RNA Nanostructures: From Structure to Function.

Nucleic-acid nanostructures, which have been designed and constructed with atomic precision, have been used as scaffolds for different molecules and proteins, as nanomachines, as computational components, and more. In particular, RNA has garnered tremendous interest as a building block for the self-assembly of sophisticated and functional nanostructures by virtue of its ease of synthesis by in vivo or in vitro transcription, its superior mechanical and thermodynamic properties, and its functional roles in nature. In this Topical Review, we describe recent developments in the use of RNA for the design and construction of nanostructures. We discuss the differences between RNA and DNA that make RNA attractive as a building block for the construction of nucleic-acid nanostructures, and we present the uses of different nanostructures─RNA alone, RNA-DNA, and functional RNA nanostructures.

In situ self-assembling Au-DNA complexes for targeted cancer bioimaging and inhibition.

Cancer remains one of the most challenging diseases to treat. For accurate cancer diagnosis and targeted therapy, it is important to assess the localization of the affected area of cancers. The general approaches for cancer diagnostics include pathological assessments and imaging. However, these methods only generally assess the tumor area. In this study, by taking advantage of the unique microenvironment of cancers, we effectively utilize in situ self-assembled biosynthetic fluorescent gold nanocluster-DNA (GNC-DNA) complexes to facilitate safe and targeted cancer theranostics. In in vitro and in vivo tumor models, our self-assembling biosynthetic approach allowed for precise bioimaging and inhibited cancer growth after one injection of DNA and gold precursors. These results demonstrate that in situ bioresponsive self-assembling GNC-PTEN (phosphatase and tensin homolog) complexes could be an effective noninvasive technique for accurate cancer bioimaging and treatment, thus providing a safe and promising cancer theranostics platform for cancer therapy.

Single Particle Hopping as an Indicator for Evaluating Electrocatalysts.

The design and screening of electrocatalysts for gas evolution reactions suffer from little understanding of multiphase processes at the electrode-electrolyte interface. Due to the complexity of the multiphase interface, it is still a great challenge to capture gas evolution dynamics under operando conditions to precisely portray the intrinsic catalytic performance of the interface. Here, we establish a single particle imaging method to real-time monitor a potential-dependent vertical motion or hopping of electrocatalysts induced by electrogenerated gas nanobubbles. The hopping feature of a single particle is closely correlated with intrinsic activities of electrocatalysts and thus is developed as an indicator to evaluate gas evolution performance of various electrocatalysts. This optical indicator diminishes interference from heterogeneous morphologies, non-Faradaic processes, and parasitic side reactions that are unavoidable in conventional electrochemical measurements, therefore enabling precise evaluation and high-throughput screening of catalysts for gas evolution systems.

Publisher Correction: Regioselective surface encoding of nanoparticles for programmable self-assembly.

In the version of this Article originally published, the diblock copolymer structure in Fig. 2a showed a single bond between the carbon and the oxygen atoms; it should have been a double bond. This has been corrected in all versions of the Article.

Regioselective surface encoding of nanoparticles for programmable self-assembly.

Surface encoding of colloidal nanoparticles with DNA is fundamental for fields where recognition interaction is required, particularly controllable material self-assembly. However, regioselective surface encoding of nanoparticles is still challenging because of the difficulty associated with breaking the identical chemical environment on nanoparticle surfaces. Here we demonstrate the selective blocking of nanoparticle surfaces with a diblock copolymer (polystyrene-b-polyacrylic acid). By tuning the interfacial free energies of a ternary system involving the nanoparticles, solvent and copolymer, controllable accessibilities to the nanoparticles' surfaces are obtained. Through the modification of the polymer-free surface region with single-stranded DNA, regioselective and programmable surface encoding is realized. The resultant interparticle binding potential is selective and directional, allowing for an increased degree of complexity of potential self-assemblies. The versatility of this regioselective surface encoding strategy is demonstrated on various nanoparticles of isotropic or anisotropic shape and a total of 24 distinct complex nanoassemblies are fabricated.

The deoxyribose phosphate lyase of DNA polymerase ß suppresses a processive DNA synthesis to prevent trinucleotide repeat instability.

