Scholar 

  78. Batzer AG, Rotin D, Urena JM, et al. Hierarchy of binding sites for Grb2 and Shc on the epidermal growth factor receptor. Mol Cell Biol 1994; 14(8): 5192–201

    PubMed  CAS  Google Scholar 

  79. Shliom O, Huang M, Sachais B, et al. Novel interactions between urokinase and its receptor. J Biol Chem 2000; 275(32): 24304–12

    Article  PubMed  CAS  Google Scholar 

  80. De Crescenzo G, Grothe S, Lortie R, et al. Real-time kinetic studies on the interaction of transforming growth factor alpha with the epidermal growth factor receptor extracellular domain reveal a conformational change model. Biochemistry 2000; 39(31): 9466–76

    Article  CAS  Google Scholar 

  81. Poiesi C, Albertini A, Ghielmi S, et al. Kinetic analysis of TNF-alpha oligomermonomer transition by surface plasmon resonance and immunochemical methods. Cytokine 1993; 5(6): 539–45

    Article  PubMed  CAS  Google Scholar 

  82. Lijnen HR, De Cock F, Collen D. Characterization of the binding of urokinase-type plasminogen activator (u-PA) to plasminogen, to plasminogen-activator inhibitor-1 and to the u-PA receptor. Eur J Biochem 1994; 224(2): 567–74

    Article  PubMed  CAS  Google Scholar 

  83. Lijnen HR, DeCock F, Van Hoef B, et al. Characterization of the interaction between plasminogen and staphylokinase. Eur J Biochem 1994; 224(1): 143–9

    Article  PubMed  CAS  Google Scholar 

  84. Batzer AG, Rotin D, Urena JM, et al. Hierarchy of binding sites for Grb2 and Shc on the epidermal growth factor receptor. Mol Cell Biol 1994; 14(8): 5192–201

    PubMed  CAS  Google Scholar 

  85. Jansson M, Uhlen M, Nilsson B. Structural changes in insulin-like growth factor (IGF) I mutant proteins affecting binding kinetic rates to IGF binding protein 1 and IGF-I receptor. Biochemistry 1997; 36(14): 4108–17

    Article  PubMed  CAS  Google Scholar 

  86. Al-Shamkhani A, Mallett S, Brown MH, et al. Affinity and kinetics of the interaction between soluble trimeric OX40 ligand, a member of the tumor necrosis factor superfamily, and its receptor OX40 on activated T cells. J Biol Chem 1997; 272(8): 5275–82

    Article  PubMed  CAS  Google Scholar 

  87. Liparoto SF, Ciardelli TL. Biosensor analysis of the interleukin-2 receptor complex. J Mol Recognit 1999; 12(5): 316–21

    Article  PubMed  CAS  Google Scholar 

  88. Karlsson R, Kullman-Magnusson M, Hamalainen MD, et al. Biosensor analysis of drug-target interactions: direct and competitive binding assays for investigation of interactions between thrombin and thrombin inhibitors. Anal Biochem 2000; 278(1): 1–13

    Article  PubMed  CAS  Google Scholar 

  89. Wu Z, Johnson KW, Choi Y, et al. Ligand binding analysis of soluble interleukin-2 receptor complexes by surface plasmon resonance. J Biol Chem 1995; 270(27): 16045–51

    Article  PubMed  CAS  Google Scholar 

  90. Park BW, Zhang HT, Wu C, et al. Rationally designed anti-HER2/neu peptide mimetic disables P185HER2/neu tyrosine kinases in vitro and in vivo. Nat Biotechnol 2000; 18(2): 194–8

    Article  PubMed  CAS  Google Scholar 

  91. Myszka DG, Arulanantham PR, Sana T, et al. Kinetic analysis of ligand binding to interleukin-2 receptor complexes created on an optical biosensor surface. Protein Sci 1996; 5(12): 2468–78

    Article  PubMed  CAS  Google Scholar 

  92. Sadana A. Analyte-receptor binding kinetics for biosensor applications. An analysis of the influence of the fractal dimension on the binding rate coefficient. Appl Biochem Biotechnol 1998; 73: 89–112

    Article  PubMed  CAS  Google Scholar 

  93. Markgren PO, Hamalainen M, Danielson UH. Kinetic analysis of the interaction between HIV-1 protease and inhibitors using optical biosensor technology. Anal Biochem 2000; 279(1): 71–8

