Ronald G. Sosnowski, Brian Chambers, Gene Tu, Kevin McElfresh, James P. O’Connell and Michael Heller
Nanogen, Inc., San Diego, CA

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The technologies of microfabrication and chemistry have been combined to investigate the effect of electric fields on biomolecular reactions. Other efforts in this area have emphasized miniaturization, array or microfabrication techniques; however, the kinetics of the molecular biology reactions remain controlled by conventional means. This work demonstrates direct manipulation of these interactions.

We have developed an addressable microelectrode array that provides electric field control over a variety of biomolecular reactions. Regulation of the electric field strength and bias allows direction of biomolecular interactions.

A DC electric field applied to specific 80µm diameter test sites directly controls denaturation of DNA. Electric fields contained in a microelectronic device also regulate DNA transport and concentration, thereby facilitating DNA hybridization. Dehybridization discrimination among different DNA hybrids is provided by varying

the strength of the electric field. Additionally, electric field denaturation control allows single base pair mismatch discrimination to be carried out rapidly (<30 seconds) and with high resolution. Electric field denaturation takes place at temperatures well below the melting point of the hybrids, and may constitute a novel method of DNA denaturation.

DNA fingerprinting loci have been examined with this device. In addition to single base pair mismatch discrimination, which can be used for single nucleotide polymorphisms and restriction site polymorphisms, this technology has been applied to discrimination of short tandem repeat sequences (STR). Specifically, the STR locus TH01 has been used as a model system for repeat unit discrimination.