Nucleic Acids Research Advance Access published online on August 31, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp675
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Methods Online |
Real-time DNA microarray analysis
1Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, 2Electrical Engineering Department, California Institute of Technology, Pasadena, CA 91125, 3Electrical and Computer Engineering Department, University of Texas at Austin, Austin, TX 78712 and 4Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
*To whom correspondence should be addressed. Tel: +1 512 232 7916; Fax: +1 512 471 8967; Email: arjang{at}mail.utexas.edu
Received May 18, 2009. Revised July 27, 2009. Accepted July 30, 2009.
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 in the capturing spots, washing artifacts, microarray spot-to-spot variations, and other signal amplitude-affecting non-idealities. We demonstrate in both theory and practice that the time-constant of target capturing in microarrays, similar to all affinity-based biosensors, is inversely proportional to the concentration of the target analyte, which we subsequently use as the fundamental parameter to estimate the concentration of the analytes. Furthermore, to empirically 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.