Analyzing DNA-Protein Interactions on a Chip

  • Limin Lin
  • James P. Brody
Part of the Biotechnology Intelligence Unit book series (BIOIU)


Gene expression is regulated by multi-protein complexes binding to short noncoding regions of genomic DNA, called cis-regulatory elements. A long-term goal of genomics is to identify and annotate all essential elements of the genome. Most coding elements of the genome have been identified and annotated; however, most regulatory elements have not. This chapter describes a method for the high throughput identification of DNA-protein interactions to identify cis-regulatory elements.


Surface Plasmon Resonance Single Base Pair Surface Plasmon Resonance Imager Surface Plasmon Resonance Angle Surface Plasmon Resonance Signal 
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. 1.
    Lemon B, Tjian R. Orchestrated response: a symphony of transcription factors for gene control. Genes Dev 2000; 14(20):2551–2569.PubMedCrossRefGoogle Scholar
  2. 2.
    Wilson WD. Tech Sight. Analyzing biomolecular interactions. Science 2002; 295(5562):2103–2105.PubMedCrossRefGoogle Scholar
  3. 3.
    Davidson EH. Genomic regulatory systems: development and evolution. San Diego: Academic Press 2001.Google Scholar
  4. 4.
    Travers AA, Buckle M. DNA, protein interactions: a practical approach, New York: Oxford University Press 2000.Google Scholar
  5. 5.
    Ausubel FM. Current protocols in molecular biology. Media, Pa.: Greene Publishing Associates 1987.Google Scholar
  6. 6.
    Galas DJ. The invention of footprinting. Trends Biochem Sci 2001; 26(11):690–693.PubMedCrossRefGoogle Scholar
  7. 7.
    Michelson AM. Deciphering genetic regulatory codes: a challenge, for functional genomics. Proc Natl Acad Sci USA 2002; 99(2):546–548.PubMedCrossRefGoogle Scholar
  8. 8.
    Tompa M, Li N, Bailey TL et al. Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 2005; 23(1):137–144.PubMedCrossRefGoogle Scholar
  9. 9.
    Hasty J, McMillen D, Isaacs F et al. Computational studies of gene regulatory networks: in numero molecular biology. Nat Rev Genet 2001; 2(4):268–279.PubMedCrossRefGoogle Scholar
  10. 10.
    Pilpel Y, Sudarsanam P, Church GM. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet 2001; 29(2):153–159.PubMedCrossRefGoogle Scholar
  11. 11.
    Qian J, Lin J, Luscombe NM et al. Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics 2003; 19(15):1917–1926.PubMedCrossRefGoogle Scholar
  12. 12.
    Cooper MA. Optical biosensors in drug discovery. Nat Rev Drug Discov 2002; 1(7):515–528.PubMedCrossRefGoogle Scholar
  13. 13.
    Mozsolits H, Thomas WG, Aguilar MI. Surface plasmon resonance spectroscopy in the study of membrane-mediated cell signalling. J Pept Sci 2003; 9(2):77–89.PubMedCrossRefGoogle Scholar
  14. 14.
    Mullett WM, Lai EP, Yeung JM. Surface plasmon resonance-based immunoassays. Methods 2000; 22(1):77–91.PubMedCrossRefGoogle Scholar
  15. 15.
    Gonzales NR, Schuck P, Schlom J et al. Surface plasmon resonance-based competition assay to assess the sera reactivity of variants of humanized antibodies. J Immunol Methods 2002; 268(2):197–210.PubMedCrossRefGoogle Scholar
  16. 16.
    Rich RL, Myszka DG. Spying on HIV with SPR. Trends Microbiol 2003; 11(3):124–133.PubMedCrossRefGoogle Scholar
  17. 17.
    Kukanskis K, Elkind J, Melendez J et al. Detection of DNA hybridization using the TISPR-1 surface plasmon resonance biosensor. Anal Biochem 1999; 274(1):7–17.PubMedCrossRefGoogle Scholar
  18. 18.
    Baird CL, Myszka DG. Current and emerging commercial optical biosensors. J Mol Recognit 2001; 14(5):261–268.PubMedCrossRefGoogle Scholar
  19. 19.
