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.

The AGLO strategy generates complex gold nanostructures with user-designed morphologies in solution, using only a simple 2D DNA origami sheet as a versatile transient template. The products are robust and stable as standalone gold nanostructures.     

Persistent organic room temperature phosphorescence: what is the role of molecular dimers?

Molecular dimers have been frequently found to play an important role in room temperature phosphorescence (RTP), but its inherent working mechanism has remained unclear. Herein a series of unique characteristics, including singlet excimer emission and thermally activated delayed fluorescence, were successfully integrated into a new RTP luminogen of CS-2COOCH₃ to clearly reveal the excited-state process of RTP and the special role of molecular dimers in persistent RTP emission.

The first purely organic room temperature phosphorescence (RTP) luminogen, with singlet excimer emission and thermally activated delayed fluorescence (TADF) effect, was successfully developed.      

Singlet fission in a hexacene dimer: energetics dictate dynamics

Singlet fission (SF) is an exciton multiplication process with the potential to raise the efficiency limit of single junction solar cells from 33% to up to 45%. Most chromophores generally undergo SF as solid-state crystals. However, when such molecules are covalently coupled, the dimers can be used as model systems to study fundamental photophysical dynamics where a singlet exciton splits into two triplet excitons within individual molecules. Here we report the synthesis and photophysical characterization of singlet fission of a hexacene dimer. Comparing the hexacene dimer to analogous tetracene and pentacene dimers reveals that excess exoergicity slows down singlet fission, similar to what is observed in molecular crystals. Conversely, the lower triplet energy of hexacene results in an increase in the rate of triplet pair recombination, following the energy gap law for radiationless transitions. These results point to design rules for singlet fission chromophores: the energy gap between singlet and triplet pair should be minimal, and the gap between triplet pair and ground state should be large.

We report the synthesis and photophysical characterization of highly exoergic singlet fission in a hexacene dimer revealing exciton dynamics that follow the energy gap law.     

Robust selenium-doped carbon nitride nanotubes for selective electrocatalytic oxidation of furan compounds to maleic acid

Selective oxidation of biomass-derived furan compounds to maleic acid (MA), an important bulk chemical, is a very attractive strategy for biomass transformation. However, achieving a high MA selectivity remains a great challenge. Herein, we for the first time successfully designed and fabricated Se-doped graphitic carbon nitride nanotubes with a chemical formula of C_3.0N-Se_0.03. The prepared C_3.0N-Se_0.03 was highly efficient for electrocatalytic oxidation of various biomass-derived furan compounds to generate MA. At ambient conditions, the MA yield could reach 84.2% from the electro-oxidation of furfural. Notably, the substituents on the furan ring significantly affected the selectivity to MA, following the order: carboxyl group > aldehyde group > hydroxyl group. Detailed investigation revealed that Se doping could tune the chemical structure of the materials (e.g., C_3.0N-Se_0.03 and g-C₃N₄), thus resulting in the change in catalytic mechanism. The excellent performance of C_3.0N-Se_0.03 originated from the suitable amount of graphitic N and its better electrochemical properties, which significantly boosted the oxidation pathway to MA. This work provides a robust and selective metal-free electrocatalyst for the sustainable synthesis of MA from oxidation of biomass-derived furan compounds.

Biomass-derived furan compounds could be selectively electro-oxidized into maleic acid over a robust selenium-doped carbon nitride nanotube catalyst.     

Amplified detection of nucleic acids and proteins using an isothermal proximity CRISPR Cas12a assay

Herein, we describe an isothermal proximity CRISPR Cas12a assay that harnesses the target-induced indiscrimitive single-stranded DNase activity of Cas12a for the quantitative profiling of gene expression at the mRNA level and detection of proteins with high sensitivity and specificity. The target recognition is achieved through proximity binding rather than recognition by CRISPR RNA (crRNA), which allows for flexible assay design. A binding-induced primer extension reaction is used to generate a predesigned CRISPR-targetable sequence as a barcode for further signal amplification. Through this dual amplification protocol, we were able to detect as low as 1 fM target nucleic acid and 100 fM target protein isothermally. The practical applicability of this assay was successfully demonstrated for the temporal profiling of interleukin-6 gene expression during allergen-mediated mast cell activation.

