Chem Commun (Camb). 2017 Sep 19;53(75):10378-10381. doi: 10.1039/c7cc02911j.

Single-molecule conductance of DNA gated and ungated by DNA-binding molecules.

Takanori Harashima1, Chie Kojima2, Shintaro Fujii1, Manabu Kiguchi1 and Tomoaki Nishino1.

1 Department of Chemistry, School of Science, Tokyo Institute of Technology, Tokyo, Japan.

2 Department of Applied Chemistry, Graduate School of Engineering, Osaka Japan.



The single-molecule conductance of DNA was found to increase by over four fold upon intercalation, while the conductance nearly unaltered upon groove-binding. These effects are interpreted on the basis of the electronic interaction of the DNA-binding molecules with the stacked DNA bases.



A single-molecule junction, composed of the single molecule bridging in the metal nanogap, is one of the promising elements for the novel electronic devices. Development of the single molecule devices using such molecular junctions could lead to realization of the ultimately miniaturized electronic devices with low power consumption. Extensive research has been devoted to developing various single molecule devices, and it has been demonstrated that the elaborate design of the constituent molecule improves their functionalities.

DNA has attracted much attention as a building block of the molecular devices because of its ability for the self-organization even with Bohr radius resolution. Therefore, transport properties in DNA molecular junction has been thoroughly investigated based on the conductance measurement by scanning tunneling microscopy (STM).1 The next challenge for realizing DNA based nanoelectronics lies in the active control of the conduction properties of a single DNA molecule by, e.g., structural modulation or external perturbation. In the electron transport of DNA, the π stack system of DNA bases plays central role. We thus anticipate that the electron transport of DNA can be controlled by the perturbation of the π stack system.

We investigated how a DNA-binding molecule, ethidium bromide (EB) or Hoechst 33258 (HOE), affects the electron transport of a single DNA molecule (Fig. 1). EB has been known to bind within DNA base stacking (intercalation). In contrast, HOE binds to the minor groove of the DNA helix (groove binding).

We found that the single-molecule conductance considerably increased by intercalation of EB, while HOE binding has little effect on the conductance of DNA. Furthermore, the electronic interaction between these ligands and DNA in the molecular junction was investigated in detail from current–voltage (I–V) characterization. We concluded that gated and ungated single-molecule conductances for the EB and HOE bindings are dominantly affected by the π–π stacking interactions between DNA bases and the ligands. This research demonstrates an effective way for the active control of DNA transport properties.



Fig. 1 Schematic illustration of molecular junctions composed of DNA–ligand complexes. The two binding configurations, i.e., intercalation and groove binding for EB and HOE, respectively, were shown.


Conductance measurement of a single DNA molecule

First, we investigated single-molecule conductance of DNA without any ligands using the STM break-junction (BJ) technique. In this technique, a gold STM tip was approached to the DNA-modified surface and then pulled up to record the tunneling current as a function of the tip displacement. When the DNA molecule bridges the gap between the STM tip and substrate to form the single-molecule junction, the current or conductance, calculated by dividing the current by the voltage, traces exhibited characteristic features: the current or conductance stayed constant despite the increased gap width. Fig. 2A showed the conductance histogram constructed from these traces. A clear peak appeared at (0.79 ± 0.12) × 10−3G0 (G0 is the fundamental conductance quantum and equals to 2e2/h) in the histogram suggested the formation of the reproducible molecular junction of single DNA junction. The conductance of ligand-free-DNA reasonably agrees with those reported earlier.2

We performed similar measurements for DNA treated with EB or HOE ligands (Fig. 2B, C). The single-molecule conductance increased by a factor of 4.4 upon the binding of EB. Thus, addition of the EB molecule enables a switching function of a single DNA molecule. In contrast, the binding of HOE resulted in negligible change in the conductance.



Fig. 2 Conductance histograms for the molecular junctions of (A) dye-free DNA, (B) EB–DNA complex, and (C) HOE–DNA complex. Inset shows representative conductance traces. The plateaus in the trace indicates the formation of the DNA molecular junction. The single-molecule conductance can be determined on the basis of the peak position in the histogram.


I–V characteristics of DNA single molecule junction

Next, we investigated the electronic property of the DNA molecular junctions to reveal the origin of the significant or negligible change in the single-molecule conductance induced by EB or HOE. To this end, measurement of I-V properties and transition voltage spectra (TVS) analyses were used. TVS reveals the energy difference between the conduction orbital (HOMO in the present case) of the molecular junction and the Fermi level of the electrode. It has been well known that the efficiency of electron transport depends on this energy difference.3 In TVS, the I–V behavior is transformed with following procedure: ln(I/V2) is plotted against 1/V, and the voltage at which this plot reaches the minimum is called the transition voltage, Vtrans. The Vtrans value is proportional to the energy difference.4

The I-V curve of the single DNA molecule was obtained by sweeping the bias voltage in molecular junction. Numerous I-V curves were measured to construct the 2D histograms, as shown in Fig. 3. The I-V curves of EB-bound DNA (Fig. 3B) clearly showed higher current responses than the dye-free DNA (Fig. 3A). In contrast, with HOE-bound DNA (Fig. 3C), a similar behavior to the dye-free DNA was observed.



Fig. 3 I–V histograms for the molecular junctions of (A) dye-free, (B) EB-bound, and (C) HOE-bound DNAs. The count number, represented by the color scale, was normalized by its total sample points. Averaged I–V spectra were overlaid as black lines.


Each I-V curve was analyzed by TVS (Fig. 4A) to construct the histogram of Vtrans (Fig. 4B). It can be clearly seen that the EB-DNA exhibits significantly smaller Vtrans compared to the dye-free DNA. On the other hand, Vtrans of HOE-DNA was comparable to that of the dye-free DNA. These relationships of Vtrans well explain the changes in the single-molecule conductance of the EB- and HOE-bound DNA: the large (small) change in Vtrans results in the significant (negligible) change in the single-molecule conductance. The degree of the change in the HOMO energy was predominantly determined by the difference in the interaction between the dye and the π–π stacking of base pairing. The binding mode of EB is known to be an intercalation. The aromatic orbital of EB overlaps with π stacked orbital in DNA bases and causes a strong electronic interaction, giving rise to the large change in Vtrans. The HOE, on the other hand, interacts with the DNA by groove binding, which causes little interaction between the dye and the π–π stacking. This results in the negligible change in Vtrans, and in turn the negligible change in the single-molecule conductance for the HOE-bound DNA.



Fig. 4 (A) Transition voltage spectra and (B) histograms for free (top, green), EB-bound (middle, orange), and HOE-bound (bottom, blue) DNAs. Arrowheads indicate the TVS minima, and the insets show typical I–V traces from which TVS was transformed. (C) Illustration of the relationship between the conduction orbital and the Fermi energy of STM electrodes.


In summary, our study revealed that the DNA single-molecule conductance can be gated or ungated by binding of the DNA-binding molecules. Conductance are increased by 4.4 times upon intercalation because of the reduced gap between the HOMO of the DNA and the Fermi level of the electrode. The perturbation of the π – π interaction between the DNA bases are induced by the intercalation, which results in the decreased energy gap. In contrast, the groove binding molecules unchanged the single molecular conductance, since the groove binding hardly affects the stacked bases, causing little change in the energy gap. The present research paves a way for designing DNA-based nanoelectronic devices.



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