The Experts below are selected from a list of 15486 Experts worldwide ranked by ideXlab platform
Elizabeth Kilbride - One of the best experts on this subject based on the ideXlab platform.
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Determinants of Product Topology in a hybrid Cre-Tn3 resolvase site-specific recombination system.
Journal of molecular biology, 2005Co-Authors: Elizabeth Kilbride, Martin R. Boocock, Mary E. Burke, W. Marshall StarkAbstract:Many natural DNA site-specific recombination systems achieve directionality and/or selectivity by making recombinants with a specific DNA Topology. This property requires that the DNA architecture of the synapse and the mechanism of strand exchange are both under strict control. Previously we reported that Tn3 resolvase-mediated synapsis of the accessory binding sites from the Tn3 recombination site res can impose topological selectivity on Cre/loxP recombination. Here, we show that the Topology of these reactions is profoundly affected by subtle changes in the hybrid recombination site les. Reversing the orientation of loxP relative to the res accessory sequence, or adding 4 bp to the DNA between loxP and the accessory sequence, can switch between two-noded and four-noded catenane Products. By analysing Holliday junction intermediates, we show that the innate bias in the order of strand exchanges at loxP is maintained despite the changes in Topology. We conclude that a specific synaptic structure formed by resolvase and the res accessory sequences permits Cre to align the adjoining loxP sites in several distinct ways, and that resolvase-mediated intertwining of the accessory sequences may be less than has been assumed previously.
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Topological selectivity of a hybrid site-specific recombination system with elements from Tn3 res/resolvase and bacteriophage P1 loxP/Cre.
Journal of molecular biology, 1999Co-Authors: Elizabeth Kilbride, Martin R. Boocock, W M StarkAbstract:In order to investigate the functions of the parts of the Tn 3 recombination site res, we created hybrid recombination sites by placing the loxP site for Cre recombinase adjacent to the "accessory" resolvase-binding sites II and III of res. The efficiency and Product Topology of in vitro recombination by Cre between two of these hybrid sites were affected by the addition of Tn 3 resolvase. The effects of resolvase addition were dependent on the relative orientation and spacing of the elements of the hybrid sites. Substrates with sites II and III of res close to loxP gave specific catenated or knotted Products (four-noded catenane, three-noded knot) when resolvase and Cre were added together. The Product topological complexity increased when the length of the spacer DNA segment between loxP and res site II was increased. Similar resolvase-induced effects on Cre recombination Product Topology were observed in reactions of substrates with loxP sites adjacent to full res sites. The results demonstrate that the res accessory sites are sufficient to impose topological selectivity on recombination, and imply that intertwining of two sets of accessory sites defines the simple catenane Product Topology in normal resolvase-mediated recombination. They are also consistent with current models for the mechanism of catalysis by Cre.
David J. Sherratt - One of the best experts on this subject based on the ideXlab platform.
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Topological Selectivity in Xer Site-Specific Recombination
Cell, 1997Co-Authors: Sean D. Colloms, Jonathan Bath, David J. SherrattAbstract:The Product Topology of Xer-mediated site-specific recombination at plasmid sites has been determined. The Product of deletion at pSC101 psi is a right-handed antiparallel 4-noded catenane. The ColE1 cer deletion Product has an identical Topology, except that only one pair of strands is exchanged. These specific Product topologies imply that the Productive synaptic complex and the strand exchange mechanism have fixed topologies. Further analysis suggests that synapsis traps exactly three negative supercoils between recombining sites, and that strand exchange introduces a further negative topological node in the deletion reaction. We present a model in which the requirement for a specific synaptic stucture, with two recombination sites interwrapped around the accessory proteins ArgR and PepA, ensures that recombination only occurs efficiently between directly repeated sites on the same DNA molecule.
W. Marshall Stark - One of the best experts on this subject based on the ideXlab platform.
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Determinants of Product Topology in a hybrid Cre-Tn3 resolvase site-specific recombination system.
