In‐Situ Configuration Studies on Segmented DNA Origami Nanotubes

Abstract

One-dimensional nanotubes are of considerable interest in materials and biochemical sciences.Aparticular desire is to create DNA nanotubes with user-defined structural features and biological relevance, which will facilitate the application of these nanotubes in the controlled release of drugs,t emplating of other materials into linear arrays and the construction of artificial membrane channels. However,l ittle is knowna bout the structures of assembled DNA nanotubes in solution.H ere we report an in situ exploration of segmented DNA nanotubes, composed of multiple units with set length distributions, by using synchrotron small-angle X-ray scattering (SAXS). Through joint experimental and theoretical studies, we show that the SAXS data are highly informativei nt he context of heterogeneous mixtures of DNA nanotubes. The structural parameters obtained by SAXS are in good agreement with those determined by atomicf orce microscopy (AFM), transmission electron microscopy (TEM), andd ynamic light scattering (DLS). In particular,t he SAXS data revealed important structurali nformation on these DNA nanotubes, such as the in-solution diameters ( % 25 nm), which could be obtained only with difficulty by use of other methods. Our resultsestablish SAXS as areliable structural analysism ethod for long DNA nanotubes and could assist in the rational design of these structures.Genetically encoded nanotubes made from biomacromolecules, such as cytoskeletal filaments, [1] channeling protein nanotubes, [2] and membrane channels, [3] are critical cellular components. They provide structural support for intracellular transport, intercellularc ommunication, and transmembrane ion/molecule channeling. [4,5] Inspired by the natural protein nanotubes widely encountered in vivo, in vitro construction of biomimetic DNA nanotubes has attracted growing interest with the development of structuralD NA nanotechnology. [6][7][8][9][10] In general, at ypical DNA nanotube can be fabricated either by parallel alignmento fD NA duplexes or throughw rapping of DNA tile lattices. [11][12][13] These biomimetic DNA nanotubes have shown great potentiali nawide number of areas, such as cargo delivery, [14] templated arrangement of other materials, artificial membrane channels, and nanoscale reaction containers.Although severalD NA nanotubes have been successfully createdb yu sing rational design, little is knowna bout their structures in solution.C urrently employed characterization methods generally rely on atomic force microscopy (AFM) or transmission electron microscopy (TEM), [15][16][17][18][19] which cannoti nterprett he in situ status of DNA nanotubes very well. Synchrotron small-angle X-ray scattering (SAXS), however,has emerged as ap owerful tool for in situ analysis of DNA nanostructures, especially for DNA nanotubes. SAXS has been used to study the interhelical spacingo fa24-helixb undle of DNA origami and the globalt wisting of planar DNA origami into nanotubes. [20,21] Further,t he positioning of chiral gold nanoparticles (AuNPs) decorated on ...

Switchable supracolloidal 3D DNA origami nanotubes mediated through fuel/antifuel reactions

“…34,37 Saccà and coworkers showed 3D DNA origami fibrils formed by base stacking and reconfigured their stiffness using DNA hybridization. 38 However, reports on DNA origami-based nanotubes are still scarce, [39][40][41][42] and triggers giving additional external control for reversible growth have not been employed for DNA-origami based fibrils so far. 43 Growing interest in DNA strand displacement has shown the extreme potential of using DNA itself as trigger.…”

“…Toehold-mediated strand displacement uses the thermodynamic gain offered by the DNA toehold to Isolated nanocylinders and their polymerized nanotubes would be of general interest for controlled drug delivery, templated material growth, as membrane channels or even as artificial filaments for biomaterials. 19,22,39,44 Here, we present a first approach towards switchable supracolloidal nanotube assemblies based on distinct 3D DNA nanocylinders (3D-DNA-NC), that are monodisperse in their size and cavity. We report how external fuel strands bridging the ssDNA overhangs emanating from the two faces of these 3D-DNA-NC guide the supracolloidal self-assembly as a function of overhang connector density, salt content and hybridization length.…”

Dominant Analytical Techniques in DNA Nanotechnology for Various Applications

“… In another application, a DNA origami switch was able to change conformations (open/closed) with the addition of MgCl 2 , and the rate at which this happens was able to be determined using time-resolved SAXS. , This technique has also shown success in determining the heterogeneity of DNA origami mixtures. DNA nanotubes composed of multiple subunits of set length were analyzed simultaneously using SAXS, and based on the output, the DNA nanotubes were able to be successfully differentiated and quantified by size . Using SAXS for this purpose offers a groundbreaking level of detail, allowing researchers to explore the limitations of their nanostructures under different conditions.…”

Minimalist Design of Wireframe DNA Nanotubes: Tunable Geometry, Size, Chirality, and Dynamics

“…In contrast, the DNA origami method permits complete rational design and precise regulation of nanotube length, circumference, and shape, with the challenge of requiring hundreds of distinct DNA sequences to assemble these structures [34–37] . Although the length of each origami tube is constrained by the size of the origami scaffold, longer nanotubes can be created hierarchically [38–39] …”

“…[34][35][36][37] Although the length of each origami tube is constrained by the size of the origami scaffold, longer nanotubes can be created hierarchically. [38][39] Tile-based, brick-based and DNA origami nanotubes are composed of densely packed DNA helices, which impart rigidity to the structures but generally require high-salt buffer solutions (e.g., Mg 2 + ) for stable assembly. This limits their ability to function in biologically relevant conditions with low salt concentrations.…”