title: Programming a topologically constrained DNA nanostructure into a sensor.
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.
authors.affiliation: Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1.|Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4O3.
authors.forename: Meng
authors.initials: M
authors.lastname: Liu
authors.affiliation: Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4O3.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1.
authors.forename: Zhongping
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1.
authors.forename: Jimmy
authors.initials: J
authors.lastname: Gu
authors.affiliation: Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4O3.
authors.forename: John D
authors.initials: JD
authors.lastname: Brennan
authors.affiliation: Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1.|Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4O3.
authors.forename: Yingfu
authors.initials: Y
authors.lastname: Li
mesh_terms: D015374:Biosensing Techniques; D004269:DNA, Bacterial; D043864:DNA, Catenated / Q000737:chemistry*; D048168:Escherichia coli K12; D049329:Nanostructures; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*
chemical_list: D004269:DNA, Bacterial; D043864:DNA, Catenated