    Article  PubMed  CAS  Google Scholar 

  94. Takano E, Hatanaka M, Maki M. Real-time-analysis of the calcium-dependent interaction between calmodulin and a synthetic oligopeptide of calcineurin by a surface plasmon resonance biosensor. FEBS Lett 1994; 352(2): 247–50

    Article  PubMed  CAS  Google Scholar 

  95. Shepard HM, Lewis GD, Sarup JC, et al. Monoclonal antibody therapy of human cancer: taking the HER2 protooncogene to the clinic. J Clin Immunol 1991; 11(3): 117–27

    Article  PubMed  CAS  Google Scholar 

  96. Berg OG, VonHippel PH. Selection of DNA binding sites by regulatory proteins. Trends Biochem Sci 1988; 13: 207–11

    Article  PubMed  CAS  Google Scholar 

  97. Faisst S, Meyer S. Compilation of vertebrate-encoded transcription factors. Nucleic Acids Res 1992; 20: 3–26

    Article  PubMed  CAS  Google Scholar 

  98. Mitchell PJ, Tjian R. Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science 1989; 2: 371–8

    Article  Google Scholar 

  99. Weis L, Reinberg D. Transcription by RNA polymerase II: initiator-directed formation of transcription-competent complexes. FASEB J 1992; 6: 3300–9

    PubMed  CAS  Google Scholar 

  100. Fisher RJ, Fivash M, Casas-Finet J, et al. Real-time DNA binding measurements of the ETS1 recombinant oncoproteins reveal significant kinetic differences between the p42 and p51 isoforms. Protein Sci 1994; 3(2): 257–66

    Article  PubMed  CAS  Google Scholar 

  101. Terenzi H, Petropoulos I, Ellouze C, et al. Interaction of DNA binding domain of HNF-3 alpha with its transferrin enhancer DNA specific target site. FEBS Lett 1995; 369(2-3): 277–82

    Article  PubMed  CAS  Google Scholar 

  102. Malmborg AC, Johansson K, Sigvardsson M, et al. Real-time analysis of Oct protein-octamer interaction and transcription complex assembly. Mol Immunol 1995; 32: 1429–42

    Article  PubMed  CAS  Google Scholar 

  103. Paal K, Baeuerle PA, Schmitz ML. Basal transcription factors TBP and TFIIB and the viral coactivator E1A 13S bind with distinct affinities and kinetics to the transactivation domain of NF-kappaB p65. Nucleic Acids Res 1997; 25(5): 1050–5

    Article  PubMed  CAS  Google Scholar 

  104. Gambari R, Bianchi N, Rutigliano C, et al. Surface plasmon resonance for real-time detection of molecular interactions between chromomycin and target DNA sequences. Int J Oncol 1997; 11: 145–9

    PubMed  CAS  Google Scholar 

  105. Cheskis BJ, Karathanasis S, Lyttle CR. Estrogen receptor ligands modulate its interaction with DNA. J Biol Chem 1997; 272(17): 11384–91

    Article  PubMed  CAS  Google Scholar 

  106. Aramburu J, Garcia-Cozar F, Raghavan A, et al. Selective inhibition of NFAT activation by a peptide spanning the calcineurin targeting site of NFAT. Mol Cell 1998; 1(5): 627–37

    Article  PubMed  CAS  Google Scholar 

  107. Cornille F, Emery P, Schuler W, et al. Protein, Nucleotide, Structure DNA binding properties of a chemically synthesized DNA binding domain of hRFX1. Nucleic Acids Res 1998; 26: 2143–9

    Article  PubMed  CAS  Google Scholar 

  108. Bryan D, Aylwin SJ, Newman DJ, et al. Steroidogenic factor 1-DNA binding: a kinetic analysis using surface plasmon resonance. J Mol Endocrinol 1999; 22(3): 241–9

    Article  PubMed  CAS  Google Scholar 

  109. Azuma Y, Renault L, Garcia-Ranea JA, et al. A. model of the ran-RCC1 interaction using biochemical and docking experiments. J Mol Biol 1999; 289(4): 1119–30

