Investigation of specific interactions between Nile blue and single type oligonucleotides and its application in electrochemical detection of hepatitis C 3a virus

In this study, development of an electrochemical DNA biosensor based on a hepatitis C virus probe was introduced using an electrochemically pre-treated pencil graphite electrode (PPGE) as a transducer and Nile blue (NB) as an electroactive indicator. At first, the electrochemical behaviour of NB on the PPGE was investigated. Then, elucidating the specific interaction of NB with each of the nucleotides of DNA, the interactions of NB with oligonucleotides containing only one base type were studied. In this study, four 18-mer oligonucleotides of poly A, poly T, poly C, and poly G were used as probe and were used as related complementary/non-complementary sequences in the hybridization section. The extent of hybridization was evaluated based on the difference between DPV signals of NB accumulated on the probe-PPGE and NB accumulated on the probe-target-PPGE. Then, the developed biosensor was applied successively for the detection of short sequences of Hepatitis C 3a virus (14 pic). The hybridization between the probe (14 pic) and its complementary sequence (C(2)Comp) as the target was studied. Some hybridization experiments with non-complementary oligonucleotides also showed that the suggested DNA sensor responds selectively to the target. Diagnostic performance of the developed biosensor was described and the detection limit was found to be 1.1 nM with a relative standard deviation of 3.5 % in the 0.1-M Tris-HCl buffer solution (pH 7.0) containing 20 mM NaCl.