Programming a topologically constrained DNA nanostructure into a sensor

Meng Liu, Qiang Zhang, Zhongping Li, Jimmy Gu, John D. Brennan () and Yingfu Li ()
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Meng Liu: McMaster University
Qiang Zhang: Biointerfaces Institute, McMaster University
Zhongping Li: McMaster University
Jimmy Gu: McMaster University
John D. Brennan: Biointerfaces Institute, McMaster University
Yingfu Li: McMaster University

Nature Communications, 2016, vol. 7, issue 1, 1-7

Abstract: Abstract Many rationally engineered DNA nanostructures use mechanically interlocked topologies to connect individual DNA components, and their physical connectivity is achieved through the formation of a strong linking duplex. The existence of such a structural element also poses a significant topological constraint on functions of component rings. Herein, we hypothesize and confirm that DNA catenanes with a strong linking duplex prevent component rings from acting as the template for rolling circle amplification (RCA). However, by using an RNA-containing DNA [2] catenane with a strong linking duplex, we show that a stimuli-responsive RNA-cleaving DNAzyme can linearize one component ring, and thus enable RCA, producing an ultra-sensitive biosensing system. As an example, a DNA catenane biosensor is engineered to detect the model bacterial pathogen Escherichia coli through binding of a secreted protein, with a detection limit of 10 cells ml−1, thus establishing a new platform for further applications of mechanically interlocked DNA nanostructures.

Date: 2016
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DOI: 10.1038/ncomms12074

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