DNA charge transport over 34 nm

Journal name:
Nature Chemistry
Volume:
3,
Pages:
228–233
Year published:
DOI:
doi:10.1038/nchem.982
Received
Accepted
Published online

Abstract

Molecular wires show promise in nanoscale electronics, but the synthesis of uniform, long conductive molecules is a significant challenge. Deoxyribonucleic acid (DNA) of precise length, by contrast, is synthesized easily, but its conductivity over the distances required for nanoscale devices has not been explored. Here we demonstrate DNA charge transport (CT) over 34 nm in 100-mer monolayers on gold. Multiplexed gold electrodes modified with 100-mer DNA yield sizable electrochemical signals from a distal, covalent Nile Blue redox probe. Significant signal attenuation upon incorporation of a single base-pair mismatch demonstrates that CT is DNA-mediated. Efficient cleavage of these 100-mers by a restriction enzyme indicates that the DNA adopts a native conformation accessible to protein binding. Similar electron-transfer rates measured through 100-mer and 17-mer monolayers are consistent with rate-limiting electron tunnelling through the saturated carbon linker. This DNA-mediated CT distance of 34 nm surpasses that of most reports of molecular wires.

At a glance

Figures

  1. Illustration of the DNAs used on the electrodes.
    Figure 1: Illustration of the DNAs used on the electrodes.

    Shown are (top to bottom) a well-matched 17-mer, a well-matched 100-mer, a 100-mer with a single mismatched base pair, the six-carbon alkanethiol linker and the Nile Blue redox probe coupled through a uracil. The green sections of the 100-mer mark the approximate location of the RsaI restriction enzyme binding site, and the red X shows the approximate location of the single CA mismatch, 69 bases from the thiolated end of the duplex. The asterisks on the sugar phosphate backbone of the 100-mers indicate the location of nicks. The specific sequences are given in the Methods section.

  2. Electrochemistry of 100-mer well-matched and mismatched monolayers.
    Figure 2: Electrochemistry of 100-mer well-matched and mismatched monolayers.

    a, The chip layout used to compare monolayer electrochemistry between well-matched 100-mers and 100-mers with a single base-pair mismatch. A mismatch (CA) is generated in the 36-mer segment by substitution of a C for a T at the position 69 bases from the thiolated end of the duplex. b, Average CV curves from well-matched (blue) and mismatched (red) 100-mer DNA, each modified with a Nile Blue redox probe. Data were obtained at a 50 mV s−1 scan rate in Tris buffer (10 mM Tris-HCl, 50 mM NaCl, 10 mM MgCl2 and 4 mM spermidine, pH 7) and averaged over similar electrodes on the chip.

  3. Kinetics of CT through 100-mer and 17-mer monolayers.
    Figure 3: Kinetics of CT through 100-mer and 17-mer monolayers.

    a, The chip layout used to test for electron-transfer kinetics. b, CV peak splitting versus scan rate for well-matched (WM) and mismatched (MM) 100-mer DNA monolayers along with well-matched 17-mer monolayers as averaged over four devices on a single chip. Error bars indicate standard deviations in the peak shift. Data were obtained in 10 mM Tris-HCl, 50 mM NaCl, 10 mM MgCl2 and 4 mM spermidine, pH 7. By applying Laviron analysis in this linear regime, the electron-transfer coefficient and electron-transfer rate were obtained. Values were α = 0.6 and k = 30–40 s−1 for well-matched 100-mer, mismatched 100-mer and well-matched 17-mer monolayers.

  4. Electrochemistry and enzymatic activity on various DNA films.
    Figure 4: Electrochemistry and enzymatic activity on various DNA films.

    a, The chip layout used to measure the electrochemical characteristics and RsaI activity on four DNA films (from top left to bottom right), including the well-matched 100-mer that contains the RsaI binding site, a well-matched 17-mer that does not contain the RsaI binding site, the single-stranded 25-mer modified by Nile Blue (ssNB) and the 100-mer without the central 36-mer segment. As illustrated, the 25-mer and 100-mer without the central 36-mer were reduced through direct surface adsorption and contact. (a) also illustrates restriction of the well-matched 100-mer DNA films upon addition of RsaI and Mg2+. b, CV scans of the four DNA films prior to addition of enzyme (blue) and after the addition of RsaI (red). The enzyme reaction was carried out in 10 mM Tris-HCl, 50 mM NaCl, 10 mM MgCl2, 4 mM spermidine, pH 7.9. Scans were taken before and after the enzyme reaction in phosphate buffer (5 mM phosphate, 50 mM NaCl, 4 mM MgCl2, 4 mM spermidine, 10% glycerol, pH 7). CV scans were measured versus Ag/AgCl at a scan rate of 100 mV s−1. For the 100-mer, 17-mer and single-stranded 25-mer, respectively, the peak splittings were 80 mV, 60 mV and 15mV, the midpoint potentials were –180 mV, –180mV and –170 mV, and k100 = k17 = 39 kss25. Values could not be determined accurately for the 100-mer that did not have the 36-mer strand.

  5. Figure 5:

    Enzymatic activity on 100-mer monolayers as a function of time. Integrated cathodic CV peak area versus time for various DNA monolayers exposed to RsaI (blue) and 100-mer DNA in the absence of enzyme (red). The types of DNA tested include the well-matched 100-mer, a well-matched 17-mer and the mismatched 100-mer, all of which contain the RsaI binding site. The charge was obtained by integrating the cathodic Nile Blue CV peaks obtained at a 100 mV s−1 scan rate.

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Author information

Affiliations

  1. Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA

    • Jason D. Slinker,
    • Natalie B. Muren,
    • Sara E. Renfrew &
    • Jacqueline K. Barton

Contributions

J.K.B., J.D.S. and N.B.M. conceived and designed the experiments. J.D.S., N.B.M. and S.E.R. carried out the experiments. J.D.S., N.B.M. and J.K.B. analysed the results and co-wrote the paper.

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The authors declare no competing financial interests.

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