Exploiting G-Quadruplex-DNA Damage as a Tool to Quantify Singlet Oxygen Production

G-Quadruplexes (G4s) are highly dynamic and polymorphic nucleic acid structures that can adopt a variety of conformations. When exposed to oxidative conditions, more specifically singlet oxygen, the guanosine nucleobases can be oxidized, which in turn can affect the conformation and folding of the G4. Based on this peculiar phenomenon, it is rationalized that G4s can serve as quantification sensors for the production of singlet oxygen. Here, a method for determining the quantum yield of singlet oxygen generation for visible as well as UV-light excited photosensitizers, using a short G4 DNA sequence, readily available from common DNA companies, as a biological and water-soluble probe, is presented.

Monosulfonated dibenzo-24-crown-8 and its properties

In this paper, we describe a method for preparing a monosulfonated dibenzo-24-crown-8 ether, SDB24C8, by direct sulfonation of the parent crown (DB24C8). Since neutral DB24C8 readily interacts with cationic guests, permanently charged SDB24C8 is an advantageous candidate for future supramolecular applications. SDB24C8 can be isolated as a sulfonic acid to be used as it is or converted to a salt of choice. The crystallographic analysis provides the first known host-guest assembly with a DB24C8-based scaffold complexing hydronium and potassium cations. Supramolecular investigations of the interactions of this anionic macrocycle with alkali cations were also performed. According to the expectations, the introduction of the sulfonic group into the DB24C8 scaffold increases the affinities of the receptor. An unusual selectivity of SDB24C8 towards a sodium cation was also observed and further investigated with DFT calculations.

Ternary host-guest complexes with rapid exchange kinetics and photoswitchable fluorescence

Confinement within molecular cages can dramatically modify the physicochemical properties of the encapsulated guest molecules, but such host-guest complexes have mainly been studied in a static context. Combining confinement effects with fast guest exchange kinetics could pave the way toward stimuli-responsive supramolecular systems—and ultimately materials—whose desired properties could be tailored “on demand” rapidly and reversibly. Here, we demonstrate rapid guest exchange between inclusion complexes of an open-window coordination cage that can simultaneously accommodate two guest molecules. Working with two types of guests, anthracene derivatives and BODIPY dyes, we show that the former can substantially modify the optical properties of the latter upon noncovalent heterodimer formation. We also studied the light-induced covalent dimerization of encapsulated anthracenes and found large effects of confinement on reaction rates. By coupling the photodimerization with the rapid guest exchange, we developed a new way to modulate fluorescence using external irradiation.

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A coordination cage encapsulates various anthracenes and BODIPY dyes as homodimers

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Mixing the two homodimers leads to the formation of anthracene-BODIPY heterodimers

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Encapsulation can either promote or suppress the photodimerization of anthracenes

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The homodimer/heterodimer equilibrium can be tuned by light-induced guest exchange

Confinement of small molecules within the cavities of natural and synthetic hosts can greatly affect the physicochemical properties of the bound species; however, to date, such host-guest complexes have been studied mainly in a static context. An important direction is the development of host-guest systems, whereby encapsulation and release of guest molecules can be reversibly controlled using light. Here, we report ternary inclusion complexes comprising an open-window coordination cage and two kinds of photoactive guests, namely, the photodimerizable anthracenes and BODIPY dyes. Alternating exposure to two different colors of light shifts the equilibrium between the encapsulated homodimers and heterodimers, thus dramatically affecting the system’s optical properties. We also find that the rates of both processes—anthracene dimerization and guest exchange—strongly depend on the substitution pattern on both types of guests, which highlights the importance of confinement effects.

Emerging properties from mechanical tethering within a post-synthetically functionalised catenane scaffold

Using a post-synthetic modification strategy we have prepared a series of functionalised [2]catenanes to study the impact of mechanically-enforced proximity on functional group properties, including emission, electrochemistry and photoreactivity.

