Photocontrolled binding and binding-controlled photochromism within anthracene-modified DNA

Sculpting photoproducts with DNA origami

Natural light-harvesting systems spatially organize densely packed dyes in different configurations to either transport excitons or convert them into charge photoproducts, with high efficiency. In contrast, artificial photosystems like organic solar cells and light-emitting diodes lack this fine structural control, limiting their efficiency. Thus, biomimetic multi-dye systems are needed to organize dyes with the sub-nanometer spatial control required to sculpt resulting photoproducts. Here, we synthesize 11 distinct perylene diimide (PDI) dimers integrated into DNA origami nanostructures and identify dimer architectures that offer discrete control over exciton transport versus charge separation. The large structural-space and site-tunability of origami uniquely provides controlled PDI dimer packing to form distinct excimer photoproducts, which are sensitive to interdye configurations. In the future, this platform enables large-scale programmed assembly of dyes mimicking natural systems to sculpt distinct photophysical products needed for a broad range of optoelectronic devices, including solar energy converters and quantum information processors.

Monocarboxylate-protected two-electron superatomic silver nanoclusters with high photothermal conversion performance

The first series of monocarboxylate-protected superatomic silver nanoclusters was synthesized and fully characterized by X-ray diffraction, fourier-transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS), and electrospray ionization mass spectrometry (ESI-MS). Specifically, compounds [Ag₁₆(L)₈(9-AnCO₂)₁₂]²⁺ (L = Ph₃P (I), (4-ClPh)₃P (II), (2-furyl)₃P (III), and Ph₃As (IV)) were prepared by a solvent-thermal method under alkaline conditions. These clusters exhibit a similar unprecedented structure containing a [Ag₈@Ag₈]⁶⁺ metal kernel, of which the 2-electron superatomic [Ag₈]⁶⁺ inner core shows a flattened and puckered hexagonal bipyramid of S₆ symmetry. Density functional theory calculations provide a rationalization of the structure and stability of these 2-electron superatoms. Results indicate that the 2 superatomic electrons occupy a superatomic molecular orbital 1S that has a substantial localization on the top and bottom vertices of the bipyramid. The π systems of the anthracenyl groups, as well as the 1S HOMO, are significantly involved in the optical and photothermal behavior of the clusters. The four characterized nanoclusters show high photothermal conversion performance in sunlight. These results show that the unprecedented use of mono-carboxylates in the stabilization of Ag nanoclusters is possible, opening the door for the introduction of various functional groups on their cluster surface.

Photo-Controlled [4+4] Cycloaddition of Anthryl-Polymer Systems: A Versatile Approach to Fabricate Functional Materials

The reversible photo-induced [4+4] cycloaddition reaction of anthracene enables multiple cycles of dimerization and scission, allowing phototunable linkage of molecular fragments for the synthesis of polymer scaffolds. New functional materials ranging from hydrogels to shape-memory polymers were designed from anthryl-polymer systems because of their diverse photochemical reactivity and responsiveness. Light as an external stimulus allows for the remote and precise spatiotemporal control of materials without the need for additional reagents. Depending on how the photoreactive anthracene moieties were introduced, the interaction of anthryl-polymer systems with light results in various processes such as polymerization, cyclization, and cross-linking. Structural modifications of anthracene derivatives could shift their absorption from the ultraviolet to the visible light region, widening their range of applications including biologically relevant studies. These applications are further diversified and enhanced by the reversibility of the dimerization reaction using light and heat as stimuli. In this review, current developments in the synthesis and photodimerization of anthracene-containing polymers and their emerging applications in the fabrication of new materials are discussed.

Insights into the Effect of Trans-to-Cis Photoisomerization of a Co-coordinated Stilbene Derivative on the Luminescence of Di-β-diketonate Lanthanide Complexes

