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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 AN, Emilsson G, Nyberg LK, Noble C, Stadler LS, Fritzsche J, Moore ER, Tegenfeldt JO, Ambjörnsson T, Westerlund F - Nucleic Acids Res. (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden.

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Comparing the SBR and IS under three experimental conditions. Gray circles: 0.5× TBE, open squares: 0.05× TBE and full squares: mixed at 5× TBE and diluted to 0.05× TBE. SBR and IS are defined in the Materials and Methods section.
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Figure 5: Comparing the SBR and IS under three experimental conditions. Gray circles: 0.5× TBE, open squares: 0.05× TBE and full squares: mixed at 5× TBE and diluted to 0.05× TBE. SBR and IS are defined in the Materials and Methods section.

Mentions: Firstly, the IS for each barcode should be as high as possible. The degree of stretching of nanoconfined DNA increases with decreasing ionic strength (34), which increases the potential resolution of the barcode, in terms of base-pairs/pixel and therefore increases IS. In our proof-of-principle study, all experiments were conducted in 0.5× TBE buffer (16). Figure 5 shows SBR plotted as a function of IS for T4-DNA in 0.5× and 0.05× TBE. A vast majority of the molecules have a significantly larger IS at the lower ionic strength when the molecules are more stretched out. However, there is also a much larger spread in both SBR and IS at the lower ionic strength.


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

Nilsson AN, Emilsson G, Nyberg LK, Noble C, Stadler LS, Fritzsche J, Moore ER, Tegenfeldt JO, Ambjörnsson T, Westerlund F - Nucleic Acids Res. (2014)

Comparing the SBR and IS under three experimental conditions. Gray circles: 0.5× TBE, open squares: 0.05× TBE and full squares: mixed at 5× TBE and diluted to 0.05× TBE. SBR and IS are defined in the Materials and Methods section.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150756&req=5

Figure 5: Comparing the SBR and IS under three experimental conditions. Gray circles: 0.5× TBE, open squares: 0.05× TBE and full squares: mixed at 5× TBE and diluted to 0.05× TBE. SBR and IS are defined in the Materials and Methods section.
Mentions: Firstly, the IS for each barcode should be as high as possible. The degree of stretching of nanoconfined DNA increases with decreasing ionic strength (34), which increases the potential resolution of the barcode, in terms of base-pairs/pixel and therefore increases IS. In our proof-of-principle study, all experiments were conducted in 0.5× TBE buffer (16). Figure 5 shows SBR plotted as a function of IS for T4-DNA in 0.5× and 0.05× TBE. A vast majority of the molecules have a significantly larger IS at the lower ionic strength when the molecules are more stretched out. However, there is also a much larger spread in both SBR and IS at the lower ionic strength.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden.

Show MeSH
Related in: MedlinePlus