Post-Synthetic Macrocyclization of Rotaxane Building Blocks

Although not often encountered, cyclic interlocked molecules are appealing molecular targets because of their restrained tridimensional structure which is related to both the cyclic and interlocked shapes. Interlocked molecules such as rotaxane building blocks may be good candidates for post-synthetic intramolecular cyclization if the preservation of the mechanical bond ensures the interlocked architecture throughout the reaction. This is obviously the case if the modification does not involve the cleavage of either the macrocycle's main chain or the encircled part of the axle. However, among the post-synthetic reactions, the chemical linkage between two reactive sites belonging to embedded elements of rotaxanes still consists of an underexploited route to interlocked cyclic molecules. This Review lists the rare examples of macrocyclization through chemical connection between reactive sites belonging to a surrounding macrocycle and/or an encircled axle of interlocked rotaxanes.

Damming an electronic energy reservoir: ion-regulated electronic energy shuttling in a [2]rotaxane

We demonstrate the first example of bidirectional reversible electronic energy transfer (REET) between the mechanically bonded components of a rotaxane. Our prototypical system was designed such that photoexcitation of a chromophore in the axle results in temporary storage of electronic energy in a quasi-isoenergetic “reservoir” chromophore in the macrocycle. Over time, the emissive state of the axle is repopulated from this reservoir, resulting in long-lived, delayed luminescence. Importantly, we show that cation binding in the cavity formed by the mechanical bond perturbs the axle chromophore energy levels, modulating the REET process, and ultimately providing a luminescence read-out of cation binding. Modulation of REET processes represents an unexplored mechanism in luminescent molecular sensor development.

Delayed emission due to reversible electronic energy transfer (REET) between chromophores in the axle and macrocycle components of a rotaxane is demonstrated. The REET process can be modulated by metal ion binding in the cavity of the rotaxane.

Expected and unexpected photoreactions of 9-(10-)substituted anthracene derivatives in cucurbit[n]uril hosts

By arranging substrates in a "reaction ready" state through noncovalent interactions, supramolecular nanoreactors/catalysts show high selectivity and/or rate acceleration features. Herein, we report the host-guest complexation of 9-(10-)substituted anthracene derivatives (G1-G3) with cucurbit[n]uril (CB[n], n = 8, 10), and the photoreactions of these derivatives in the presence of CB[n] hosts. Both CB[10] and CB[8] showed no obvious effects on the photoreaction of 9,10-disubstituted derivative G1. For G2 and G3, CB[10] operated as either a nanoreactor or catalyst (10%) for the photodimerization of two compounds with high selectivity and high yield. However, although CB[8] formed a 1 : 2 complex with G2, as also observed with CB[10], the photosolvolysis product (9-anthracenemethanol) was obtained quantitatively after photoirradiation of the CB[8]·2G2 complex. This unexpected photosolvolysis was rationalized by a plausible catalytic cycle in which anthracene acts as a photoremovable protecting group (PPG) and the carbonium ion intermediate is stabilized by CB[8].

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.

Photochromic rotaxanes and pseudorotaxanes

Among stimulus-responsive molecular ring-on-thread rotaxanes and pseudorotaxanes, variants incorporating photochromic sub-units are attracting considerable attention as their properties and structure can be remotely and precisely controlled, additionally without producing chemical waste. The focus herein is on photoswitching-driven assembly/disassembly and modulation of properties resulting from light-activated isomerization or changes in electronic properties.

Photoactive Molecular-Based Devices, Machines and Materials: Recent Advances

Molecular and supramolecular-based systems and materials that can perform predetermined functions in response to light stimulation have been extensively studied in the past three decades. Their investigation continues to be a highly stimulating topic of chemical research, not only because of the inherent scientific value related to a bottom-up approach to functional nanostructures, but also for the prospective applications in diverse fields of technology and medicine. Light is an important tool in this context, as it can be conveniently used both for supplying energy to the system and for probing its states and transformations. In this microreview we recall some basic aspects of light-induced processes in (supra)molecular assemblies, and discuss their exploitation to implement novel functionalities with nanostructured devices, machines and materials. To this aim we illustrate a few examples from our own recent work, which are meant to illustrate the trends of current research in the field.

