Orthogonal light-triggered multiple effects based on photochromic nanoparticles for DNA cleavage and beyond

Efficient and spatiotemporally controllable cleavage of deoxyribonucleic acid (DNA) is of great significance for both disease treatment (e.g. tumour, bacterial infection, etc) and molecular biology applications (e.g. gene editing). The recently developed light-induced cleavage strategy based on catalytic nanoparticles has been regarded as a promising strategy for DNA controllable cleavage. Although the regulation based on orthogonal light in biomedical applications holds more significant advantages than that based on single light, nanoparticle-mediated DNA cleavage based on orthogonal light has yet to be reported. In this article, for the first time, we demonstrated an orthogonal light-regulated nanosystem for efficient and spatiotemporal DNA cleavage. In this strategy, tungsten oxide (WO₃) nanoparticles with photochromic properties were used as nano-antennae to convert the photoenergy from the orthogonal visible light (405 nm) and near-infrared light (808 nm) into chemical energy for DNA cleavage. We verified that only the orthogonal light can trigger high cleavage efficiency on different types of DNA. Moreover, such an orthogonal light-response nano-system can not only induce significant apoptosis of tumour cells, but also effectively eliminate bacterial biofilms.

Gold nanoclusters: Photophysical properties and photocatalytic applications

Atomically precise gold nanoclusters (Au NCs) have high specific surface area and abundant unsaturated active sites. Traditionally, Au NCs are employed as thermocatalysts for multielectron transfer redox catalysis. Meanwhile, Au NCs also exhibit discrete energy levels, tunable photophysical and electrochemical properties, including visible to near infrared absorption, microsecond long-lived excited-state lifetime, and redox chemistry. In recent years, Au NCs are increasingly employed as visible to near infrared photocatalysts for their high photocatalytic activity and unique selectivity. This review focuses on the photophysical properties of a variety of Au NCs and their employment as photocatalysts in photocatalytic reactions and related applications including solar energy conversion and photodynamic therapies.

Visible-Light-Mediated Modification and Manipulation of Biomacromolecules

Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.

A Comprehensive Review on Fused Heterocyclic as DNA Intercalators: Promising Anticancer Agents

Since the discovery of DNA intercalating agents (by Lerman, 1961), a growing number of organic, inorganic, and metallic compounds have been developed to treat life-threatening microbial infections and cancers. Fused-heterocycles are amongst the most important group of compounds that have the ability to interact with DNA. DNA intercalators possess a planar aromatic ring structure that inserts itself between the base pairs of nucleic acids. Once inserted, the aromatic structure makes van der Waals interactions and hydrogen-bonding interactions with the base pairs. The DNA intercalator may also contain an ionizable group that can form ionic interactions with the negatively charged phosphate backbone. After the intercalation, other cellular processes could take place, leading ultimately to cell death. The heterocyclic nucleus present in the DNA intercalators can be considered as a pharmacophore that plays an instrumental role in dictating the affinity and selectivity exhibited by these compounds. In this work, we have carried out a revision of small organic molecules that bind to the DNA molecule via intercalation and cleaving and exert their antitumor activity. A general overview of the most recent results in this area, paying particular attention to compounds that are currently under clinical trials, is provided. Advancement in spectroscopic techniques studying DNA interaction can be examined in-depth, yielding important information on structure-activity relationships. In this comprehensive review, we have focused on the introduction to fused heterocyclic agents with DNA interacting features, from medicinal point of view. The structure-activity relationships points, cytotoxicity data, and binding data and future perspectives of medicinal compounds have been discussed in detail.

Lorenz A, Taratula O, Henary M, Grant KB. DNA Photocleavage in the Near-Infrared Wavelength Range by 2-Quinolinium Dicarbocyanine Dyes

Here, we report the syntheses of two pentamethine cyanine dyes containing quinolinium rings and substituted with either hydrogen (3) or bromine (4) at the meso carbon. The electron withdrawing bromine atom stabilizes dye 4 in aqueous buffer, allowing complex formation to occur between the dye and double-helical DNA. UV–visible, CD, and fluorescence spectra recorded at low DNA concentrations suggest that dye 4 initially binds to the DNA as a high-order aggregate. As the ratio of DNA to dye is increased, the aggregate is converted to monomeric and other low-order dye forms that interact with DNA in a non-intercalative fashion. The brominated dye 4 is relatively unreactive in the dark, but, under 707–759 nm illumination, generates hydroxyl radicals that cleave DNA in high yield (pH 7.0, 22 °C). Dye 4 is also taken up by ES2 ovarian carcinoma cells, where it is non-toxic under dark conditions. Upon irradiation of the ES2 cells at 694 nm, the brominated cyanine reduces cell viability from 100 ± 10% to 14 ± 1%. Our results suggest that 2-quinolinium-based carbocyanine dyes equipped with stabilizing electron withdrawing groups may have the potential to serve as sensitizing agents in long-wavelength phototherapeutic applications.

