Analysis of the mechanism of DNA recombination using tangles

Sumners, D. W.; Ernst, Claus; Spengler, Sylvia J.; Cozzarelli, Nicholas R.

doi:10.1017/s0033583500003498

Cited by 85 publications

(79 citation statements)

References 68 publications

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“…The parity of a tangle [29] describes which pairs of points in {NE, NW, SE, SW } are connected by each tangle arc. A tangle (A, t) has parity (0) (denoted by A ≈ (0)), if the arcs of t connect NW to NE, and SW to SE; A has parity (1) if the arcs connect NW to SE and SW to NE; and, A has parity (0, 0) if the arcs connect NW to SW and NE to SE.…”

Section: Results: Tangle Analysis Of Gin Recombinationmentioning

confidence: 99%

“…We study the case where, prior to recombination, the phage genome is a single circular DNA molecule, effectively the unknot in S 3 . Recombination can then be analyzed by using tangles to model an enzyme such as Gin together with the DNA bound to the enzyme (see: [29]). Tangles, defined formally below, are …”

Section: Preview and Motivationmentioning

confidence: 99%

“…The computation of the solutions (O, R) in Theorem 4·2 does not take into account equation (i), however the theorem shows that the system of four tangle equations has a unique solution pair (O,R). It is possible to argue, on biological grounds, that P = (0) [29,30]. Note that assuming P = (0) would lead to a unique solution to the system with only equations (i)-(iii).…”

Section: Theorem 4·2 (Inversely Repeated Sites) Suppose That the Tanmentioning

confidence: 99%

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Tangle analysis of Gin site-specific recombination

Vázquez¹,

Sumners²

2004

Math. Proc. Camb. Phil. Soc.

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We use the tangle model to study the action of the site-specific recombinase Gin, an enzyme that can introduce topological changes on circular DNA molecules. Gin and its bound DNA are modelled as a 2-string tangle which undergoes changes during recombination, thereby changing the topology of the DNA substrate. We show that the tangles involved in the analysis are all rational tangles. This technique allows us to prove that, under the model's assumptions, there is a unique topological description of the enzymatic action. The Gin system is one of the few to date where tangle analysis can be carried out systematically and rigorously, yielding a single, biologically reasonable solution. Preview and motivationSite-specific recombination alters the genome of an organism by moving, inserting or inverting DNA segments. When acting on circular DNA molecules, site-specific recombinases can change the topology and geometry of the molecules [25,31]. The tangle model provides mathematical tools to analyze such changes [26,27,28]. The detailed tangle formalism and an application of the model to the Tn3 resolvase system were first presented in [10].Here we analyze the enzymatic action of Gin, a site-specific recombinase encoded by bacteriophage Mu (a virus that infects bacteria). Gin inverts a DNA segment within the phage genome to extend the phage's range of infection. The phage genome contains two recombination sites that Gin recognizes, cleaves and rearranges to complete one round of recombination (Figure 1). Gin recombination is processive, i.e. it can carry out more than one recombination round while binding only once to its substrate. We study the case where, prior to recombination, the phage genome is a single circular DNA molecule, effectively the unknot in S 3 . Recombination can then be analyzed by using tangles to model an enzyme such as Gin together with the DNA bound to the enzyme (see: [29]). Tangles, defined formally below, are

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Section: Results: Tangle Analysis Of Gin Recombinationmentioning

confidence: 99%

Section: Preview and Motivationmentioning

confidence: 99%

Section: Theorem 4·2 (Inversely Repeated Sites) Suppose That the Tanmentioning

confidence: 99%

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Tangle analysis of Gin site-specific recombination

Vázquez¹,

Sumners²

2004

Math. Proc. Camb. Phil. Soc.

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“…The same forces that cause computer cables to become entangled also apply to long strings of DNA. Mathematical models, involving geometric and topological concepts, help shed light on these processes, and may be used to engage both mathematics and biology students in interdisciplinary exploration of DNA structure and function [6,7,8,9]. Does DNA simply "unzip" in DNA replication, the process through which DNA makes copies of itself?…”

Section: How Does Dna "Unzip" During Replication?mentioning

confidence: 99%

Unraveling the Tangled Complexity of DNA: Combining Mathematical Modeling and Experimental Biology to Understand Replication, Recombination and Repair

Robic

Jungck

2011

Math. Model. Nat. Phenom.

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Abstract. How does DNA, the molecule containing genetic information, change its three-dimensional shape during the complex cellular processes of replication, recombination and repair? This is one of the core questions in molecular biology which cannot be answered without help from mathematical modeling. Basic concepts of topology and geometry can be introduced in undergraduate teaching to help students understand counterintuitive complex structural transformations that occur in every living cell. Topoisomerases, a fascinating class of enzymes involved in replication, recombination and repair, catalyze a change in DNA topology through a series of highly coordinated mechanistic steps. Undergraduate biology and mathematics students can visualize and explore the principles of topoisomerase action by using easily available materials such as Velcro, ribbons, telephone cords, zippers and tubing. These simple toys can be used as powerful teaching tools to engage students in hands-on exploration with the goal of learning about both the mathematics and the biology of DNA structure.

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“…21 The tangle model has since been used to determine various features of protein-DNA interactions for a number of specific proteins. [22][23][24][25][26][27][28][29][30][31] With the exception of 29 discussed below, the previous topological treatments began with the precise, biologically determined knot or catenane types of (at least some of) the products. This input was then harnessed in topological arguments that probed various features of the pathway and/or mechanism.…”

Section: Introductionmentioning

confidence: 99%

Predicting Knot or Catenane Type of Site-Specific Recombination Products

Buck¹,

Flapan²

2007

Journal of Molecular Biology

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Site-specific recombination on supercoiled circular DNA yields a variety of knotted or catenated products. We develop a model of this process, and give extensive experimental evidence that the assumptions of our model are reasonable. We then characterize all possible knot or catenane products that arise from the most common substrates. We apply our model to tightly prescribe the knot or catenane type of previously uncharacterized data.

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Analysis of the mechanism of DNA recombination using tangles

Cited by 85 publications

References 68 publications

Tangle analysis of Gin site-specific recombination

Tangle analysis of Gin site-specific recombination

Unraveling the Tangled Complexity of DNA: Combining Mathematical Modeling and Experimental Biology to Understand Replication, Recombination and Repair

Predicting Knot or Catenane Type of Site-Specific Recombination Products

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