Single-molecule mechanical identification and sequencing

Fangyuan Ding, Maria Manosas, Michelle M. Spiering, Stephen J. Benkovic, David Bensimon, Jean François Allemand, Vincent Croquette

Research output: Contribution to journalArticlepeer-review

35 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)367-372
Number of pages6
JournalNature methods
Volume9
Issue number4
DOIs
StatePublished - Apr 2012

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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