Universal Strategy To Engineer Catalytic DNA Hairpin Assemblies for Protein Analysis

Nucleic acids can be programmed into enzyme-free catalytic DNA circuits (CDCs) to carry out various functions ranging from DNA computing to signal amplifications for biosensing. Catalytic hairpin assembly (CHA), the accelerated hybridization between two DNA hairpins catalyzed by a DNA input, is one of the most widely studied and used CDCs for amplified detection of nucleic acids and small molecules. So far, it is still challenging to expand CHAs to proteins largely due to the lack of a universal strategy to construct protein-responsive CHAs. To address this challenge, we demonstrate that a rationally designed protein-DNA binding complex can be used as an effective catalyst to accelerate CHA reactions. On the basis of this principle, we developed specific CHAs for a number of important protein biomarkers, including human α-thrombin, human prostate specific antigen, and human epidermal growth factor receptor 2. Upon establishing this panel of protein-responsive CHAs, we further explore their potential applications to the detection of specific protein biomarkers from human serum samples and cancer cells.