Synthesis and Light-Induced Actuation of Photo-Labile 2-Pyridyl-1,2,3-Triazole Ru(bis-bipyridyl) Appended Ferrocene Rotors

To realise useful control over molecular motion in the future an extensive toolbox of both actionable molecules and stimuli-responsive units must be developed. Previously, our laboratory has reported 1,1'-disubstituted ferrocene (Fc) rotor units which assume a contracted/π-stacked conformation until complexation of cationic metal ions causes rotation about the Ferrocene (Fc) molecular 'ball-bearing'. Herein, we explore the potential of using the photochemical ejection of [Ru(2,2'-bipyridyl)₂]2+ units as a stimulus for the rotational contraction of new ferrocene rotor units. Fc rotors with both 'regular' and 'inverse' 2-pyridyl-1,2,3-triazole binding pockets and their corresponding [Ru(2,2'-bipyridyl)₂]2+ complexes were synthesised. The rotors and complexes were characterised using nuclear magnetic resonance (NMR) and ultraviolet (UV)-visible spectroscopies, Electro-Spray Ionisation Mass Spectrometry (ESI⁻MS), and electrochemistry. The 1,1'-disubstituted Fc ligands were shown to π-stack both in solution and solid state. Density Functional Theory (DFT) calculations (CAM-B3LYP/6-31G(d)) support the notion that complexation to [Ru(2,2'-bipyridyl)₂]2+ caused a rotation from the syn- to the anti-conformation. Upon photo-irradiation with UV light (254 nm), photo-ejection of the [Ru(2,2'-bipyridyl)₂(CH₃CN)₂]2+ units in acetonitrile was observed. The re-complexation of the [Ru(2,2'-bipyridyl)₂]2+ units could be achieved using acetone as the reaction solvent. However, the process was exceedingly slowly. Additionally, the Fc ligands slowly decomposed when exposed to UV irradiation meaning that only one extension and contraction cycle could be completed.

Light-initiated reversible conversion of macrocyclic endoperoxides derived from half-sandwich rhodium-based metallarectangles

A series of metallarectangles were synthesized by an anthracene-based ligand and three different half-sandwich rhodium precursors. The photochemical reactions show that these metallarectangles can be reversibly converted to the macrocyclic endoperoxides.

An Unprecedented Photochemical Reaction for Anthracene-Containing Derivatives

A series of anthracene-containing derivatives have been synthesised and characterised. The photochemical behaviour of these derivatives have been investigated by ¹ H NMR spectroscopy. An unprecedented photolysis reaction for anthracene-containing derivatives was observed in the case of anthracenes directly armed with a -CH₂ O-R group upon UV irradiation. The photolysis reaction process has been demonstrated to occur in three steps. Firstly, the anthracene-containing derivatives are converted into the corresponding endoperoxide intermediate upon UV irradiation in the presence of air; then, the endoperoxide intermediate is decomposed to the corresponding starting compound and 9-anthraldehyde; finally, 9-anthraldehyde is further oxidised to anthraquinone. Additionally, the photolysis reaction of anthracene-containing derivatives is significantly promoted in the presence of a thiacalix[4]arene platform.

Synthesis of linear [5]catenanes via olefin metathesis dimerization of pseudorotaxanes composed of a [2]catenane and a secondary ammonium salt

[5]Catenanes were synthesized by olefin metathesis dimerization.

Versatile control of the submolecular motion of di(acylamino)pyridine-based [2]rotaxanes

A cyclic network of chemical reactions has been conceived for exchanging the dynamic behaviour of di(acylamino)pyridine-based rotaxanes and surrogates. X-ray diffraction studies revealed the intercomponent interactions in these interlocked compounds and were consistent with those found in solution by dynamic NMR experiments. This particular binding site was incorporated into a molecular shuttle enabled for accessing two states with an outstanding positional discrimination through chemical manipulation. Furthermore, the ability of the di(acylamino)pyridine domain to associate with external binders with a complementary array of HB donor and acceptor sites was exploited for the advance of an unprecedented electrochemical switch operating through a reversible anion radical recognition process.

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.