Tangle Solutions for a Family of DNA-Rearranging Proteins

Classification of Tangle Solutions for Integrases, A Protein Family that Changes DNA Topology

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 classify the tangle solutions for each of the two systems. A key step is to combine work of our previous paper with recent results of Kronheimer, Mrowka, Ozsvath and Szabo, and Ernst to show a certain prim…

Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex

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. By investigating planarity conditions on these graphs we show that there is a unique biologically relevant solution. That is, we show there is a unique rational tangle solution, which is also the unique…

From tangle fractions to DNA

This paper is an introduction to rational tangles, rational knots and links and their applications to DNA. The paper can be read as an introduction to our more technical papers on rational tangles (math.GT/0311499) and on rational knots (math.GT/0212011). The present paper includes a self-contained account of the tangle fraction from the point of view of the bracket polynomial, accounts of the classification theorems for rational tangles and rational knots (and of our new proofs of these results) and a description of the use of rational tangles in studying DNA recombination.

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.

Non-hyperbolic solutions to tangle equations involving composite links

Solving tangle equations is deeply connected with studying enzyme action on DNA. The main goal of this paper is to solve the system of tangle equations $N(O+X_1)=b_1$ and $N(O+X_2)=b_2 \# b_3$, where $X_1$ and $X_2$ are rational tangles, and $b_i$ is a 2-bridge link, for $i=1,2,3$, with $b_2$ and $b_3$ nontrivial. We solve this system of equations under the assumption $\widetilde{O}$, the double branched cover of $O$, is not hyperbolic, i.e.$O$ is not $π$-hyperbolic. Besides, we also deal with tangle equations involving 2-bridge links only under the assumption $O$ is an algebraic tangle.

缠结方程、Jones猜想、缠结补空间中曲面的斜率以及q-变形有理数

Tangle Equations, the Jones conjecture, slopes of surfaces in tangle complements, and q-deformed rationals

本文研究2-缠结方程组的解的唯一性，证明带标架有理解至多一个，并指出Jones解结猜想蕴含一般唯一性；同时引入Kauffman括号比并猜想其与曲面斜率及q-有理数的关系，还关联了两个著名猜想。