title: Single-molecule mechanical identification and sequencing.
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.
authors.affiliation: Laboratoire de Physique Statistique, Ecole Normale Supérieure, Université Pierre et Marie Curie Université Paris 06, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France.
authors.forename: Fangyuan
authors.initials: F
authors.lastname: Ding
authors.forename: Maria
authors.initials: M
authors.lastname: Manosas
authors.forename: Michelle M
authors.initials: MM
authors.lastname: Spiering
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Benkovic
authors.forename: David
authors.initials: D
authors.lastname: Bensimon
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Allemand
authors.forename: Vincent
authors.initials: V
authors.lastname: Croquette
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D011088:DNA Ligases / Q000378:metabolism; D020862:GC Rich Sequence; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation / Q000379:methods*; D008280:Magnetics; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D013698:Templates, Genetic
chemical_list: D004247:DNA; D011088:DNA Ligases