Kinetics of charge transport through self-assembled DNA monolayers: Influence of DNA defects and applications for biosensing

Charge transport (CT) through DNA is not yet well understood, but is of importance both fundamentally and in applications such as biosensing. The kinetics of charge transport through self-assembled DNA monolayers was examined using the electrochemical techniques of cyclic voltammetry (CV) and square wave voltammetry (SWV) as complimentary methods for verification of extracted kinetic parameters. DNA, synthesized with and without defects to the base pair pi-stack, was attached to gold working electrodes through incorporation of a six-carbon thiolated linker. Electrical properties were monitored by following the redox signal of Nile blue covalently attached to a modified thymine. Controlled variation in temperature revealed from CV and SWV that DNA CT increases dramatically with temperature until the dehybridization of the DNA causes the single strand containing the redox probe to no longer be coupled to the monolayer. 17-mer DNA containing a single CA mismatch was compared directly to fully well-matched DNA of otherwise identical sequence using multiplexed chips. The mismatch defect was found to greatly attenuate CT at low temperatures and gradually approximate a well-matched sequence as temperature increased. In contrast, DNA containing a single missing base (abasic) site showed only marginal CT decrease relative to well-matched DNA at low temperature, but diverged from the well-matched DNA as temperature increased. Experimental data acquired via SWV was fit to theoretical curves using a modified Nelder-Mead simplex algorithm and kinetic parameters were determined. The electron transfer rate constant k0 was compared across different types of DNA monolayers and Arrhenius behavior was observed. CT implications to disruptions in the pi-stack were then utilized for the sensing of enzymes formamidopyrimidine DNA glycosylase (FPG) and uracil-DNA glycosylase (UDG) by incorporation of defects 8-oxoguanine and uracil into DNA monolayers. Sensitive and selective detection of both enzymes was achieved. Additionally, signal loss due to specific enzyme binding activities was monitored in real-time to determine temperature dependent kinetics of enzyme reactions with target DNA substrates. Versatility of the DNA-mediated electrochemical sensing platform was demonstrated through detection of FPG on gold-coated polyacrylonitrile (PAN) nanofibers. These results are important for the improved understanding of DNA CT properties and to the field of biosensing.