Trinucleotide repeat (TNR) instability is associated with over 42 neurodegenerative diseases and cancer, for which the molecular mechanisms remain to be elucidated. We have shown that the DNA base excision repair (BER) pathway and its central component, DNA polymerase ß (pol ß), in particular, its polymerase activity plays an active role in regulating somatic TNR instability. Herein, we revealed a unique role of the pol ß dRP lyase in preventing somatic TNR instability. We found that deficiency of pol ß deoxyribose phosphate (dRP) lyase activity locked the pol ß dRP lyase domain to a dRP group, and this 'tethered' pol ß to its template forcing the polymerase to perform a processive DNA synthesis. This subsequently promoted DNA strand slippage allowing pol ß to skip over a template loop and causing TNR deletion. We showed that the effects were eliminated by complementation of the dRP lyase deficiency with wild-type pol ß protein. The results indicate that pol ß dRP lyase activity restrained the pol ß-dRP interaction to suppress a pol ß processive DNA synthesis, thereby preventing TNR deletion. This further implicates a potential of pol ß dRP lyase inhibition as a novel treatment of TNR-expansion diseases.

Selective Induction of Optical Magnetism.

An extension of the Maxwell-Faraday law of electromagnetic induction to optical frequencies requires spatially appropriate materials and optical beams to create resonances and excitations with curl. Here we employ cylindrical vector beams with azimuthal polarization to create electric fields that selectively drive magnetic responses in dielectric core-metal nanoparticle "satellite" nanostructures. These optical frequency magnetic resonances are induced in materials that do not possess spin or orbital angular momentum. Multipole expansion analysis of the scattered fields obtained from electrodynamics simulations show that the excitation with azimuthally polarized beams selectively enhances magnetic vs electric dipole resonances by nearly 100-fold in experiments. Multipolar resonances (e.g., quadrupole and octupole) are enhanced 5-fold by focused azimuthally versus linearly polarized beams. We also selectively excite electric multipolar resonances in the same identical nanostructures with radially polarized light. This work opens new opportunities for spectroscopic investigation and control of "dark modes", Fano resonances, and magnetic modes in nanomaterials and engineered metamaterials.

Plasmonic Photothermal Gold Bipyramid Nanoreactors for Ultrafast Real-Time Bioassays.

Nucleic acid amplification techniques have been among the most powerful tools for biological and biomedical research, and the vast majority of the bioassays rely on thermocycling that uses time-consuming and expensive Peltier-block heating. Here, we introduce a plasmonic photothermal method for quantitative real-time PCR, using gold bipyramids and light to achieve ultrafast thermocycling. Moreover, we successfully extend our photothermal system to other biological assays, such as isothermal nucleic acid amplification and restriction enzyme digestion.

Live Cell MicroRNA Imaging Using Cascade Hybridization Reaction.

Recent advances in RNA research have posed new directives in biology and chemistry to uncover the complex roles of ribonucleic acids in cellular processes. Innovative techniques to visualize native RNAs, particularly, short, low-abundance RNAs in live cells, can dramatically impact current research on the roles of RNAs in biology. Herein, we report a novel method for real-time, microRNA imaging inside live cells based on programmable oligonucleotide probes, which self-assemble through the Cascade Hybridization Reaction (CHR).

Enzymatic synthesis of periodic DNA nanoribbons for intracellular pH sensing and gene silencing.

We report the construction of periodic DNA nanoribbons (DNRs) by a modified DNA origami method. Unlike the conventional DNA origami, the DNR scaffold is a long, single-stranded DNA of tandem repeats, originating from the rolling circular amplification (RCA). Consequently, the number of folding staple strands tremendously decreases from hundreds to a few, which makes the DNR production scalable and cost-effective, thus potentially removing the barrier for practical applications of DNA nanostructures. Moreover, the co-replicational synthesis of scaffold and staple strands by RCA-based enzymatic reactions allows the generation of DNRs in one pot, further reducing the cost. Due to their unique periodicity, rigidity, and high aspect ratio, DNRs are efficiently internalized into cells and escape from endosomal entrapment, making them potential nanocarriers for imaging agents and biological therapeutics. We demonstrated proof-of-concept applications of DNRs as an intracellular pH sensor and an efficient small interfering RNA delivery vehicle in human cancer cells.

Light-induced MOF synthesis enabling composite photothermal materials.

Metal-organic frameworks (MOFs) are a class of porous materials known for their large surface areas. Thus, over the past few decades the development of MOFs and their applications has been a major topic of interest throughout the scientific community. However, many current conventional syntheses of MOFs are lengthy solvothermal processes carried out at elevated temperatures. Herein, we developed a rapid light-induced synthesis of MOFs by harnessing the plasmonic photothermal abilities of bipyramidal gold nanoparticles (AuBPs). The generality of the photo-induced method was demonstrated by synthesizing four different MOFs utilizing three different wavelengths (520 nm, 660 nm and 850 nm). Furthermore, by regulating light exposure, AuBPs could be embedded in the MOF or maintained in the supernatant. Notably, the AuBPs-embedded MOF (AuBP@UIO-66) retained its plasmonic properties along with the extraordinary surface area typical to MOFs. The photothermal AuBP@UIO-66 demonstrated a significant light-induced heating response that was utilized for ultrafast desorption and MOF activation.

