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Electrochemical detection of single-nucleotide mismatches using an electrode microarray.

Li X, Lee JS, Kraatz HB

Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada S7N 5E5.

Gold electrode arrays with electrode diameters of 10 mum were used for the detection of eight single-nucleotide mismatches in unlabeled and prehybridized DNA by electrochemical impedance spectroscopy (EIS). Because of the differences in the electrical properties of films of duplex DNA (normal duplex DNA in B-form) in the presence and absence of Zn(2+) at pH > or = 8.6, Randles equivalent circuits were employed to evaluate the EIS results. The difference in the charge-transfer resistance (DeltaR(CT)) between B-DNA (absence of Zn(2+) at pH > or = 8.6) and M-DNA (presence of Zn(2+) at pH > or = 8.6) allows unequivocal detection of all eight single-nucleotide mismatches within a 20-mer DNA sequence. After dehybridization/rehybridization with target DNA, DeltaR(CT) allows the discrimination of single-nucleotide mismatches with concentrations of the target strand as low as 10 fM. Although the presence of protein impurities (bovine serum albumin, 10 microg/mL) interferes with the detection of the target strand (1 pM detection limit), the presence of nontarget DNA (calf thymus DNA, 10(-8) M) does not interfere, and the detection limit for recognition of the target strand remains at 10 fM.

Published 1 September 2006 in Anal Chem, 78(17): 6096-101.
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