November 02, 2015

Bootstrapping Atomic Precision using adjustable DNA origami triangle hinge

A new study demonstrates that researchers can control the distance between two molecules such that they can adjust the step size to as small as Bohr's radius. This proof-of-concept study using DNA origami techniques shows how molecular positioning can be fine-tuned at the atomic level at room temperature in solution. This work has applications for molecular architecture as well as templated chemical reactions

Funke and Dietz controlled the distance of the distal endpoints suing an adjuster helix, a DNA helix whose length is increased by adding base pairs.

The intersecting pieces are also DNA helices meaning that as the angle converges, the distance between one helix and the other decreases. The base pairs on each helix are a certain distance apart from the base pairs on the other helix. As this work demonstrates, that distance is adjustable.

Funke and Dietz demonstrated that the angle changes with increasing length of adjuster helix by making helices of lengths from ten base pairs to fifty base pairs. TEM studies showed a smoothly increasing angle as length of the adjuster helix increased. The DNA arms and adjuster helices provide the scaffold to control distance between two interacting molecules placed on the arms.

Alex Klotz describes the work Alex did graduate research on using top-down nanotechnology to study DNA in part because he thought DNA origami, which was only a few years old at the time, was really cool. One aspect of his master’s project was about controlling what structure DNA will fold into at equilibrium, although my Ph.D. was more quantitative.

The authors created a hinge out of DNA which they selectively open or close by varying the length of one of the DNA molecules, which allows them to adjust the positions of molecules attached to the hinge by as little 0.04 nanometers, much less than the typical spacing between atoms in a solid.

They created what essentially amounts to an adjustable DNA hinge: two comparatively rigid backbones made of DNA origami structures, with a triangle of DNA double-helices controlling the interior angle of the two structures. By dictating the number of base-pairs in the supporting leg of the triangle, they could control the opening angle. By adjusting it one base-pair at a time, from 10 to 50 base-pairs, roughly 3 to 17 nanometers (a good rule of thumb is that double stranded DNA has three base-pairs per nanometer), they adjusted in opening angle of the hinge in 41 discrete steps. Looking at the hinges with a transmission electron microscope, it is clear that the angle can be precisely controlled.

To see how well they could position molecules using this hinge, they attached two fluorescent molecules to the interior arms of the hinge triangle, on equivalent positions (the coloured dots in the above picture). These molecules undergo Förster resonant energy transfer (FRET), a phenomenon where optically excited molecules transfer their excess energy to unexcited molecules through dipole forces

Nature Nanotechnology - Placing molecules with Bohr radius resolution using DNA origami

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 nmand 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.

32 pages of supplemental material

SOURCES - Phys Org, Nature Nanotechnology, Alex Klotz at physicsforums

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