DNA gated photochromism and fluorescent switch in a thiazole orange modified diarylethene

DNA G-quadruplexes in the genome of Trypanosoma cruzi as potential therapeutic targets for Chagas disease: Dithienylethene ligands as effective antiparasitic agents

Chagas disease is caused by the parasite Trypanosoma cruzi and affects over 7 million people worldwide. The two actual treatments, Benznidazole (Bzn) and Nifurtimox, cause serious side effects due to their high toxicity leading to treatment abandonment by the patients. In this work, we propose DNA G-quadruplexes (G4) as potential therapeutic targets for this infectious disease. We have found 174 PQS per 100,000 nucleotides in the genome of T. cruzi and confirmed G4 formation of three frequent motifs. We synthesized a family of 14 quadruplex ligands based in the dithienylethene (DTE) scaffold and demonstrated their binding to these identified G4 sequences. Several DTE derivatives exhibited micromolar activity against epimastigotes of four different strains of T. cruzi, in the same concentration range as Bzn. Compounds L3 and L4 presented remarkable activity against trypomastigotes, the active form in blood, of T. cruzi SOL strain (IC50 = 1.5-3.3 μM, SI = 25-40.9), being around 40 times more active than Bzn and displaying much better selectivity indexes.

Innovative Synthesis of Photo-Responsive, Self-Healing Silicone Elastomers with Enhanced Mechanical Properties and Thermal Stability

Photo-responsive materials have garnered significant interest for their ability to react to non-contact stimuli, though achieving self-healing under gentle conditions remains an elusive goal. In this research, an innovative and straightforward approach for synthesizing silicone elastomers is proposed that not only self-heal at room temperature but also possess unique photochromic properties and adjustable mechanical strength, along with being both transparent and reprocessable. Initially, aldehyde-bifunctional dithiophene-ethylene molecules with dialdehyde groups (DTEM) and isocyanurate (IPDI) is introduced into the aminopropyl-terminated polydimethylsiloxane (H2N-PDMS-NH2) matrix. Subsequently, palladium is incorporated to enhance coordination within the matrix. These silicone elastomers transition to a blue state under 254 nm UV light and revert to transparency under 580 nm light. Remarkably, they demonstrate excellent thermal stability at temperatures up to 100 °C and show superior fatigue resistance. The optical switching capabilities of the silicone elastomers significantly affect both their mechanical characteristics and self-healing abilities. Notably, the PDMS-DTEM-IPDI-@Pd silicone elastomer, featuring closed-loop photo-switching molecules, exhibits a fracture toughness that is 1.3 times greater and a room temperature self-healing efficiency 1.4 times higher than its open-loop counterparts. This novel photo-responsive silicone elastomer offers promising potential for applications in data writing and erasure, UV protective coatings, and micro-trace development.

Photochromic Nucleosides and Oligonucleotides

Photochromism is a reversible phenomenon wherein a material undergoes a change in color upon exposure to light. In organic photochromes, this effect often results from light-induced isomerization reactions, leading to alterations in either the spatial orientation or electronic properties of the photochrome. The incorporation of photochromic moieties into biomolecules, such as proteins or nucleic acids, has become a prevalent approach to render these biomolecules responsive to light stimuli. Utilizing light as a trigger for the manipulation of biomolecular structure and function offers numerous advantages compared to other stimuli, such as chemical or electrical treatments, due to its non-invasive nature. Consequently, light proves particularly advantageous in cellular and tissue applications. In this review, we emphasize recent advancements in the field of photochromic nucleosides and oligonucleotides. We provide an overview of the design principles of different classes of photochromes, synthetic strategies, critical analytical challenges, as well as structure-property relationships. The applications of photochromic nucleic acid derivatives encompass diverse domains, ranging from the precise photoregulation of gene expression to the controlled modulation of the three-dimensional structures of oligonucleotides and the development of DNA-based fluorescence modulators. Moreover, we present a future perspective on potential modifications and applications.

