Affinity interactions between strands of oligonucleotides to bare gold surfaces has been previously established using infrared-based analysis techniques (Kimura-suda et al., 2003). The gradient of affinity interactions has been the basis of detecting methylation in a nucleotide sequence. For example, eMethylsorb detects the percent of DNA methylation using differential pulse voltammetry to determine amount of adsorbed methylated DNA on gold surfaces compared to nonmethylated sequences (Koo et al., 2014). Sensing DNA methylation electrochemically can lead to the development of a point-of-care sensor to diagnose diseases (e.g. cancer, psychiatric disorders) linked to DNA methylation. A sensor that could evaluate global methylation levels without the need of a more expensive genetic sequencing method could be very useful for initial detection.

While differential pulse voltammetry is a useful technique, we hypothesize that electrochemical impedance spectroscopy can provide greater sensitivity. In addition, we are interested in the effect of chain-length on the ability to look at affinity of DNA via electrochemical methods. While electrochemical studies have previously analyzed longer methylated sequences (Koo et al., 2015), we will report on individual nucleic acid bases and smaller repetitive oligonucleotide sequences.

Although there is value at looking in longer sequence adsorption, it requires the isolation of a specific sequence, leading to a larger required sample size, higher cost, and more time. A budding technique in the epigenetic field is examining global levels of methylation which looks at the overall DNA instead of a certain section (Kurdyukov and Bullock, 2016). Individual nucleobases have been characterized through modeling to predict gold interactions, but the affinity interactions between individual nucleobases and gold surfaces have never been characterized electrochemically (Piana and Bilic, 2006). We first propose to investigate the measurement of individual nucleic acid bases before investigating the global DNA makeup.

The fundamental aspect of this approach is to understand the resolution and reproducibility of electrochemical characterization of nucleobases. We will discuss the effect of the solvent used to dissolve nucleobases, oligonucleotide length, and detection technique (e.g. electrochemical impedance spectroscopy, cyclic voltammetry) on the ability to electrochemically distinguish nucleobases. We will conclude with a set of electrochemical conditions to optimally deduce nucleobase absorption on gold surfaces.

References:

Kimura-suda, H., Petrovykh, D.Y., Tarlov, M.J., and Whitman, L.J. (2003). Base-Dependent Competitive Adsorption of Single-Stranded DNA on Gold. JACS 9014–9015.

Koo, K.M., Ibn Sina, A.A., Carrascosa, L.G., Shiddiky, M.J.A., and Trau, M. (2014). eMethylsorb: rapid quantification of DNA methylation in cancer cells on screen-printed gold electrodes. Analyst 139, 6178–6184.

Koo, K.M., Sina, A.A.I., Carrascosa, L.G., Shiddiky, M.J.A., and Trau, M. (2015). DNA–bare gold affinity interactions: mechanism and applications in biosensing. Anal. Methods 7, 7042–7054.

Kurdyukov, S., and Bullock, M. (2016). DNA Methylation Analysis: Choosing the Right Method. Biology (Basel). 5, 3.

Piana, S., and Bilic, A. (2006). The nature of the adsorption of nucleobases on the gold [111] surface. J. Phys. Chem. B 110, 23467–23471.