Electrochemistry of DNA Monolayers Modified With a Perylenediimide Base Surrogate

Abstract

Electrochemistry of self-assembled DNA monolayers represents an attractive strategy for understanding the intrinsic properties of DNA and for developing DNA-based sensors. Thus, there is much interest in the discovery and characterization of new redox-active probes for application in DNA-based technologies. Herein, we report a detailed study of the electrochemical properties of a perylene-3,4,9,10-tetracarboxylic diimide base surrogate, when incorporated at various positions within a DNA monolayer. We demonstrate that the redox chemistry of this perylenediimide probe is mediated by the DNA base pair stack, dependent on its location within the DNA monolayer, and activated thermally. The electrochemical features and general synthetic flexibility of the perylenediimide base surrogate appear favorable for assays that leverage DNA-mediated charge transport.

The Electronic Influence of Abasic Sites in DNA

“…An average activation energy of 326 ± 6 meV was observed for T17-A monolayers. A similar value for E A was also found for T17, which is higher than previously reported for Nile blue monolayers 26,28 and similar constructs, 34,47,48 but closer to theoretically anticipated values for CT through DNA. 49,50 Laviron analysis of the T17-A monolayer was also performed and found to give similar rate results (see Supporting Information Figure 4).…”

“…Thus, the lower values of CT yield through abasic site monolayers as estimated by CV and SWV follow the observed trend that yield is proportional to the stability of the duplex. 28, 34 To further explore the nature of the attenuation of CT yield by an abasic site, we followed the temperature dependence of the square wave peak height from 0°C (near the freezing point of the buffer) up through 55°C, which is beyond the melting transition of the T17-A duplex where the probe strand will no longer be bound to the duplex ( Figure 3A). This figure represents peak heights averaged across the T17 and T17-A monolayers of a single chip and hence compares the monolayers under the same assembly and environmental conditions.…”

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.…”

Length‐Independent Charge Transport in Chimeric Molecular Wires

“…We proceeded to self‐assemble and spectroscopically characterize monolayers from P1 , P2 , P3 , and P4 . As illustrated in Figure B, we incubated clean gold substrates in solutions of each of our thiol‐modified constructs, allowing for the formation of specific covalent S−Au bonds, and then treated the modified substrates with mercaptohexanol to enforce upright macromolecular orientations and displace non‐specifically physisorbed species . We subsequently confirmed the average orientations of the four monolayers’ constituent macromolecules with near edge X‐ray absorption fine structure spectroscopy (NEXAFS), which is a surface‐sensitive technique that can elucidate the electronic characteristics and orientations of surface‐confined molecules.…”

“…First, we selected perylene‐3,4,9,10 tetracarboxylic diimide (PTCDI) as the π‐conjugated building block for our constructs because of this molecule's well‐known electrochemical properties, propensity for adapting stacked columnar arrangements, and excellent stability under various conditions . Next, we used standard automated oligonucleotide synthesis techniques, which are compatible with PTCDI derivatives, to prepare, purify, and characterize thiol‐ and ferrocene‐modified macromolecules featuring one, two, three, or four PTCDIs arranged on a phospho‐alkane backbone (Supporting Information, Figures S1–16). Notably, our constructs’ negatively‐charged backbone and solubilizing hexaethylene glycol imide substituents facilitated processing and mitigated intermolecular aggregation.…”