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RAPID DISCRIMINATION AMONG INDIVIDUAL DNA MOLECULES IN MICROLITER VOLUMES.   W. Vercoutere¹, S. Winters-Hilt², H. Olsen¹, D. Deamer¹, D. Haussler²  and M. Akeson^1,2*. ¹Department of Chemistry and Biochemistry, and ²Center for Biomolecular Science and Engineering, University of California, Santa Cruz  95064. 

We are developing a lightweight instrument that can discriminate between individual DNA molecules. The apparatus consists of two 70-μl chambers separated by a lipid bilayer barrier in which a single protein channel α-hemolysin is inserted; a potential is applied and the resulting ionic current through the channel is recorded by standard patch-clamp instrumentation. A signature current blockade is produced each time a molecule of DNA enters the pore. Hundreds of DNA molecules can be detected in a minute-long recording. Recognition of current signatures and identification of DNA is done in part by using a machine learning algorithm called a 'Support Vector Machine'. This system can be used to distinguish differences in length, composition and concentration of DNA. No modification of DNA is necessary, unlike other high-resolution DNA techniques. Most recently we used DNA hairpins to model duplex DNA, and have shown that single base-pair and single nucleotide differences can be resolved. This instrument would be useful for detecting damage to DNA caused by radiation. The size of this device and the sensitivity to small differences in DNA make this promising for use in laboratories with close confines such as a space station.

(Supported by NASA: NAG5-9403; and NIH: HG01826-01.)