Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells.

Fluorescent RNAs, aptamers that bind and activate small fluorogenic dyes, have provided a particularly attractive approach to visualizing RNAs in live cells. However, the simultaneous imaging of multiple RNAs remains challenging due to a lack of bright and stable fluorescent RNAs with bio-orthogonality and suitable spectral properties. Here, we develop the Clivias, a series of small, monomeric and stable orange-to-red fluorescent RNAs with large Stokes shifts of up to 108 nm, enabling the simple and robust imaging of RNA with minimal perturbation of the target RNA's localization and functionality. In combination with Pepper fluorescent RNAs, the Clivias enable the single-excitation two-emission dual-color imaging of cellular RNAs and genomic loci. Clivias can also be used to detect RNA-protein interactions by bioluminescent imaging both in live cells and in vivo. We believe that these large Stokes shift fluorescent RNAs will be useful tools for the tracking and quantification of multiple RNAs in diverse biological processes.

Structural basis of a small monomeric Clivia fluorogenic RNA with a large Stokes shift.

RNA-based fluorogenic modules have revolutionized the spatiotemporal localization of RNA molecules. Recently, a fluorophore named 5-((Z)-4-((2-hydroxyethyl)(methyl)amino)benzylidene)-3-methyl-2-((E)-styryl)-3,5-dihydro-4H-imidazol-4-one (NBSI), emitting in red spectrum, and its cognate aptamer named Clivia were identified, exhibiting a large Stokes shift. To explore the underlying molecular basis of this unique RNA-fluorophore complex, we determined the tertiary structure of Clivia-NBSI. The overall structure uses a monomeric, non-G-quadruplex compact coaxial architecture, with NBSI sandwiched at the core junction. Structure-based fluorophore recognition pattern analysis, combined with fluorescence assays, enables the orthogonal use of Clivia-NBSI and other fluorogenic aptamers, paving the way for both dual-emission fluorescence and bioluminescence imaging of RNA molecules within living cells. Furthermore, on the basis of the structure-based substitution assay, we developed a multivalent Clivia fluorogenic aptamer containing multiple minimal NBSI-binding modules. This innovative design notably enhances the recognition sensitivity of fluorophores both in vitro and in vivo, shedding light on future efficient applications in various biomedical and research contexts.

Imaging the dynamics of messenger RNA with a bright and stable green fluorescent RNA.

Fluorescent RNAs (FRs) provide an attractive approach to visualizing RNAs in live cells. Although the color palette of FRs has been greatly expanded recently, a green FR with high cellular brightness and photostability is still highly desired. Here we develop a fluorogenic RNA aptamer, termed Okra, that can bind and activate the fluorophore ligand ACE to emit bright green fluorescence. Okra has an order of magnitude enhanced cellular brightness than currently available green FRs, allowing the robust imaging of messenger RNA in both live bacterial and mammalian cells. We further demonstrate the usefulness of Okra for time-resolved measurements of ACTB mRNA trafficking to stress granules, as well as live-cell dual-color superresolution imaging of RNA in combination with Pepper620, revealing nonuniform and distinct distributions of different RNAs throughout the granules. The favorable properties of Okra make it a versatile tool for the study of RNA dynamics and subcellular localization.

Rapid fabrication of physically robust hydrogels.

Hydrogel materials show promise for diverse applications, particular as biocompatible materials due to their high water content. Despite advances in hydrogel technology in recent years, their application is often severely limited by inadequate mechanical properties and time-consuming fabrication processes. Here we report a rapid hydrogel preparation strategy that achieves the simultaneous photo-crosslinking and establishment of biomimetic soft-hard material interface microstructures. These biomimetic interfacial-bonding nanocomposite hydrogels are prepared within seconds and feature clearly separated phases but have a strongly bonded interface. Due to effective interphase load transfer, biomimetic interfacial-bonding nanocomposite gels achieve an ultrahigh toughness (138 MJ m-3) and exceptional tensile strength (15.31 MPa) while maintaining a structural stability that rivals or surpasses that of commonly used elastomer (non-hydrated) materials. Biomimetic interfacial-bonding nanocomposite gels can be fabricated into arbitrarily complex structures via three-dimensional printing with micrometre-level precision. Overall, this work presents a generalizable preparation strategy for hydrogel materials and acrylic elastomers that will foster potential advances in soft materials.