Real-time detection of telomerase activity using the exponential isothermal amplification of telomere repeat assay.

As crucial pieces in the puzzle of cancer and human aging, telomeres and telomerase are indispensable in modern biology. Here we describe a novel exponential isothermal amplification of telomere repeat (EXPIATR) assay--a sensitive, simple, and reliable in vitro method for measuring telomerase activity in cell extracts. Through a strategically designed path of nucleic acid isothermal amplifications, EXPIATR abandons the expensive thermal cycling protocol and achieves ultrafast detection: telomerase activity equivalent to a single HeLa cancer cell can be detected in ∼25 min.

Point-of-care nucleic acid tests: assays and devices.

The COVID-19 pandemic (caused by the SARS_CoV_2 virus) has emphasized the need for quick, easy-to-operate, reliable, and affordable diagnostic tests and devices at the Point-of-Care (POC) for homes/fields/clinics. Such tests and devices will contribute significantly to the fight against the COVID-19 pandemic and any future infectious disease epidemic. Often, academic research studies and those from industry lack knowledge of each other's developments. Here, we introduced DNA Polymerase Chain Reaction (PCR) and isothermal amplification reactions and reviewed the current commercially available POC nucleic acid diagnostic devices. In addition, we reviewed the history and the recent advancements in an effort to develop reliable, quick, portable, cost-effective, and automatic point-of-care nucleic acid diagnostic devices, from sample to result. The purpose of this paper is to bridge the gap between academia and industry and to share important knowledge on this subject.

Photothermally heated colloidal synthesis of nanoparticles driven by silica-encapsulated plasmonic heat sources.

Using photons to drive chemical reactions has become an increasingly important field of chemistry. Plasmonic materials can provide a means to introduce the energy necessary for nucleation and growth of nanoparticles by efficiently converting visible and infrared light to heat. Moreover, the formation of crystalline nanoparticles has yet to be included in the extensive list of plasmonic photothermal processes. Herein, we establish a light-assisted colloidal synthesis of iron oxide, silver, and palladium nanoparticles by utilizing silica-encapsulated gold bipyramids as plasmonic heat sources. Our work shows that the silica surface chemistry and localized thermal hotspot generated by the plasmonic nanoparticles play crucial roles in the formation mechanism, enabling nucleation and growth at temperatures considerably lower than conventional heating. Additionally, the photothermal method is extended to anisotropic geometries and can be applied to obtain intricate assemblies inaccessible otherwise. This study enables photothermally heated nanoparticle synthesis in solution through the plasmonic effect and demonstrates the potential of this methodology.

Plasmonic visible-near infrared photothermal activation of olefin metathesis enabling photoresponsive materials.

Light-induced catalysis and thermoplasmonics are promising fields creating many opportunities for innovative research. Recent advances in light-induced olefin metathesis have led to new applications in polymer and material science, but further improvements to reaction scope and efficiency are desired. Herein, we present the activation of latent ruthenium-based olefin metathesis catalysts via the photothermal response of plasmonic gold nanobipyramids. Simple synthetic control over gold nanobipyramid size results in tunable localized surface plasmon resonance bands enabling catalyst initiation with low-energy visible and infrared light. This approach was applied to the ROMP of dicyclopentadiene, affording plasmonic polymer composites with exceptional photoresponsive and mechanical properties. Moreover, this method of catalyst activation was proven to be remarkably more efficient than activation through conventional heating in all the metathesis processes tested. This study paves the way for providing a wide range of photoinduced olefin metathesis processes in particular and photoinduced latent organic reactions in general by direct photothermal activation of thermally latent catalysts.

DNA-CNT nanowire networks for DNA detection.

The ability to detect biological analytes in a rapid, sensitive, operationally simple, and cost-effective manner will impact human health and safety. Hybrid biocatalyzed-carbon nanotube (CNT) nanowire-based detection methods offer a highly sensitive and specific platform for the fabrication of simple and effective conductometric devices. Here, we report a conductivity-based DNA detection method utilizing carbon nanotube-DNA nanowire devices and oligonucleotide-functionalized enzyme probes. Key to our sensor design is a DNA-linked-CNT wire motif, which forms a network of interrupted carbon nanotube wires connecting two electrodes. Sensing occurs at the DNA junctions linking CNTs, followed by amplification using enzymatic metalization leading to a conductimetric response. The DNA analyte detection limit is 10 fM with the ability to discriminate single, double, and triple base pair mismatches. DNA-CNT nanowires and device sensing gaps were characterized by scanning electron microscopy (SEM) and confocal Raman microscopy, supporting the enhanced conductometric response resulting from nanowire metallization.

