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Competitive binding...
Competitive binding-based optical DNA mapping for fast identification of bacteria - multi-ligand transfer matrix theory and experimental applications on Escherichia coli.
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- Nilsson, Adam (author)
- Lund University,Lunds universitet,Fysiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Department of Physics,Departments at LTH,Faculty of Engineering, LTH
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- Emilsson, Gustav, 1989 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Nyberg, Lena, 1979 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Noble, Charleston (author)
- Lund University,Lunds universitet,Fasta tillståndets fysik,Fysiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Beräkningsbiologi och biologisk fysik - Genomgår omorganisation,Institutionen för astronomi och teoretisk fysik - Genomgår omorganisation,Naturvetenskapliga fakulteten,Solid State Physics,Department of Physics,Departments at LTH,Faculty of Engineering, LTH,Computational Biology and Biological Physics - Undergoing reorganization,Department of Astronomy and Theoretical Physics - Undergoing reorganization,Faculty of Science
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- Svensson-Stadler, Liselott, 1971 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Institute of Biomedicine, Department of Infectious Medicine
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- Fritzsche, Joachim, 1977 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Moore, Edward R.B. 1954 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Institute of Biomedicine, Department of Infectious Medicine
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- Tegenfeldt, Jonas (author)
- Lund University,Lunds universitet,Fasta tillståndets fysik,Fysiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Solid State Physics,Department of Physics,Departments at LTH,Faculty of Engineering, LTH
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- Ambjörnsson, Tobias (author)
- Lund University,Lunds universitet,Beräkningsbiologi och biologisk fysik - Genomgår omorganisation,Institutionen för astronomi och teoretisk fysik - Genomgår omorganisation,Naturvetenskapliga fakulteten,Computational Biology and Biological Physics - Undergoing reorganization,Department of Astronomy and Theoretical Physics - Undergoing reorganization,Faculty of Science
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- Westerlund, Fredrik, 1978 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
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(creator_code:org_t)
- 2014-07-10
- 2014
- English.
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In: Nucleic Acids Research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 42:15, s. 118-118
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Abstract
Subject headings
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- 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.
Subject headings
- NATURVETENSKAP -- Biologi -- Biofysik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biophysics (hsv//eng)
- NATURVETENSKAP -- Fysik -- Den kondenserade materiens fysik (hsv//swe)
- NATURAL SCIENCES -- Physical Sciences -- Condensed Matter Physics (hsv//eng)
- NATURVETENSKAP -- Fysik -- Annan fysik (hsv//swe)
- NATURAL SCIENCES -- Physical Sciences -- Other Physics Topics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
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- By the author/editor
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Nilsson, Adam
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Emilsson, Gustav ...
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Nyberg, Lena, 19 ...
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Noble, Charlesto ...
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Svensson-Stadler ...
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Fritzsche, Joach ...
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Moore, Edward R. ...
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Tegenfeldt, Jona ...
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Ambjörnsson, Tob ...
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Westerlund, Fred ...
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Biophysics
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Physical Science ...
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and Condensed Matter ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Physical Science ...
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and Other Physics To ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Biochemistry and ...
- Articles in the publication
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Nucleic Acids Re ...
- By the university
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Lund University
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Chalmers University of Technology
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University of Gothenburg