Herein, we develop an isothermal proximity CRISPR Cas12a assay that harnesses the target-induced collateral cleavage activity of Cas12a for the quantitative profiling of gene expression and detection of proteins with high sensitivity and specificity.     

A helical amplification system composed of artificial nucleic acids

Herein we report an amplification system of helical excess triggered by nucleic acid hybridization for the first time. It is usually impossible to prepare achiral nanostructures composed of nucleic acids because of their intrinsic chirality. We used serinol nucleic acid (SNA) oligomers for the preparation of achiral nanowires because SNA oligomers with symmetrical sequences are achiral. Nanowire formation was confirmed by atomic force microscopy and size exclusion chromatography. When a chiral nucleic acid with a sequence complementary to SNA was added to the nanostructure, helicity was induced and a strong circular dichroism signal was observed. The SNA nanowire could amplify the helicity of chiral nucleic acids through nucleobase stacks. The SNA nanostructures have potential for use as platforms to detect chiral biomolecules under aqueous conditions because SNA can be readily functionalized and is water-soluble.

Herein we report an amplification system of helical excess triggered by nucleic acid hybridization for the first time.     

TMTHSI,a superior 7-membered ring alkyne containing reagent for strain-promoted azide–alkyne cycloaddition reactions

We describe the development of TMTH-SulfoxImine (TMTHSI) as a superior click reagent. This reagent combines a great reactivity, with small size and low hydrophobicity and compares outstandingly with existing click reagents. TMTHSI can be conveniently functionalized with a variety of linkers allowing attachment of a diversity of small molecules and (peptide, nucleic acid) biologics.

TMTHSI was developed as new reagent for strain-promoted azide–alkyne cycloaddition reactions, enabling connection of a diversity of small to large molecular constructs.     

Design and enhanced gene silencing activity of spherical 2′-fluoroarabinose nucleic acids (FANA-SNAs)

Drug delivery vectors for nucleic acid therapeutics (NATs) face significant barriers for translation into the clinic. Spherical nucleic acids (SNAs) – nanoparticles with an exterior shell made up of DNA strands and a hydrophobic interior – have recently shown great potential as vehicles to improve the biodistribution and efficacy of NATs. To date, SNA design has not taken advantage of the powerful chemical modifications available to NATs. Here, we modify SNAs with 2′-deoxy-2′-fluoro-d-arabinonucleic acid (FANA-SNA), and show increased stability, enhanced gene silencing potency and unaided uptake (gymnosis) as compared to free FANA. By varying the spacer region between the nucleic acid strand and the attached hydrophobic polymer, we show that a cleavable DNA based spacer is essential for maximum activity. This design feature will be important when implementing functionalized nucleic acids into nanostructures for gene silencing. The modularity of the FANA-SNA was demonstrated by silencing two different targets. Transfection-free delivery was superior for the modified SNA compared to the free FANA oligonucleotide.

Optimizing FANA modified spherical nucleic acids (FANA-SNAs) for highly efficient delivery of nucleic acid therapeutics.     

A minimal hybridization chain reaction (HCR) system using peptide nucleic acids

The HCR represents a powerful tool for amplification in DNA-based circuitry and sensing applications, yet requires the use of long DNA sequences to grant hairpin metastability. Here we describe a minimal HCR system based on peptide nucleic acids (PNAs). A system comprising a 5-mer stem and 5-mer loop/toehold hairpins was found to be suitable to achieve rapid amplification. These hairpins were shown to yield >10-fold amplification in 2 h and be suitable for the detection of a cancer biomarker on live cells. The use of γ-peg-modified PNA was found to be beneficial.

