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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/4582979
- author
- 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
- organization
- publishing date
- 2014
- 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
- pmid:25013180
- ISSN
- 1362-4962
- DOI
- 10.1093/nar/gku556
- language
- English
- LU publication?
- yes
- additional info
- The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Solid State Physics (011013006), Computational biology and biological physics (000006113), Physics, Faculty of Technology (011013200)
- id
- a4ab1be1-7893-4c17-a068-6a90a7dedadc (old id 4582979)
- date added to LUP
- 2016-04-01 09:50:09
- date last changed
- 2024-02-20 21:56:17
@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}},
doi = {{10.1093/nar/gku556}},
volume = {{42}},
year = {{2014}},
}