Structure-based investigation of fluorogenic Pepper aptamer.

Pepper fluorescent RNAs are a recently reported bright, stable and multicolor fluorogenic aptamer tag that enable imaging of diverse RNAs in live cells. To investigate the molecular basis of the superior properties of Pepper, we determined the structures of complexes of Pepper aptamer bound with its cognate HBC or HBC-like fluorophores at high resolution by X-ray crystallography. The Pepper aptamer folds in a monomeric non-G-quadruplex tuning-fork-like architecture composed of a helix and one protruded junction region. The near-planar fluorophore molecule intercalates in the middle of the structure and is sandwiched between one non-G-quadruplex base quadruple and one noncanonical G·U wobble helical base pair. In addition, structure-based mutational analysis is evaluated by in vitro and live-cell fluorogenic detection. Taken together, our research provides a structural basis for demystifying the fluorescence activation mechanism of Pepper aptamer and for further improvement of its future application in RNA visualization.

Visible-light activatable coumarin-based phototriggers for fluorescence imaging with ultra-high photolysis efficiency.

Photoactivated fluorophores (PAFs) are powerful imaging tools for observing subcellular structures and tracking dynamic biological processes. However, photoremovable protecting groups (PPGs) widely used to construct PAFs suffer from the drawbacks of short-wavelength excitation and/or low photolysis efficiency. Herein, a class of coumarin-based PPGs with electron-rich thiophene derived substitutions at the C3-position of a coumarin scaffold were prepared. The modification not only leads to the redshift of the absorption band to the blue light region (400-500 nm), but also the increases of uncaging quantum yield (Φu) as well as molar extinction coefficient (εmax), thus enhancing the photolysis efficiency (Φu × Îµmax) up to 34.2 × 103 M-1 cm-1. The exceptionally high photolysis efficiency enables efficient photolysis in blue light as weak as 2 mW cm-2 or in blue light from a Luminol chemiluminescence system. Based on the excellent photolysis properties, the PAF constructed by the new PPG exhibits fast photoactivation and a low background signal, and the resulting fluorescence images display a signal-to-noise ratio greater than 780. It is anticipated that the superior photolysis performance makes the PPGs a novel platform for the construction of photo responsive systems in a variety of applications.

One-Step Manufacturing of Supramolecular Liquid-Crystal Elastomers by Stress-Induced Alignment and Hydrogen Bond Exchange.

Liquid-crystal elastomers (LCEs) capable of performing large and reversible deformation in response to an external stimulus are an important class of soft actuators. However, their manufacturing process typically involves a multistep approach that requires harsh conditions. For the very first time, LCEs with customized geometries that can be manufactured by a rapid one-step approach at room temperature are developed. The LCEs are hydrogen bond (H-bond) crosslinked main chain polymers comprising flexible short side chains. Applying a stretching/shear force to the LCE can simultaneously induce mesogen alignment and H-bond exchange, allowing for the formation of well-aligned LCE networks stabilized by H-bonds. Based on this working principle, soft actuators in fibers and 2D/3D objects can be manufactured by mechanical stretching or melt extrusion within a short time (e.g. <1 min). These actuators can perform reversible macroscopic motions with large, controlled deformations up to 38 %. The dynamic nature of H-bonds also provides the actuators with reprocessability and reprogrammability. Thus, this work opens the way for the one-step and custom manufacturing of soft actuators.

A Light-Driven Molecular Machine Controls K+ Channel Transport and Induces Cancer Cell Apoptosis.

