Conformational flexibility facilitates self-assembly of complex DNA nanostructures

Abstract

Molecular self-assembly is a promising approach to the preparation of nanostructures. DNA, in particular, shows great potential to be a superb molecular system. Synthetic DNA molecules have been programmed to assemble into a wide range of nanostructures. It is generally believed that rigidities of DNA nanomotifs (tiles) are essential for programmable self-assembly of well defined nanostructures. Recently, we have shown that adequate conformational flexibility could be exploited for assembling 3D objects, including tetrahedra, dodecahedra, and buckyballs, out of DNA three-point star motifs. In the current study, we have integrated tensegrity principle into this concept to assemble well defined, complex nanostructures in both 2D and 3D. A symmetric five-point-star motif (tile) has been designed to assemble into icosahedra or large nanocages depending on the concentration and flexibility of the DNA tiles. In both cases, the DNA tiles exhibit significant flexibilities and undergo substantial conformational changes, either symmetrically bending out of the plane or asymmetrically bending in the plane. In contrast to the complicated natures of the assembled structures, the approach presented here is simple and only requires three different component DNA strands. These results demonstrate that conformational flexibility could be explored to generate complex DNA nanostructures. The basic concept might be further extended to other biomacromolecular systems, such as RNA and proteins.

Fig. 1.

Self-assembly of DNA icosahedra. Three different types of DNA single strands stepwise assemble into sticky-ended five-point-star motifs (tiles), which then further assemble into icosahedra. Each vertex in the icosahedra is a five-point-star tile; one of them is highlighted as golden. Note that the red colored central loops are 5 bases long.

Fig. 2.

Characterization of the self-assembled DNA iscosahedron. (A) Native PAGE (2.5%) analysis. The sample compositions are indicated above the gel image, and the identity of each band is suggested on the right. (B) DLS analysis of the mass distribution along the hydrodynamic radius of the DNA complexes.

Fig. 3.

Cryogenic transimission electron microscopy (cryo-EM) analysis of DNA icosahedron. (A) A representative raw cryo-EM image. White boxes indicate the DNA particles. (B) Comparison of raw images of individual particles at a high magnification (Left) and the corresponding computer-generated model projections (Right). (C) Comparison of class average of particle images with similar views (Upper) and the corresponding computer-generated model projections (Lower). (D) Three views of the DNA icosahedron structure reconstructed from cryo-EM images.

Fig. 4.

Characterization of DNA cages assembled from five-point-star tiles with 4-base-long central loops. (A) DLS analysis of the assembled DNA cages. (B) A representative AFM image of the assembled DNA cages. (C) Zoom-in view. Note that the DNA structures are double-layered. (D) After the top layer is swiped away, AFM imaging reveals the detailed structures of the DNA lattices. (Inset) Corresponding Fourier transform pattern.

Fig. 5.

Proposed assembly process of DNA five-point-star tiles at high DNA concentrations. On the surface of the assembled DNA nanocages, DNA tiles are arranged into tetragonal 2D crystals. Compared with the free-DNA five-point-star tile, the branches in the final structure have asymmetrical bends in the molecular plane. The angles between two neighboring branches varies (three 60° and two 90°) in the final structure and are all different from the angle (72°) in the free tiles.