The Electronic Influence of Abasic Sites in DNA

Abstract

Abasic sites in DNA are prevalent as both naturally forming defects and as synthetic inclusions for biosensing applications. The electronic impact of these defects in DNA sensor and device configurations has yet to be clarified. Here we report the effect of an abasic site on the rate and yield of charge transport through temperature-controlled analysis of DNA duplex monolayers on multiplexed devices. Transport yield through the abasic site monolayer strongly increases with temperature, but the yield relative to an undamaged monolayer decreases with temperature. This is opposite to the increasing relative yield with temperature from a mismatched base pair, and these effects are accounted for by the unique structural impact of each defect. Notably, the effect of the abasic site is nearly doubled when heated from room temperature to 37 °C. The rate of transport is largely unaffected by the abasic site, showing Arrhenius-type behavior with an activation energy of ∼300 meV. Detailed abasic site investigation elucidates the electrical impact of these biologically spontaneous defects and aids development of biological sensors.

Application of Electrochemical Devices to Characterize the Dynamic Actions of Helicases on DNA

“…26,29 In brief, 1 mm thick Si wafers featuring a 10000 Å thick oxide layer (Silicon Quest, Inc.) were patterned via a two-layer process. For the first layer, the gold electrodes were deposited by a lift-off technique.…”

“…24–29 DNA electrochemistry has been utilized in identifying single nucleotide polymorphisms, 26,30–33 base lesions, 34 protein binding, and enzymatic activity. 31,35–39 One study has investigated the electrochemistry of DNA bound XPD helicases using DNA modified electrodes.…”

Using DNA devices to track anticancer drug activity

“…In the first purification round, DNA oligonucleotides with the 4,4′-dimethoxytrityl group on were eluted, while in the second purification round, DNA oligonucleotides with the 4,4′-dimethoxytrityl group off (removed according to Glen Research procedures for each strand) were purified, each according to previous reports (McWilliams et al 2015; Wohlgamuth et al 2014). The identity of the desired products was confirmed by matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) on a Shimadzu Axima Confidence mass spectrometer.…”

“…The chips/substrates featuring multiplexed gold electrodes for DNA self-assembly and electrochemical experiments were prepared as previously described (McWilliams et al 2015; Slinker et al 2010). In brief, 1 mm thick Si wafers featuring a 10 000 Å thick oxide layer (Silicon Quest, Inc.) were patterned via a two-layer process.…”

Sensing DNA through DNA Charge Transport

“…35 Larger scale structural changes such as dehybridization or melting of the duplex may be used to provide necessary confirmation of DNA CT in some context, especially when they are used in the sensing experiment that is being established. 36 Careful use of multiple redox probes, some that are able to undergo DNA CT, such as an intercalator, and others that are unable to undergo DNA CT, for example ruthenium hexammine, can also be used to confirm a DNA-mediated signal.…”