Ion valence-gated photochromism of an aza-crowned diarylethene

A non-photochromic diarylethene 2o with an N-phenylaza-15-crown-5 was synthesized. When the nitrogen atom in the aza-crown ring was protonated, it became photochromic due to the prevention of a twisted intramolecular charge transfer (TICT). Although addition of a monovalent metal cation (Li+, Na+, K+, Rb+, Cs+, Cu+, Ag+) in acetonitrile could not stop the TICT so that it was not photochromic, the addition of a multivalent metal cation (Mg2+, Ca2+, Sr2+, Ba2+, Fe2+, Ni2+, Al3+, Sb5+) changed 2o to be photochromic due to the strong attraction of the lone pair on the nitrogen atom. In the presence of excess Cu2+, 2o was oxidized to be EPR-detectable 2o·+, which was thermally unstable as well as inert towards visible-light irradiation. However, 2o·+ was further oxidized to be fairly stable 2o2+ by the irradiation of 365-nm light in the presence of Cu2+. ESI-MS measurements strongly suggested the generation of 2o·+ by mixing 2o with Cu(ClO4)2 in acetonitrile, and the transformation of 2o·+ to 2o2+ by successive 365-nm light irradiation. Fe3+ similarly worked as the oxidant, but the two-step oxidation of 2o to 2o2+ occurred more easily.

Small-molecule photoswitches for fluorescence bioimaging: engineering and applications

Fluorescence microscopy has revolutionised our understanding of biological systems, enabling the visualisation of biomolecular structures and dynamics in complex systems. The possibility to reversibly control the optical or biochemical properties of fluorophores can unlock advanced applications ranging from super-resolution microscopy to the design of multi-stimuli responsive and functional biosensors. In this Highlight, we review recent progress in small-molecule photoswitches applied to biological imaging with an emphasis on molecular engineering strategies and promising applications, while underlining the main challenges in their design and implementation.

Dual and sequential locked/unlocked photo-switching effects on FRET processes by tightened/loosened nano-loops of diarylethene-based [1]rotaxanes

The self-trapping nano-loop structures of [1]rotaxanes exhibited multiple Förster resonance energy transfer (FRET) patterns via dual and sequential locking/unlocking of pH-gated and UV exposure processes. As a tightened and constrained nano-loop in the acidic condition, dithienylethene (DTE) unit was locked in the highly bending open form to forbid ring closure upon UV irradiation.

Light responsive nucleic acid for biomedical application

Nucleic acids are widely used in biomedical applications because of their programmability and biocompatibility. The light responsive nucleic acids have attracted wide attention due to their remote control and high spatiotemporal resolution. In this review, we summarized the latest developments in biomedicine of light responsive molecules. The molecules which confer light responsive properties to nucleic acids were summarized. The binding sites of molecules to nucleic acids, the induced structural changes, and functional regulation of nucleic acids were reviewed. Then, the biomedical applications of light responsive nucleic acids were listed, such as drug delivery, biosensing, optogenetics, gene editing, etc. Finally, the challenges were discussed and possible future directions of light-responsive nucleic acids were proposed.

Future-Oriented Advanced Diarylethene Photoswitches: From Molecular Design to Spontaneous Assembly Systems

Diarylethene (DAE) photoswitch is a new and promising family of photochromic molecules and has shown superior performance as a smart trigger in stimulus-responsive materials. During the past few decades, the DAE family has achieved a leap from simple molecules to functional molecules and developed toward validity as a universal switching building block. In recent years, the introduction of DAE into an assembly system has been an attractive strategy that enables the photochromic behavior of the building blocks to be manifested at the level of the entire system, beyond the DAE unit itself. This assembly-based strategy will bring many unexpected results that promote the design and manufacture of a new generation of advanced materials. Here, recent advances in the design and fabrication of diarylethene as a trigger in materials science, chemistry, and biomedicine are reviewed.

Extending the Legible Time of Light-Responsive Rewritable Papers with a Tunable Photochromic Diarylethene Molecule

Inkless printing based on rewritable papers has recently made great progress because it can improve the utilization rate of papers, which is of great significance for saving resources and protecting the environment. Among them, light-responsive rewritable papers (LRPs) are a hot research topic because light is clean, easily available, wavelength and intensity adjustable, and noncontacting. However, the photochromic material, as the imaging substance of LRPs, is easily affected by environmental conditions, resulting in insufficient time to read the information. In view of this, we designed and constructed an acid/base tunable diarylethene molecular system that can effectively adjust the photochromic properties by reversibly changing the electron density of the diarylethene photoreaction center through protonation and demonstrated its potential as an imaging material with a longer legible time. What makes us more satisfied is that the acidification can not only extend the legible time of carrying information but also bring a clear and stable absorption/fluorescence imaging dual mode, which can better reflect details and improve contrast. Therefore, we believe that this tunable photochromic diarylethene molecule is a potential imaging material for the development of new LRPs.