The design of artificial ion channels with high activity, selectivity and gating function is challenging. Herein, we designed the light-driven motor molecule MC2, which provides new design criteria to overcome these challenges. MC2 forms a selective K+ channel through a single molecular transmembrane mechanism, and the light-driven rotary motion significantly accelerates ion transport, which endows the irradiated motor molecule with excellent cytotoxicity and cancer cell selectivity. Mechanistic studies reveal that the rotary motion of MC2 promotes K+ efflux, generates reactive oxygen species and eventually activates caspase-3-dependent apoptosis in cancer cells. Combined with the spatiotemporally controllable advantages of light, we believe this strategy can be exploited in the structural design and application of next-generation synthetic cation transporters for the treatment of cancer and other diseases.

Highly Tough, Stretchable, and Enzymatically Degradable Hydrogels Modulated by Bioinspired Hydrophobic ß-Sheet Peptides.

Peptide-based supramolecular hydrogels have attracted great attention due to their good biocompatibility and biodegradability and have become promising candidates for biomedical applications. The bottom-up self-assembly endows the peptides with a highly ordered secondary structure, which has proven to be an effective strategy to improve the mechanical properties of hydrogels through strong physical interactions and energy dissipation. Inspired by the excellent mechanical properties of spider-silk, which can be attributed to the rich ß-sheet crystal formation by the hydrophobic peptide fragment, a hydrophobic peptide (HP) that can form a ß-sheet assembly was designed and introduced into a poly(vinyl alcohol) (PVA) scaffold to improve mechanical properties of hydrogels by the cooperative intermolecular physical interactions. Compared with hydrogels without peptide grafting (P-HP0), the strong ß-sheet self-assembly domain endows the hybrid hydrogels (P-HP20, P-HP29, and P-HP37) with high strength and toughness. The fracture tensile strength increased from 0.3 to 2.1 MPa (7 times), the toughness increased from 0.4 to 21.6 MJ m-3 (54 times), and the compressive strength increased from 0.33 to 10.43 MPa (31 times) at 75% strain. Moreover, the hybrid hydrogels are enzymatically degradable due to the dominant contribution of the ß-sheet assembly for network cross-linking. Combining the good biocompatibility and sustained drug release of the constructed hydrogels, this hydrophobic ß-sheet peptide represents a promising candidate for the rational design of hydrogels for biomedical applications.

A Light-Operated Molecular Cable Car for Gated Ion Transport.

Inspired by the nontrivial and controlled movements of molecular machines, we report an azobenzene-based molecular shuttle PR2, which can perform light-gated ion transport across lipid membranes. The amphiphilicity and membrane-spanning molecular length enable PR2 to insert into the bilayer membrane and efficiently transport K+ (EC50 =4.1 µm) through the thermally driven stochastic shuttle motion of the crown ether ring along the axle. The significant difference in shuttling rate between trans-PR2 and cis-PR2 induced by molecular isomerization enables a light-gated ion transport, i.e., ON/OFF in situ regulation of transport activity and single-channel current. This work represents an example of using a photoswitchable molecular machine to realize gated ion transport, which demonstrates the value of molecular machines functioning in biomembranes.

Genetically encoded fluorescent sensors reveal dynamic regulation of NADPH metabolism.

Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is essential for biosynthetic reactions and antioxidant functions; however, detection of NADPH metabolism in living cells remains technically challenging. We develop and characterize ratiometric, pH-resistant, genetically encoded fluorescent indicators for NADPH (iNap sensors) with various affinities and wide dynamic range. iNap sensors enabled quantification of cytosolic and mitochondrial NADPH pools that are controlled by cytosolic NAD+ kinase levels and revealed cellular NADPH dynamics under oxidative stress depending on glucose availability. We found that mammalian cells have a strong tendency to maintain physiological NADPH homeostasis, which is regulated by glucose-6-phosphate dehydrogenase and AMP kinase. Moreover, using the iNap sensors we monitor NADPH fluctuations during the activation of macrophage cells or wound response in vivo. These data demonstrate that the iNap sensors will be valuable tools for monitoring NADPH dynamics in live cells and gaining new insights into cell metabolism.