    Jonsson U, Fagerstam L, Ivarsson B et al. Real-time biospecific interaction analysis using surface plasmon resonance and a sensor chip technology. Biotechniques 1991; 11(5):620–627.PubMedGoogle Scholar
  20. 20.
    Sjolander S, Urbaniczky C. Integrated fluid handling system for biomolecular interaction analysis. Anal Chem 1991; 63(20):2338–2345.PubMedCrossRefGoogle Scholar
  21. 21.
    Malmqvist M. Biospecific interaction analysis using biosensor technology. Nature 1993; 361(6408):186–187.PubMedCrossRefGoogle Scholar
  22. 22.
    Melendez J, Carr R, Bartholomew DU et al. A commercial solution for surface plasmon sensing. Sens Actuators B Chem 1996; 35(1–3):212–216.CrossRefGoogle Scholar
  23. 23.
    Elkind JL, Stimpson DI, Strong AA et al. Integrated analytical sensors: the use of the TISPR-1 as a biosensor. Sens Actuators B Chem 1999; 54(1–2):182–190.CrossRefGoogle Scholar
  24. 24.
    Liedberg B, Nylander C, Lundstrom I. Surface-Plasmon Resonance for Gas-Detection and Biosensing. Sens Actuators 1983; 4(2):299–304.Google Scholar
  25. 25.
    Rothenhausler B, Knoll W. Surface-Plasmon Microscopy. Nature 1988; 332(6165):615–617.CrossRefGoogle Scholar
  26. 26.
    Fu E, Foley J, Yager P. Wavelength-tunable surface plasmon resonance microscope. Rev Sci Instrum 2003; 74(6):3182–3184.CrossRefGoogle Scholar
  27. 27.
    Wegner GJ, Lee HJ, Marriott G et al. Fabrication of histidine-tagged fusion protein arrays for surface plasmon resonance imaging studies of protein-protein and protein-DNA interactions. Anal Chem 2003; 75(18):4740–4746.PubMedCrossRefGoogle Scholar
  28. 28.
    Naimushin AN, Soelberg SD, Nguyen DK et al. Detection of Staphylococcus aureus enterotoxin B at femtomolar levels with a miniature integrated two-channel surface plasmon resonance (SPR) sensor. Biosens Bioelectron 2002; 17(6–7):573–584.PubMedCrossRefGoogle Scholar
  29. 29.
    Whelan RJ, Wohland T, Neumann L et al. Analysis of biomolecular interactions using a miniaturized surface plasmon resonance sensor. Anal Chem 2002; 74(17):4570–4576.PubMedCrossRefGoogle Scholar
  30. 30.
    Marejka P, Hruby P, Volka K. Surface plasmon resonance and Raman scattering effects studied for layers deposited on Spreeta sensors. Anal Bioanal Chem 2003; 375(8):1240–1245.Google Scholar
  31. 31.
    Yi SJ, Yuk JS, Jung SH et al. Investigation of selective protein immobilization on charged protein array by wavelength interrogation-based SPR sensor. Mol Cells 2003; 15(3):333–340.PubMedGoogle Scholar
  32. 32.
    Kyo M, Yamamoto T, Motohashi H et al. Evaluation of MafG interaction with Maf recognition element arrays by surface plasmon resonance imaging technique. Genes Cells 2004; 9(2):153–164.PubMedCrossRefGoogle Scholar
  33. 33.
    Shumaker-Parry JS, Zareie MH, Aebersold R et al. Microspotting streptavidin and double-stranded DNA arrays on gold for high-throughput studies of protein-DNA interactions by surface plasmon resonance microscopy. Anal Chem 2004; 76(4):918–929.PubMedCrossRefGoogle Scholar
  34. 34.
    Green NM. Avidin. Adv Protein Chem 1975; 29:85–133.PubMedCrossRefGoogle Scholar
  35. 35.
    Jung LS, Nelson KE, Campbell CT et al. Surface plasmon resonance measurement of binding and dissociation of wild-type and mutant streptavidin on mixed biotin-containing alkylthiolate monolayers, Sens Actuators B Chem 1999; 54(1–2):137–144.CrossRefGoogle Scholar
  36. 36.
    Thompson HG, Harris JW, Wold BJ et al. p62 overexpression in breast tumors and regulation by prostate-derived Ets factor in breast cancer cells. Oncogene 2003; 22(15):2322–2333.PubMedCrossRefGoogle Scholar

Copyright information

© Landes Bioscience and Springer Science+Business Media 2007

Authors and Affiliations

  1. 1.Department of Biomedical EngineeringUniversity of CaliforniaIrvineUSA

Personalised recommendations