Five lanthanide complexes constructed from a stilbene derivative, (E)-N',N'-bis(pyridin-2-ylmethyl)-4-styrylbenzoyl hydrazide (HL), and two β-diketonates (2-thenoyltrifluoroacetonate, tta), with or without a trifluoroacetate anion (CF₃CO₂ ^-), namely, [Ln(tta)₂(HL) (CF₃CO₂)] [LnC₄₅H₃₂F₉N₄O₇S₂, Ln = La (1), Nd (2), Eu (3), or Gd (4)] and [Yb(tta)₂(L)] (YbC₄₃H₃₁F₆N₄O₅S₂ (5), L = deprotonated HL), were synthesized and characterized. Crystals of these five complexes were obtained and analyzed by single-crystal X-ray diffraction. These complexes all belonged to the monoclinic P2₁/c space group. For La³⁺, Nd³⁺, Eu³⁺, and Gd³⁺, the central lanthanide ion was nine-coordinate with a monocapped twisted square antiprism polyhedron geometry. The central Yb³⁺ ion of complex 5 was eight-coordinate with a distorted double-capped triangular prism polyhedron geometry. Among the five complexes, trans-to-cis photoisomerization of the stilbene group in gadolinium complex 4 showed the largest quantum yield. Complexes 2, 3, and 4 showed dual luminescence and photoisomerization functions. The luminescence change of complex 3 was reversible upon the trans-to-cis photoisomerization process. The sensitization efficiencies of luminescent europium complex 3 in acetonitrile solutions and in the solid state were 49.9 and 42.6%, respectively. These medium sensitization efficiencies led to the observation of simultaneous photoisomerization and luminescence, which further confirmed our previous report that photoisomerization of the stilbene group within complexes was related to the lanthanide ion energy level and whether a ligand-to-metal center or ligand-to-ligand charge-transfer process was present. In complexes 1-5, in addition to the intramolecular absorption transition of the ligand itself (IL, π_HL-π_HL ^* and π_tta-π_tta*), the presence of a ligand-to-ligand charge-transfer transition between tta and HL (LLCT, π_tta-π_HL ^* or π_HL-π_tta ^*) indicated whether the triplet-state energy of HL was able to transfer to the excited energy level of the lanthanide ions, leading to different extents of HL photoisomerization. These results provide an important route for the design of new dual-function lanthanide-based optical switching materials.

Supramolecular-controlled regioselective photochemical [4+4] cycloaddition within Cp*Rh-based metallarectangles

Photochemical reactions are vital synthetic means for the synthesis of natural products as well as highly strained molecules. However, it remains an inherent challenge to control the chemo- and regioselectivity...

Supramolecular-induced regiocontrol over the photochemical [4 + 4] cyclodimerization of NHC- or azole-substituted anthracenes

Thanks to the impressive control that microenvironments within enzymes can have over substrates, many biological reactions occur with high regio- and stereoselectivity. However, comparable regio- and stereoselectivity is extremely difficult to achieve for many types of reactions, particularly photochemical cycloaddition reactions in homogeneous solutions. Here, we describe a supramolecular templating strategy that enables photochemical [4 + 4] cycloaddition of 2,6-difunctionalized anthracenes with unique regio- and stereoselectivity and reactivity using a concept known as the supramolecular approach. The reaction of 2,6-azolium substituted anthracenes H₄-L(PF₆)₂ (L = 1a–1c) with Ag₂O yielded complexes anti-[Ag₂L₂](PF₆)₄ featuring an antiparallel orientation of the anthracene groups. Irradiation of complexes anti-[Ag₂L₂](PF₆)₄ proceeded under [4 + 4] cycloaddition linking the two anthracene moieties to give cyclodimers anti-[Ag₂(2)](PF₆)₂. Reaction of 2,6-azole substituted anthracenes with a dinuclear complex [Cl-Au-NHC–NHC-Au-Cl] yields tetranuclear assemblies with the anthracene moieties oriented in syn-fashion. Irradiation and demetallation gives a [4 + 4] syn-photodimer of two anthracenes. The stereoselectivity of the [4 + 4] cycloaddition between two anthracene moieties is determined by their orientation in the metallosupramolecular assemblies.

A supramolecular templating strategy that enables the photochemical [4 + 4] cycloaddition of 2,6-difunctionalized anthracene derivatives with unique stereoselectivity has been developed based on metal-NHC units.

Synthesis of Anthracene Conjugates of Truncated Antifreeze Protein Sequences: Effect of the End Group and Photocontrolled Dimerization on Ice Recrystallization Inhibition Activity

Biomacromolecular antifreezes distinguish ice from water, function by binding to specific planes of ice, and could have many applications from cryobiology to aerospace where ice is a problem. In biology, antifreeze protein (AFP) activity is regulated by protein expression levels via temperature and light-regulated expression systems, but in the laboratory (or applications), the antifreeze activity is "always on" without any spatial or temporal control, and hence methods to enable this switching represent an exciting synthetic challenge. Introduction of an abiotic functionality into short peptides (e.g., from solid-phase synthesis) to enable switching is also desirable rather than on full-length recombinant proteins. Here, truncated peptide sequences based on the consensus repeat sequence from type-I AFPs (TAANAAAAAAA) were conjugated to an anthracene unit to explore their photocontrolled dimerization. Optimization of the synthesis to ensure solubility of the hydrophobic peptide included the addition of a dilysine solubilizing linker. It was shown that UV-light exposure triggered reversible dimerization of the AFP sequence, leading to an increase in molecular weight. Assessment of the ice recrystallization inhibition activity of the peptides before and after dimerization revealed only small effects on activity. However, it is reported here for the first time that addition of the anthracene unit to a 22-amino-acid truncated peptide significantly enhanced ice recrystallization inhibition compared to the free peptide, suggesting an accessible synthetic route to allow AFP activity using shorter, synthetically accessible peptides with a photoreactive functionality.

