“Printing” DNA Strand Patterns on Small Molecules with Control of Valency, Directionality, and Sequence

Modular Assembled Localized Hybridization Chain Reaction for In Situ mRNA Amplified Imaging

As a nonenzymatic DNA signal amplification technique, localized hybridization chain reaction (LHCR) was designed to improve the limitations in response speed and low sensitivity of conventional free diffusional HCR (hybridization chain reaction). However, it is still confronted with the challenges of complicated DNA scaffolds with low loading capacity and a time-consuming process of diffusion. Herein, we introduced modular assembly of a DNA minimal scaffold for coassembly of DNA hairpins for amplified fluorescence imaging of mRNA in situ. DNA hairpins were spatially bound to two Y-shaped modules to form H-shaped DNA modules, and then multiple H-shaped DNA modules can further assemble into an H-module-based hairpin scaffold (HHS). Benefiting from highly spatial localization and high loading capacity, the HHS system showed higher sensitivity and faster speed. It has also been proven to work perfectly in vitro and in vivo, which could provide a promising bioanalysis system for low abundance biomolecule detection.

DNA-Mediated Peptide Assembly into Protein Mimics

The design of new protein structures is challenging due to their vast sequence space and the complexity of protein folding. Here, we report a new modular DNA-templated strategy to construct protein mimics. We achieve the spatial control of multiple peptide units by conjugation with DNA and hybridization to a branched DNA trimer template followed by covalent stapling of the preorganized peptides into a single unit. A library of protein mimics with different lengths, sequences, and heptad registers has been efficiently constructed. DNA-templated protein mimics show an α-helix or coiled-coil motif formation even when they are constructed from weakly interacting peptide units. Their attached DNA handles can be used to exert dynamic control over the protein mimics' secondary and tertiary structures. This modular strategy will facilitate the development of DNA-encoded protein libraries for the rapid discovery of new therapeutics, enzymes, and antibody mimics.

Nano-Bio Interactions between DNA Nanocages and Human Serum Albumin

DNA nanostructures have emerged as promising nanomedical tools due to their biocompatibility and tunable behavior. Recent work has shown that DNA nanocages decorated with organic dendrimers strongly bind human serum albumin (HSA), yet the dynamic structures of these complexes remain uncharacterized. This theoretical and computational investigation elucidates the fuzzy interactions between dendritically functionalized cubic DNA nanocages and HSA. The dendrimer-HSA interactions occur via nonspecific binding with the protein thermodynamically and kinetically free to cross the open faces of the cubic scaffold. However, the rigidity of the DNA scaffold prevents the binding energetics from scaling with the number of dendrimers. These discoveries not only provide a useful framework by which to model general interactions of DNA nanostructures complexed with serum proteins but also give valuable molecular insight into the design of next-generation DNA nanomedicines.

Self-Assembly of Hybrid Peptide-DNA Nanostructures using Homotrimeric Coiled-Coil/Nucleic Acid Building Blocks

Peptides and DNA are two of the most commonly used self-assembling biological molecules for the construction of nanomaterials. However, there are only a few examples that combine these two self-assembly motifs as key structural elements in a nanostructure. We report on the synthesis of a peptide-DNA conjugate that self-assembles into a stable homotrimer based on the coiled-coil motif. The hybrid peptide-DNA trimer was then used as a novel three-way junction to link together either small DNA tile nanostructures, or to close up a triangular wireframe DNA structure. The resulting nanostructures were characterized by atomic force microscopy, and compared with a scrambled, non-assembling peptide as a control. These hybrid nanostructures enable the integration of peptide motifs and potentially bio-functionality with DNA nanostructures, and open the door to novel nano-materials that have the advantages of both molecules.

DNA-Scaffolded Synergistic Catalysis

We report DNA-scaffolded synergistic catalysis, a concept that combines the diverse reaction scope of synergistic catalysis with the ability of DNA to precisely preorganize abiotic groups and undergo stimuli-triggered conformational changes. As an initial demonstration of this concept, we focus on Cu-TEMPO-catalyzed aerobic alcohol oxidation, using DNA as a scaffold to hold a copper cocatalyst and an organic radical cocatalyst (TEMPO) in proximity. The DNA-scaffolded catalyst maintained a high turnover number upon dilution and exhibited 190-fold improvement in catalyst turnover number relative to the unscaffolded cocatalysts. By incorporating the cocatalysts into a DNA hairpin-containing scaffold, we demonstrate that the rate of the synergistic catalytic reaction can be controlled through a reversible DNA conformational change that alters the distance between the cocatalysts. This work demonstrates the compatibility of synergistic catalytic reactions with DNA scaffolding, opening future avenues in reaction discovery, sensing, responsive materials, and chemical biology.

