Strategies to Build Hybrid Protein-DNA Nanostructures

DNA functionalized programmable hybrid biomaterials for targeted multiplexed applications

With the advent of DNA nanotechnology, DNA-based biomaterials have emerged as a unique class of materials at the center of various biological advances. Owing to DNA's high modification capacity via programmable Watson-Crick base-pairing, DNA structures of desired design with increased complexity have been developed. However, the limited scalability, along with poor mechanical properties, high synthesis costs, and poor stability, reduced the adaptability of DNA-based materials to complex biological applications. DNA-based hybrid biomaterials were designed to overcome these limitations by conjugating DNA with functional materials. Today, DNA-based hybrid materials have attracted significant attention in biological engineering with broad application prospects in biomedicine, clinical diagnosis, and nanodevices. Here, we summarize the recent advances in DNA-based hybrid materials with an in-depth understanding of general molecular design principles, functionalities, and applications. Finally, the challenges and prospects associated with DNA-based hybrid materials are discussed at the end of this review.

Biomimetic synthesis of protein-DNA-CaHPO4 hybrid nanosheets for biosensing: Detection of thrombin as an example

Traditional strategies for coupling of proteins with DNA involve the additional modifications on protein or DNA to construct protein-DNA conjugates, resulting in complex or time-consuming coupling process. This study presented a biomimetic synthesis strategy to elaborately synthesize a new type of biomolecule-inorganic hybrid nanosheets. Horseradish peroxidase (HRP) and DNA aptamer can be easily combined with CaHPO₄ via coprecipitation simultaneously to form all-inclusive HRP-aptamer-CaHPO₄ hybrid (HAC) nanosheets integrating bifunction of biorecognition and signal amplification, which was proceeded in the green environment at room temperature and required no additional modifications on CaHPO₄, protein and DNA. Therefore, it avoided tedious linking and purification procedures. The HAC nanosheets were then employed as the signal labels and showed excellent performance for detecting thrombin. This bioinspired approach provides great possibilities to facile and efficient immobilization of protein, DNA or even other types of biomolecules (e.g., RNA and peptide) on inorganic nanomaterials and endows great potential in the preparation of a variety of multifunctional biomolecule-CaHPO₄ two-dimensional (2D) nanobiohybrids for various applications extending from biosensing to energy, biomedicine, environmental science and catalysis.

Graphene Oxide and Biomolecules for the Production of Functional 3D Graphene-Based Materials

Graphene and its derivatives have been widely employed in the manufacturing of novel composite nanomaterials which find applications across the fields of physics, chemistry, engineering and medicine. There are many techniques and strategies employed for the production, functionalization, and assembly of graphene with other organic and inorganic components. These are characterized by advantages and disadvantages related to the nature of the specific components involved. Among many, biomolecules and biopolymers have been extensively studied and employed during the last decade as building blocks, leading to the realization of graphene-based biomaterials owning unique properties and functionalities. In particular, biomolecules like nucleic acids, proteins and enzymes, as well as viruses, are of particular interest due to their natural ability to self-assemble via non-covalent interactions forming extremely complex and dynamic functional structures. The capability of proteins and nucleic acids to bind specific targets with very high selectivity or the ability of enzymes to catalyse specific reactions, make these biomolecules the perfect candidates to be combined with graphenes, and in particular graphene oxide, to create novel 3D nanostructured functional biomaterials. Furthermore, besides the ease of interaction between graphene oxide and biomolecules, the latter can be produced in bulk, favouring the scalability of the resulting nanostructured composite materials. Moreover, due to the presence of biological components, graphene oxide-based biomaterials are more environmentally friendly and can be manufactured more sustainably compared to other graphene-based materials assembled with synthetic and inorganic components. This review aims to provide an overview of the state of the art of 3D graphene-based materials assembled using graphene oxide and biomolecules, for the fabrication of novel functional and scalable materials and devices.

