April 14, 2017
- New research into the physics of nanochannel mapping published this week in the journal Biomicrofluidics, from AIP Publishing, may help overcome a (literal) knot in the process and advance genome mapping technology. A team of researchers from the University of Minnesota partnered with BioNano Genomics, a company commercializing genome mapping in nanochannels, to understand the basic physics that underlies the mapping, and use that understanding to improve the technology. BioNano Genomics maps genomes by encoding DNA with sequence-specific, fluorescent labels before injecting it into nanochannels that cause the molecule to stretch out. The structural mapping information is read from the stretched DNA.
DNA knots, however, would put a kink in this method as the molecular tangle could be read incorrectly as a structural variation in the genome sequence. To better understand these nanoknots, the group uses computer simulations to model nanochannel configurations of DNA and compares the predictions to measurement-based characterizations.
“We looked at the probability that the DNA would form a knot inside the channel and predicted the size of the knots,” said Kevin Dorfman, a member of the research team and lead author of the work. “This is important in mapping because knots could be incorrectly characterized as changes in DNA sequence structure when, in fact, they are just rearrangements of the DNA within the channel.”
The work did reveal that these knots are not an intrinsic problem in genome mapping. If knot formation was frequent, this would make the processing of genome mapping data much more challenging. If the apparent knots in the experiments come from some other sources, then they can be removed by changing other parts of the experimental protocol.
Excerpt from news release written by Julia Majors, "What's a Knot--and What's Not--in Genomic Mapping." Read the full news release via the link below. Article title: Simulations of knotting of DNA during genome mapping.
Related Link: https://publishing.aip.org/publishing/journal-highlights/whats-knot-and-whats-not-genomic-mapping