A Dual-Enzyme-Assisted Three-Dimensional DNA Walking Machine Using T4 Polynucleotide Kinase as Activators and Application in Polynucleotide Kinase Assays

T4 polynucleotide kinase (T4 PNK), an intracellular kinase, catalyzes the phosphorylation of 5'-hydroxyl termini in nucleic acids and plays a crucial role in DNA-related physiological activities. Malfunctioning of PNK is associated with the deregulation of many cellular activities and eventually induces a variety of human diseases. Herein, we report a smart three-dimensional (3D) DNA walking machine using PNK as an effective activator when coupled with the duplex DNA nuclease-assisted cleavage reaction. The 3D DNA tracks benefit from high DNA loading capacity of gold nanoparticles, and the high efficiency of duplex nuclease-mediated cyclic cleavage facilitates the movement of the DNA machine in response to T4 PNK. The DNA machine is also applied for the PNK assay based on the signal amplification from point to area during the DNA walking process. The method achieves an excellent detection limit of 0.0067 U/mL with a linear range from 0.01 to 0.3 U/mL and a favorable specificity even in complex serum samples. Therefore, the 3D DNA machine shows great potential in biochemical and molecular biology studies, drug discovery, and clinic diagnostics.