Localized DNA Hybridization Chain Reactions on DNA Origami

Abstract

The field of DNA nanoscience has demonstrated many exquisite DNA nanostructures and intricate DNA nanodevices. However, the operation of each step of prior demonstrated DNA nanodevices requires the diffusion of DNA strands, and the speed of these devices is limited by diffusion kinetics. Here we demonstrate chains of localized DNA hybridization reactions on the surface of a self-assembled DNA origami rectangle. The localization design for our DNA nanodevices does not rely on the diffusion of DNA strands for each step, thus providing faster reaction kinetics. The locality also provides considerable increased scalability, since localized components of the devices can be reused in other locations. A variety of techniques, including atomic force microscopy, total internal reflection fluorescence, and ensemble fluorescence spectroscopy, are used to confirm the occurrence of localized DNA hybridization reactions on the surface of DNA origami. There are many potential biological applications for our localized DNA nanodevices, and the localization design is extensible to applications involving DNA nanodevices operating on other molecular surfaces, such as those of the cell.

DNA Microsystems for Biodiagnosis

“…Although the LAMP method appears to be similar to the PCR method, there are at least three factors that allows the LAMP method to be distinct. The first factor is the use of secondary structures of the template (e.g., hairpin's loop) [78,79]. The second factor is the use of polymerase-assisted strand displacement.…”

“…In general, the field of dynamic DNA nanotechnology aims to design systems that are often inspired by the behavior of molecular protein motors. In particular, DNA walkers are an example of a cascade reaction which translates multiple DNA hybridization reactions into a successive step-by-step linear motion [78,79,102,119]. These structures can potentially be used for transporting functional molecules or for designing active molecular transport and autonomous DNA nanomachines [97,120].…”

“…Micromachines 2020, 11, x 11 of 29 motion [78,79,102,119]. These structures can potentially be used for transporting functional molecules or for designing active molecular transport and autonomous DNA nanomachines [97,120].…”

Utilizing the Organizational Power of DNA Scaffolds for New Nanophotonic Applications

“…Accessing far more dynamic signal changes within the latter types of systems makes them optimal for creating logic gates where changes in their fluorescent readouts serve to reflect their function. Molecular logic gates are the building blocks for more complex computational tasks, but to function they should present robust photonic signals, both in signal intensity and readout speed . In general, the inputs for DNA logic gates are most often other DNA strands, but RNA, enzymes, or small molecules can all function as input signals 192a,194.…”

Biocomputing with Nanostructures on Lipid Bilayers

“…Elementary logic gates and multi‐input logic circuits, whose computational tasks could be completed within minutes, were demonstrated. In a recent example, hybridization chain reactions were implemented by origami‐bound hairpins . This result is particularly intriguing because cascaded DNA reactions on origami templates were implemented without relying on fuel strands in solution.…”