A minimal peptide nucleic acid (PNA) HCR system based on a 5-mer stem and 5-mer loop/toehold hairpins was developed. The system was applied to the detection of a cancer biomarker on the surface of living cells.     

Biosynthetic access to the rare antiarose sugar via an unusual reductase-epimerase

Rubrolones, isatropolones, and rubterolones are recently isolated glycosylated tropolonids with notable biological activity. They share similar aglycone skeletons but differ in their sugar moieties, and rubterolones in particular have a rare deoxysugar antiarose of unknown biosynthetic provenance. During our previously reported biosynthetic elucidation of the tropolone ring and pyridine moiety, gene inactivation experiments revealed that RubS3 is involved in sugar moiety biosynthesis. Here we report the in vitro characterization of RubS3 as a bifunctional reductase/epimerase catalyzing the formation of TDP-d-antiarose by epimerization at C3 and reduction at C4 of the key intermediate TDP-4-keto-6-deoxy-d-glucose. These new findings not only explain the biosynthetic pathway of deoxysugars in rubrolone-like natural products, but also introduce RubS3 as a new family of reductase/epimerase enzymes with potential to supply the rare antiarose unit for expanding the chemical space of glycosylated natural products.

Rubrolones, isarubrolones, and rubterolones are recently isolated glycosylated tropolonids with notable biological activity.     

Simultaneous detection of small molecules,proteins and microRNAs using single molecule arrays

Biological samples such as blood, urine, cerebrospinal fluid and saliva contain a large variety of proteins, nucleic acids, and small molecules. These molecules can serve as potential biomarkers of disease and therefore, it is desirable to simultaneously detect multiple biomarkers in one sample. Current detection techniques suffer from various limitations including low analytical sensitivity and complex sample processing. In this work, we present an ultrasensitive method for simultaneous detection of small molecules, proteins and microRNAs using single molecule arrays (Simoa). Dye-encoded beads modified with specific capture probes were used to quantify each analyte. Multiplex competitive Simoa assays were established for simultaneous detection of cortisol and prostaglandin E2. In addition, competitive and sandwich immunoassays were combined with a direct nucleic acid hybridization assay for simultaneous detection of cortisol, interleukin 6 and microRNA 141. The multi-analyte Simoa assay shows high sensitivity and specificity, which provides a powerful tool for the analysis of many different samples.

The first example of multiplexed detection of proteins, nucleic acids, and small molecules using single molecule measurement methodology.     

Long-lived triplet charge-separated state in naphthalenediimide based donor–acceptor systems

1,4,5,8-Naphthalenediimides (NDIs) are widely used motifs to design multichromophoric architectures due to their ease of functionalisation, their high oxidative power and the stability of their radical anion. The NDI building block can be incorporated in supramolecular systems by either core or imide functionalization. We report on the charge-transfer dynamics of a series of electron donor–acceptor dyads consisting of a NDI chromophore with one or two donors linked at the axial, imide position. Photo-population of the core-centred π–π* state is followed by ultrafast electron transfer from the electron donor to the NDI. Due to a solvent dependent singlet–triplet equilibrium inherent to the NDI core, both singlet and triplet charge-separated states are populated. We demonstrate that long-lived charge separation in the triplet state can be achieved by controlling the mutual orientation of the donor–acceptor sub-units. By extending this study to a supramolecular NDI-based cage, we also show that the triplet charge-separation yield can be increased by tuning the environment.

Ultrafast electron transfer from singlet and triplet excited states in equilibrium results in the population of both singlet and triplet charge-separated states.     

