Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli.
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.
Affiliation: Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden.Show MeSH
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Mentions: We are now in a position to introduce the transfer matrices (27,28). Briefly, for each base pair we introduce an M × M transfer matrix with elements T(i; m, m′). These matrix elements give the statistical weight for site i to be in state m provided that site i + 1 is in state m′. Most of the elements in the transfer matrix are zero since, for example, if site i + 1 is occupied by the last monomer of a type 1 ligand, then site i cannot also be occupied by the last monomer of another type 1 ligand (if λ1 ≥ 2). With the statistical weights presented in Figure 2 and our choice of enumeration in mind, it is straightforward to provide expressions for the elements of the transfer matrix . Explicit results are given in Figure 3. In the Supplementary Information, we provide explicit forms for T(i:m, m′) which allow straightforward automated computation of these transfer matrices for arbitrary S and λi (see Equations (2)–(7) in the Supplementary Information).
Affiliation: Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden.