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
Related in: MedlinePlus
Mentions: To obtain a time-averaged experimental ‘barcode’, one must account for center-of-mass diffusion in the channel and conformational fluctuations. To that end, we applied a slightly modified version of the ‘local box stretching’ approach in (30). We complemented the algorithm by applying a moving average on the experimental signal, for alignment purposes. We also introduced a rough method for aligning the start and finish pixel of the region containing the DNA (see Supplementary Information for details and for an analysis of the noise properties of the aligned experimental barcodes). See Figure 4 for an example of the result of the alignment and data fitting.
Affiliation: Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden.