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FRET-Based Real-Time DNA Microarrays

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

Abstract

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 

Notes

Acknowledgments

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.

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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

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