Journal of molecular biology, 2005Co-Authors: Elizabeth Kilbride, Martin R. Boocock, Mary E. Burke, W. Marshall StarkAbstract:Many natural DNA site-specific recombination systems achieve directionality and/or selectivity by making recombinants with a specific DNA Topology. This property requires that the DNA architecture of the synapse and the mechanism of strand exchange are both under strict control. Previously we reported that Tn3 resolvase-mediated synapsis of the accessory binding sites from the Tn3 recombination site res can impose topological selectivity on Cre/loxP recombination. Here, we show that the Topology of these reactions is profoundly affected by subtle changes in the hybrid recombination site les. Reversing the orientation of loxP relative to the res accessory sequence, or adding 4 bp to the DNA between loxP and the accessory sequence, can switch between two-noded and four-noded catenane Products. By analysing Holliday junction intermediates, we show that the innate bias in the order of strand exchanges at loxP is maintained despite the changes in Topology. We conclude that a specific synaptic structure formed by resolvase and the res accessory sequences permits Cre to align the adjoining loxP sites in several distinct ways, and that resolvase-mediated intertwining of the accessory sequences may be less than has been assumed previously.
Martin R. Boocock - One of the best experts on this subject based on the ideXlab platform.
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Determinants of Product Topology in a hybrid Cre-Tn3 resolvase site-specific recombination system.
Journal of molecular biology, 2005Co-Authors: Elizabeth Kilbride, Martin R. Boocock, Mary E. Burke, W. Marshall StarkAbstract:Many natural DNA site-specific recombination systems achieve directionality and/or selectivity by making recombinants with a specific DNA Topology. This property requires that the DNA architecture of the synapse and the mechanism of strand exchange are both under strict control. Previously we reported that Tn3 resolvase-mediated synapsis of the accessory binding sites from the Tn3 recombination site res can impose topological selectivity on Cre/loxP recombination. Here, we show that the Topology of these reactions is profoundly affected by subtle changes in the hybrid recombination site les. Reversing the orientation of loxP relative to the res accessory sequence, or adding 4 bp to the DNA between loxP and the accessory sequence, can switch between two-noded and four-noded catenane Products. By analysing Holliday junction intermediates, we show that the innate bias in the order of strand exchanges at loxP is maintained despite the changes in Topology. We conclude that a specific synaptic structure formed by resolvase and the res accessory sequences permits Cre to align the adjoining loxP sites in several distinct ways, and that resolvase-mediated intertwining of the accessory sequences may be less than has been assumed previously.
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Topological selectivity of a hybrid site-specific recombination system with elements from Tn3 res/resolvase and bacteriophage P1 loxP/Cre.
Journal of molecular biology, 1999Co-Authors: Elizabeth Kilbride, Martin R. Boocock, W M StarkAbstract:In order to investigate the functions of the parts of the Tn 3 recombination site res, we created hybrid recombination sites by placing the loxP site for Cre recombinase adjacent to the "accessory" resolvase-binding sites II and III of res. The efficiency and Product Topology of in vitro recombination by Cre between two of these hybrid sites were affected by the addition of Tn 3 resolvase. The effects of resolvase addition were dependent on the relative orientation and spacing of the elements of the hybrid sites. Substrates with sites II and III of res close to loxP gave specific catenated or knotted Products (four-noded catenane, three-noded knot) when resolvase and Cre were added together. The Product topological complexity increased when the length of the spacer DNA segment between loxP and res site II was increased. Similar resolvase-induced effects on Cre recombination Product Topology were observed in reactions of substrates with loxP sites adjacent to full res sites. The results demonstrate that the res accessory sites are sufficient to impose topological selectivity on recombination, and imply that intertwining of two sets of accessory sites defines the simple catenane Product Topology in normal resolvase-mediated recombination. They are also consistent with current models for the mechanism of catalysis by Cre.
Amol Sasane - One of the best experts on this subject based on the ideXlab platform.
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On the density of stabilizable plants in the class of unstabilizable plants: The real symmetric disk algebra case
Journal of the Franklin Institute, 2009Co-Authors: Rudolf Rupp, Amol SasaneAbstract:Abstract Let A R denote the set of functions from the disk algebra having real Fourier coefficients. Generalizing a result of Quadrat we show that every unstabilizable multi-input multi-output plant is as close as we want to a stabilizable multi-input multi-output plant in the Product Topology.
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ON THE DENSITY OF STABILIZABLE PLANTS IN THE CLASS OF UNSTABILIZABLE PLANTS
2008Co-Authors: Rudolf Rupp, Amol SasaneAbstract:Let AR denote the set of functions from the disk algebra having real Fourier coefficients. Generalizing a result of A.Quadrat we show that every unstabilizable multi-input multi-output plant is as close as we want to a stabilizable multi-input multi-output plant in the Product Topology.
