Placing molecules with Bohr radius resolution using DNA origami

Abstract

Molecular self-assembly with nucleic acids can be used to fabricate discrete objects with defined sizes and arbitrary shapes. It relies on building blocks that are commensurate to those of biological macromolecular machines and should therefore be capable of delivering the atomic-scale placement accuracy known today only from natural and designed proteins. However, research in the field has predominantly focused on producing increasingly large and complex, but more coarsely defined, objects and placing them in an orderly manner on solid substrates. So far, few objects afford a design accuracy better than 5 nm, and the subnanometre scale has been reached only within the unit cells of designed DNA crystals. Here, we report a molecular positioning device made from a hinged DNA origami object in which the angle between the two structural units can be controlled with adjuster helices. To test the positioning capabilities of the device, we used photophysical and crosslinking assays that report the coordinate of interest directly with atomic resolution. Using this combination of placement and analysis, we rationally adjusted the average distance between fluorescent molecules and reactive groups from 1.5 to 9 nm in 123 discrete displacement steps. The smallest displacement step possible was 0.04 nm, which is slightly less than the Bohr radius. The fluctuation amplitudes in the distance coordinate were also small (±0.5 nm), and within a factor of two to three of the amplitudes found in protein structures.

Uncovering the forces between nucleosomes using DNA origami

“…We used a previously calibrated high-resolution DNA-based positioning device ( 32 ) to place two nucleosomes close to each other in a defined relative orientation (Fig. 1B).…”

“…1C) and count the number of spectrometer particles that realize particular nucleosome-nucleosome distances. The shape of our spectrometer, together with a previously obtained calibration ( 32 ), enables relating with subnanometer resolution the scale-independent and easy-to-measure opening angles of single particles to actual nucleosome-nucleosome distances. To provide an independent readout in solution, our spectrometer also features a set of dyes that report the conformation via a complementary fluorescence resonance energy transfer (FRET) signal.…”

Protein Coating of DNA Nanostructures for Enhanced Stability and Immunocompatibility

“…[10][11][12] The computational tools [11][12][13] for designing such objects have emerged along with these techniques, and this progress has opened up new possibilities for the researchers to effortlessly build their own nanostructures for tailored uses. [14] Recently demonstrated applications based on customized DNA nanostructures include artificial ion channels, [15] optical (plasmonic and photonic) structures, [16,17] high-precision molecular positioning devices, [18] modifiable templates for arranging, e.g., proteins, [19][20][21] polymers, [22] and nanotubes, [23] as well as DNA-assisted techniques for creating arbitrarily shaped metal nanoparticles. [24][25][26] Fully addressable DNA nanostructures, especially DNA origami, possess huge potential to serve as inherently biocompatible and versatile molecular platforms.…”

Engineering Cell Surface Function with DNA Origami

“…DNA origami devices have wide-ranging applications including drug delivery [10–12] , sensing [13, 14] , molecular manipulation [15] , and measurement [16, 17] .…”