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

Nilsson, Adam LU ; Emilsson, Gustav; Nyberg, Lena K; Noble, Charleston LU ; Svensson Stadler, Liselott; Fritzsche, Joachim; Moore, Edward R B; Tegenfeldt, Jonas LU ; Ambjörnsson, Tobias LU and Westerlund, Fredrik (2014) In Nucleic Acids Research 42(15). p.118-118
Abstract
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... (More)
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. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Nucleic Acids Research
volume
42
issue
15
pages
118 - 118
publisher
Oxford University Press
external identifiers
  • pmid:25013180
  • wos:000343220300002
  • scopus:84964315694
ISSN
1362-4962
DOI
10.1093/nar/gku556
language
English
LU publication?
yes
id
a4ab1be1-7893-4c17-a068-6a90a7dedadc (old id 4582979)
date added to LUP
2014-09-10 10:18:17
date last changed
2017-09-10 03:00:55
@article{a4ab1be1-7893-4c17-a068-6a90a7dedadc,
  abstract     = {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.},
  author       = {Nilsson, Adam and Emilsson, Gustav and Nyberg, Lena K and Noble, Charleston and Svensson Stadler, Liselott and Fritzsche, Joachim and Moore, Edward R B and Tegenfeldt, Jonas and Ambjörnsson, Tobias and Westerlund, Fredrik},
  issn         = {1362-4962},
  language     = {eng},
  number       = {15},
  pages        = {118--118},
  publisher    = {Oxford University Press},
  series       = {Nucleic Acids Research},
  title        = {Competitive binding-based optical DNA mapping for fast identification of bacteria - multi-ligand transfer matrix theory and experimental applications on Escherichia coli.},
  url          = {http://dx.doi.org/10.1093/nar/gku556},
  volume       = {42},
  year         = {2014},
}