Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2008 Jun;36(11):3515-21.
doi: 10.1093/nar/gkn192. Epub 2008 Apr 24.

3D visualization software to analyze topological outcomes of topoisomerase reactions

I K Darcy  1 , R G Scharein, A Stasiak
Affiliations

3D visualization software to analyze topological outcomes of topoisomerase reactions

I K Darcy et al. Nucleic Acids Res. 2008 Jun.

Abstract

The action of various DNA topoisomerases frequently results in characteristic changes in DNA topology. Important information for understanding mechanistic details of action of these topoisomerases can be provided by investigating the knot types resulting from topoisomerase action on circular DNA forming a particular knot type. Depending on the topological bias of a given topoisomerase reaction, one observes different subsets of knotted products. To establish the character of topological bias, one needs to be aware of all possible topological outcomes of intersegmental passages occurring within a given knot type. However, it is not trivial to systematically enumerate topological outcomes of strand passage from a given knot type. We present here a 3D visualization software (TopoICE-X in KnotPlot) that incorporates topological analysis methods in order to visualize, for example, knots that can be obtained from a given knot by one intersegmental passage. The software has several other options for the topological analysis of mechanisms of action of various topoisomerases.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
(A) The substrate (top) and product (bottom) knots are each shown in two different configurations. The configurations on the right are standard minimal crossing representations of the substrate knot (top right) and product knot (bottom right). The representations on the left are shown in such a way such that the one crossing on which topoisomerase acts has been separated from the other crossings. A circle has been drawn around this crossing. The topoisomerase action is modeled by changing the overcrossing segment to an undercrossing segment (and vice versa), via intersegmental passage. (B) The top left knot after the DNA conformation not bound by topoisomerase has been simplified. White mesh sphere represents the topoisomerase.
Figure 2.
Figure 2.
All possible topoisomerase-mediated reaction pathways from the unknot to 5.1 involving rational knots with less than 14 crossings.
Figure 3.
Figure 3.
A portion of the table showing rational knots with less than 14 crossings that may be obtained from the knot 5.2 via one round of topoisomerase action.
Figure 4.
Figure 4.
Converting the knot 5.2 to 5.1 via one crossing change.
See this image and copyright information in PMC

References

    1. Shishido K, Ishii S, Komiyama N. The presence of the region on pBR322 that encodes resistance to tetracycline is responsible for high levels of plasmid DNA knotting in Escherichia coli DNA topoisomerase I deletion mutant. Nucleic Acids Res. 1989;17:9749–9759. - PMC - PubMed
    1. Sogo JM, Stasiak A, Martinez-Robles ML, Krimer DB, Hernandez P, Schvartzman JB. Formation of knots in partially replicated DNA molecules. J. Mol. Biol. 1999;286:637–643. - PubMed
    1. Arsuaga J, Vazquez M, McGuirk P, Trigueros S, Sumners DW, Roca J. DNA knots reveal a chiral organization of DNA in phage capsids. Proc. Natl Acad. Sci. USA. 2005;102:9165–9169. - PMC - PubMed
    1. Wang JC. Moving one DNA double helix through another by a type II DNA topoisomerase: the story of a simple molecular machine. Q. Rev. Biophys. 1998;31:107–144. - PubMed
    1. Corbett KD, Berger JM. Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases. Annu. Rev. Biophys. Biomol. Struct. 2004;33:95–118. - PubMed

Publication types