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Creating complex molecular topologies by configuring DNA four-way junctions

Abstract

The realization of complex topologies at the molecular level represents a grand challenge in chemistry. This necessitates the manipulation of molecular interactions with high precision. Here we show that single-stranded DNA (ssDNA) knots and links can be created by utilizing the inherent topological properties that pertain to the DNA four-way junction, at which the two helical strands form a node and can be configured conveniently and connected for complex topological construction. Using this strategy, we produced series of ssDNA topoisomers with the same sequences. By finely designing the curvature and torsion, double-stranded DNA knots were accessed by hybridizing and ligating the complementary strands with the knotted ssDNA templates. Furthermore, we demonstrate the use of a constructed ssDNA knot both to probe the topological conversion catalysed by DNA topoisomerase and to study the DNA replication under topological constraint.

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Figure 1: DNA-junction-based strategy for topological construction.
Figure 2: Constructing trefoil knots of both handedness.
Figure 3: Topoisomers of two- and three-component links.
Figure 4: Design and construction of dsDNA knots.
Figure 5: Study of DNA topoisomerase and polymerases with the ssDNA trefoil knot.

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Acknowledgements

We thank J. Piccirilli and B. Tian for their critical reading of the manuscript, J. Birac for providing the GIDEON software for preparing the DNA structures, W. Sherman for helpful information about the tensegrity-triangle design and T. Witten and G. Zocchi for insightful discussions. D.L. acknowledges the Martha Ann and Joseph A. Chenicek Graduate Research Fund and the HHMI International Student Research Fellowship. This work is supported by the University of Chicago and the NSF CAREER Award (DMR-1555361) to Y.W.

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D.L. and Y.W. conceived the project. D.L. designed the experiments. D.L., G.C. and U.A. performed the research. D.L., G.C. and Y.W. analysed the data and wrote the paper. T.M.C. helped revise the manuscript.

Corresponding author

Correspondence to Yossi Weizmann.

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The authors declare no competing financial interests.

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Liu, D., Chen, G., Akhter, U. et al. Creating complex molecular topologies by configuring DNA four-way junctions. Nature Chem 8, 907–914 (2016). https://doi.org/10.1038/nchem.2564

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