publication . Other literature type . Article . 2017

Simulations of knotting of DNA during genome mapping.

Aashish Jain; Kevin D. Dorfman;
Open Access
  • Published: 01 Mar 2017
  • Publisher: AIP Publishing
Abstract
Genome mapping involves the confinement of long DNA molecules, in excess of 150 kilobase pairs, in nanochannels near the circa 50 nm persistence length of DNA. The fidelity of the map relies on the assumption that the DNA is linearized by channel confinement, which assumes the absence of knots. We have computed the probability of forming different knot types and the size of these knots for long chains (approximately 164 kilobase pairs) via pruned-enriched Rosenbluth method simulations of a discrete wormlike chain model of DNA in channel sizes ranging from 35 nm to 60 nm. Compared to prior simulations of short DNA in similar confinement, these long molecules exhi...
Subjects
arXiv: Quantitative Biology::GenomicsQuantitative Biology::BiomoleculesMathematics::Geometric Topology
Medical Subject Headings: stomatognathic systemfood and beveragessurgical procedures, operative
free text keywords: Regular Articles
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