A polycatenated DNA scaffold for the one-step assembly of hierarchical nanostructures.

A unique DNA scaffold was prepared for the one-step self-assembly of hierarchical nanostructures onto which multiple proteins or nanoparticles are positioned on a single template with precise relative spatial orientation. The architecture is a topologically complex ladder-shaped polycatenane in which the "rungs" of the ladder are used to bring together the individual rings of the mechanically interlocked structure, and the "rails" are available for hierarchical assembly, whose effectiveness has been demonstrated with proteins, complementary DNA, and gold nanoparticles. The ability of this template to form from linear monomers and simultaneously bind two proteins was demonstrated by chemical force microscopy, transmission electron microscopy, and confocal fluorescence microscopy. Finally, fluorescence resonance energy transfer between adjacent fluorophores confirmed the programmed spatial arrangement between two different nanomaterials. DNA templates that bring together multiple nanostructures with precise spatial control have applications in catalysis, biosensing, and nanomaterials design.

Regiospecific synthesis of Au-nanorod/SWCNT/Au-nanorod heterojunctions.

The synthesis of precisely defined nanoscale hybrid materials remains a challenge at the frontier of chemistry and material science. In particular, the assembly of diverse high-aspect ratio one-dimensional materials such as gold nanorods and carbon nanotubes into functional systems is of ever increasing interest due to their electronic and sensing applications. To meet these challenges, methods for interfacing gold nanorods with carbon materials such as single-walled carbon nanotubes (SWCNTs) in a regio-controlled manner are needed. Herein, we report a method for the regiospecific synthesis of terminally linked gold nanorod-SWCNTs based on a nanotube surface protection strategy. The key to our approach is a SWCNT surface protection procedure allowing for selective functionalization of the SWCNT termini.

Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution.

Although advances in nanotechnology have enabled the construction of complex and functional synthetic nucleic acid­based nanoarchitectures, high-resolution discrete structures are lacking because of the difficulty in obtaining good diffracting crystals. Here, we report the design and construction of RNA nanostructures based on homooligomerizable one-stranded tiles for x-ray crystallographic determination. We solved three structures to near-atomic resolution: a 2D parallelogram, a 3D nanobracelet unexpectedly formed from an RNA designed for a nanocage, and, eventually, a bona fide 3D nanocage designed with the guidance of the two previous structures. Structural details of their constituent motifs, such as kissing loops, branched kissing loops, and T-junctions, that resemble natural RNA motifs and resisted x-ray determination are revealed, providing insights into those natural motifs. This work unveils the largely unexplored potential of crystallography in gaining high-resolution feedback for nanoarchitectural design and suggests a route to investigate RNA motif structures by configuring them into nanoarchitectures.

Intelligent Bio-Responsive Fluorescent Au-shRNA Complexes for Regulated Autophagy and Effective Cancer Bioimaging and Therapeutics.

The long non-coding RNA (lncRNA) MALAT1 acts as an oncogene. RNA interference (RNAi) is an effective method to control the expression of specific genes and can be used for the treatment of tumors, but an effective and safe carrier system is a significant obstacle to gene therapy. Herein, we explored the possibility of constructing an in situ bio-responsive self-assembled fluorescent gold-short hairpin RNA nanocomplex (Au-shRNA NCs) delivery system by co-incubating gold and MALAT1-shRNA for precise hepatocellular carcinoma (HCC) imaging and treatment. Due to the characteristics of the cancer microenvironment, Au-shRNA NCs self-assembled in HCC cells (HepG2) but did not occur in control cells (L02) under the same conditions. The in situ bio-responsive self-assembled Au-shRNA NCs delivery system can realize cancer cell bioimaging and promote cell uptake and endosomal escape mechanism, thereby realizing effective transfection. They effectively silenced target gene MALAT1, and with the downregulation of MALAT1, we found that several molecules involved in autophagic flux were also regulated. In vitro and tumor-bearing mouse model experiments demonstrated that the as-prepared fluorescent Au-shRNA NCs can readily realize tumor bioimaging and effectively silence the target gene MALAT1, and those autophagy-related pathway molecules were significantly downregulated, thereby exerting a tumor suppressor efficiency. This raises the possibility of realizing accurate multi-scale bio-imaging from the molecular-level with targeted gene-recognition to cancer cell imaging as well as in vivo tumor tissue imaging for the simultaneous precise cancer therapy.