    Article  PubMed  CAS  Google Scholar 

  110. Oda M, Furukawa K, Sarai A, et al. Kinetic analysis of DNA binding by the c-Myb DNA-binding domain using surface plasmon resonance. FEBS Lett 1999; 454(3): 288–92

    Article  PubMed  CAS  Google Scholar 

  111. Pio F, Assa-Munt N, Yguerabide J, et al. Mutants of ETS domain PU.1 and GGAA/T recognition: free energies and kinetics. Protein Sci 1999; 8(10): 2098–109

    Article  PubMed  CAS  Google Scholar 

  112. Galio L, Briquet S, Cot S, et al. Analysis of interactions between huGATA-3 transcription factor and three GATA regulatory elements of HIV-1 long terminal repeat, by surface plasmon resonance. Anal Biochem 1997; 253(1): 70–7

    Article  PubMed  CAS  Google Scholar 

  113. Michalopoulos I, Hay RT. Role of the conserved lysine 80 in stabilisation of NF-kappaB p50 DNA binding. Nucleic Acids Res 1999; 27(2): 503–9

    Article  PubMed  CAS  Google Scholar 

  114. Young ET, Kacherovsky N, Cheng C. An accessory DNA binding motif in the zinc finger protein Adr1 assists stable binding to DNA and can be replaced by a third finger. Biochemistry 2000; 39(3): 567–74

    Article  PubMed  CAS  Google Scholar 

  115. Peng H, Begg GE, Harper SL, et al. Biochemical analysis of the Kruppel-associated box (KRAB). J Biol Chem 2000; 275(24): 18000–10

    Article  PubMed  CAS  Google Scholar 

  116. Tanaka Y, Shimoike T, Ishii K, et al. Selective binding of hepatitis C virus core protein to synthetic oligonucleotides corresponding to the 5′ untranslated region of the viral genome. Virology 2000; 270(1): 229–36

    Article  PubMed  CAS  Google Scholar 

  117. Ohno T, Umeda S, Hamasaki N, et al. Binding of human mitochondrial transcription factor A, an HMG box protein, to a four-way DNA junction. Biochem Biophys Res Commun 2000; 271(2): 492–8

    Article  PubMed  CAS  Google Scholar 

  118. Saijo M, Kuraoka I, Masutani C, et al. Sequential binding of DNA repair proteins RPA and ERCC1 to XPA in vitro. Nucleic Acids Res 1996; 24(23): 4719–24

    Article  PubMed  CAS  Google Scholar 

  119. Wang M, Mahrenholz A, Lee SH. RPA stabilizes the XPA-damaged DNA complex through protein-protein interaction. Biochemistry 2000; 39(21): 6433–9

    Article  PubMed  CAS  Google Scholar 

  120. Hosfield DJ, Mol CD, Shen B, et al. Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity. Cell 1998; 95(1): 135–46

    Article  PubMed  CAS  Google Scholar 

  121. Tang L, Li J, Katz DS, et al. Determining the DNA bending angle induced by non-specific high mobility group-1 (HMG-1) proteins: a novel method. Biochemistry 2000; 39(11): 3052–60

    Article  PubMed  CAS  Google Scholar 

  122. Burch LR, Midgley CA, Currie RA, et al. Mdm2 binding to a conformationally sensitive domain on p53 can be modulated by RNA. FEBS Lett 2000; 472(1): 93–8

    Article  PubMed  CAS  Google Scholar 

  123. DeZutter JK, Knight KL. The hRad51 and RecA proteins show significant differences in cooperative binding to single-stranded DNA. J Mol Biol 1999; 293(4): 769–80

    Article  PubMed  CAS  Google Scholar 

  124. Cheskis B, Freedman LP. Modulation of nuclear receptor interactions by ligands: kinetic analysis using surface plasmon resonance. Biochemistry 1996; 35(10): 3309–18

    Article  PubMed  CAS  Google Scholar 

  125. Suen CS, Berrodin TJ, Mastroeni R, et al. A transcriptional coactivator, steroid receptor coactivator-3, selectively augments steroid receptor transcriptional activity. J Biol Chem 1998; 273(42): 27645–53

    Article  PubMed  CAS  Google Scholar 

  126. Galio L, Briquet S, Vaquero C. Real-time study of interactions between a composite DNA regulatory region (HIV-1 LTR NRE) and several transcription factors of nuclear extracts. Biochem Biophys Res Commun 1999; 264(1): 6–13

