A DNA Walker as a Fluorescence Signal Amplifier

Abstract

Sensing nucleic acids typically involves the recognition of a specific sequence and reporting by, for example, a fluorogenic reaction yielding one activated dye molecule per detected nucleic acid. Here, we show that after binding to a DNA origami track a bound DNA target (a "DNA walker") can release the fluorescence of many molecules by acting as the catalyst of an enzymatic nicking reaction. As the walking kinetics sensitively depends on the walker sequence, the resulting brightness distribution of DNA origamis is a sequence fingerprint with single-nucleotide sensitivity. Using Monte Carlo simulations, we rationalize that the random self-avoiding walk is mainly terminated when steps to nearest neighbors are exhausted. Finally, we demonstrate that the DNA walker is also active in a plasmonic hotspot for fluorescence enhancement, indicating the potential of combining different amplification mechanisms enabled by the modularity of DNA nanotechnology.

Programming Motions of DNA Origami Nanomachines

“…One of the pioneering examples of DNA nanomachines is a switch based on the B–Z transition of DNA, reported by Mao and his colleagues . With the ease of synthesis and excellent biocompatibility, DNA has been extensively utilized as the material to design and engineer nanomechanical machines that display specific structures (such as walkers and gears ) and functions (such as biosensing and drug‐release). To perform controlled directional motion, DNA nanomachines have to overcome the unavoidable random Brownian motion by converting other types of energy to kinetic energy.…”

“…Recently developed DNA nanomachines are mainly powered by the addition and removal of designed single DNA strands, to induce the hybridization and dehybridization between two complementary strands as the driving force . In addition, enzymatic reactions and external applied fields could also provide energy to initiate and maintain the machine motion.…”

“…Various enzymes, including nuclease, DNAzyme, and polymerases, have been employed to power the operation of DNA machines . The cleavage of oligo strands by nuclease or DNAzyme induces the release of a short DNA fragment, which could hybridize with another anchor on DNA origami.…”

“…The translational motion of DNA machine on origami surface is critically dependent on the motion paths that are designed and preprogrammed on origami platform . Lund et al developed a nanoscale DNA “spider” that performs directional movement along precisely defined tracks on DNA origami ( Figure a–c) .…”

“…Rational design and fabrication of synthetic nanomachines that can convert energy into nanoscale motions has become one of the most fascinating research topics of nanotechnology. Inspired by the vast range of protein‐based molecular machines in living cells, various artificial nanoscale machines in response to certain inputs have been reported, which hold great promise for performing diverse functions, such as biomolecule mimicking, molecule sensing, drug delivery, and nanosurgery . Pioneering contributions by Jean‐Pierre Sauvage, Fraser Stoddart, Ben Feringa, and others during the late 1990s led to a rapid progress in the development of autonomous synthetic molecular machines.…”