Electrophoretic mobility of DNA knots

Stasiak, Andrzej; Katritch, Vsevolod; Bednář, Jan; Michoud, Didier; Dubochet, Jacques

doi:10.1038/384122a0

Cited by 189 publications

(187 citation statements)

References 13 publications

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“…For instance, their gel mobility coefficients are essentially different 16,17 . In general, polymeric materials in their phases in which the fraction of knotted molecules is considerable, should display interesting physical properties 4 .…”

Section: Discussionmentioning

confidence: 99%

Tight open knots

Pierański

Przybyl

Stasiak

2001

The European Physical Journal E

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Section: Discussionmentioning

confidence: 99%

Tight open knots

Pierański

Przybyl

Stasiak

2001

The European Physical Journal E

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“…Reaction products were fractionated by gel electrophoresis. Roughly speaking, DNA knots and links with same, small, crossing number migrate in the gel with same velocity [24], resulting in an array of discrete bands in the gel. Gin recombination is processive, i.e.…”

Section: Gin the Site-specific Recombination System Of Bacteriophage Mumentioning

confidence: 99%

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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“…To verify this, DNA in the reactions was nicked with DNase I in order to remove DNA supercoils and to separate the products according to their electrophoretic properties (i.e. the number of catenation nodes they contain; Stasiak et al ., 1996).…”

Section: The Presence Of Dr1 and Dr2 Imposes A Specific Topology To Tmentioning

confidence: 99%

Self‐control in DNA site‐specific recombination mediated by the tyrosine recombinase TnpI

Vanhooff

Galloy

Agaisse

et al. 2006

Molecular Microbiology

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SummaryTn 4430 is a distinctive transposon of the Tn 3 family that encodes a tyrosine recombinase (TnpI) to resolve replicative transposition intermediates. The internal resolution site of Tn 4430 (IRS, 116 bp) contains two inverted repeats (IR1 and IR2) at the crossover core site, and two additional TnpI binding motifs (DR1 and DR2) adjacent to the core. Deletion analysis demonstrated that DR1 and DR2 are not required for recombination in vivo and in vitro . Their function is to provide resolution selectivity to the reaction by stimulating recombination between directly oriented sites on a same DNA molecule. In the absence of DR1 and/ or DR2, TnpI-mediated recombination of supercoiled DNA substrates gives a mixture of topologically variable products, while deletion between two wild-type IRSs exclusively produces two-noded catenanes. This demonstrates that TnpI binding to the accessory motifs DR1 and DR2 contributes to the formation of a specific synaptic complex in which catalytically inert recombinase subunits act as architectural elements to control recombination sites pairing and strand exchange. A model for the organization of TnpI/IRS recombination complex is presented.

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Electrophoretic mobility of DNA knots

Cited by 189 publications

References 13 publications

Tight open knots

Tight open knots

Tangle analysis of Gin site-specific recombination

Self‐control in DNA site‐specific recombination mediated by the tyrosine recombinase TnpI

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