    Article  PubMed  CAS  Google Scholar 

  127. Matsuda T, Morikawa M, Haruki M, et al. Isolation of TBP-interacting protein (TIP) from a hyperthermophilic archaeon that inhibits the binding of TBP to TATA-DNA. FEBS Lett 1999; 457(1): 38–42

    Article  PubMed  CAS  Google Scholar 

  128. Passadore M, Bianchi N, Feriotto G, et al. Differential effects of distamycin analogues on amplification of human gene sequences by polymerase-chain reaction. Biochem J 1995; 308: 513–9

    PubMed  CAS  Google Scholar 

  129. Sastry M, Fiala R, Patel DJ. Solution structure of mithramycin dimers bound to partially overlapping sites on DNA. J Mol Biol 1995; 251: 674–689

    Article  PubMed  CAS  Google Scholar 

  130. Welch JJ, RausherIII FJ, Beerman TA. Targeting DNA-binding drugs to sequence-specific transcription factor. DNA complexes. J Biol Chem 1994; 269: 31051–31058

    PubMed  CAS  Google Scholar 

  131. Bischoff G, Bischoff R, Birch-Hirschfeld E, et al. DNA-drug interaction measurements using surface plasmon resonance. J Biomol Struct Dyn 1998; 16(2): 187–203

    Article  PubMed  CAS  Google Scholar 

  132. Gambari R, Feriotto G, Rutigliano C, et al. Biospecific interaction analysis (BIA) of low-molecular weight DNA-binding drugs. J Pharmacol Exp Ther 2000; 294(1): 370–7

    PubMed  CAS  Google Scholar 

  133. Boger DL, Saionz KW. DNA binding properties of key sandramycin analogues: systematic examination of the intercalation chromophore. Bioorg Med Chem 1999; 7(2): 315–21

    Article  PubMed  CAS  Google Scholar 

  134. Xavier KA, Eder PS, Giordano T. RNA as a drug target: methods for biophysical characterization and screening. Trends Biotechnol 2000; 18: 349–56

    Article  PubMed  CAS  Google Scholar 

  135. Wong CH, Hendrix M, Priestley ES, et al. Specificity of aminoglycoside antibiotics for the A-site of the decoding region of ribosomal RNA. Chem Biol 1998; 5(7): 397–406

    Article  PubMed  CAS  Google Scholar 

  136. VanRyk DI, Venkatesan S. Real-time kinetics of HIV-1 Rev-Rev response element interactions. Definition of minimal binding sites on RNA and protein stoichiometric analysis. J Biol Chem 1999; 274: 17452–63

    Article  PubMed  Google Scholar 

  137. Tanious FA, Ding D, Patrick DA, et al. Effects of compound structure on Carbazole-DNA complexes: tests of the minor-groove complex models. Biochemistry 2000; 39: 12091–101

    Article  PubMed  CAS  Google Scholar 

  138. Reichert J, Jabs A, Slickers P, et al. The IMB Jena Image Library of Biological Macromolecules. Nucleic Acids Res 2000; 28: 246–9, and available at http://www.imb.jena.de/IMAGE.html

    Article  PubMed  CAS  Google Scholar 

  139. Mizushina Y, Kamisuki S, Mizuno T, et al. Dehydroaltenusin: A mammalian DNA polymerase alpha inhibitor. J Biol Chem 2000; 275: 33957–61

    Article  PubMed  CAS  Google Scholar 

  140. Quinn JG, O’Neill S, Doyle A, et al. Development and application of surface plasmon resonance-based biosensors for the detection of cell-ligand interactions. Anal Biochem 2000; 281(2): 135–43

    Article  PubMed  CAS  Google Scholar 

  141. Affinity Sensors On Line. IAsys{R} Application Note 5.2. Available at: URL: http://w.affinity-sensors.com/pdf/appnotes/APPNOTES5-2.PDF [Accessed 2001 April]

  142. Affinity Sensors On Line. IAsys{R} Application Note 5.3 Available at: URL: http://w.affinity-sensors.com/pdf/appnotes/APPNOTES5-3.PDF [Accessed 2001 April]

