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Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

This article presents a detailed protocol for synthesis of small circular DNA molecules, annealing of circular DNA motifs, and construction of 1D and 2D ...

Nanjing University

RNA nanoparticles are designed and self-assembled according to noncanonical interactions of naturally conserved RNA motifs and/or canonical Watson-Crick base-pairing interactions, which have potential applications in gene therapy and nanomedicine. These artificially engineered nanoparticles are mainly synthesized from in vitro transcribed RNAs, purified by denaturing and native polyacrylamide gel electrophoresis (PAGE), and characterized with native PAGE, AFM, and TEM technologies. The protocols of in vitro transcription, denaturing and native PAGE, and RNA nanoparticle self-assembly are described in detail.

Assembling RNA Nanoparticles.

Using small circular DNA molecules of different lengths as scaffolds, we successfully synthesised DNA nanotubes consisting of Mao's DNA tensegrity triangle tiles with four-arm junctions (Holliday junctions) at all vertices. Due to the intrinsic curvature of the triangle tile and the consecutive tile alignment, the 2D arrays are organised in the form of nanotubes. Two sized triangle tiles with equilateral side lengths of 1.5 and 2.5 full helical turns are connected by the sticky ended cohesion of a duplex with a length of 2.5 helical turns respectively, and their parallel lozenge tiling lattices were demonstrated by high resolution AFM images, where the former lozenge unit cell has a lattice constant of 13.6 nm, and the latter has a larger lattice constant of 17.0 nm. Modification of the triangle tile with infinitesimal disturbance on side lengths and insertion of one thymine single stranded loop at every vertex resulted in comparably similar nanotubes.

DNA nanotubes assembled from tensegrity triangle tiles with circular DNA scaffolds.

Small DNA tiles built from linear oligonucleotides for the construction of DNA nanostructures often have even widths in the lateral direction against the DNA helical axis. Herein we present an example of DNA dumbbell tiles with uneven widths between the central double helical stem and the two head loops after association with helper strands. A characteristic of DNA dumbbell tiles is that the stem length controls the stereostructure of the two head motifs. A stem at 11 bp twists two head motifs of a dumbbell tile into parallel conformations, wheareas a stem at 16 bp twists two head motifs into antiparallel conformations. We successfully constructed four DNA dumbbell tiles and assembled them into two-dimensional (2D) arrays of planar nanoribbons with zebra-like patterns and fine nanotubes as well.

Shou-Jun Xiao

State Key Laboratory of Coordination Chemistry,
School of Chemistry and Chemical Engineering,
State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering

Nanjing University

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

Shou-Jun Xiao

State Key Laboratory of Coordination Chemistry,School of Chemistry and Chemical Engineering,State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering

Nanjing University

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

State Key Laboratory of Coordination Chemistry,
School of Chemistry and Chemical Engineering,
State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering