Capsule-like DNA Hydrogels with Patterns Formed by Lateral Phase Separation of DNA Nanostructures

Phase separation is a key phenomenon in artificial cell construction. Recent studies have shown that the liquid–liquid phase separation of designed-DNA nanostructures induces the formation of liquid-like condensates that eventually become hydrogels by lowering the solution temperature. As a compartmental capsule is an essential artificial cell structure, many studies have focused on the lateral phase separation of artificial lipid vesicles. However, controlling phase separation using a molecular design approach remains challenging. Here, we present the lateral liquid–liquid phase separation of DNA nanostructures that leads to the formation of phase-separated capsule-like hydrogels. We designed three types of DNA nanostructures (two orthogonal and a linker nanostructure) that were adsorbed onto an interface of water-in-oil (W/O) droplets via electrostatic interactions. The phase separation of DNA nanostructures led to the formation of hydrogels with bicontinuous, patch, and mix patterns, due to the immiscibility of liquid-like DNA during the self-assembly process. The frequency of appearance of these patterns was altered by designing DNA sequences and altering the mixing ratio of the nanostructures. We constructed a phase diagram for the capsule-like DNA hydrogels by investigating pattern formation under various conditions. The phase-separated DNA hydrogels did not only form on the W/O droplet interface but also on the inner leaflet of lipid vesicles. Notably, the capsule-like hydrogels were extracted into an aqueous solution, maintaining the patterns formed by the lateral phase separation. In addition, the extracted hydrogels were successfully combined with enzymatic reactions, which induced their degradation. Our results provide a method for the design and control of phase-separated hydrogel capsules using sequence-designed DNAs. We envision that by incorporating various DNA nanodevices into DNA hydrogel capsules, the capsules will gain molecular sensing, chemical-information processing, and mechanochemical actuating functions, allowing the construction of functional molecular systems

Correction to “Triplex-Forming Peptide Nucleic Acid Probe Having Thiazole Orange as a Base Surrogate for Fluorescence Sensing of Double-stranded RNA”

Correction to “Triplex-Forming Peptide Nucleic Acid Probe Having Thiazole Orange as a Base Surrogate for Fluorescence Sensing of Double-stranded RNA

Triplex-Forming Peptide Nucleic Acid Probe Having Thiazole Orange as a Base Surrogate for Fluorescence Sensing of Double-stranded RNA

We have developed a new fluorescent sensing probe for double-stranded RNA (dsRNA) by integrating thiazole orange (TO) as a base surrogate into triplex-forming PNA. Our probe forms the thermally stable triplex with the target dsRNA at acidic pH; and the triplex formation is accompanied by the remarkable light-up response of the TO unit. The binding of our probe to the target dsRNA proceeds very rapidly, allowing real-time monitoring of the triplex formation. Importantly, we found the TO base surrogate in our probe functions as a universal base for the base pair opposite the TO unit in the triplex formation. Furthermore, the TO unit is significantly more responsive for the fully matched dsRNA sequence compared to the mismatch-containing sequences, which enables the analysis of the target dsRNA sequence at the single-base pair resolution. The binding and sensing functions of our probe are described for the development of fluorescent probes applicable to sensing biologically relevant dsRNA

Platinum-Catalyzed Dehydroalkoxylation−Cyclization Cascade via N−O Bond Cleavage

Platinum-Catalyzed Dehydroalkoxylation−Cyclization Cascade via N−O Bond Cleavag

Stereoelectronic Effect on Stereoselective Olefination of Ketones Providing Tetrasubstituted Olefins via Ynolates

Stereoelectronic Effect on Stereoselective Olefination of Ketones Providing Tetrasubstituted Olefins via Ynolate

Deep-Red Light-up Signaling of Benzo[<i>c</i>,<i>d</i>]indole–Quinoline Monomethine Cyanine for Imaging of Nucleolar RNA in Living Cells and for Sequence-Selective RNA Analysis

RNA-binding small probes with deep-red emission are promising for RNA analysis in biological media without suffering from background fluorescence. Here benzo­[c,d]­indole–quinoline (BIQ), an asymmetric monomethine cyanine analogue, was newly developed as a novel RNA-selective probe with light-up signaling ability in the deep-red spectral range. BIQ features a significant light-up response (105-fold) with an emission maximum at 657 nm as well as improved photostability over the commercially available RNA-selective probe, SYTO RNA select. BIQ was successfully applied to the fluorescence imaging of nucleolar RNAs in living cells with negligible cytotoxicity. Furthermore, we found the useful ability of BIQ as a base surrogate integrated in peptide nucleic acid (PNA) oligonucleotides for RNA sequence analysis. BIQ base surrogate functioned as a deep-red light-up base surrogate in forced intercalation (FIT) and triplex-forming FIT (tFIT) systems for the sequence-selective detection of single-stranded and double-stranded RNAs, respectively

A Novel Tandem [2 + 2] Cycloaddition−Dieckmann Condensation: Facile One-Pot Process To Obtain 2,3-Disubstituted-2-cycloalkenones from Ynolates

A Novel Tandem [2 + 2] Cycloaddition−Dieckmann Condensation:  Facile One-Pot Process To Obtain 2,3-Disubstituted-2-cycloalkenones from Ynolate

Self-Assembly and Disassembly of Membrane Curvature-Sensing Peptide-Based Deep-Red Fluorescent Probe for Highly Sensitive Sensing of Exosomes

With increasing knowledge of the diverse roles of exosomes in biological processes, much attention has been paid to the development of analytical methods for exosome analysis. Here, we developed a new class of amphipathic helical (AH) peptide-based fluorescent probes for highly sensitive detection of exosomes in a mix and read manner. Membrane curvature-sensing AH peptide (ApoC) was coupled with lipophilic tail (C12)-carrying thiazole red (TR) for construction of a self-assembly/disassembly based fluorescence “off-on” sensing system for target exosomes. ApoC-TRC12 has extremely weak emission due to the formation of the aggregates, whereas it becomes emissive in response to the target exosomes through the binding-induced disassembly of ApoC-TRC12. We demonstrated that the C12 unit attached to the TR unit had a favorable effect on both fluorescence response (signal-to-background: S/B) and binding affinity. ApoC-TRC12 was applicable to rapid and simple detection of exosomes with high detection sensitivity (limit of detection ≈ 103 particles/μL)

A Novel Tandem [2 + 2] Cycloaddition−Dieckmann Condensation with Ynolate Anions. Efficient Synthesis of Substituted Cycloalkenones and Naphthalenes via Formal [<i>n</i> + 1] Cycloaddition

A novel tandem [2 + 2] cycloaddition−Dieckmann condensation via ynolate anions is described. Ynolate anions are useful for the formation of reactive β-lactone enolates via a pathway not involving the enolization of the corresponding β-lactones. The [2 + 2] cycloaddition of ynolate anions with δ- or γ-keto esters, followed by Dieckmann condensation, gives bicyclic β-lactones, which are easily decarboxylated to produce synthetically useful 2,3-disubstituted cyclopentenones and cyclohexenones in one pot. This tandem reaction was applied to a novel, one-pot synthesis of highly substituted naphthalenes

The First Tandem [2 + 2] Cycloaddition−Michael Reaction Using Ynolates: Facile Construction of Substituted Carbocycles

A tandem [2 + 2] cycloaddition−Michael reaction using ynolate anions followed by decarboxylation produced polysubstituted five-, six-, and seven-membered cycloalkenes