Self-assembled DNA hydrogel as switchable material for aptamer-based fluorescent detection of protein

The methodology based on target-responsive structural switching is powerful in bioanalysis with the controllability and sensitivity. In this paper, an aptamer-functionalized DNA hydrogel was designed as a specifically target-responsive switchable material for protein detection. This pure DNA hydrogel was constructed by using a Y-shaped DNA and an aptamer linker through a DNA self-assembly without synthetic polymer backbone. With use of thrombin as the model analyte, the DNA hydrogel was first applied to visual detection with the entrapped Au nanoparticles (AuNPs) as indicating agent. Furthermore, the positively charged quantum dots (QDs) as the fluorophore were synthesized by using polyethyleneimine (PEI) as wrapper and characterized with spectroscopy, transmission electron micrograph, ζ potential, and dynamic laser scattering techniques. Along with a gel-to-sol transition in the presence of the target, the released negatively charged AuNPs from the hydrogel could approach the positively charged QDs. Due to the electrostatic interaction, fluorescence resonance energy transfer between PEI-QDs and AuNPs therefore occurred and quenched the fluorescence signal for the sensitive detection of thrombin. This assay for the detection of thrombin showed a good linear relationship in a range of 0.075 to 12.5 μM with a detection limit of 67 nM at 3σ, and demonstrated excellent feasibility in complex serum matrixes. The biocompatible DNA hydrogel provides a universal switchable material for signal transduction and significantly demonstrates proof-of-concept for the detection of proteins.