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Nucleic Acids Research, 2000, Vol. 28, No. 7 E17-e17
© 2000 Oxford University Press

Rapid, high fidelity analysis of simple sequence repeats on an electronically active DNA microchip

Ray Radtkey, Lana Feng, M. Muralhidar, Melanie Duhon, David Canter, Deborah DiPierro1, Sylvia Fallon, Eugene Tu, Kevin McElfresh1, Michael Nerenberg and Ron Sosnowski*

Nanogen Inc., 10398 Pacific Center Court, San Diego, CA 92121, USA and 1The Bode Technology Group, Springfield, VA 22150, USA

We describe a method for the discrimination of short tandem repeat (STR) alleles based on active microarray hybridization. An essential factor in this method is electronic hybridization of the target DNA, at high stringency, in <5 min. High stringency is critical to avoid slippage of hybrids along repeat tracts at allele-specific test sites in the array. These conditions are attainable only with hybridization kinetics realized by electronic concentration of DNA. A sandwich hybrid is assembled, in which proper base stacking of juxtaposed terminal nucleotides results in a thermodynamically favored complex. The increased stability of this complex relative to non-stacked termini and/or base pair mismatches is used to determine the identification of STR alleles. This method is capable of simultaneous and precise identification of alleles containing different numbers of repeats, as well as mutations within these repeats. Given the throughput capabilities of microarrays our system has the potential to enhance the use of microsatellites in forensic criminology, diagnostics and genetic mapping.

* To whom correspondence should be addressed. Tel: +1 858 410 4600; Fax: +1 858 410 4848; Email: rsosnowski@nanogen.com


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