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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.

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.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Nilsson AN,Emilsson G,Nyberg LK,Noble C,Stadler LS,Fritzsche J,Moore ER,Tegenfeldt JO,Ambjörnsson T,Westerlund F

doi

10.1093/nar/gku556

subject

Has Abstract

pub_date

2014-09-01 00:00:00

pages

e118

issue

15

eissn

0305-1048

issn

1362-4962

pii

gku556

journal_volume

42

pub_type

杂志文章

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