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Face of Tobias Ambjörnsson. Photo.

Tobias Ambjörnsson

Senior lecturer

Face of Tobias Ambjörnsson. Photo.

Competitive binding-based optical DNA mapping for fast identification of bacteria - multi-ligand transfer matrix theory and experimental applications on Escherichia coli.

Author

  • Adam Nilsson
  • Gustav Emilsson
  • Lena K Nyberg
  • Charleston Noble
  • Liselott Svensson Stadler
  • Joachim Fritzsche
  • Edward R B Moore
  • Jonas Tegenfeldt
  • Tobias Ambjörnsson
  • Fredrik Westerlund

Summary, in English

We demonstrate a single DNA molecule optical mapping assay able to resolve a specific Escherichia coli strain from other strains. The assay is based on competitive binding of the fluorescent dye YOYO-1 and the AT-specific antibiotic netropsin. The optical map is visualized by stretching the DNA molecules in nanofluidic channels. We optimize the experimental conditions to obtain reproducible barcodes containing as much information as possible. We implement a multi-ligand transfer matrix method for calculating theoretical barcodes from known DNA sequences. Our method extends previous theoretical approaches for competitive binding of two types of ligands to many types of ligands and introduces a recursive approach that allows long barcodes to be calculated with standard computer floating point formats. The identification of a specific E. coli strain (CCUG 10979) is based on mapping of 50-160 kilobasepair experimental DNA fragments onto the theoretical genome using the developed theory. Our identification protocol introduces two theoretical constructs: a P-value for a best experiment-theory match and an information score threshold. The developed methods provide a novel optical mapping toolbox for identification of bacterial species and strains. The protocol does not require cultivation of bacteria or DNA amplification, which allows for ultra-fast identification of bacterial pathogens.

Department/s

  • Department of Physics
  • Computational Biology and Biological Physics
  • Solid State Physics

Publishing year

2014

Language

English

Pages

118-118

Publication/Series

Nucleic Acids Research

Volume

42

Issue

15

Document type

Journal article

Publisher

Oxford University Press

Topic

  • Biophysics
  • Condensed Matter Physics

Status

Published

ISBN/ISSN/Other

  • ISSN: 1362-4962