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Application of tangle theory to DNA topology
by
Soojeong Kim
Yonsei University, South Korea
Coauthors: Isabel K. Darcy
During biological processes, enzyme (protein) interaction with DNA can change the topology of DNA which results in knotted or linked DNA. The topology of DNA can sometimes be determined by biological methods. However, it is a difficult and laborious process which often doesn't work. Thus tangle analysis was introduced to study various enzyme(protein) actions mathematically.
A tangle is a 3-dimensionalball with strings properly embedded in it. In a tangle model, we assume the protein complex as a 3-dimensional ball and the DNA segments bound by protein as strings embedded inside the ball. When a protein binds to DNA at n-sites, then the DNA-protein complex can be modeled by an n-string tangle.
In the early 1990's, C. Ernst and D. Sumners used 2-string tangle to analyze the conformation of DNA segments within the Tn3 and Phase lamda proteins based on N. Cozzarelli's experiments. In late 2000's, a 3-string tangle analysis of DNA topology within Mu-protein is introducedby I. Darcy et. al. Their work is motivated by S. Pathaniaet. al.'s difference experiment of Mu-transpososome. Recently, the author and I. Darcy developed 4-string tangle analysis of DNA-protein complexes and this theory is generalized to n-string tangle analysis.
Date received: February 22, 2015
Copyright © 2015 by the author(s). The author(s) of this work and the organizers of the conference have granted their consent to include this abstract in Topology Atlas. Document # cbkp-10.