Development of Acrylamide-Based Rapid and Multicolor Fluorogenic Probes for High Signal-to-Noise Live Cell Imaging.

Protein covalent labeling is dramatically useful for studying protein function in living cells and organisms. In this field, the chemical tag technique combined with fluorogenic probes has emerged as a powerful tool. Herein, a series of TMP tag fluorogenic probes have been developed to span the green to full blue spectral range. These probes feature an acrylamide unit that acts as a linker group to conjugate the fluorophore and the ligand as well as a quencher and a covalent reaction group. After the probes bind to eDHFR:L28C, the acrylamide unit specifically reacts with the thiol group of the L28C residue beside the ligand binding pocket, achieving protein-specific labeling without any liberation of leaving groups. With these probes, multicolor and specific protein labeling with a fast reaction rate ( t1/2 = 33 s) and dramatic fluorescence enhancement (4000-fold) were obtained. Furthermore, no-wash protein labeling in both living cells and zebrafish was successfully achieved. We expect it may provide a general and highly effective chemical tool for the study of protein function in living cells and organisms.

An Artificial Molecular Shuttle Operates in Lipid Bilayers for Ion Transport.

Inspired by natural biomolecular machines, synthetic molecular-level machines have been proven to perform well-defined mechanical tasks and measurable work. To mimic the function of channel proteins, we herein report the development of a synthetic molecular shuttle, [2]rotaxane 3, as a unimolecular vehicle that can be inserted into lipid bilayers to perform passive ion transport through its stochastic shuttling motion. The [2]rotaxane molecular shuttle is composed of an amphiphilic molecular thread with three binding stations, which is interlocked in a macrocycle wheel component that tethers a K+ carrier. The structural characteristics enable the rotaxane to transport ions across the lipid bilayers, similar to a cable car, transporting K+ with an EC50 value of 1.0 µM (3.0 mol % relative to lipid). We expect that this simple molecular machine will provide new opportunities for developing more effective and selective ion transporters.

Coumarin Photocaging Groups Modified with an Electron-Rich Styryl Moiety at the 3-Position: Long-Wavelength Excitation, Rapid Photolysis, and Photobleaching.

A new class of coumarin photocaging groups modified with an electron-rich styryl moiety at the 3-position was constructed. The large π-conjugated structure and stabilization of the carbocation intermediates by electron donors endowed the new photocaging groups with excellent long-wavelength absorption, large two-photon absorption cross-sections, and high uncaging quantum yields. Moreover, the new photocaging groups displayed unique photobleaching properties after photocleavage as a result of the intramolecular cyclization rearrangement of a carbocation intermediate to form five-membered ring byproducts and block the styryl conjugation at the 3-position. These superior properties of the new photocaging groups are extremely beneficial for high-concentration samples and thick specimens, thus extending the application of photocaging groups in many fields.

Sequential control over thiol click chemistry by a reversibly photoactivated thiol mechanism of spirothiopyran.

A novel photocontrolled thiol click chemistry based on spirothiopyran and maleimide is reported. Upon irradiation with λ=365 nm light, the spirothiopyran can isomerize to the open merocyanine form, a thiophenolate group, which can rapidly react with maleimide. The unreacted MC will readily isomerize back to the starting spirothiopyran, which can be repeatedly photoactivated as needed. Thus, this reversible photoactivated thiol confers spatiotemporal sequential control on the thiol-maleimide reaction using only one type of photochemical reaction. Polymer post-functionalization and hydrogel building with subsequent multipatterning using different maleimide molecules in a temporal sequential manner indicate that this photocontrolled Michael addition reaction can modulate the specific chemical events in a sequence.

Intracellular thiols and photo-illumination sequentially activate doubly locked molecular probes for long-term cell highlighting and tracking with precise spatial accuracy.