Designing a highly stable coordination-driven metallacycle for imaging-guided photodynamic cancer theranostics

Coordination-driven self-assembly features good predictability and directionality in the construction of discrete metallacycles and metallacages with well-defined sizes and shapes, but their medicinal application has been limited by their low stability and solubility. Herein, we have designed and synthesized a highly stable coordination-driven metallacycle with desired functionality derived from a perylene-diimide ligand via a spontaneous deprotonation self-assembly process. Brilliant chemical stability and singlet oxygen production ability of this emissive octanuclear organopalladium macrocycle make it a good candidate toward biological studies. After cellular uptake by endocytosis, the metallacycle exhibits potent fluorescence cell imaging properties and cancer photodynamic therapeutic ability through enhancing ROS production, with high biocompatibility and safety. This study not only provides a rational design strategy for highly stable luminescent organopalladium metallacycles, but also sheds light on their application in imaging-guided photodynamic cancer therapy.

A highly-luminescent metallacycle with chemical stability and singlet oxygen production ability were obtained by a spontaneous deprotonation self-assembly process, which exhibits application potential in imaging-guided photodynamic cancer therapy.     

Construction of chiral α-tert-amine scaffolds via amine-catalyzed asymmetric Mannich reactions of alkyl-substituted ketimines

Stereoselective Mannich reactions of aldehydes with ketimines provide chiral β-amino aldehydes that bear an α-tert-amine moiety. However, the structural variation of the ketimines is limited due to the formation of inseparable E/Z isomers, low reactivity, and other synthetic difficulties. In this study, a highly diastereodivergent synthesis of hitherto difficult-to-access β-amino aldehydes that bear a chiral α-tert-amine moiety was achieved using the amine-catalyzed Mannich reactions of aldehydes with less-activated Z-ketimines that bear both alkyl and alkynyl groups.

Stereoselective Mannich reactions of aldehydes with ketimines provide chiral β-amino aldehydes that bear an α-tert-amine moiety.     

Expedient synthesis of conjugated triynes via alkyne metathesis

The first synthesis of conjugated triynes by molybdenum-catalysed alkyne metathesis is reported. Strategic to the success of this approach is the utilization of sterically-hindered diynes that allowed for the site-selective alkyne metathesis to produce the desired conjugated triyne products. The steric hindrance of the alkyne moiety was found to be crucial in preventing the formation of diyne byproducts. This novel synthetic strategy was amenable to self- and cross-metathesis providing straightforward access to the corresponding symmetrical and dissymmetrical triynes with high selectivity.

The first synthesis of symmetrical and dissymmetrical conjugated triynes by self- and cross-metathesis was successfully achieved thanks to the use of hindered diynes.     

Templates direct the sequence-specific anchoring of the C-terminus of peptido RNAs

When amino acids and ribonucleotides react in aqueous condensation buffer, they form peptido RNA with a phosphoramidate bond between the N-terminus of the peptide and the 5′-terminal phosphate of a ribonucleotide. If peptido RNA was the product of spontaneous reactions of amino acids and nucleotides, there must have been a transition to peptidyl tRNAs, where the C-terminus of the peptide is ester-linked to the 2′,3′-terminus of an oligonucleotide. Here we report how short peptido RNAs react with the 3′-terminus of oligodeoxynucleotides, templated by RNA strands. In our model system, the rate and yield of the anchoring of the C-terminus of the dipeptido dinucleotides to an amino group was found to depend on the sequence of the peptide, the 5′-terminal nucleotide of the dinucleotide and the RNA template. In all cases tested, highest yields were found for dinucleotides hybridizing next to the primer terminus. For the most reactive species, GlyPro-AA, anchoring yields ranged from 8–99%, depending on the template. When LeuLeu-AA, PhePhe-AA and GlyGly-AA were allowed to compete for anchoring on 3′-UUC-5′ as templating sequence, they gave a product ratio of 1 : 2 : 6, and this selectivity was almost independent of the terminal base of the primer. Our results show the control that a simple duplex context has over the covalent anchoring of peptido RNAs at a position known from peptidyl tRNAs. Processes of this type may have bridged the gap between untemplated condensation reactions and the highly specific processes of ribosomal protein synthesis.

