Tuning porosity and radial mechanical properties of DNA origami nanotubes via crossover design

Abstract

DNA origami nanotubes are utilized as structural platforms for the fabrication of various micro/nanosystems for drug delivery, optical or biological sensing, and even nanoscale robots. Their radial structural and mechanical properties, which play a crucial role in the effective use of micro/nanosystems, have not been fully studied. In particular, the effects of crossovers, which are basic structures for rationally assembling double-stranded DNA (dsDNA) helices into a nanotube configuration, have not yet been characterized experimentally. To investigate the effects of crossovers on the porosity and the radial mechanical properties of DNA origami nanotubes, we fabricated a DNA origami nanotube with varied crossover designs along the nanotube axis. The radial geometry of the DNA origami nanotube is experimentally characterized by both atomic force microscopy (AFM) and electron cryomicroscopy (cryo-EM). Moreover, the radial mechanical properties of the DNA origami nanotube including the radial modulus are directly measured by force–distance-based AFM. These measurements reveal that the porosity and the radial modulus of DNA origami nanotubes can be tuned by adjusting the crossover design, which enables the optimal design and construction of DNA origami nanostructures for various applications.

Environment‐Dependent Stability and Mechanical Properties of DNA Origami Six‐Helix Bundles with Different Crossover Spacings

“…[30][31][32][33][34][35][36][37][38][39] Therefore, DNA origami design choices such as lattice type, staple lengths, crossover location and spacing, twist correction, and so on all affect the structural and mechanical properties and thus the environment-dependent behavior of the nano structures. [25,37,[39][40][41][42][43][44][45][46] This means DNA stability can be manipulated also by rational design, instead of solely by outer factors. For example, deliberate design can be used for additional benefit in devising tools like drug carriers with engineered release profiles.…”

Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures

“…29 The moduli associated with radial compression of rod-like origamis have also been probed by atomic-force microscopy. 39 Most explorations of the mechanical limits of DNA origami have focused on the effects of tension typically applied by optical tweezers or an atomic-force microscope. [40][41][42][43] These studies have revealed saw-tooth force-extension profiles, where the origamis yield through multiple unravelling events.…”

Biotechnological and Therapeutic Applications of Natural Nucleic Acid Structural Motifs

“…Paul Rothemund utilized multiple branched junctions as structural motifs to fold single stranded bacteriophage DNA, M13mp18, creating the DNA origami technique (Figure 10a). [117,118] Peng Yin developed the self-assembly of DNA tiles and bricks to further expand the rapidly growing number of structures that can be made using short DNA oligonucleotides (Figures 10b and 10c). The precise placement of ligands has enabled development of 'molecular pegboards' as tools to study individual molecular interactions, distance requirements, and enzymatic cascades.…”