Predicting Knot or Catenane Type of Site-Specific Recombination Products

Abstract

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.

KNOTTED AND LINKED PRODUCTS OF RECOMBINATION ON T (2, n)#T (2, m) SUBSTRATES

“…However, we have tried to state our assumptions in a more explicit and self-contained way than in [3,5], and hence our wording is somewhat different. The biological justifications for the three assumptions are given in [2,6].…”

“…In particular, these conditions prevent B ∪ R from having one of the forms illustrated in Figure 5. Biological arguments are given in [2,6] explaining why these types of configurations are unlikely to occur. We now assume that Assumption 2 holds for our substrate-enzyme complex, and fix the surface R and sphere P , as well as the representation of R by the decorated planar surface S ⊆ P satisfying the conditions in Assumption 2.…”

Determining the topology of stable protein–DNA complexes

“…Mathematical analysis can be applied directly to study the topological mechanism of proteins that knot/catenate circular DNA [11,[19][20][21][22][23][24][25][26][27][28][29]. The configuration of DNA bound by Tn3 resolvase ( Figure 1B) was proposed using the experimentally determined product topologies [9,10,[12][13][14][15].…”

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

“…Together with torus knots and catenanes, twist knots are the most common products of site-specific recombination both in vivo [41] and in vitro [13-16, 41, 42], mediated by serine recombinases and tyrosine recombinases on unknotted, unlinked and torus knot and torus catenane substrates (see Table 1 in [43] and references therein). For example, recombination mediated by λ Int on the torus catenane T (2, −2) with attP and attB bacteriophage lambda attachment sites, one on each of the components of the catenane substrate, yields the twist knot products C(−2, 3), C(−2, 5), C(−2, 7) and C(−2, 9) ( Table 7 in [16], see also the top image of Figure 5).…”