FRET-Based Real-Time DNA Microarrays

  • Arjang HassibiEmail author
  • Haris Vikalo
  • José Luis Riechmann
  • Babak Hassibi
Part of the Methods in Molecular Biology book series (MIMB, volume 815)


We present a quantification method for affinity-based DNA microarrays which is based on the real-time measurements of hybridization kinetics. This method, i.e., real-time DNA microarrays, enhances the detection dynamic range of conventional systems by being impervious to probe saturation, washing artifacts, microarray spot-to-spot variations, and other intensity-affecting impediments. We demonstrate in both theory and practice that the time-constant of target capturing is inversely proportional to the concentration of the target analyte, which we take advantage of as the fundamental parameter to estimate the concentration of the analytes. Furthermore, to experimentally validate the capabilities of this method in practical applications, we present a FRET-based assay which enables the real-time detection in gene expression DNA microarrays.

Key words

Microarray Real-time Gene expression Time-constant FRET 



We are grateful to Vijaya Kumar for experimental assistance with microarray manufacture and target labeling. We also want to thank Professor Scott Fraser at Caltech for technical feedback in the imaging aspects of this project.


  1. 1.
    Monitoring of Gene Expression Patterns with a Complementary DNA Microarray, Science, 270, 467–470.Google Scholar
  2. 2.
    Chee, M., Yang, R., Hubbell, E., Berno, A., Huang, X.C., Stern, D., Winkler, J., Lockhart, D.J., Morris, M.S. and Fodor, S.P. (1996) Accessing Genetic Information with High-Density DNA Arrays, Science, 274, 610–614.Google Scholar
  3. 3.
    Lockhart, D.J. and Winzeler, E.A., (2000) Genomics, Gene Expression and DNA Arrays, Nature, 405, 827–836.Google Scholar
  4. 4.
    Wang, D.G., Fan, J.–B., Siao, C.–J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Winchester, E., Spencer, J., et al. (1998) Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymor­phisms in the Human Genome, Science, 280, 1077–1082.Google Scholar
  5. 5.
    Hardenbol, P., Baner, J., Jain, M., Nilsson, M., Namsaraev, E.A., Karlin-Neumann, G.A., Fakhrai-Rad, H., Ronaghi, M., Willis, T.D., Landegren, U. et. al., (2003) Multiplexed Genotyping with Sequence-Tagged Molecular Inversion Probes, Nat. Biotechnol., 21, 673–678.Google Scholar
  6. 6.
    Hassibi, A., Zahedi, S., Navid, R., Dutton, R.W. and Lee, T.H., (2005) Biological Shot-Noise and Quantum-Limited Signal-to-Noise Ratio in Affinity-Based Biosensors, J. Appl. Phys., 97–084701:1–10.Google Scholar
  7. 7.
    Hassibi, A., Vikalo, H. and Hajimiri, A., (2007) On Noise Processes and Limits of Performance in Biosensors, J. Appl. Phys., 102–014909:1–12.Google Scholar
  8. 8.
    Tu, Y., Stolovitzky, G. and Klein, U., (2002) Quantitative Noise Analysis for Gene Expression Microarray Experiments, Proc. Natl. Acad. Sci., 99–22:14031–14036.Google Scholar
  9. 9.
    Hassibi, A., Vikalo, H., Riechmann, J.L. and Hassibi, B. (2009) Real-time DNA Microarray Analysis, Nucleic Acids Research, doi: 10.1093/nar/gkp 675, 1–12.
  10. 10.
    Okamura, Y., Kondo, S., Sase, I., Suga, T., Mise, K., Furusawa, I., Kawakami, S. and Watanabe, Y. (2000) Double-Labeled Donor Probe can Enhance the Signal of Fluorescence Resonance Energy Transfer (FRET) in Detection of Nucleic Acid Hybridization, Nucleic Acids Research, 28, e107.Google Scholar
  11. 11.
    Rajendran, M. and Ellington, A.D. (2003) In vitro Selection of Molecular Beacons, Nucleic Acids Research, 31–19, 5700–5713.Google Scholar
  12. 12.
    Marras, S.A.E., Tyagi, S. and Kramer, F.R. (2006) Real-time Assays with Molecular Beacons and other Fluorescent Nucleic Acid Hybridization Orobes, Clin Chim Acta, 363, 48–60.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Arjang Hassibi
    • 1
    Email author
  • Haris Vikalo
    • 2
  • José Luis Riechmann
    • 3
  • Babak Hassibi
    • 4
  1. 1.Institute for Cellular and Molecular Biology, University of TexasAustinUSA
  2. 2.Electrical and Computer Engineering DepartmentUniversity of TexasAustinUSA
  3. 3.Division of BiologyCalifornia Institute of TechnologyPasadenaUSA
  4. 4.Electrical Engineering DepartmentCalifornia Institute of TechnologyPasadenaUSA

Personalised recommendations