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Electrochemical DNA array for simultaneous genotyping of single-nucleotide polymorphisms associated with the therapeutic effect of interferon.

Approximately 170 million people worldwide are affected by the hepatitis C virus (HCV). Interferon has been developed to treat HCV hepatitis, but its effectiveness depends on factors including the type and copy number of the infecting viruses and individual patient characteristics. Some single-nucleotide polymorphisms (SNPs) in the host are correlated with responsiveness (1)(2)(3)(4). Two SNPs are at nucleotide positions −88 (G or T) and −123 (C or A) within an interferon-stimulated response element-like sequence in the promoter region of the MxA gene (1)(2). The MxA protein is interferon-inducible and is known to inhibit the replication of a wide variety of single-stranded RNA viruses (5). Two other of these SNPs are at nucleotide position −221 (C or G; X/Y) within the promoter region of the mannose-binding lectin (MBL) gene and at codon 54 (A or G; A/B) within exon 1 of this gene (3)(4). The functions of MBL include the elimination of pathogens (6). The identification of these genetic variations in patients can help predict the efficacy of interferon in the treatment of HCV.

DNA microarrays or DNA chip-based technologies can be used for the simultaneous genotyping of polymorphisms. The technologies used in recently reported DNA hybridization devices or indicators include gold nanoparticles (7)(8), enzyme-amplified electronic transduction (9), electrocatalysis (10), conducting polymers(11), surfactant bilayers (12), surface-attached molecular beacons (13), and ferrocene-labeled signaling probes (14). Most studies involved fundamental investigations of their properties, however, and despite the advances in these detection strategies, there has been relatively little progress toward the goal of simultaneous genotyping of multiple significant genetic variations in real clinical samples.

In previous studies, we have found that Hoechst 33258, which is a minor-groove binder and specifically binds to double-stranded DNA, is electrochemically active and useful for …