Spiropyran Meets Guanine Quadruplexes: Isomerization Mechanism and DNA Binding Modes of Quinolizidine-Substituted Spiropyran Probes

DELFI: a computer oracle for recommending density functionals for excited states calculations

Density functional theory (DFT) is the workhorse of computational quantum chemistry. One of its main limitations is that choosing the right functional is a non-trivial task left for human experts. The choice is particularly hard for excited state calculations when using its time-dependent formulation (TD-DFT). This is due to the approximations of the method, but also because the photophysical properties of a molecule are defined by a manifold of states that all need to be properly described. This includes not only the relative energy of the states, but also capturing the correct character, order, and intensity of the transitions. In this work, we developed a neural network to recommend functionals to be used on molecules for TD-DFT calculations, by simultaneously considering all these properties for a manifold of states. This was possible by developing a scoring system to define the accuracy of an excited state's calculation against a higher-accuracy reference. The scoring system is generalizable to any level of theory; we here applied it to evaluate the performance of common functionals of different rungs against a higher accuracy method on a large set of organic molecules. The results are collected in a database that we released and made open, providing four million data points to the community for future applications. The scoring system assigns a value between zero and one hundred to each functional for each molecule, transforming the complicated task of learning photophysical properties into a simpler regression task. We used the dataset to train a graph attention neural network to predict the scores for unseen molecules. We call this oracle DELFI (Data-driven EvaLuation of Functionals by Inference), which can be used to quickly screen and predict the ranking of functionals to calculate the optical properties of organic molecules. We validated DELFI in two in silico experiments: choosing a common functional for a series of spiropyran-merocyanine isomers and a unique functional to screen a large dataset of over 50 000 organic photovoltaic molecules, for which an extensive benchmark would be unfeasible. A corresponding web application allows DELFI to be easily run and the results to be analyzed, alleviating the hurdle of choosing the right functional for TD-DFT calculations.

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.

Good Vibrations Report on the DNA Quadruplex Binding of an Excited State Amplified Ruthenium Polypyridyl IR Probe

The nitrile containing Ru(II)polypyridyl complex [Ru(phen)2(11,12-dCN-dppz)]2+ (1) is shown to act as a sensitive infrared probe of G-quadruplex (G4) structures. UV-visible absorption spectroscopy reveals enantiomer sensitive binding for the hybrid htel(K) and antiparallel htel(Na) G4s formed by the human telomer sequence d[AG3(TTAG3)3]. Time-resolved infrared (TRIR) of 1 upon 400 nm excitation indicates dominant interactions with the guanine bases in the case of Λ-1/htel(K), Δ-1/htel(K), and Λ-1/htel(Na) binding, whereas Δ-1/htel(Na) binding is associated with interactions with thymine and adenine bases in the loop. The intense nitrile transient at 2232 cm-1 undergoes a linear shift to lower frequency as the solution hydrogen bonding environment decreases in DMSO/water mixtures. This shift is used as a sensitive reporter of the nitrile environment within the binding pocket. The lifetime of 1 in D2O (ca. 100 ps) is found to increase upon DNA binding, and monitoring of the nitrile and ligand transients as well as the diagnostic DNA bleach bands shows that this increase is related to greater protection from the solvent environment. Molecular dynamics simulations together with binding energy calculations identify the most favorable binding site for each system, which are in excellent agreement with the observed TRIR solution study. This study shows the power of combining the environmental sensitivity of an infrared (IR) probe in its excited state with the TRIR DNA "site effect" to gain important information about the binding site of photoactive agents and points to the potential of such amplified IR probes as sensitive reporters of biological environments.

A Modern Look at Spiropyrans: From Single Molecules to Smart Materials

Photochromic compounds of the spiropyran family have two main isomers capable of inter-switching with UV or visible light. In the current review, we discuss recent advances in the synthesis, investigation of properties, and applications of spiropyran derivatives. Spiropyrans of the indoline series are in focus as the most promising representatives of multi-sensitive spirocyclic compounds, which can be switched by a number of external stimuli, including light, temperature, pH, presence of metal ions, and mechanical stress. Particular attention is paid to the structural features of molecules, their influence on photochromic properties, and the reactions taking place during isomerization, as the understanding of the structure-property relationships will rationalize the synthesis of compounds with predetermined characteristics. The main prospects for applications of spiropyrans in such fields as smart material production, molecular electronics and nanomachinery, sensing of environmental and biological molecules, and photopharmacology are also discussed.

Multistimuli-responsive fluorescent probes based on spiropyrans for the visualization of lysosomal autophagy and anticounterfeiting

Lysosomes, as the main degradative organelles, play an important role in a variety of cellular metabolic activities including autophagy and apoptosis, catabolism and transporting substances. Lysosomal autophagy is an important physiological process and causes a slight change in the intra-lysosomal pH to facilitate the breakdown of macromolecular proteins. Therefore, detecting the fluctuation of intra-lysosomal pH is of great significance in monitoring physiological and pathological activities in living organisms. However, few probes have enabled the ratiometric monitoring of lysosomal pH and lysosomal autophagy in dual channels. Fortunately, spiropyrans, as compounds with multistimuli-responsive discoloration properties, form two different isomers under acid induction and ultraviolet induction. To fill this gap, in this work, two novel multistimuli-responsive fluorescent probes with lysosomal targeting in dual channels based on spiropyrans were rationally designed and synthesized. Notably, the two probes exhibited different absorption wavelengths in their UV-responsive and pH-responsive moieties due to their different electron-donating groups. Moreover, bioimaging experiments clearly demonstrate that the probes Lyso-SP and Lyso-SQ monitor lysosomal autophagy by facilitating the visualization of fluctuations in intra-lysosomal pH. Meanwhile, their potential applications in the field of dual-anticounterfeiting were explored based on their photoluminescence ability. We expect that more multistimuli-responsive fluorescent probes can be developed by this design approach.

Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine

Guanine radical cation (G^•+) is a key intermediate in many oxidative processes occurring in nucleic acids. Here, by combining mixed Quantum Mechanical/Molecular Mechanics calculations and Molecular Dynamics (MD) simulations, we study how the structural behaviour of a tract GGG(TTAGGG)₃ (hereafter Tel21) of the human telomeric sequence, folded in an antiparallel quadruple helix, changes when one of the G bases is ionized to G^•+ (Tel21⁺). Once assessed that the electron-hole is localized on a single G, we perform MD simulations of twelve Tel21⁺ systems, differing in the position of G^•+ in the sequence. When G^•+ is located in the tetrad adjacent to the diagonal loop, we observe substantial structural rearrangements, which can decrease the electrostatic repulsion with the inner Na⁺ ions and increase the solvent exposed surface of G^•+. Analysis of solvation patterns of G^•+ provides new insights on the main reactions of G^•+, i.e. the deprotonation at two different sites and hydration at the C8 atom, the first steps of the processes producing 8oxo-Guanine. We suggest the main structural determinants of the relative reactivity of each position and our conclusions, consistent with the available experimental trends, can help rationalizing the reactivity of other G-quadruplex topologies.

Molecular photoswitches in aqueous environments

Molecular photoswitches enable dynamic control of processes with high spatiotemporal precision, using light as external stimulus, and hence are ideal tools for different research areas spanning from chemical biology to smart materials. Photoswitches are typically organic molecules that feature extended aromatic systems to make them responsive to (visible) light. However, this renders them inherently lipophilic, while water-solubility is of crucial importance to apply photoswitchable organic molecules in biological systems, like in the rapidly emerging field of photopharmacology. Several strategies for solubilizing organic molecules in water are known, but there are not yet clear rules for applying them to photoswitchable molecules. Importantly, rendering photoswitches water-soluble has a serious impact on both their photophysical and biological properties, which must be taken into consideration when designing new systems. Altogether, these aspects pose considerable challenges for successfully applying molecular photoswitches in aqueous systems, and in particular in biologically relevant media. In this review, we focus on fully water-soluble photoswitches, such as those used in biological environments, in both in vitro and in vivo studies. We discuss the design principles and prospects for water-soluble photoswitches to inspire and enable their future applications.

Rational design of a photoswitchable DNA glue enabling high regulatory function and supramolecular chirality transfer

Short, complementary DNA single strands with mismatched base pairs cannot undergo spontaneous formation of duplex DNA (dsDNA). Mismatch binding ligands (MBLs) can compensate this effect, inducing the formation of the double helix and thereby acting as a molecular glue. Here, we present the rational design of photoswitchable MBLs that allow for reversible dsDNA assembly by light. Careful choice of the azobenzene core structure results in excellent band separation of the E and Z isomers of the involved chromophores. This effect allows for efficient use of light as an external control element for duplex DNA formation and for an in-depth study of the DNA-ligand interaction by UV-Vis, SPR, and CD spectroscopy, revealing a tight mutual interaction and complementarity between the photoswitchable ligand and the mismatched DNA. We also show that the configuration of the switch reversibly dictates the conformation of the DNA strands, while the dsDNA serves as a chiral clamp and translates its chiral information onto the ligand inducing a preference in helical chirality of the Z isomer of the MBLs.

Enhanced Rigidity Changes Ultraviolet Absorption: Effect of a Merocyanine Binder on G-Quadruplex Photophysics

The urge to discover selective fluorescent binders to G-quadruplexes (G4s) for rapid diagnosis must be linked to understand the effect that those have on the DNA photophysics. Herein, we report on the electronic excited states of a bound merocyanine dye to c-Myc G4 using extensive multiscale quantum mechanics/molecular mechanics calculations. We find that the absorption spectra of c-Myc G4, both without and with the intercalated dye, are mainly composed of exciton states and mixed local/charge-transfer states. The presence of merocyanine hardly affects the energy range of the guanine absorption or the number of guanines excited. However, it triggers a substantial amount (16%) of detrimental pure charge-transfer states involving oxidized guanines. We identify the rigidity introduced by the probe in G4, reducing the overlap among guanines, as the one responsible for the changes in the exciton and charge-transfer states, ultimately leading to a redshift of the absorption maximum.

Spiropyran Meets Guanine Quadruplexes: Isomerization Mechanism and DNA Binding Modes of Quinolizidine-Substituted Spiropyran Probes

The recent delivery of a fluorescent quinolizidine-substituted spiropyran, which is able to switch in vivo and bind to guanine quadruplexes (G4) at physiological pH values, urged us to elucidate its molecular switching and binding mechanism. Combining multiscale dynamical studies and accurate quantum chemical calculations, we show that, both in water and in the G4 environment, the switching of the spiropyran ring is not promoted by an initial protonation event-as expected by the effect of low pH solutions-but that the deprotonated merocyanine form is an intermediate of the reaction leading to the protonated open species. Additionally, we investigate the binding of both deprotonated and protonated open forms of merocyanine to c-MYC G4s. Both species bind to G4s albeit with different hydrogen-bond patterns and provide distinct rotamers around the exocyclic double bond of the merocyanine forms. Altogether, our study sheds light on the pharmacophoric points for the binding of these probes to DNA, and thereby, contributes to future developments of new G4 binders of the remarkable family of quinolizidine-substituted spiropyrans.