Nanochannel-based DNA Barcoding for Plasmid Characterisation

Sammanfattning: Plasmids are circular DNA molecules found in bacteria. These molecules often contain genes coding for resilience against harmful substances such as antibiotics, in its environment. To be able to classify plasmids fast, and with small samples would be of great gain for medical care, to improve the efficiency of treatments, and to reduce the spread of antibiotics resistance. Our experimental collaborators (Fredrik Westerlund group, Chalmers) stain DNA molecules in a predictable way with a fluorescent chemical, and by doing so they create patterns (barcodes) for plasmids, which are observed through microscopes. We use the transfer matrix method to compute predicted barcodes from genetic sequences. By comparing barcodes, both from theory and from experiments, we identify types of plasmids, and find manipulations to the plasmids, such as missing or added genes. By combining barcodes with more conventional sequencing, the barcodes are used as scaffolds for the shorter fragments.