A topological characterization of knots and links arising from site-specific recombination

DOI10.1088/1751-8113/40/41/008MaRDI QIDQ5423658zbMATH OpenOpenAlexFDO

Authors Dorothy Buck, Erica Flapan

Publication date 31 October 2007

Published in Journal of Physics A: Mathematical and Theoretical (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0707.3896

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10)

Abstract: We develop a topological model of knots and links arising from a single (or multiple processive) round(s) of recombination starting with an unknot, unlink, or (2,m)-torus knot or link substrate. We show that all knotted or linked products fall into a single family, and prove that the size of this family grows linearly with the cube of the minimum number of crossings. Additionally, we prove that the only possible products of an unknot substrate are either clasp knots and links or (2,m)-torus knots and links. Finally, in the (common) case of (2,m)-torus knot or link substrates whose products have minimal crossing number m+1, we prove that the types of products are tightly prescribed, and use this to examine previously uncharacterized experimental data.

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Cited in

(14)

• A topological characterization of the products arising from site-specific recombination on \(T(2,n) \# C(2,r)\) DNA substrates
• The classification of rational subtangle replacements between rational tangles
• The local topological free energy of proteins
• Knotted and linked products of recombination on \(T(2,n)\#T(2,m)\) substrates
• A model of DNA knotting and linking
• Characterization of knots and links arising from site-specific recombination on twist knots
• Knotting of replication intermediates is narrowly restricted
• Topological analysis of enzymatic actions on DNA polyhedral links
• BIOLOGICAL DISTANCES ON DNA KNOTS AND LINKS: Applications to XER recombination
• Topological model for recombination of DNA and RNA
• Site-specific recombination on unknot and unlink substrates producing two-bridge links
• A topological model of site-specific recombination that predicts the knot and link type of DNA products
• Wavelet multifractal modeling and prediction of transmembrane proteins series
• DNA topology review

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