Photoinduced Cross-Linking of Short Furan-Modified DNA on Surfaces

A Photosensitized Singlet Oxygen (1O2) Toolbox for Bio-Organic Applications: Tailoring 1O2 Generation for DNA and Protein Labelling, Targeting and Biosensing

Singlet oxygen (1O2) is the excited state of ground, triplet state, molecular oxygen (O2). Photosensitized 1O2 has been extensively studied as one of the reactive oxygen species (ROS), responsible for damage of cellular components (protein, DNA, lipids). On the other hand, its generation has been exploited in organic synthesis, as well as in photodynamic therapy for the treatment of various forms of cancer. The aim of this review is to highlight the versatility of 1O2, discussing the main bioorganic applications reported over the past decades, which rely on its production. After a brief introduction on the photosensitized production of 1O2, we will describe the main aspects involving the biologically relevant damage that can accompany an uncontrolled, aspecific generation of this ROS. We then discuss in more detail a series of biological applications featuring 1O2 generation, including protein and DNA labelling, cross-linking and biosensing. Finally, we will highlight the methodologies available to tailor 1O2 generation, in order to accomplish the proposed bioorganic transformations while avoiding, at the same time, collateral damage related to an untamed production of this reactive species.

Tuning the Acceptor Unit of Push-Pull Porphyrazines for Dye-Sensitized Solar Cells

A family of four push–pull porphyrazines of A₃B type, where each unit A contains two peripheral propyl chains and the unit B is endowed with a carboxylic acid, were prepared. The carboxylic acid was attached to the β-position of the pyrrolic unit, either directly (Pz 10), or through cyanovinyl (Pz 11) and phenyl (Pz 7) groups. The fourth Pz (14) consisted in a pyrazinoporphyrazine wherein the dinitrogenated heterocycle provided intrinsic donor–acceptor character to the macrocycle and contained a carboxyphenyl substituent. The direct attachment of the carboxylic acid functions and their linkers to the porphyrazine core produces stronger perturbation on the electronic properties of the macrocycle, with respect to their connection through fused benzene or pyrazine rings in TT112 and 14, respectively. The HOMO and LUMO energies of the Pzs, which were estimated with DFT calculations, show little variation within the series, except upon introduction of the cyanovinyl spacer, which produces a decrease in both frontier orbital energetic levels. This effective interaction of cyanovinyl substitution with the macrocycle is also evidenced in UV/Vis spectroscopy, where a large splitting of the Q-band indicates strong desymmetrization of the Pz. The performance of the four Pzs as photosensitizers in DSSCs were also investigated.

Visible-light triggered templated ligation on surface using furan-modified PNAs

Oligonucleotide-templated reactions are frequently exploited for target detection in biosensors and for the construction of DNA-based materials and probes in nanotechnology. However, the translation of the specifically used template chemistry from solution to surfaces, with the final aim of achieving highly selective high-throughput systems, has been difficult to reach and therefore, poorly explored. Here, we show the first example of a visible light-triggered templated ligation on a surface, employing furan-modified peptide nucleic acids (PNAs). Tailored photo-oxidation of the pro-reactive furan moiety is ensured by the simultaneous introduction of a weak photosensitizer as well as a nucleophilic moiety in the reacting PNA strand. This allows one to ensure a localized production of singlet oxygen for furan activation, which is not affected by probe dilution or reducing conditions. Simple white light irradiation in combination with target-induced proximity between reactive functionalities upon recognition of a short 22mer DNA or RNA sequence that functions as a template, allows sensitive detection of nucleic acid targets in a 96 well plate format.

An Anticaffeine Antibody-Oligonucleotide Conjugate for DNA-Directed Immobilization in Environmental Immunoarrays

The development of fast and cheap high-throughput platforms for the detection of environmental contaminants is of particular importance to understand the human-related impact on the environment. The application of DNA-directed immobilization (DDI) of IgG molecules is currently limited to the clinical diagnostics scenario, possibly because of the high costs of production of such addressable platforms. We here describe the efficient and specific hybridization of an antibody-oligonucleotide conjugate to a short 12-mer capture probe. The specific antibody used is a monoclonal antibody against caffeine, a stimulant and important anthropogenic marker. With this work, we hope to contribute to broadening the application potential of DDI to environmental markers in order to develop cheaper and more stable high-throughput screening platforms for standard routine analysis of pollutants in a variety of complex matrices.

Study of Photochemical Cytosine to Uracil Transition via Ultrafast Photo-Cross-Linking Using Vinylcarbazole Derivatives in Duplex DNA

Gene therapies, including genome editing, RNAi, anti-sense technology and chemical DNA editing are becoming major methods for the treatment of genetic disorders. Techniques like CRISPR-Cas9, zinc finger nuclease (ZFN) and transcription activator-like effector-based nuclease (TALEN) are a few such enzymatic techniques. Most enzymatic genome editing techniques have their disadvantages. Thus, non-enzymatic and non-invasive technologies for nucleic acid editing has been reported in this study which might possess some advantages over the older methods of DNA manipulation. 3-cyanovinyl carbazole (^CNVK) based nucleic acid editing takes advantage of photo-cross-linking between a target pyrimidine and the ^CNVK to afford deamination of cytosine and convert it to uracil. This method previously required the use of high temperatures but, in this study, it has been optimized to take place at physiological conditions. Different counter bases (inosine, guanine and cytosine) complementary to the target cytosine were used, along with derivatives of ^CNVK (^NH2VK and ^OHVK) to afford the deamination at physiological conditions.

Decoration of trastuzumab with short oligonucleotides: synthesis and detailed characterization

Trastuzumab (Herceptin®) is an FDA-approved therapeutic antibody currently employed in the treatment of metastatic stages of breast cancer. Herein, we propose a simple, fast and cost-effective methodology to conjugate trastuzumab with 22-mer 5' thiol-modified oligonucleotides using a bifunctional crosslinker. The conjugates were successfully characterized by MALDI-ToF MS and SDS-PAGE, obviating the need for enzymatic digestion and difficult chromatographic separations. Furthermore, ELISA was performed to ensure that trastuzumab activity is not affected by oligonucleotide conjugation.

Porphyrinoid biohybrid materials as an emerging toolbox for biomedical light management

The present article reviews the most important developing strategies in light-induced nanomedicine, based on the combination of porphyrinoid photosensitizers with a wide variety of biomolecules and biomolecular assemblies.

Panchromatic Photosensitizers Based on Push-Pull, Unsymmetrically Substituted Porphyrazines

A series of five push-pull porphyrazines of A₃ B type, in which unit B is an isoindole 4-carboxylic acid, has been prepared. The units A have been endowed with thioether, amine, ether and alkyl functions, either directly attached to the β-position of the pyrrolic units, or connected to the porphyrazine core through p-substituted phenyl groups. Attaching the electron-donor functions to the porphyrazine periphery produces strong perturbations in the electronic and redox properties of the dyes. Their HOMO and LUMO energies, estimated from the optical and redox data, as well as with DFT calculations, raise upon functionalization with amines, while the corresponding frontier orbital energetic levels lower upon functionalization with thioethers, p-methoxyphenyl or p-tert-butylphenyl groups. The effective interaction of peripheral substitution with the macrocycle produces chromophores with panchromatic absorption between 300 and 750-850 nm.