Electrochemical Characterization of Synthetic Hybrid DNA Molecular Wires
Authors: Golkar Narenji Alaleh , Goshi Noah , Coste Michael , Burns Dillon , Lee Raymond , Ngo Katrina , Purse Byron , Kassegne Sam 
Published: February 2020

Over the past several years, considerable amount of research have been conducted on DNA conductivity studies and charge transfer mechanisms for potential applications in micro and nano-scale electronic devices. In general, there is a consensus that DNA molecule behaves as a one-dimensional aromatic crystal with π-electron conductivity. Along these lines, our recent work has shown that DNA molecular wire’s electrical properties are strongly influenced by the ionization potential and percentage content of its base-pairs that form these π-orbital stacking. Our previous work has also shown the effect of external effects such as humidity, electrical fields, and UV illumination on the long-term stability of DNA molecular wires. In general, with time, there is measurable significant decrease in the conductivity in DNA wires exposed to ambient conditions. Such external effects could also result in the physical change of DNA molecular wires that in turn compromise their suitability as nanoelectronic component.
As a viable solution to long-term stability problems with DNA molecular wires and also tuning their conductivity, we are currently working on synthesizing hybrid DNA molecular wires made of natural base-pairs and synthetic base-pairs with lower ionization potentials and more π-orbital overlapping. One strong candidate is tricyclic cytosine analogue (such as (8-MeO) tC0), a synthetic unnatural base, which possesses (i) a lower ionization potential (~ 0.65 V) compared to natural bases, G (1.29 V), C (1.6 V), A (1.42 V), T (1.7 V) and (ii) more π-orbital stacking than the natural bases due to its tricyclic structure. This unnatural base can be a good choice as it minimally perturbs the structure of B-form DNA. Subsequently, we investigate the charge transfer mechanism of short hybrid doubled stranded DNA (16 bp) consisting of both natural and unnatural bases and compared it to the natural DNA strand of the same length. The whole hybrid DNA sequence is NH2-5’-AtC0TACAGTCATCGCtC0tC0-3’ where some bases were substitute with tricyclic cytosine analogues (tC0).
Two methods are used to study the charge transport through hybrid DNA wires. One is based on the charge transport between donor and acceptor (oxidant and hole trap). The oxidant (donor) is the metallointercalator which has positive charge with either Ru or Rh complex. This intercalator does not perturb the structure of the DNA π stacking as it binds covalently with DNA. The hole trap is two (8-MeO) tC0 molecules in a row, as it can potentially have the lowest ionization potential in the DNA sequence. The donor is then photo-excited and the fluorescence of the donor quenched through the DNA strand during charge transfer to the acceptor. The Ru or Rh complex are positioned at the 5’ of the DNA sequence, apart from the hole trap. A DNA 5 ‘terminus has to be terminated with amine group in order to interact with carboxyl group of Ru or Rh complex through EDC-NHS reaction. The other method is based on electrochemical detection. The sequence to be used is the same as the first method, however, it is terminated with the thiol group SH-5’-AtC0TACAGTCATCGCtC0tC0-3’ in order to be attached easily to gold electrodes. The radox active material (Methylen Blue) acts as an intercalator and its electrocatalytic signal is measured while the electrons pass through the DNA strands attached to the surface. The DNA strands are in the Ferrocyanide solution [Fe(CN)6]-3 which can be reduced by the reduction of methyl blue. The chronocoulometry techniques is then used to measure the electron transport in DNA strand. Between the two methods, we demonstrate that synthetic molecular wires consisting of both natural and strategically placed synthetic bases with lower ionization potential and π stacking will offer a stable and electrically tunable molecular wire.