DNA Walkers: Emerging Analytical Applications, Biomolecular-Nanomaterial Probes and Biomolecule Sensors

Abstract

DNA walkers are a unique class of dynamic DNA devices that move nucleic acid walkers processively along designated one-, two-, or three-dimensional tracks. Because of the unique mechanical motion, dynamic interaction, and capabilities for signal amplification, programmable signal transduction, high directionality, and predictable analytical performance on the basis of Watson-Crick base paring rules, this class of dynamic DNA nanodevice has gained great attention from the analytical community in the recent years. This includes bioanalytical applications that range from nucleic acid sensing, to protein detection and to cellular imaging and analysis. The research described herein focuses on improving the understanding of biophysical processes involved in the design and operation of DNA walkers. Specifically, we developed a series of stochastic DNA walkers capable of probing dynamic interactions occurring at the biomolecule-nanoparticle (bio-nano) interface. By monitoring dynamics of DNA walkers on spherical nucleic acid (SNA) tracks, we systematically investigated effects of varying interfacial factors, including intramolecular interactions, orientation, cooperativity, steric effect, multivalence, and binding hindrance on enzymatic activities at the bio-nano interface. Leveraging the newly gained knowledge at the interface, we also fabricated ultrasensitive biosensors for amplified detection of nucleic acids and antibodies. Our study revealed critical roles of interfacial factors to enzyme activities and performance of enzyme-driven nanodevices. We also demonstrate that improvement in understanding bio-nano interfaces will facilitate the design and operation of biosensors and inspire new sensing mechanisms.