The overwinding and underwinding of DNA duplexes between junctions have been used in designing left-and righthanded DNA origami nanostructures, respectively. For DNA tubes obtained from self-assembled tiles, only a theoretical approach of the intrinsic curvature of the tiles has been previously used to explain their formation. Details regarding the quantitative and structural descriptions of the tile's intrinsic curvature in DNA nanostructures have so far never been addressed. In this work, we designed three types of tile cores built around a circular scaffold using three-and four-branched junctions. Joining the tile cores with arms having two kinds of inter-tile distances, an odd and an even number of DNA half-turns, tended to form planar 2D lattices and tubes, respectively. Streptavidin bound to biotin was used as a labeling technique to characterize the inside and outside surfaces of the tubes and thereby the tile conformation of dihedrals with addressable faces. DNA tubes with either right-or left-handed chirality were obtained by the coupling of the intrinsic curvature of the tiles with the arm twist. We were able to assign the chiral indices (n,m) to a tube with its structure resolved by AFM at the single-tile level and therefore to estimate the global curvature of the tube (or its component tile) using a regular polygon model that approximated its transverse section. A deeper understanding of the integrated actions of different types of twisting forces on DNA tubes will be extremely helpful in engineering more elaborate DNA nanostructures in the future.
By rationally adjusting the weaving modes of point‐star tiles, the curvature inherent in the tiles can be changed, and various DNA nanostructures can be assembled, such as planar wireframe meshes, perforated wireframe tubes, and curved wireframe polyhedra. Based on the weaving and tiling architectures for traditional point‐star tiles with the core arm length at two DNA half‐turns, we improved the weaving modes of our newly reported four‐point‐star tiles with the core arm length at three half‐turns to adjust their curvature and rigidity for assembling 2D arrays of DNA grids and tubes. Following our previous terms and methods to analyze the structural details of E‐tiling tubes, we used the chiral indices (n,m) to describe the most abundant tube of typical assemblies; especially, we applied both one‐locus and/or dual‐locus biotin/streptavidin (SA) labelling strategies to define the configurations of two specific tubes, along with the absolute conformations of their component tiles. Such structural details of the DNA tubes composed of tiles with addressable concave and convex faces and packing directions should help us understand their physio‐chemical and biological properties, and therefore promote their applications in drug delivery, biocatalysis, biomedicine, etc.
The overwinding and underwinding of duplex segments between junctions have been used in designing both left-handed and right-handed DNA origami nanostructures. For a variety of DNA tubes obtained from self-assembled tiles, only a theoretical approach of the intrinsic curvature of the DNA tile (specified as the intrinsic tile curvature) has been previously used to explain their formation. Details regarding the quantitative and structural descriptions of the tile curvature and its evolution in DNA tubes by the coupling of the twist of the inter-tile arm (specified as the arm twist) have never been addressed. In this work, we designed three types of tile cores built around a circular 128 nucleotide scaffold by using longitudinal weaving (LW), bridged longitudinal weaving (bLW) and transverse weaving (TW). Joining the tiles with inter-tile arms having the length of an odd number of DNA half-turns (termed O-tiling) almost resulted into planar 2D lattices, whereas joining the tiles with the arms having the length of an even number of DNA half-turns (termed E-tiling) nearly generated tubes. Streptavidin bound to biotin was used as a labeling technique to characterize the inside and outside surfaces of the E-tiling tubes and thereby the conformations of their component tiles with addressable concave and convex curvatures. When the arms have the normal winding at the relaxed B-form of DNA, the intrinsic tile curvature deter-mines the chirality of the E-tiling tubes. By regulating the arm length and the sticky end length of the bLW-Ep/q (E-tiling of the bLW cores with the arm length of p-bp and the sticky end length of q-nt) assemblies, the arm can be overwound, resulting in a left-handed twist, and can also be underwound, resulting in a right-handed twist. Chiral bLW-Ep/q tubes with either a right-handed curvature or a left-handed curvature can also be formed by the coupling of the intrinsic tile curvature and the arm twist. We were able to assign the chiral indices (n,m) to each tube using high-resolution AFM images, and therefore were able to estimate the tile curvature using a regular polygon model that approximated the transverse section of the tube. A deeper understanding of the integrated actions of dif-ferent types of twisting forces on the DNA tubes will be extremely helpful in engineering more elaborate DNA nanostructures in the future.
Using oligonucleotides to weave 2D tiles such as double crossovers (DX) and multi‐arm junction (mAJ) tiles and arrays is well‐known, but weaving 3D tiles is rare. Here, we report the construction of two new bilayer tiles in high yield using small circular 84mer oligonucleotides as scaffolds. Further, we designed five E‐tiling approaches to construct porous nanotubes of microns long in medium yield via solution assembly and densely covered planar microscale arrays via surface‐mediated assembly.
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