Programming a "Crab Claw"-like DNA Nanomachine as a Super Signal Amplifier for Ultrasensitive Electrochemical Assay of Hg2

Herein, with skillfully engaging stable T-Hg²⁺-T bonding, a "Crab Claw"-like DNA nanomachine with concise and highly efficient assembly and enhanced recognition/conversion efficiency was engineered as a super signal amplifier, which was united with Pd@Cu@Pt multimetallic mesoporous nanomaterials (Pd@Cu@Pt MMNs) for ultrasensitive electrochemical assay of mercury ions (Hg²⁺). Specifically, the formed "Crab Claw"-like DNA nanomachine could simultaneously trigger four same cascade DNAzyme cleavage reactions with the help of Mg²⁺ DNAzyme for markedly converting target Hg²⁺ to enormous DNA segments labeled with ferrocene (Fc), improving the detection sensitivity. Subsequently, the prepared Pd@Cu@Pt MMNs could not only show commendable electrochemical catalysis to Fc but also act as an excellent immobilization matrix for capturing and accumulating abundant Fc around them to further strengthen the electrochemical signal. As a result, the well-designed electrochemical sensor could achieve a low limit of detection of 3.58 fM in the range from 10 fM to 100 nM for Hg²⁺detection. This strategy offers a simple and rapid avenue to detect heavy metal ions and shows promising application potential for environmental pollutant monitoring.

Responsive optical probes for deep-tissue imaging: Photoacoustics and second near-infrared fluorescence

Optical imaging has played a vital role in development of biomedicine and image-guided theragnostic. Nevertheless, the clinical translation of optical molecular imaging for deep-tissue visualization is still limited by poor signal-to-background ratio and low penetration depth owing to light scattering and tissue autofluorescence. Hence, to facilitate precise diagnosis and accurate surgery excision in clinical practices, the responsive optical probes (ROPs) are broadly designed for specific reaction with biological analytes or disease biomarkers via chemical/physical interactions for photoacoustic and second near-infrared fluorescence (NIR-II, 900-1700 nm) fluorescence imaging. Herein, the recent advances in the development of ROPs including molecular design principles, activated mechanisms and treatment responses for photoacoustic and NIR-II fluorescence imaging are reviewed. Furthermore, the present challenges and future perspectives of ROPs for deep-tissue imaging are also discussed.

Organic Semiconductor-DNA Hybrid Assemblies

Organic semiconductors are photonic and electronic materials with high luminescence, quantum efficiency, color tunability, and size-dependent optoelectronic properties. The self-assembly of organic molecules enables the establishment of a fabrication technique for organic micro- and nano-architectures with well-defined shapes, tunable sizes, and defect-free structures. DNAs, a class of biomacromolecules, have recently been used as an engineering material capable of intricate nanoscale structuring while simultaneously storing biological genetic information. Here, the up-to-date research on hybrid materials made from organic semiconductors and DNAs is presented. The trends in photonic and electronic phenomena discovered in DNA-functionalized and DNA-driven organic semiconductor hybrids, comprising small molecules and polymers, are observed. Various hybrid forms of solutions, arrayed chips, nanowires, and crystalline particles are discussed, focusing on the role of DNA in the hybrids. Furthermore, the recent technical advances achieved in the integration of DNAs in light-emitting devices, transistors, waveguides, sensors, and biological assays are presented. DNAs not only serve as a recognizing element in organic-semiconductor-based sensors, but also as an active charge-control material in high-performance optoelectronic devices.

The assemble, grow and lift-off (AGLO) strategy to construct complex gold nanostructures with pre-designed morphologies

The construction of metallic nanostructures with customizable morphologies and complex shapes has been an essential pursuit in nanoscience. DNA nanotechnology has enabled the fabrication of increasingly complex DNA nanostructures with unprecedented specificity, programmability and sub-nanometer precision, which makes it an ideal approach to rationally organize metallic nanostructures. Here we report an Assemble, Grow and Lift-Off (AGLO) strategy to construct robust standalone gold nanostructures with pre-designed customizable shapes in solution, using only a simple 2D DNA origami sheet as a versatile transient template. Gold nanoparticle (AuNP) seeds were firstly assembled onto the pre-designed binding sites of the DNA origami template and then additional gold was slowly deposited onto the AuNP seeds. The growing seed surfaces eventually merge with adjacent seeds to generate one continuous gold nanostructure in a pre-designed shape, which can then be lifted off the origami template. Diverse customized patterns of templated AuNP seeds were successfully transformed into corresponding gold nanostructures with the target structure transformation percentage over 80%. Moreover, the AGLO strategy can be incorporated with a magnetic bead separation platform to enable the easy recycling of the excess AuNP seeds and DNA components.