Single photon DNA photocleavage at 830 nm by quinoline dicarbocyanine dyes

We have synthesized symmetrical carbocyanine dyes in which two 4-quinolinium rings are joined by a pentamethine bridge that is meso-substituted with H or Cl. Irradiation of the halogenated dye at 830 nm produces hydroxyl radicals that generate DNA direct strand breaks. This represents the first reported example of DNA photocleavage upon single photon excitation of a chromophore at wavelengths above 800 nm.

Targeting G-quadruplexes with Organic Dyes: Chelerythrine-DNA Binding Elucidated by Combining Molecular Modeling and Optical Spectroscopy

The DNA-binding of the natural benzophenanthridine alkaloid chelerythrine (CHE) has been assessed by combining molecular modeling and optical absorption spectroscopy. Specifically, both double-helical (B-DNA) and G-quadruplex sequences—representative of different topologies and possessing biological relevance, such as telomeric or regulatory sequences—have been considered. An original multiscale protocol, making use of molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations, allowed us to compare the theoretical and experimental circular dichroism spectra of the different DNA topologies, readily providing atomic-level details of the CHE–DNA binding modes. The binding selectivity towards G-quadruplexes is confirmed by both experimental and theoretical determination of the binding free energies. Overall, our mixed computational and experimental approach is able to shed light on the interaction of small molecules with different DNA conformations. In particular, CHE may be seen as the building block of promising drug candidates specifically targeting G-quadruplexes for both antitumoral and antiviral purposes.

Selective parallel G-quadruplex recognition by a NIR-to-NIR two-photon squaraine

Fluorescence imaging probes for specific G-quadruplex (G4) conformations are of considerable interest in biomedical research. Herein, we present the synthesis and the binding properties of a new water-soluble near-infrared (NIR) amphiphilic squaraine dye (CAS-C1) which is capable of selective detection of parallel over non-parallel and non G4 topologies. The striking changes in its linear optical response upon binding to parallel G4s give rise to high fluorescence quantum yields (Φ f ≈ 0.7) and one-photon molecular brightness in the far-red-NIR region. The outstanding recognition process of CAS-C1 for parallel G4s via end-stacking provides binding constants in the nanomolar regime (K b = 107 to 108 M-1) awarding it as one of the most potent parallel G4 binders currently available. Moreover, the CAS-C1-parallel G4 system exhibits large two-photon absorption (TPA) cross-sections and molecular brightness in the second NIR biological transparency window (λ ≈ 1275 nm), making it an ideal candidate for NIR-to-NIR ultrasensitive two-photon procedures.

Spin-Forbidden Excitation: A New Approach for Triggering Photopharmacological Processes with Low-Intensity NIR Light

Exposure to low-intensity radiation in the near-infrared (NIR) spectral region matching the optically transparent "phototherapeutic window" of biological tissues can be applied to directly populate spin-restricted excited states of light-responsive compounds. This unconventional and unprecedented approach is introduced herein as a new strategy to overcome some of the major unresolved problems observed in the rapidly emerging fields of photopharmacology and molecular photomedicine, where practical applications in living cells and organisms are still limited by undesired side reactions and insufficient light penetration. Water-soluble and biocompatible metal complexes with a significant degree of spin-orbit coupling were identified as target candidates for testing our new hypothesis. As a first example, a dark-stable manganese carbonyl complex acting as a visible-light-triggered CO-releasing molecule (Photo-CORM) is shown to be photoactivated by NIR radiation, although apparently no spectroscopically evident absorption bands are detectable in this low-energy region. This quite remarkable effect is ascribed to a strongly restricted, but obviously not completely forbidden optical population of the lowest triplet excited state manifold of the diamagnetic complex from the singlet ground state.

From non-covalent binding to irreversible DNA lesions: nile blue and nile red as photosensitizing agents

We report a molecular modeling study, coupled with spectroscopy experiments, on the behavior of two well known organic dyes, nile blue and nile red, when interacting with B-DNA. In particular, we evidence the presence of two competitive binding modes, for both drugs. However their subsequent photophysical behavior is different and only nile blue is able to induce DNA photosensitization via an electron transfer mechanism. Most notably, even in the case of nile blue, its sensitization capabilities strongly depend on the environment resulting in a single active binding mode: the minor groove. Fluorescence spectroscopy confirms the presence of competitive interaction modes for both sensitizers, while the sensitization via electron transfer, is possible only in the case of nile blue.