Abstract

With the development of DNA self-assembly, DNA-protein interactions are increasingly applied to synthesize nano-architectures. The assemblies whom based on DNA templates attracting proteins show great potential in many fields due to the functional diversity of proteins. TMV, the most promising biomolecular complex in nanotechnology application, starts up self-assembly progress via strong interaction between quantity of coat protein (CP) and a specific single strand RNA. Here we designed a transformable DNA nano-cage through Chain Displacement Reaction by DNA origami, which used for catching the self-assembled TMV CP specifically through a particular sequence of RNA containing the TMV origin of assembly. We hope our DNA nano-structure would apply to not only capture or delivery but also catalysis, enrichment, biosensor and etc.

Video

Introduction

DNA origami has been widely applied in various fields in the past decade due to its strong designability and diversity. Complex shapes and lattices can be constructed based on a scaffold, a single DNA strand derived from plasmid, and numerous ssDNA staples, such as nanoscale DNA box, intricate interior cavities and tunnels.^1-5Several studies about the binding, encapsulation, load and release of certain protein by DNA-based nanodevice were reported continuously, demonstrating the feasibility and potential of DNA origami in protein-related application.^6-9The capture of enzyme horseradish peroxidase by DNA cage have been achieved via the denaturation and renaturation of DNA hairpin by temperature alteration, which provides a new path for DNA-cage-conducted protein encapsulation.^10-11Thus, new design to enhance both the cavity volume and detection accuracy on DNA cage for protein seizure would be of great interest.

Great efforts have been devoted to constructing DNA-protein conjugation for multi-purpose, with a wide range of strategies emerging, such as biotin-streptavidin¹², aptamer-protein¹³, antigen-antibody¹⁴, junction-binding proteins¹⁵, oligonucleotide linkers¹⁶, polyamide recognition¹⁷, amyloid self-assembly¹⁰and etc. Recently, new strategies of virus coat protein (CP) conjugation to DNA inspired by virus DNA-guided protein assembly came into view and raised many researchers’ interest¹⁸. Although one-dimensional DNA-templated protein assembly strategy has been adopted to construct virus-like nanotube with CP, there’s no report about virus CP binding to DNA nanodevice¹⁹, which let us to sketch out an idea of CP encapsulation by DNA cage.

Tobacco mosaic virus (TMV) has attracted enormous attention in self-assembly technology by utilizing the specific recognition between TMV RNA and CP subunits.^20-21The strong and precise interaction of CPs to a characteristic RNA loop (origin of assembly, OA) is believed as the start-up of TMV self-assembly, which is often employed to build programmed biomolecular materials.^22-24Hybridizing the OA-containing RNA with modified DNA had facilitated the controllable synthesis and regulation of protein-inorganic composites: the TMV-liked nanorod²⁵,the nanostar colloids of gold core with TMV-liked tubes²⁶and the TMV derived nanotube array²⁷were reported before. Therefore, it’s entirely possible to modify DNA origami with functional RNA for additional versatilities.

Inspired by the convenient RNA-directed bottom-up assembly strategy, we introduce the OA RNA into a three-dimensional DNA origami structure for virus protein detection without any chemical modification on DNA strand. In this study, we chose tetrahedron, the simplest structure among all of polyhedrons, for DNA cage design. The elaborate cage can be opened and closed manually by adding and removing ‘fuel’ strand of DNA that controls CPs entry. One protruding strand of OA-containing RNA was added into the cage to detect CPs and induce the subsequent self-assembly. We expect that our boldly proposed design can contribute to the enrichment of DNA-origami-based protein encapsulation and give some inspirations for new design of reconfigurable three-dimensional DNA nanostructure.

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