  143. Uhlmann E, Peyman A. Antisense oligonucleotides: a new therapeutic principle. Chem Rev 1990; 90: 543–84

    Article  CAS  Google Scholar 

  144. McShean WM, Rossen RD, Laughter AH, et al. Inhibition of transcription of HIV-1 in infected human cells by oligodeoxynucleotides designed to form DNA triple helices. J Biol Chem 1992; 267: 5712–21

    Google Scholar 

  145. Morishita R, Sugimoto T, Aoki M, et al. In vivo transfection of cis element ‘decoy’ against nuclear factor-kappaB binding site prevents myocardial infarction. Nat Med 1997; 3: 894–9

    Article  PubMed  CAS  Google Scholar 

  146. Good L, Nielsen PE. Progress in developing PNA as a gene-targeted drug. Antisense Nucleic Acid Drug Dev 1997; 7: 431–7

    Article  PubMed  CAS  Google Scholar 

  147. Simoes-Wust AP, Olie RA, Gautschi O, et al. Bcl-xl antisense treatment induces apoptosis in breast carcinoma cells. Int J Cancer 2000; 87(4): 582–90

    Article  PubMed  CAS  Google Scholar 

  148. Agarwal N, Gewirtz AM. Oligonucleotide therapeutics for hematologic disorders. Biochim Biophys Acta 1999; 1489(1): 85–96

    Article  PubMed  CAS  Google Scholar 

  149. Lacerra G, Sierakowska H, Carestia C, et al. Restoration of hemoglobin A synthesis in erythroid cells from peripheral blood of thalassemic patients. Proc Natl Acad Sci U S A 2000; 97(17): 9591–6

    Article  PubMed  CAS  Google Scholar 

  150. Persson B, Stenhag K, Nilsson P, et al. Analysis of oligonucleotide probe affinities using surface plasmon resonance: a means for mutational scanning. Anal Biochem 1997; 246(1): 34–44

    Article  PubMed  CAS  Google Scholar 

  151. Jensen KK, Orum H, Nielsen PE, et al. Kinetics for hybridization of peptide nucleic acids (PNA) with DNA and RNA studied with the BIAcore technique. Biochemistry 1997; 36(16): 5072–7

    Article  PubMed  CAS  Google Scholar 

  152. Rutigliano C, Bianchi N, Tomassetti M, et al. Surface plasmon resonance for real-time monitoring of molecular interactions between a triple helix forming oligonucleotide and the Sp1 binding sites of human Ha-ras promoter: effects of the DNA-binding drug chromomycin. Int J Oncol 1998; 12(2): 337–43

    PubMed  CAS  Google Scholar 

  153. Krone JR, Nelson RW, Dogruel D, et al. BIA/MS: interfacing biomolecular interaction analysis with mass spectrometry. Anal Biochem 1997; 244(1): 124–32

    Article  PubMed  CAS  Google Scholar 

  154. Nelson RW, Krone JR, Jansson O. Surface plasmon resonance biomolecular interaction analysis mass spectrometry. 1. Chip-based analysis. Anal Chem 1997; 69(21): 4363–8

    Article  PubMed  CAS  Google Scholar 

  155. Sonksen CP, Nordhoff E, Jansson O, et al. Combining MALDI mass spectrometry and biomolecular interaction analysis using a biomolecular interaction analysis instrument. Anal Chem 1998; 70(13): 2731–6

    Article  PubMed  CAS  Google Scholar 

  156. Nelson RW, Nedelkov D, Tubbs KA. Biosensor chip mass spectrometry: a chip-based proteomics approach. Electrophoresis 2000; 21(6): 1155–63

    Article  PubMed  CAS  Google Scholar 

  157. Danelian E, Karlen A, Karlsson R, et al. SPR biosensor studies of the direct interaction between 27 drugs and a liposome surface: correlation with fraction absorbed in humans. J Med Chem 2000; 43(11): 2083–6

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

Acknowledgments: We thank ISS (AIDS 1998), CNR (Target Project on Biotechnology), MURST (PRIN-1998) and Ministero della Sanità (Progetto per la Ricerca Finalizzata 1998) for financial support.

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  1. Department of Biochemistry and Molecular Biology, and Biotechnology Center, Ferrara University, Ferrara, Italy

    Roberto Gambari

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Gambari, R. Biospecific Interaction Analysis. Am J Pharmacogenomics 1, 119–135 (2001). https://doi.org/10.2165/00129785-200101020-00005

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