______________________________________________________________________ Introduction DNA detection via redox mediators was employed using various mediators such as [Ru(bpy)3] 2+ , [Co(phen)3] 3+ , ferrocene or [Fe(CN)6] 3-/4- (Figure 1.15, a). Catalytic oxidation of guanine using [Ru(bpy)3] 2+ on indium tin oxide (ITO) electrodes is a well-known example 60 . The approach involves addition of DNA into a solution containing the ruthenium complex, while the electrode is held at a potential suitable for the oxidation of the reduced form of the complex. The complex is regenerated by the oxidation of guanine from DNA. Consequently, the signal is enhanced proportionally to the amount of guanine available for oxidation, since the direct guanine oxidation is not possible at ITO electrodes. The characteristics of non-covalently interacting indicators are a different affinity towards dsand ssDNA. They can interact with DNA either by electrostatic binding, binding to the groove of dsDNA or intercalate into dsDNA (Figure 1.15, b). The most widely used indicators are daunomycin, proflavine, antraquinone, methylene blue, [Co(phen)3] 3+ and [Ru(NH3)6] 3+ . One of the initial studies on non-covalent interaction of compounds with DNA was done by Mikkelsen et al., using [Co(phen)3] 3+ as a dsDNA minor groove binder. The metal complex is positively charged and attracted by negatively charged DNA, resulting in a higher current for the more negatively charged dsDNA 61 . Furthermore, Barton and coworkers pioneered the work on long-range charge transfer resistance through DNA, using electrochemically active intercalators 62 (methylene blue and daunomycin). Interaction of non-electrochemically active intercalating compounds was investigated using EIS 63 . First covalently bound DNA markers were investigated in the beginning of the 1980s 46 . Labelling of the DNA can be performed using the probe DNA, where the label is positioned at the distant end of the probe (Figure 1.15, c). Due to the flexibility of the ssDNA, without the presence of target DNA, the label is close enough to the surface and the signal is detected. Upon hybridization the signal switches off due to the rigidity of the dsDNA. Namely, after the hybridization the label is too far away from the surface for the electron transfer to occur. Labelling of the target DNA is also possible, and it is usually done at the end that is close to the surface upon hybridization (Figure 1.15, d). Therefore, after hybridization the signal is switched on. However, this approach requires a preparation step in which the target DNA from the sample needs to be labelled, which prolongs the assay time. In a sandwich-type assay, immobilized probe DNA is initially hybridized with a portion of the non-labelled target DNA from the sample, and subsequently a labelled signal DNA is hybridized with the overhang of the target DNA (Figure 1.15, e). Enzymes are readily used as labels for this approach 64 . In this case, DNA 1.4 Hybridization detection 24
______________________________________________________________________ Introduction detection can be performed using a redox mediator in solution. An alternative approach is to hybridize a signal DNA with an overhang from the target DNA that is placed close to the surface 65 . This way there is no need for the redox mediator to obtain the signal. Figure 1.15. Indirect DNA detection using a) electrochemical mediators, b) non-covalently interacting indicators, c-d) labelling of probe or target DNA and e) sandwich type detection. 1.4 Hybridization detection 25