Programming molecular topologies from single-stranded nucleic acids

Xiaodong Qi,Shuoxing Jiang,Hao Yan,Wah Chiu,Fei Zhang,Dongran Han,Zhaoming Su,Hao Yan,Baoquan Ding,Peng Yin,Yan Liu,Yan Liu

doi:10.1038/s41467-018-07039-7

Abstract

Molecular knots represent one of the most extraordinary topological structures in biological polymers. Creating highly knotted nanostructures with well-defined and sophisticated geometries and topologies remains challenging. Here, we demonstrate a general strategy to design and construct highly knotted nucleic acid nanostructures, each weaved from a single-stranded DNA or RNA chain by hierarchical folding in a prescribed order. Sets of DNA and RNA knots of two- or three-dimensional shapes have been designed and constructed (ranging from 1700 to 7500 nucleotides), and they exhibit complex topological features, with high crossing numbers (from 9 up to 57). These single-stranded DNA/RNA knots can be replicated and amplified enzymatically in vitro and in vivo. This work establishes a general platform for constructing nucleic acid nanostructures with complex molecular topologies.

Highlights

Molecular knots represent one of the most extraordinary topological structures in biological polymers
Synthetic topological DNA nanostructures have previously been constructed by creating topological nodes based on B-form/Z-form double-stranded DNA helices[11,12,13,14], paranemic crossovers[15,16], and DNA four-way junctions[17]
The 3D knots were characterized by cryogenic transmission electronic microscopy single particle reconstruction, which confirmed their designated geometries

Summary

Introduction

Molecular knots represent one of the most extraordinary topological structures in biological polymers. In contrast to the strategies that rely on the design of individual topological nodes and finding the appropriate DNA motifs/interactions with which to assemble such nodes, a different approach is to fold one long single-stranded DNA (ssDNA) chain into programmable topologies This strategy presents an important yet unanswered question: can partially paired, dsDNA thread through its own entanglement to form highly knotted topological structures?. A crossing number is a knot invariant that shows the smallest number of crossings in any diagram of the knot, representing the topological complexity of a knot[18] Each of these ssDNA or ssRNA knots are folded and self-assembled from a replicable single-stranded nucleic acid molecule with sizes ranging from 1700 to 7500 nucleotides (nt). This ability to construct such structures may allow us to create more intricate diverse transformative applications in nanotechnology and molecular science, such as nanophotonics[19,20], drug delivery[21], cryo-EM analysis[22], and DNA-based memory storage[23,24]

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Results

Conclusion