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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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Related in: MedlinePlus

List of the different statistical weights for a base-pair i when in contact with bulk consisting of S different ligand species (here, S = 3 for illustrative purposes). The quantity cs (s = 1, ..., S) is the bulk concentration of ligand type s, Ks is the associated binding constant and  are the different cooperativity parameters between the ligands species.
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Figure 2: List of the different statistical weights for a base-pair i when in contact with bulk consisting of S different ligand species (here, S = 3 for illustrative purposes). The quantity cs (s = 1, ..., S) is the bulk concentration of ligand type s, Ks is the associated binding constant and are the different cooperativity parameters between the ligands species.

Mentions: The goal of the theoretical calculations is to calculate the probability, ps(i), that a base-pair i is occupied by (one of the monomers of) a ligand of type s. To that end, we here introduce an extension of the transfer matrix approach, described in (27,28) for two types of ligands, to multi-ligand CB. As in (27,28) we write:(3)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} p_s(i) = \frac{Z_s(i)}{Z} \end{equation*}\end{document}where Z is the partition function and Zs(i) is a sum over all allowed Boltzmann-weighted states consistent with base-pair i being covered by a type s ligand. Below we show that Zs(i) and Z can be calculated using transfer matrices. The various statistical weights needed for the transfer matrix approach are illustrated in Figure 2.


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)

List of the different statistical weights for a base-pair i when in contact with bulk consisting of S different ligand species (here, S = 3 for illustrative purposes). The quantity cs (s = 1, ..., S) is the bulk concentration of ligand type s, Ks is the associated binding constant and  are the different cooperativity parameters between the ligands species.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: List of the different statistical weights for a base-pair i when in contact with bulk consisting of S different ligand species (here, S = 3 for illustrative purposes). The quantity cs (s = 1, ..., S) is the bulk concentration of ligand type s, Ks is the associated binding constant and are the different cooperativity parameters between the ligands species.
Mentions: The goal of the theoretical calculations is to calculate the probability, ps(i), that a base-pair i is occupied by (one of the monomers of) a ligand of type s. To that end, we here introduce an extension of the transfer matrix approach, described in (27,28) for two types of ligands, to multi-ligand CB. As in (27,28) we write:(3)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} p_s(i) = \frac{Z_s(i)}{Z} \end{equation*}\end{document}where Z is the partition function and Zs(i) is a sum over all allowed Boltzmann-weighted states consistent with base-pair i being covered by a type s ligand. Below we show that Zs(i) and Z can be calculated using transfer matrices. The various statistical weights needed for the transfer matrix approach are illustrated in Figure 2.

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