Sensors 2010, 10(8), 7371-7385; doi:10.3390/s100807371
Article

Use of a Multiplexed CMOS Microarray to Optimize and Compare Oligonucleotide Binding to DNA Probes Synthesized or Immobilized on Individual Electrodes

Karl Maurer 1 email, Nina Yazvenko 1 email, Jodi Wilmoth 1 email, John Cooper 1 email, Wanda Lyon 2 email and David Danley 1,* email
1 CombiMatrix Corporation, 6500 Harbour Heights Parkway, Suite #202, Mukilteo WA 98275, USA 2 AFRL/RHPB, Wright Patterson AFB, 2729 R Street, Area B B837, Dayton, OH 45433, USA
* Author to whom correspondence should be addressed.
Received: 20 June 2010; in revised form: 15 July 2010 / Accepted: 30 July 2010 / Published: 5 August 2010
(This article belongs to the Section Biosensors)
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Abstract: The CombiMatrix microarray with 12,544 electrodes supports in situ electrochemical synthesis of user-defined DNA probes. As an alternative, we immobilized commercially synthesized DNA probes on individual electrodes coated with electropolymerized polypyrrole (Ppy). Hybridization was measured using a biotinylated target oligonucleotide and either Cy5-streptavidin and fluorescence detection or horseradish peroxidase-streptavidin and enzyme-enhanced electrochemical detection. Detection efficiencies were optimized by varying the deposition of the Ppy, the terminal groups on the DNA probes, and other factors that impacted fluorescence quenching and electrical conductivity. Optimized results were compared against those obtained using a microarray with the same DNA sequences synthesized in situ. Immobilized probes produced higher fluorescence signals, possibly by providing a greater stand off between the Cy5 on the target oligonucleotide and the quenching effects of the Ppy and the platinum electrode.
Keywords: CombiMatrix microarray; biosensor; electrochemical detection; DNA; hybridization; polypyrrole

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MDPI and ACS Style

Maurer, K.; Yazvenko, N.; Wilmoth, J.; Cooper, J.; Lyon, W.; Danley, D. Use of a Multiplexed CMOS Microarray to Optimize and Compare Oligonucleotide Binding to DNA Probes Synthesized or Immobilized on Individual Electrodes. Sensors 2010, 10, 7371-7385.

AMA Style

Maurer K, Yazvenko N, Wilmoth J, Cooper J, Lyon W, Danley D. Use of a Multiplexed CMOS Microarray to Optimize and Compare Oligonucleotide Binding to DNA Probes Synthesized or Immobilized on Individual Electrodes. Sensors. 2010; 10(8):7371-7385.

Chicago/Turabian Style

Maurer, Karl; Yazvenko, Nina; Wilmoth, Jodi; Cooper, John; Lyon, Wanda; Danley, David. 2010. "Use of a Multiplexed CMOS Microarray to Optimize and Compare Oligonucleotide Binding to DNA Probes Synthesized or Immobilized on Individual Electrodes." Sensors 10, no. 8: 7371-7385.

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