On-Demand Chirality Transfer of Human Serum Albumin to Bis(thiophen-2-yl)hexafluorocyclopentenes through Their Photochromic Ring Closure

Photochromic 1,2-bis(5-carboxy-3-methyl-2-thienyl)hexafluorocyclopentene and its dimethyl ester incorporated in human serum albumin (HSA) showed highly enantioselective photochromic ring-closing reactions upon 366 nm light irradiation. The absolute stereochemistry of the major ring-closed form of the dicarboxylic acid at the newly formed sp³ carbon atoms was determined to be (S,S) by the process of docking simulation of the diarylethene molecule and HSA followed by molecular dynamics calculations and comparison of the measured and calculated CD spectra. Esterification of the major closed form of the diacid gave the minor closed form of the diester. The absolute stereochemistry of the major diester was thus determined to be (R,R).

A dual-mode visual detector for toxic hydrazine

Hydrazine (N₂H₄) is one of the commonly used chemical reagents in numerous industries and applications but its toxicity to humans poses a need to develop simple visual detection methods. Herein, we demonstrate a novel dual-mode system to detect and simultaneously consume hydrazine in vapour and solution by using a small photoresponsive molecule that has altered optical response (both colourimetric and fluorescent) after reacting with hydrazine.

A small photoresponsive molecule changes colour from blue to colourless when exposed to hydrazine vapours. It also becomes emissive providing two convenient ways of detecting the presence of this toxic chemical.

Turn-on mode diarylethenes for bioconjugation and fluorescence microscopy of cellular structures

In superresolution fluorescence microscopy, employing synthetic dyes that can be reversibly photoswitched between a nonfluorescent (“dark”) and a fluorescent (“bright”) state has been an attractive alternative to using photoswitchable fluorescent proteins. However, employing such synthetic dyes has been elusive because they have defied reliable attachment to proteins and required UV light for photoswitching. Here we prepared “turn-on mode” fluorescent diarylethenes (fDAEs) that are switchable with visible rather than UV light and blink between a bright fluorescent and a dark state in aqueous buffers. Moreover, our thienyl-substituted fDAEs effectively labeled two thiol groups on nanobodies bearing a single maleimide tag. With these small-sized probes, we acquired superresolution images of vimentin filaments in cells by applying just yellow (561 nm) light.

The use of photoswitchable fluorescent diarylethenes (fDAEs) as protein labels in fluorescence microscopy and nanoscopy has been limited by labeling inhomogeneity and the need for ultraviolet light for fluorescence activation (on-switching). To overcome these drawbacks, we prepared “turn-on mode” fDAEs featuring thienyl substituents, multiple polar residues, and a reactive maleimide group in the core structure. Conjugates with antibodies and nanobodies displayed complete on-switching and excitation with violet (405 nm) and yellow-green (<565 nm) light, respectively. Besides, they afforded high signal-to-noise ratios and low unspecific labeling in fluorescence imaging. Irradiation with visible light at 532 nm or 561 nm led to transient on-off switching (“blinking”) of the fDAEs of double-labeled nanobodies so that nanoscale superresolution images were readily attained through switching and localization of individual fluorophores.

Photoswitchable Fluorescent Self-Assembled Metallacycles with High Photostability

In this study, photoswitchable fluorescent supramolecular metallacycles with high fatigue-resistance have been constructed by coordination-driven self-assembly by using bithienylethene with dipyridyl units (BTE) as a coordination donor and a fluorescent di-platinum(II) (Pt-F) as a coordination acceptor. The photo-triggered reversible transformation between the ring-open and ring-closed form of the metallacycles was confirmed by ¹ H NMR, ³¹ P NMR, and UV/Vis spectroscopy. This unique property enabled a reversible noninvasive "off-on" switching of fluorescence through efficient Förster resonance energy transfer (FRET). Importantly, the metallacycles remained structurally intact after up to 10 photoswitching cycles. The photoresponsive property and exceptional photostability of the metallacycles posit their potential promising application in optical switching, image storage, and super-resolution microscopy.

Controlled Fluorescence Enhancement of DNA-Binding Dye Through Chain Length Match between Oligoguanine and TOTO

Fluorescent DNA-binding dyes are extensively employed as probe and biosensing in biological detection and imaging. Experiments and theoretical calculations of thiazole orange homodimeric (TOTO) dye binding to a single-strand DNA (ssDNA), poly(dG)_n (n = 2, 4, 6, 8), reveal that the n = 6 complex shows about 300-fold stronger fluorescence than n = 2, 4 and a slightly stronger one than n = 8 complexes, which is benefited from the length match between TOTO and poly(dG)₆. The machine learning, based on molecular dynamics trajectories, indicates that TOTO is featured by the dihedral angle along its backbone and its end-to-end distance, in which the latter one defines the stretch and hairpin structures of TOTO, respectively. The time-dependent density functional theory calculations on the low-lying excited states show that the stretched TOTO with π-π end-stacking binding mode can bring about strong fluorescence with localized π-π^* transitions. For the n = 2, 4, and 8 complexes, the linear scaling quantum mechanics calculations indicate that the dominant hairpin TOTO with intercalative binding modes have relatively larger binding energies, leading to fluorescence quenching by intramolecular charge transfer. Our results may provide an insight for modulating the DNA-dye binding modes to tune the degree of charge transfer and designing fluorescent probes for the recognition of specific DNA sequences.

