Abstract
High-throughput, low-cost DNA sequencing has emerged as one of the challenges of the postgenomic era. Here we present the proof of concept for a single-molecule platform that allows DNA identification and sequencing. In contrast to most present methods, our scheme is not based on the detection of the fluorescent nucleotides but on DNA hairpin length. By pulling on magnetic beads tethered by a DNA hairpin to the surface, the molecule can be unzipped. In this open state it can hybridize with complementary oligonucleotides, which transiently block the hairpin rezipping when the pulling force is reduced. By measuring from the surface to the bead of a blocked hairpin, one can determine the position of the hybrid along the molecule with nearly single-base precision. Our approach can be used to identify a DNA fragment of known sequence in a mix of various fragments and to sequence an unknown DNA fragment by hybridization or ligation.
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Acknowledgements
We acknowledge useful suggestions by M. Volovitch, T. Lionnet and K. Neuman. This work was supported by an ERA-MolMachines grant (to D.B.), a Human Frontier Science Program grant (RGP003/2007 to V.C. and S.J.B.) and the European Research Council grant 'MagRepS' 267862 (to V.C., F.D., M.M. and S.J.B.). We thank J. Quintas for providing mechanical expertise on the instrument.
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J.-F.A. and V.C. designed the apparatus; F.D., S.J.B., M.M., M.M.S. and V.C. discussed the T4 system that led to the concept of sequencing; F.D. and M.M. performed experiments on magnetic tweezers; F.D. and M.M.S. prepared DNA hairpins; F.D., D.B. and V.C. performed hybridization and ligation assays; F.D. and V.C. analyzed data; F.D., M.M., M.M.S., S.J.B., J.-F.A., D.B. and V.C. prepared the manuscript.
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D.B., J-F.A. and V.C. are collaborating with the company PicoTwist that manufactures magnetic tweezers. F.D., M.M., D.B., J-F.A. and V.C. have three patent applications on the work described here (EP 10305563.8, EP 10305564.6 and EP 11306743).
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Supplementary Figures 1–10, Supplementary Discussion, Supplementary Note 1 (PDF 1441 kb)
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Ding, F., Manosas, M., Spiering, M. et al. Single-molecule mechanical identification and sequencing. Nat Methods 9, 367–372 (2012). https://doi.org/10.1038/nmeth.1925
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DOI: https://doi.org/10.1038/nmeth.1925
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