A novel photoconvertible fluorescent probe, which can be activated by intracellular thiols, has been synthesized. Such a molecular probe comprises three parts: a 7-aminocoumarin phototrigger, a thiol-removable energy acceptor, and a caged fluorescein scaffold with intracellular thiols reactivity as the fluorescent reporter. Extracellularly, the energy acceptor blocks the emission of the coumarin that regulates the photocleavage and photoactivation of the fluorescein. Intracelluarly, the high concentration of thiols releases the energy acceptor, thus activating the S1 state of the phototrigger, which emits coumarin blue fluorescence for pre-visualization and liberates the caged green-fluorescent fluorescein to highlight the specific cell upon illumination. Compared to traditional photoactivated organic dyes, the intracellular thiols activated probe requires double activations: one by intracellular thiols and the other by light activation. The dual activations restrict fluorescence precisely inside live cells and at the particular spatial region of light activation, thus a probe with precise spatial accuracy in live cells.

Biohybrid Nanorobots Carrying Glycoengineered Extracellular Vesicles Promote Diabetic Wound Repair through Dual-Enhanced Cell and Tissue Penetration.

Considerable progress has been made in the development of drug delivery systems for diabetic wounds. However, underlying drawbacks, such as low delivery efficiency and poor tissue permeability, have rarely been addressed. In this study, a multifunctional biohybrid nanorobot platform comprising an artificial unit and several biological components is constructed. The artificial unit is a magnetically driven nanorobot surface modified with antibacterial 2-hydroxypropyltrimethyl ammonium chloride chitosan, which enables the entire platform to move and has excellent tissue penetration capacity. The biological components are two-step engineered extracellular vesicles that are first loaded with mangiferin, a natural polyphenolic compound with antioxidant properties, and then glycoengineered on the surface to enhance cellular uptake efficiency. As expected, the platform is more easily absorbed by endothelial cells and fibroblasts and exhibits outstanding dermal penetration performance and antioxidant properties. Encouraging results are also observed in infected diabetic wound models, showing improved wound re-epithelialization, collagen deposition, angiogenesis, and accelerated wound healing. Collectively, a biohybrid nanorobot platform that possesses the functionalities of both artificial units and biological components serves as an efficient delivery system to promote diabetic wound repair through dual-enhanced cell and tissue penetration and multistep interventions.

A light-activated polymer with excellent serum tolerance for intracellular protein delivery.

The design of efficient materials for intracellular protein delivery has attracted great interest in recent years; however, most current materials for this purpose are limited by poor serum stability due to the early release of cargoes triggered by abundant serum proteins. Here, we propose a light-activated crosslinking (LAC) strategy to prepare efficient polymers with excellent serum tolerance for intracellular protein delivery. A cationic dendrimer engineered with photoactivatable O-nitrobenzene moieties co-assembles with cargo proteins via ionic interactions, followed by light activation to yield aldehyde groups on the dendrimer and the formation of imine bonds with cargo proteins. The light-activated complexes show high stability in buffer and serum solutions, but dis-assemble under low pH conditions. As a result, the polymer successfully delivers cargo proteins green fluorescent protein and ß-galactosidase into cells with maintained bioactivity even in the presence of 50% serum. The LAC strategy proposed in this study provides a new insight to improve the serum stability of polymers for intracellular protein delivery.

Correction: Reinforced hydrogel network building by a rapid dual-photo-coupling reaction for 3D printing.

Correction for 'Reinforced hydrogel network building by a rapid dual-photo-coupling reaction for 3D printing' by Renjie Zhou et al., Chem. Commun., 2023, 59, 1963-1966, https://doi.org/10.1039/D2CC05677A.

Reinforced hydrogel network building by a rapid dual-photo-coupling reaction for 3D printing.

A facile hydrogel fabrication strategy based on a simultaneous dual-photo-coupling reaction (i.e., photoinduced S-nitrosylation and Schiff base reaction) was reported. This strategy allowed a strengthened three-arm crosslinking network to form in one step and the hydrogels obtained displayed rapid gelation, excellent mechanical strength and biocompatibility for cell encapsulated-3D printing in real time. Our hydrogel fabrication strategy will likely foster advances in biomaterials and the extreme speed and reinforced mechanical strength should significantly benefit 3D printing and related applications.