ArticleNucleic acids research2014
Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Chromosome-scale assembly of yeast genomes using enzyme-free, dense optical genome mapping.Nature communications · 2026Article
- DOM: Dual Optical Mapping Integrating Sequence-Specific Barcodes and A/T Density Profiles.Small methods · 2026Article
- Strain-Level Typing ofACS infectious diseases · 2025Article
- Opening and closing of a cryptic pocket in VP35 toggles it between two different RNA-binding modes.eLife · 2025Article
- Sequencing and Optical Genome Mapping for the Adventurous Chemist.Chemical & biomedical imaging · 2024Review
- Force-enhanced sensitive and specific detection of DNA-intercalative agents directly from microorganisms at single-molecule level.Nucleic acids research · 2024Article
- Comparison of CTX-M encoding plasmids present during the early phase of the ESBL pandemic in western Sweden.Scientific reports · 2024Article
- Identification and characterization of plasmids carrying the mobile colistin resistance geneJAC-antimicrobial resistance · 2023Article
- 21 Fluorescent Protein-Based DNA Staining Dyes.Molecules (Basel, Switzerland) · 2022Article
- Review
- Engineered CRISPR-Cas systems for the detection and control of antibiotic-resistant infections.Journal of nanobiotechnology · 2021Review
- A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids.Micromachines · 2021Article
- Optical DNA Mapping of Plasmids Reveals Clonal Spread of Carbapenem-ResistantAntibiotics (Basel, Switzerland) · 2021Article
- Identity ofMicroorganisms · 2021Article
- The HIV-1 nucleocapsid chaperone protein forms locally compacted globules on long double-stranded DNA.Nucleic acids research · 2021Article
- Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale.Essays in biochemistry · 2021Article
- Article
- Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach.PloS one · 2021Article
- A Predictive Model of Antibody Binding in the Presence of IgG-Interacting Bacterial Surface Proteins.Frontiers in immunology · 2021Article
- Combining dense and sparse labeling in optical DNA mapping.PloS one · 2021Article
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10 authors.
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No grant is acknowledged in the PubMed record.
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.
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