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DNA sequencing using electrical conductance measurements of a DNA polymerase

A Retraction to this article was published on 03 June 2015

An Addendum to this article was published on 04 October 2013

An Erratum to this article was published on 05 August 2013

This article has been updated

Abstract

The development of personalized medicine—in which medical treatment is customized to an individual on the basis of genetic information—requires techniques that can sequence DNA quickly and cheaply. Single-molecule sequencing technologies, such as nanopores, can potentially be used to sequence long strands of DNA without labels or amplification, but a viable technique has yet to be established. Here, we show that single DNA molecules can be sequenced by monitoring the electrical conductance of a phi29 DNA polymerase as it incorporates unlabelled nucleotides into a template strand of DNA. The conductance of the polymerase is measured by attaching it to a protein transistor that consists of an antibody molecule (immunoglobulin G) bound to two gold nanoparticles, which are in turn connected to source and drain electrodes. The electrical conductance of the DNA polymerase exhibits well-separated plateaux that are 3 pA in height. Each plateau corresponds to an individual base and is formed at a rate of 22 nucleotides per second. Additional spikes appear on top of the plateaux and can be used to discriminate between the four different nucleotides. We also show that the sequencing platform works with a variety of DNA polymerases and can sequence difficult templates such as homopolymers.

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Figure 1: The protein transistor–DNA polymerase sequencing platform.
Figure 2: Monitoring the assembly of the protein transistor–Φ29 platform and identifying the different bases with electrical conductance measurements.
Figure 3: Base-calling criteria for G, T, A and C nucleotides.
Figure 4: Conductance trajectory of the protein transistor platform sequencing a difficult template.

Change history

  • 11 July 2013

    In the version of this Article originally published, the addresses of all affiliations were incorrect; the correct addresses should have read "1Department of Biological Science and Technology, National Chiao Tung University, 1001 University Road, Hsinchu, Taiwan, ROC, 2Biomedical Electronics Translational Research Center, National Chiao Tung University, 1001 University Road, Hsinchu, Taiwan, ROC, 3Department of Materials Science and Engineering, National Chiao Tung University, 1001 University Road, Hsinchu, Taiwan, ROC, 4Institute of Electrical and Control Engineering, National Chiao Tung University, 1001 University Road, Hsinchu, Taiwan, ROC." In the Acknowledgements, the first sentence should have read "This work was partially supported by the 'Aim for the Top University Plan' of the National Chiao Tung University and the Ministry of Education, Taiwan, ROC." These errors have been corrected in the HTML and PDF versions.

  • 28 August 2013

    Editorial note: significant concerns have been raised about the validity of the data reported in this work. After an internal inquiry, we contacted the authors' institution, the National Chiao Tung University, and asked them to launch a formal investigation into the matter. This investigation is now underway.

  • 03 June 2015

    Significant concerns were raised about the validity of the data reported in this work shortly after publication. After an internal inquiry, a formal investigation was launched at the National Chiao Tung University, which focused on the reproducibility of the data. The results of the work could not be reproduced in a reasonable timeframe, and the authors could not provide the investigating committee with a complete set of raw data for the original experiments. The authors Y.-S. C., J.-C. C. and G. S. H. have therefore agreed to retract the manuscript; C.-H. L., M.-Y. H. and H.-A. P. did not respond to the journal's attempts to contact them about this retraction.

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Acknowledgements

This work was partially supported by the 'Aim for the Top University Plan' of the National Chiao Tung University and the Ministry of Education, Taiwan, ROC. This work was also partly supported by Nanotechnology National project 101-2120-M-009-008 of the National Science Counsel, Taiwan, and a National Health Research Institute grant (NHRI-EX102-10249EI). The authors acknowledge funding support from the Air Force Office of Scientific Research (AFOSR, FA2386-11-1-4094; special grant AOARD-13-4035).

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Y.S.C. and G.S.H. are responsible for the concept and design of the study. G.S.H., C.H.L. and M.Y.H. prepared the manuscript. Y.S.C., C.H.L., H.A.P., J.C.C. and M.Y.H performed the experiments and data analysis.

Corresponding author

Correspondence to G. Steven Huang.

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The authors declare no competing financial interests.

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Chen, YS., Lee, CH., Hung, MY. et al. DNA sequencing using electrical conductance measurements of a DNA polymerase. Nature Nanotech 8, 452–458 (2013). https://doi.org/10.1038/nnano.2013.71

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