A 4-string tangle analysis of DNA-protein complexes based on difference topology
نویسندگان
چکیده
منابع مشابه
Topological tangle modeling of difference topology experiments: tangle analysis of DNA-protein complexes
An n-string tangle is a three dimensional ball with n strings which are properly embedded in it. Topological tangle analysis of DNA-protein complexes based on difference topology experiments are studied for last 30 years. In this paper, A 2-string tangle analysis of DNA-Tn3 complex [5, 6] and a 3-string tangle analysis of DNA-Mu complex [3, 13] and a biologically relevant 4-string tangle analys...
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We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA segments. We analyze such experiments for the Mu protein-DNA complex. We characterize the solutions to the corresponding tangle equations by certain knotted graphs....
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Integrase proteins acting on circular double-stranded DNA often change its topology by transforming unknotted circles into torus knots and links. Two systems of tangle equations--corresponding to the two initial DNA sequences--arise when modelling this transformation: direct and inverted. With no a priori assumptions on the constituent tangles, we utilize Dehn surgery arguments to completely cl...
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Topological Analysis of Dna-protein Complexes
A tangle consists of strings properly embedded in a 3-dimensional ball. Tangles have been used to model protein-bound DNA. The protein is represented by the 3D ball and the protein-bound DNA is represented by the strings embedded in the 3D ball. We review tangle analysis of protein-DNA complexes involving three or four segments of DNA. 1. Introduction. An n-string tangle is a three dimensional ...
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ژورنال
عنوان ژورنال: Journal of Knot Theory and Its Ramifications
سال: 2015
ISSN: 0218-2165,1793-6527
DOI: 10.1142/s021821651550056x