Solution, surface, and single molecule platforms for the study of DNA-mediated charge transport

Abstract

The structural core of DNA, a continuous stack of aromatic heterocycles, the base pairs, which extends down the helical axis, gives rise to the fascinating electronic properties of this molecule that is so critical for life. Our laboratory and others have developed diverse experimental platforms to investigate the capacity of DNA to conduct charge, termed DNA-mediated charge transport (DNA CT). Here, we present an overview of DNA CT experiments in solution, on surfaces, and with single molecules that collectively provide a broad and consistent perspective on the essential characteristics of this chemistry. DNA CT can proceed over long molecular distances but is remarkably sensitive to perturbations in base pair stacking. We discuss how this foundation, built with data from diverse platforms, can be used both to inform a mechanistic description of DNA CT and to inspire the next platforms for its study: living organisms and molecular electronics.

Fig. 1

Platforms for the study of DNA CT. In solution (top), donor and acceptor molecules are covalently tethered or otherwise incorporated into opposite ends of a DNA duplex. DNA CT is initiated by photoexcitation of the donor and measured by spectroscopic or biochemical methods. On electrode surfaces (center), DNA is covalently tethered to the surface by one end and modified with a redox-active probe moiety on the distal end. An applied potential to the electrode results in DNA CT to the distal probe and produces a characteristic DNA-mediated redox signal. With single molecules (bottom), one DNA duplex is covalently attached by amide bonds across a gap that has been cut in a carbon nanotube within an electrical circuit. Current flow through the CNT-DNA device is a reflection of DNA CT through the single DNA duplex that bridges the gap and can be used to make fundamental measurements of DNA conductivity.

Fig. 2

Binding modes of donors and acceptors influence their participation in DNA CT. Δ-[Rh(phi)₂(phen)]³⁺ (top left), intercalates between the DNA bases and is thus well coupled to the DNA π-stack and can participate in DNA CT. In contrast, [Ru(NH₃)₆]³⁺ (center right) which electrostatically binds the negatively charged phosphate backbone and Λ-[Ru(phen)₃]²⁺ (bottom right) which binds within the major groove, are not well coupled and do not participate in DNA CT.

Fig. 3

Structural perturbations to the base π-stack inhibit DNA CT. For efficient DNA CT, bases in the duplex must be well stacked with each other to achieve proper π-orbital overlap and electronic coupling. This occurs naturally in the case of fully matched DNA (top left). Nicks in the sugar phosphate backbone (top right) and methylation of the DNA bases (center left) do not interfere with the base stack and thus do not inhibit DNA CT. However, attenuation of DNA CT is observed for perturbations that disrupt the base stack including single base mismatches (center right), bound proteins that severely kink the DNA (bottom right), and single base bulges (bottom left). The attenuation in DNA CT caused by these structural perturbations, and others, has been measured with solution, surface, and single molecule platforms.

Fig. 4

DNA-modified electrodes allow for the measurement of DNA CT to diverse redox-active species. As long as probe molecules are well coupled to the DNA π-stack, DNA-modified electrodes can be used to measure DNA-mediated redox processes of a variety of noncovalent (left) and covalent (center) redox probes, as well as proteins with redox-active cofactors (right). Attenuation of the redox signal by the incorporation of a mismatch or other structural perturbation to the π-stack can be used as a diagnostic to determine if the observed signal is indeed DNA-mediated.

Fig. 5

DNA-modified electrodes can be used to monitor proteins with redox-active cofactors. Here, the DNA helicase XPD which contains a [4Fe–4S] cluster is shown bound to a DNA-modified electrode. In the absence of any ATP or with the non-hydrolyzable ATP analog ATP-γ-S, a steady DNA-mediated signal from the cluster is measured (left). Upon addition of ATP, this signal increases significantly. This result reflects a conformational change in XPD during ATP hydrolysis that improves the coupling of the [4Fe–4S] cluster to the π-stack. Thus, DNA-modified electrodes report on how DNA coupling changes during protein activity and this information can provide insight into how DNA CT might be involved in the regulation and coordination of these activities.

Fig. 6

Carbon nanotube (CNT) devices allow for conductivity measurements in single molecules of DNA. In this platform, a CNT is connected into an electrical circuit (top). Then, high resolution electron beam lithography and oxygen ion plasma are used to cut a gap in the CNT that has a defined width and carboxylic acid end functionalization (center). A single, amine-modified DNA duplex of compatible length is then added and made to covalently bridge the gap by peptide coupling (bottom). Importantly, the DNA is functionalized with amines on both the 5′ and 3′ ends of just one of the strands in the duplex (shown here in blue) such that the noncovalent strand (green) may be easily exchanged for fully complementary or mismatched strands. DNA-mediated current can then be measured across this reconnected DNA–CNT device and compared to the current across the uncut CNT.

Fig. 7

Single molecule measurements of DNA CT reflect perturbations to the DNA π-stack. (From left to right) Prior to cutting a gap, current flows through the CNT device. After the gap is cut, reconnection with a single DNA strand does not allow current flow; reconnection with duplex DNA is necessary to restore current flow. Incorporation of a mismatch, cutting with a restriction enzyme, and base flipping by a bound methyltransferase all shut off current flow through the device. This sensitivity to structural perturbations of the DNA π-stack is also observed in measurements of DNA CT in solution and on surfaces and indicates that these single molecule conductivity measurements are likewise DNA-mediated.

Scheme 1

Probes used for the study of DNA CT.