Development of an enzyme-powered three dimensional DNA nanomachine for discriminating single nucleotide variants through simulation-guided engineering and noncovalent DNA catalysis.

Herein, we report a bottom-up approach to assemble a series of stochastic DNA walkers capable of probing dynamic interactions occurring at the bio–nano interface. We systematically investigated the impact of varying interfacial factors, including intramolecular interactions, orientation, cooperativity, steric effect, multivalence, and binding hindrance on enzymatic behaviors at the interfaces of spherical nucleic acids. Our mechanistic study has revealed critical roles of various interfacial factors that significantly alter molecular binding and enzymatic behaviors from bulk solutions. The improved understanding of the bio–nano interface may facilitate better design and operation of nanoparticle-based biosensors and/or functional devices. We successfully demonstrate how improved understanding of the bio–nano interface help rationalize the design of amplifiable biosensors for nucleic acids and antibodies.

There is a need for biosensing systems that can be operated at the point‐of‐care (POC) for disease screening and diagnostics and health monitoring. In spite of this, simple to operate systems with the required analytical sensitivity and specificity in clinical samples, using a sample‐in‐answer‐out approach, remain elusive. Reported here is an electrochemical bio‐barcode assay (e‐biobarcode assay) that integrates biorecognition with signal transduction using molecular (DNA/protein) machines and signal readout using nanostructured electrodes. The e‐biobarcode assay eliminates multistep processing and uses a single step for analysis following sample collection into the reagent tube. A clinically relevant performance for the analysis of prostate specific antigen (PSA) in undiluted and unprocessed human plasma: a log‐linear range of 1 ng mL−1–200 ng mL−1 and a LOD of 0.4 ng mL−1, was achieved. The e‐biobarcode assay offers a realistic solution for biomarker analysis at the POC.