Light-controlled thrombin catalysis and clot formation using a photoswitchable G-quadruplex DNA aptamer

The reversible photocontrol of an enzyme governing blood coagulation is demonstrated. The thrombin binding aptamer (TBA), was rendered photochromic by modification with two anthracene groups. Light-triggered anthracene photodimerisation distorts its structure, inhibiting binding of the enzyme thrombin, which in turn triggers catalysis and the resulting clotting process.

A phototunable anion receptor for C-HX interactions with benzoate anions

A supramolecular receptor consisting of two anthracene moieties with binding motifs for binding of benzoate anions is reported here. NMR studies indicate that the binding involves π-π interactions and CHX interactions. Upon exposure to >350 nm light, the receptor undergoes a [4 + 4] photoelectrocyclization restricting the access to the binding site for benzoate. The reverse reaction works in the presence of the dual stimuli of 254 nm light and the benzoate anions. The work thus demonstrates a light mediated dynamic control of the binding pocket of a supramolecular anion receptor.

Alkyne-Alkyne Photo-cross-linking on the Flipping-out Field

The base flip-inducing nucleic acids are expected to create a specific field for various chemical reactions. We now report a novel type of base-flip-inducing oligodeoxynucleotide and photo-cross-linking reaction. Two 3-arylethynyl-5-methyl-2-pyridone nucleosides, Ph and An, were synthesized, and their properties were investigated. The alkyne-alkyne photo-cross-linking rapidly proceeded by taking advantage of the base-flipping-out field where two alkynes overlap each other. This photo-cross-linking would be a new candidate to form cross-linked DNAs.

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.

Rationalisation of a mechanism for sensing single point variants in target DNA using anthracene-tagged base discriminating probes

The fluorescence sensing mechanism for identifying single base changes in target DNA strands has been established through detailed biophysical measurements.

Efficiency of [2 + 2] photodimerization of various stilbene derivatives within the DNA duplex scaffold

A DNA duplex was used as a scaffold to evaluate the intrinsic reactivity of [2 + 2] photodimerization between stilbene derivatives; the duplex pre-organizes the substrates avoiding the need for an association step. Unmodified stilbenes were first introduced at base-pairing positions on complementary DNA strands. The duplex was then irradiated with 340 nm UV light. HPLC analyses revealed that [2 + 2] photodimerization proceeded rapidly without side reactions. Thus, it was confirmed that the DNA duplex could be used as an ideal scaffold for [2 + 2] photodimerization of stilbenes. Next, we examined homo-photodimerization abilities of various stilbene derivatives. Homo-photodimerization of p-cyanostilbene, p-methylstilbazolium, and p-stilbazole occurred efficiently, whereas homo-photodimerization of p-dimethylaminostilbene and p-nitrostilbene did not proceed at all, probably because the reaction was quenched by dimethylamino and nitro groups. Time-dependent density functional theory calculations revealed that excitation energy was correlated with quantum yield. We further investigated hetero-photodimerization. These reactions were made possible by the use of two complementary oligodeoxyribonucleotides tethering different stilbene derivatives. Reactivities in hetero-photodimerization were highly dependent on the combination of derivatives. A high correlation was observed between the quantum yields and energy gaps of HOMO and LUMO between reactive derivatives. Unexpectedly, nitrostilbene, which was non-reactive in homo-photodimerization, cross-reacted with p-methylstilbazolium and p-stilbazole, both of which had close HOMO or LUMO with nitrostilbene. Evaluation of the intrinsic reactivity of homo- and hetero-photodimerization of stilbene derivatives was made possible by the use of DNA as a scaffold.

Exploiting anthracene photodimerization within peptides: light induced sequence-selective DNA binding

Here we detail the first example of anthracene photodimerisation in peptides, and use it to trigger a selective biomolecular recognition event.

Electroporation and microinjection successfully deliver single-stranded and duplex DNA into live cells as detected by FRET measurements

Förster resonance energy transfer (FRET) technology relies on the close proximity of two compatible fluorophores for energy transfer. Tagged (Cy3 and Cy5) complementary DNA strands forming a stable duplex and a doubly-tagged single strand were shown to demonstrate FRET outside of a cellular environment. FRET was also observed after transfecting these DNA strands into fixed and live cells using methods such as microinjection and electroporation, but not when using lipid based transfection reagents, unless in the presence of the endosomal acidification inhibitor bafilomycin. Avoiding the endocytosis pathway is essential for efficient delivery of intact DNA probes into cells.

A ferrocene nucleic acid oligomer as an organometallic structural mimic of DNA

The design, synthesis and electrochemical behaviour of an oligomer consisting of linked thymine-functionalised ferrocene units are reported, which, as a so-called form of ferrocene nucleic acid (FcNA), acts as a structural mimic of DNA.