Obtaining Precise Molecular Information via DNA Nanotechnology

Abstract

Precise characterization of biomolecular information such as molecular structures or intermolecular interactions provides essential mechanistic insights into the understanding of biochemical processes. As the resolution of imaging-based measurement techniques improves, so does the quantity of molecular information obtained using these methodologies. DNA (deoxyribonucleic acid) molecule have been used to build a variety of structures and dynamic devices on the nanoscale over the past 20 years, which has provided an accessible platform to manipulate molecules and resolve molecular information with unprecedented precision. In this review, we summarize recent progress related to obtaining precise molecular information using DNA nanotechnology. After a brief introduction to the development and features of structural and dynamic DNA nanotechnology, we outline some of the promising applications of DNA nanotechnology in structural biochemistry and in molecular biophysics. In particular, we highlight the use of DNA nanotechnology in determination of protein structures, protein-protein interactions, and molecular force.

Keywords: DNA nanotechnology; cryo-EM; molecular forces; protein–protein interactions; single-molecule techniques; structural reconstruction.

Figure 1

DNA nanostructures created by DNA tile and DNA origami assembly. (A) Artificial immobile junction assembled from four ssDNA strands, adapted with permission from [37]. (B) Double crossover structures, adapted with permission from [38]. (C) 2D DNA crystals made from DNA tiles with three and four arms, adapted with permission from [39,40] (D) DNA bricks for the assembly of 2D objects, adapted with permission from [11]. (E) An earlier 3D octahedron created prior to the birth of DNA origami, adapted with permission from [41]. (F) Cylinder model and atomistic DNA model of a honeycomb-pleated origami, adapted with permission from [27]. (G) Cylinder model of the twisted and curved 3D DNA origami, adapted with permission from [17]. (H) Models and TEM images of a twisted 10 × 6-helix DNA bundle, adapted with permission from [17]. (I) An 8 × 8 array of DNA origami with an example pattern of Mona Lisa, adapted with permission from [42].

Figure 2

Dynamic DNA nanotechnology and its application in constructing dynamic devices. (A) An example of TMSD, adapted with permission from [90]. (B) The kinetics of TMSD can be tuned by changing the length and sequence of the toehold domain, adapted with permission from [90]. (C) Schematic representation of aptamer binding to a target protein, reproduced from [91] under terms of the CC BY 4.0 license. (D) An DNA nanorobot that can be opened by receptor-induced binding with aptamers, adapted with permission from [71]. (E) pH-triggered nanoswitches that form an intramolecular triplex structure through the formation of a Watson–Crick (dashed) pH-insensitive hairpin and a second Hoogsteen (dots) pH-sensitive hairpin, adapted with permission from [80]. (F) Hoogsteen base-pairing-based box that closes in low-pH conditions, adapted from [75] under the terms of the Creative Commons CC BY license. (G,H) Ortho-nitrobenzyl functionalized DNA capsule that opens upon exposure to light, adapted with permission from [81].

Figure 3

DNA nanotechnology applied in the structural reconstruction of proteins. (A) Overlay of the cryo-EM maps of the 48-helix-brick (left) and atomic models of a twist tower derived from fitting to the cryo-EM map (right), adapted from [95] under the terms of the Creative Commons CC BY license. (B) Perspective view of the DNA origami molecular support (top) and illustration of five different settings for the p53 binding on the central dsDNA helix (bottom), adapted with permission from [9]. (C) Illustration of the DNA origami chassis (top left) and its TEM (right); 3D reconstruction of BurrH is shown on bottom left, adapted with permission from [100]. (D) Views of the design of the DNA nanobarrel with a central pore and reconstruction of a-hemolysin into the DNA nanobarrel through lipid–protein interaction, adapted with permission from [101].

Figure 4

Study of PPIs based on DNA nanotechnology methods. (A) Self-assembled 2D peptide nanostructure, adapted with permission from [106]. (B) Structure of the junctured-DNA tweezer (left) and the strategy used to attach a given protein at a given tip (right), adapted with permission from [107]. (C) Schematic of the DNA NanoComb method, adapted with permission from [10].

Figure 5

Measurement of molecular forces via DNA nanotechnology. (A) Schematic of the DNA force spectrometer featuring a spring-loaded hinge with two attached nucleosomes, reproduced from [111] under terms of the CC BY 4.0 license. (B) Structure of the DNA-origami force clamp, with ssDNA reservoirs located on each side of the clamp (left); individual origami samples were assembled for each constant-force variant (middle); TBP-induced DNA bending under force were monitored by FRET (right), adapted with permission from [112]. (C) Schematic of the integrin tension sensor, adapted with permission from [115]. (D) Schematic depicting the concept of mechanical information storage, adapted from [119] under terms of the CC BY license.