Photocaged Hoechst Enables Subnuclear Visualization and Cell Selective Staining of DNA in vivo

Selective targeting of DNA by means of fluorescent labeling has become a mainstay in the life sciences. While genetic engineering serves as a powerful technique and allows the visualization of nucleic acid by using DNA‐targeting fluorescent fusion proteins in a cell‐type‐ and subcellular‐specific manner, it relies on the introduction of foreign genes. On the other hand, DNA‐binding small fluorescent molecules can be used without genetic engineering, but they are not spatially restricted. Herein, we report a photocaged version of the DNA dye Hoechst33342 (pcHoechst), which can be uncaged by using UV to blue light for the selective staining of chromosomal DNA in subnuclear regions of live cells. Expanding its application to a vertebrate model organism, we demonstrate uncaging in epithelial cells and short‐term cell tracking in vivo in zebrafish. We envision pcHoechst as a valuable tool for targeting and interrogating DNA with precise spatiotemporal resolution in living cells and wild‐type organisms.

Multicolour fluorescent “sulfide–sulfone” diarylethenes with high photo-fatigue resistance

Compact, photochromic, reversible and fluorescent: blue and red emission from the “open” and “closed” forms (see picture) and up to 20 000 cycles in organic solvents without exclusion of air–oxygen.

Visible-light photoswitching of ligand binding mode suggests G-quadruplex DNA as a target for photopharmacology

A pyridinium-decorated photoresponsive dithienylethene selectively targets G-quadruplex DNA, allowing binding mode and toxicity to be controlled exclusively with visible light.

Photoregulation between small DNAs and reversible photochromic molecules

Oligonucleotides are widely used biological materials in the fields of biomedicine, nanotechnology, and materials science. Due to the demands for the photoregulation of DNA activities, scientists are placing more and more research interest in the interactions between reversible photochromic molecules and DNAs. Photochromic molecules can work as switches for regulating the DNAs' behavior under light irradiation; meanwhile, DNAs also exert influence over the photochromic molecules. The photochromic molecules can be attached to DNAs either by covalent bonds or by noncovalent forces, which results in different regulative functions. Azobenzenes, spiropyrans, diarylethenes, and stilbene-like compounds are important photochromic molecules working as photoswitches. By summarizing their interactions with oligonucleotides, this review intends to facilitate the relevant research on oligonucleotides/photochromic molecules in the biological and medicinal fields and in materials science.

Recent developments in reversible photoregulation of oligonucleotide structure and function

There is a growing interest in the photoregulation of biological functions, due to the high level of spatiotemporal precision achievable with light. Additionally, light is non-invasive and waste-free. In particular, the photoregulation of oligonucleotide structure and function is a rapidly developing study field with relevance to biological, physical and material sciences. Molecular photoswitches have been incorporated in oligonucleotides for 20 years, and the field has currently grown beyond fundamental studies on photochemistry of the switches and DNA duplex stability, and is moving towards applications in chemical biology, nanotechnology and material science. Moreover, the currently emerging field of photopharmacology indicates the relevance of photocontrol in future medicine. In recent years, a large number of publications has appeared on photoregulation of DNA and RNA structure and function. New strategies are evaluated and novel, exciting applications are shown. In this comprehensive review, the key strategies for photoswitch inclusion in oligonucleotides are presented and illustrated with recent examples. Additionally the applications that have emerged in recent years are discussed, including gene regulation, drug delivery and materials design. Finally, we identify the challenges that the field currently faces and look forward to future applications.

Cyanine dyes: synergistic action of hydrogen, halogen and chalcogen bonds allows discrete I42− anions in crystals

Discrete tetraiodide dianions (I₄²⁻) are formed in crystals via halogen bond coordination of I₂ by iodide anions which are pinned in their positions by a network of hydrogen bonds involving a benzoselenazole cyanine dye.

