2006
DOI: 10.1016/j.jmb.2006.06.005
|View full text |Cite
|
Sign up to set email alerts
|

Topological Information Embodied in Local Juxtaposition Geometry Provides a Statistical Mechanical Basis for Unknotting by Type-2 DNA Topoisomerases

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
3
1
1

Citation Types

16
143
0

Year Published

2007
2007
2022
2022

Publication Types

Select...
4
4

Relationship

0
8

Authors

Journals

citations
Cited by 55 publications
(159 citation statements)
references
References 75 publications
16
143
0
Order By: Relevance
“…While early models were very complex (6,7), a recent strikingly simple proposal invoked only the enzyme binding preference for inter-hooked arrangements of juxtaposed segments before performing the inter-segmental passage between those segments (12). Indeed, very recent simulation studies that used random polygons confined to a cubic lattice revealed that selection of inter-hooked arrangements of opposing segments as sites of inter-segmental passage can cause a 50-fold reduction of the steady-state knotting probability as compared to the topological equilibrium in this system (13). These studies and similar ones investigating unlinking of catenated chains (14) provided therefore a proof of principle that a preference for certain geometry of juxtaposed segments can lead DNA topoisomerases to perform very efficient unknotting.…”
Section: Introductionmentioning
confidence: 99%
“…While early models were very complex (6,7), a recent strikingly simple proposal invoked only the enzyme binding preference for inter-hooked arrangements of juxtaposed segments before performing the inter-segmental passage between those segments (12). Indeed, very recent simulation studies that used random polygons confined to a cubic lattice revealed that selection of inter-hooked arrangements of opposing segments as sites of inter-segmental passage can cause a 50-fold reduction of the steady-state knotting probability as compared to the topological equilibrium in this system (13). These studies and similar ones investigating unlinking of catenated chains (14) provided therefore a proof of principle that a preference for certain geometry of juxtaposed segments can lead DNA topoisomerases to perform very efficient unknotting.…”
Section: Introductionmentioning
confidence: 99%
“…It is not yet clear whether G-segment bending is a feature of the type IIB enzymes [8]. A related model envisages that the enzymes bind preferentially to 'hooked juxtapositions' of DNA strands ( Figure 3B), which simulations suggest are over-represented in knotted and catenated DNA [17][18][19]; this model would presumably require geometrical selection of the T segment as well as the G segment. These geometric models involving DNA bending would suggest that small circles might show an increased topology simplification effect.…”
Section: Discussionmentioning
confidence: 99%
“…In order to compare with the experiments of Rybenkov et al [8], one goal for random polygon model studies has been to estimate the knot-reduction factor, R K [10], which is the ratio of knots-to-unknots at equilibrium divided by the On the left, the strand-passage structure is shown. It consists of two sets of consecutive lattice edges: the 'top' set is defined by the vertices A, B, C and the nearest-neighbour edges joining them; and the 'bottom' set is defined by the vertices D, E, F, G, H and the nearest-neighbour edges joining them.…”
Section: The -Structure Lattice Strand-passage Modelmentioning
confidence: 99%
“…In order to identify potential mechanisms, various random polygon models of strand-passage have been studied [9][10][11][12][13][14][15][16][17][18][19].…”
Section: Introductionmentioning
confidence: 99%
See 1 more Smart Citation