journal article·2010-12Open access

Identifying single bases in a DNA oligomer with electron tunnelling

Shuo Huang, Jin He, Shuai Chang, Peiming Zhang, Feng Liang, Shengqin Li, Michael Tuchband, Alexander Fuhrmann, Robert Ros, Stuart Lindsay

Nature Nanotechnology· Volume 5· Issue 12

Abstract

It has been proposed that single molecules of DNA could be sequenced by measuring the physical properties of the bases as they pass through a nanopore. Theoretical calculations suggest that electron tunnelling can identify bases in single-stranded DNA without enzymatic processing, and it was recently experimentally shown that tunnelling can sense individual nucleotides and nucleosides. Here, we report that tunnelling electrodes functionalized with recognition reagents can identify a single base flanked by other bases in short DNA oligomers. The residence time of a single base in a recognition junction is on the order of a second, but pulling the DNA through the junction with a force of tens of piconewtons would yield reading speeds of tens of bases per second.
Source: europepmc · Quality: candidate unverified · Source record ↗

Research context

OpenAlex topics: Nanopore and Nanochannel Transport Studies · Molecular Junctions and Nanostructures · Quantum and electron transport phenomena

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

References (20)

Show source-provided references
1. Zwolak, M. & Di Ventra, M. Physical approaches to DNA sequencing and detection. Rev. Mod. Phys. 80, 141–165 (2008).10.1103/RevModPhys.80.141 ↗
2. Branton, D. et al. Nanopore sequencing. Nature Biotechnol. 26, 1146–1153 (2008).10.1038/nbt.1495 ↗
3. Lagerqvist, J., Zwolak, M. & Di Ventra, M. Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport. Biophys. J. 93, 2384–2390 (2007).10.1529/biophysj.106.102269 ↗
4. Zwolak, M. & Di Ventra, M. Electronic signature of DNA nucleotides via transverse transport. Nano Lett. 5, 421–424 (2005).10.1021/nl048289w ↗
5. Krstic, P. S., Wells, J. C., Fuentes-Cabrera, M., Xu, D. & Lee, J. W. Toward electronic conductance characterization of DNA nucleotide bases. Solid State Phenom. 121–123, 1387–1390 (2007).10.4028/www.scientific.net/SSP.121-123.1387 ↗
6. Tsutsui, M., Taniguchi, M., Yokota, K. & Kawai, T. Identification of single nucleotide via tunnelling current. Nature Nanotech. 5, 286–290 (2010).10.1038/nnano.2010.42 ↗
7. Chang, S. et al. Electronic signature of all four DNA nucleosides in a tunneling gap. Nano Lett. 10, 1070–1075 (2010).10.1021/nl1001185 ↗
8. Clarke, J. et al. Continuous base identification for single-molecule nanopore DNA sequencing. Nature Nanotech. 4, 265–270 (2009).10.1038/nnano.2009.12 ↗
9. Lindsay, S. et al. Recognition tunneling. Nanotechnology 21, 262001 (2010).10.1088/0957-4484/21/26/262001 ↗
10. Gross, L., Mohn, F., Moll, N., Liljeroth, P. & Meyer, G. The chemical structure of a molecule resolved by atomic force microscopy. Science 325, 1110–1114 (2009).10.1126/science.1176210 ↗
11. Vaught, A., Jing, T. W. & Lindsay, S. M. Non-exponential tunneling in water near an electrode. Chem. Phys. Lett. 236, 306–310 (1995).10.1016/0009-2614(95)00223-Q ↗
12. Lindsay, S. M. & Ratner, M. A. Molecular transport junctions: clearing mists. Adv. Mater. 19, 23–31 (2007).10.1002/adma.200601140 ↗
13. Fuhrmann, A., Anselmetti, D., Ros, R., Getfert, S. & Reimann, P. Refined procedure of evaluating experimantal single-molecule force spectroscopy data. Phys. Rev. E 77, 031912 (2008).10.1103/PhysRevE.77.031912 ↗
14. Getfert, S. & Reimann, P. Optimal evaluation of single-molecule force spectroscopy experiments. Phys. Rev. E 76, 052901 (2007).10.1103/PhysRevE.76.052901 ↗
15. Ramachandran, G. K. et al. A bond-fluctuation mechanism for stochastic switching in wired molecules. Science 300, 1413–1415 (2003).10.1126/science.1083825 ↗
16. Goldsmith, B. R., Coroneus, J. G., Kane, A. A., Weiss, G. A. & Collins, P. G. Monitoring single-molecule reactivity on a carbon nanotube. Nano Lett. 8, 189–194 (2008).10.1021/nl0724079 ↗
17. Keyser, U. F. et al. Direct force measurements on DNA in a solid-state nanopore. Nature Phys. 2, 473–477 (2006).10.1038/nphys344 ↗
18. Visoly-Fisher, I. et al. Conductance of a biomolecular wire. Proc. Natl Acad. Sci. USA 103, 8686–8690 (2006).10.1073/pnas.0600593103 ↗
19. Ashcroft, B. et al. An AFM/rotaxane molecular reading head for sequence-dependent DNA structure. Small 4, 1468–1475 (2008).10.1002/smll.200800233 ↗
20. Fuhrmann, A. Force Spectroscopy from Single Molecules to Whole Cells: Refined Procedures of Data Analysis. PhD thesis, Arizona State Univ. (2010).