A multi-state fluorescent switch based on a diarylethene with an acridine unit

A new asymmetrical fluorescent diarylethene derivative with an acridine unit was synthesized by Schiff base condensation. The derivative was sensitive to lights and special metal ions. Stimulated by UV/vis lights and Zn²⁺, distinct changes were observed in UV-vis and fluorescent spectra. Upon addition of Zn²⁺, the derivative emission peak was blue-shifted by 34nm and the emission intensity was enhanced by 16 fold, accompanied by the fluorescent color changed from red to light yellow, due to the formation of a 1:1 metal/ligand complex. The complex exhibited excellent fluorescence switching upon irradiation with UV light. Taking advantage of the lights and Zn²⁺ stimuli (inputs), and fluorescence intensity at 580nm (output), a molecular logic gate was constructed. Moreover, a new absorption band centered at 420-450nm emerged upon exposure to Zn²⁺. The dramatic color change of the solution made the 'naked-eyes' detection of Zn²⁺ possible.

Photochromism and molecular logic gate operation of a water-compatible bis-glycosyl diarylethene

The synthesis of a bis-glycosyl diarylethene derivative by click chemistry for the water-compatible photochromism and operation of molecular logic gates is reported.

A highly selective fluorescent chemosensor for Fe3+ based on a new diarylethene with a rhodamine 6G unit

A new multi-functional diarylethene-rhodamine 6G derivative was synthesized; its colorimetric and fluorometric sensing ability for Fe³⁺/EDTA, TFA/TEA and switching behaviors induced by light were investigated.

Combination of microbiological, spectroscopic and molecular docking techniques to study the antibacterial mechanism of thymol against Staphylococcus aureus: membrane damage and genomic DNA binding

Thymol (2-isopropyl-5-methylphenol) is a natural ingredient used as flavor or preservative agent in food products. The antibacterial mechanism of thymol against Gram-positive, Staphylococcus aureus was investigated in this work. A total of 15 membrane fatty acids were identified in S. aureus cells by gas chromatography-mass spectrometry. Exposure to thymol at low concentrations induced obvious alterations in membrane fatty acid composition, such as decreasing the proportion of branched 12-methyltetradecanoic acid and 14-methylhexadecanoic acid (from 22.4 and 17.3% to 7.9 and 10.3%, respectively). Membrane permeability assay and morphological image showed that thymol at higher concentrations disrupted S. aureus cell membrane integrity, which may decrease cell viability. Moreover, the interaction of thymol with genomic DNA was also investigated using multi-spectroscopic techniques, docking and atomic force microscopy. The results indicated that thymol bound to the minor groove of DNA with binding constant (K _a) value of (1.22 ± 0.14) × 10⁴ M^-1, and this binding interaction induced a mild destabilization in the DNA secondary structure, and made DNA molecules to be aggregated. Graphical Abstract Thymol exerts its antibacterial effect throught destruction of bacterial cell membrane and binding directly to genomic DNA.

High contrast off–on fluorescence photo-switching via copper ion recognition, trans–cis isomerization and ring closure of a thiosemicarbazide Schiff base

Two independently addressable photochromic systems based on distinct mechanisms and selective recognition for Cu²⁺were investigated in detail.

A diarylethene-based fluorescent chemosensor for the sequential recognition of Fe3+ and cysteine

A new fluorescent chemosensor based on a diarylethene was designed and synthesized for sequential recognition of Fe³⁺ and cysteine.

The effect of a “push–pull” structure on the turn-on fluorescence of photochromic thio-ketone type diarylethenes

A diarylethene with a six-membered ring carrying an electron-donating sulfur atom and an electron-withdrawing carbonyl group shows fluorescence in its ring-closed state.

Cyanine-based dithienylethenes: synthesis, characterization, photochromism and biological imaging in living cells

Photochromic materials have been widely used in many fields such as electro-optical functional materials and novel bio-materials.

CB[8] gated photochromism of a diarylethene derivative containing thiazole orange groups

Photochromism in a diarylethene derivative (1O) can be gated by a host–guest interaction where the thiazole orange groups are bound into the hydrophobic cavity of CB[8] in water.

Diarylethene based fluorescent switchable probes for the detection of amyloid-β pathology in Alzheimer's disease

Two fluorescent switchable diarylethene derivatives which can detect amyloid-β aggregates bothin vitroandin vivowere reported.

Construction of photoswitchable rotaxanes and catenanes containing dithienylethene fragments

Mechanically interlocked structures such as rotaxanes and catenanes provide a novel backbone for constructing functional materials with unique structural characteristics.