Therapeutic Applications of Programmable DNA Nanostructures

Deoxyribonucleic acid (DNA) nanotechnology, a frontier in biomedical engineering, is an emerging field that has enabled the engineering of molecular-scale DNA materials with applications in biomedicine such as bioimaging, biodetection, and drug delivery over the past decades. The programmability of DNA nanostructures allows the precise engineering of DNA nanocarriers with controllable shapes, sizes, surface chemistries, and functions to deliver therapeutic and functional payloads to target cells with higher efficiency and enhanced specificity. Programmability and control over design also allow the creation of dynamic devices, such as DNA nanorobots, that can react to external stimuli and execute programmed tasks. This review focuses on the current findings and progress in the field, mainly on the employment of DNA nanostructures such as DNA origami nanorobots, DNA nanotubes, DNA tetrahedra, DNA boxes, and DNA nanoflowers in the biomedical field for therapeutic purposes. We will also discuss the fate of DNA nanostructures in living cells, the major obstacles to overcome, that is, the stability of DNA nanostructures in biomedical applications, and the opportunities for DNA nanostructure-based drug delivery in the future.

Unified Nanotechnology Format: One Way to Store Them All

The domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate the desired structure before the wet lab assembly. To aid with these tasks, various software tools exist and are often used in conjunction. However, their interoperability is hindered by a lack of a common file format that is fully descriptive of the many design paradigms. Therefore, in this paper, we propose a Unified Nanotechnology Format (UNF) designed specifically for the biomimetic nanotechnology field. UNF allows storage of both design and simulation data in a single file, including free-form and lattice-based DNA structures. By defining a logical and versatile format, we hope it will become a widely accepted and used file format for the nucleic acid nanotechnology community, facilitating the future work of researchers and software developers. Together with the format description and publicly available documentation, we provide a set of converters from existing file formats to simplify the transition. Finally, we present several use cases visualizing example structures stored in UNF, showcasing the various types of data UNF can handle.

DNA nanotechnology-facilitated ligand manipulation for targeted therapeutics and diagnostics

Ligands, mostly binding to proteins to form complexes and catalyze chemical reactions, can serve as drug and probe molecules, as well as sensing elements. DNA nanotechnology can integrate the high editability of DNA nanostructures and the biological activity of ligands into functionalized DNA nanostructures in a manner of controlled ligand stoichiometry, type, and arrangement, which provides significant advantages for targeted therapeutics and diagnostics. As therapeutic agents, multiple- and multivalent-ligands functionalized DNA nanostructures increase ligand-receptor affinity and activate multivalent ligand-receptor interactions, enabling improved regulation of cell signaling and enhanced control of cell behavior. As diagnostic agents, multiple ligands interaction via DNA nanostructures endows DNA nanosensors with high sensitivity and excellent signal transduction capability. Herein, we review the principles and advantages of using DNA nanostructures to manipulate ligands for targeted therapeutics and diagnostics and provide future perspectives.

Nano-sandwich composite by kinetic trapping assembly from protein and nucleic acid

Design and preparation of layered composite materials alternating between nucleic acids and proteins has been elusive due to limitations in occurrence and geometry of interaction sites in natural biomolecules. We report the design and kinetically controlled stepwise synthesis of a nano-sandwich composite by programmed noncovalent association of protein, DNA and RNA modules. A homo-tetramer protein core was introduced to control the self-assembly and precise positioning of two RNA–DNA hybrid nanotriangles in a co-parallel sandwich arrangement. Kinetically favored self-assembly of the circularly closed nanostructures at the protein was driven by the intrinsic fast folding ability of RNA corner modules which were added to precursor complex of DNA bound to the protein. The 3D architecture of this first synthetic protein–RNA–DNA complex was confirmed by fluorescence labeling and cryo-electron microscopy studies. The synthesis strategy for the nano-sandwich composite provides a general blueprint for controlled noncovalent assembly of complex supramolecular architectures from protein, DNA and RNA components, which expand the design repertoire for bottom-up preparation of layered biomaterials.

Obtaining Precise Molecular Information via DNA Nanotechnology

Precise characterization of biomolecular information such as molecular structures or intermolecular interactions provides essential mechanistic insights into the understanding of biochemical processes. As the resolution of imaging-based measurement techniques improves, so does the quantity of molecular information obtained using these methodologies. DNA (deoxyribonucleic acid) molecule have been used to build a variety of structures and dynamic devices on the nanoscale over the past 20 years, which has provided an accessible platform to manipulate molecules and resolve molecular information with unprecedented precision. In this review, we summarize recent progress related to obtaining precise molecular information using DNA nanotechnology. After a brief introduction to the development and features of structural and dynamic DNA nanotechnology, we outline some of the promising applications of DNA nanotechnology in structural biochemistry and in molecular biophysics. In particular, we highlight the use of DNA nanotechnology in determination of protein structures, protein-protein interactions, and molecular force.