Multiresponsive rolling circle amplification for DNA logic gates mediated by endonuclease.

Abstract

Rolling circle amplification (RCA), an efficient isothermal amplification method allowing the polymerase-mediated generation of long single-stranded DNA molecules made of tandem repeats, has been widely used in biomedical and nanotechnology fields due to structural and compositional versatility of its components. In this work, we confer multiresponsiveness to RCA reactions by designing dumbbell-shaped DNA templates and hairpin probes containing different endonuclease cleavage sites. Endonucleases trigger the release of RCA primers or the cleavage of DNA templates, which controls subsequent RCA reactions. A set of one-input and two-input DNA logic gates, which use endonucleases or hairpin probes as inputs, including YES, NOT, AND, OR, NOR, and INHIBIT, are constructed on the basis of our proposed multiresponsive RCA reactions. We demonstrate flexibility and scalability of these logic gates by integrating them to fabricate more complex three-input logic circuits (AND-OR and NOR-AND circuits). Moreover, our strategy is used to construct an assay system for endonuclease activity. Our proposed method might be applicable in the multichannel detection of endonucleases, nucleic acids, and other biomolecules.