arXiv 1810.087512018-10-20math.GTq-bio.BMq-bio.QM

Recent advances on the non-coherent band surgery model for site-specific recombination

Allison H. Moore, Mariel Vazquez

备注：: This is an invited expository article

英文摘要：

Site-specific recombination is an enzymatic process where two sites of precise sequence and orientation along a circle come together, are cleaved, and the ends are recombined. Site-specific recombination on a knotted substrate produces another knot or a two-component link depending on the relative orientation of the sites prior to recombination. Mathematically, site-specific recombination is modeled as coherent (knot to link) or non-coherent (knot to knot) banding. We here survey recent developments in the study of non-coherent bandings on knots and discuss biological implications.

机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。

阅读原文

阅读 PDF ↗

arXiv 页面 ↗HTML 原文 ↗

本文内容

英文摘要相关论文

机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。

继续探索

相关论文

Rational tangle surgery and Xer recombination on catenanes

The protein recombinase can change the knot type of circular DNA. The action of a recombinase converting one knot into another knot is normally mathematically modeled by band surgery. Band surgeries on a 2-bridge knot N((4mn-1)/(2m)) yielding a (2,2k)-torus link are characterized. We apply this and other rational tangle surgery results to analyze Xer recombination on DNA catenanes using the tangle model for protein-bound DNA.

2011-08-03math.GT

Predicting Knot and Catenane Type of Products of Site-specific Recombination on Twist Knot Substrates

Site-specific recombination on supercoiled circular DNA molecules can yield a variety of knots and catenanes. Twist knots are some of the most common conformations of these products and they can act as substrates for further rounds of site-specific recombination. They are also one of the simplest families of knots and catenanes. Yet, our systematic understanding of their implication in DNA and important cellular processes like site-specific recombination is very limited. Here we present a topological model of site-specific recombination characterising all possible products of this reaction on …

2011-06-22math.GTq-bio.BMq-bio.QM

Characterization of Knots and Links Arising From Site-specific Recombination on Twist Knots

We develop a model characterizing all possible knots and links arising from recombination starting with a twist knot substrate, extending previous work of Buck and Flapan. We show that all knot or link products fall into three well-understood families of knots and links, and prove that given a positive integer $n$, the number of product knots and links with minimal crossing number equal to $n$ grows proportionally to $n^5$. In the (common) case of twist knot substrates whose products have minimal crossing number one more than the substrate, we prove that the types of products are tightly presc…

2011-01-07math.GTq-bio.QM

Distance one lens space fillings and band surgery on the trefoil knot

We prove that if the lens space $L(n, 1)$ is obtained by a surgery along a knot in the lens space $L(3,1)$ that is distance one from the meridional slope, then $n$ is in $\{-6, \pm 1, \pm 2, 3, 4, 7\}$. This result yields a classification of the coherent and non-coherent band surgeries from the trefoil to $T(2, n)$ torus knots and links. The main result is proved by studying the behavior of the Heegaard Floer $d$-invariants under integral surgery along knots in $L(3,1)$. The classification of band surgeries between the trefoil and torus knots and links is motivated by local reconnection proces…

2019-09-25math.GT

Knotted and linked products of recombination on $T(2,n)\#T(2,m)$ substrates

We develop a topological model of site-specific recombination that applies to substrates which are the connected sum of two torus links of the form $T(2,n)\#T(2,m)$. Then we use our model to prove that all knots and links that can be produced by site-specific recombination on such substrates are contained in one of two families, which we illustrate.

2013-11-21math.GT

A Topological Characterization Of Knots and Links Arising From Site-Specific Recombination

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 hav…

2007-07-26math.GT

更多相关论文收起更多论文

Tangle solutions for composite knots: applications to Hin recombination

We extend the tangle model, originally developed by Ernst and Sumners, to include composite knots. We show that, for any prime tangle, there are no rational tangle attachments of distance greater than one that first yield a 4-plat and then a connected sum of 4-plats. This is done by building on results on exceptional Dehn fillings at maximal distance. We then apply our results to the action of the Hin recombinase on mutated sites. In particular, after solving the tangle equations for processive recombination, we use our work to give a complete set of solutions to the tangle equations modelling…

2010-07-06math.GT