The C-terminus of dipeptido dinucleotides reacts with the 3′-terminus of a primer strand in template directed fashion with a strong dependence on the structures of peptide and template.     

Cyclodepsipeptide alveolaride C: total synthesis and structural assignment

First stereoselective total synthesis of naturally occurring bioactive cyclodepsipeptide alveolaride C has been achieved using a convergent approach. This synthetic study enabled us to establish unambiguously the stereochemistry of three unassigned chiral centres embedded in the nonpeptidic segment as well as revised the stereochemistry of the proposed β-phenylalanine counterpart of the molecule. The key strategic features of this synthesis include Sharpless asymmetric dihydroxylation for installing the vicinal diol moiety, Julia–Kocienski olefination for constructing the aliphatic side chain, the Shiina protocol for intermolecular esterification, amide coupling and macrolactamization for the ring formation.

First total synthesis of natural cyclodepsipeptide alveolaride C has been accomplished with an unambiguous solution to its structural riddle.     

Supramolecular chemistry under mechanochemical conditions: a small molecule template generated and integrated into a molecular-to-supramolecular and back-to-molecular cascade reaction

We describe the integration of a small-molecule hydrogen-bond-donor template into a cascade reaction that is comprised of a combination of molecular and supramolecular events. The cascade is performed mechanochemically and in the presence of μL amounts of water. The small-molecule template is generated (molecular) using water-assisted vortex grinding and is then used to assemble an alkene (supramolecular) to undergo an intermolecular [2 + 2] photodimerization reaction (molecular). The chemical cascade results in a cyclobutane photoproduct that we show serves as a building block of a hydrogen-bonded network with a topology that conforms to T-silica. Remarkably, the molecular–supramolecular–molecular chemical cascade occurs stepwise and entirely regioselectively within the continuous mechanochemical conditions employed.

Mechanochemistry is applied to molecular and supramolecular chemistry to support a template-directed photochemical reaction.     

Exploiting the radical reactivity of diazaphosphinanes in hydrodehalogenations and cascade cyclizations

The remarkable reducibility of diazaphosphinanes has been extensively applied in various hydrogenations, based on and yet limited by their well-known hydridic reactivity. Here we exploited their unprecedented radical reactivity to implement hydrodehalogenations and cascade cyclizations originally inaccessible by hydride transfer. These reactions feature a broad substrate scope, high efficiency and simplicity of manipulation. Mechanistic studies suggested a radical chain process in which a phosphinyl radical is generated in a catalytic cycle via hydrogen-atom transfer from diazaphosphinanes. The radical reactivity of diazaphosphinanes disclosed here differs from their well-established hydridic reactivity, and hence, opens a new avenue for diazaphosphinane applications in organic syntheses.

Unprecedented radical reactivity of diazaphosphinanes was explored to implement efficient hydrodehalogenations and cascade cyclizations.     

DNA-based constitutional dynamic networks as functional modules for logic gates and computing circuit operations

A nucleic acid-based constitutional dynamic network (CDN) is introduced as a single computational module that, in the presence of different sets of inputs, operates a variety of logic gates including a half adder, 2 : 1 multiplexer and 1 : 2 demultiplexer, a ternary multiplication matrix and a cascaded logic circuit. The CDN-based computational module leads to four logically equivalent outputs for each of the logic operations. Beyond the significance of the four logically equivalent outputs in establishing reliable and robust readout signals of the computational module, each of the outputs may be fanned out, in the presence of different inputs, to a set of different logic circuits. In addition, the ability to intercommunicate constitutional dynamic networks (CDNs) and to construct DNA-based CDNs of higher complexity provides versatile means to design computing circuits of enhanced complexity.

A nucleic acid-based constitutional dynamic network (CDN) provides a single functional computational module for diverse input-guided logic operations and computing circuits.