Annalisa Masi

The reaction of the HS^•/S^•− radical (pKa ~3.4), generated selectively from H₂S by γ-irradiated N₂-flushed aqueous solutions at pH 5, with purine nucleosides (dG or dA), a 10-mer double-stranded oligodeoxynucleotide (ds-ODNs), and calf thymus (ct) DNA was investigated, under various experimental conditions. Concurrent quantification of the four purine 5′,8-cyclo-2′-deoxynucleosides (cPu) and two 8-oxo-7,8-dihydro-2′-deoxypurines (8-oxo-Pu) by LC-MS/MS analysis using isotopomeric internal standards was achieved. The formation of 8-oxo-Pu is several tens of times larger than cPu. Mechanistic schemes for the formation of the two product groups are proposed. Hydrogen atom abstraction from C5′–H by S^•− produces the cPu via cyclization of the C5′ radical onto C8, forming a new covalent bond, C5′–C8. The unexpected formation of 8-oxo-Pu should be mechanistically more complex. We propose that an S^•− (coupled with H⁺) adds to the base rings, followed by the elimination of HS⁻ to form the corresponding radical cation; subsequent reactions with H₂O and radical disproportionation with another S^•− lead to 8-oxo-Pu. A comparison of S^•− with the available literature data for HO^• reactivity towards ct-DNA in de-oxygenated aqueous solutions is also presented. Before the present findings, cPu lesions were attributed exclusively to HO^• reactivity toward ct-DNA. The reaction of the thiyl radical (HOCH₂CH₂S^•) with ct-DNA was also investigated, yielding results similar to those of S^•− obtained under comparable experimental conditions. Our results contributed to a better understanding of DNA damage induced by reactive sulfur species (RSS), particularly the formation of purine lesions and the relative abundance of cPu versus 8-oxo-Pu.

The global rise in antimicrobial resistance (AMR) demands innovative strategies beyond traditional antibiotics. Peptide Nucleic Acids (PNAs), synthetic DNA analogues with peptide-like backbones, act as thermically, chemically, and enzymatically stable sequence-specific agents capable of silencing essential bacterial genes. Through antisense mechanisms, PNAs bind bacterial mRNA or rRNA, blocking translation or ribosome assembly and thereby inducing species-specific growth inhibition. Their programmable design enables precise targeting of multidrug-resistant pathogens while sparing commensal microbiota. Recent advances, including γ-modified backbones, cationic substitutions, and delivery platforms such as cell-penetrating peptides (CPPs), dendron conjugates, and nanoparticles, have improved solubility, stability, and cellular uptake. Studies show promising in vitro and, albeit less frequently, in vivo efficacy against both Gram-positive and Gram-negative bacteria, often with synergistic activity when combined with conventional antibiotics. Although challenges remain in delivery and large-scale production, PNAs represent a promising class of antimicrobials to combat AMR through targeted gene inhibition.

Nucleic acids and their synthetic analogs have driven modern diagnostics of versatile platforms capable of detecting disease signatures with molecular precision

Microalgae represent some of the most promising eukaryotic platforms in biotechnology due to their rapid growth, simple cultivation requirements, reliance on sunlight as a primary energy source, and ability to synthesize high-value bioactive compounds. These characteristics have made microalgae attractive candidates in various fields, including biofuel production, carbon capture, and pharmaceutical development. However, several technical limitations have limited their large-scale use as sustainable biofactories. A paradigm shift is currently occurring thanks to the genetic manipulation of microalgae, driven by CRISPR-Cas technology. Significant progress has been made in the model species Chlamydomonas reinhardtii, particularly in the targeted and efficient insertion of foreign DNA. Despite this progress, key challenges remain, and further optimization of CRISPR-Cas methodologies is needed to fully unleash the genetic potential of this organism. This review provides an overview of the convergence of CRISPR-Cas technologies in microalgae research, highlighting their impact on genetic studies, metabolic engineering, and industrial applications. It summarizes recent advances in microalgal genome editing through CRISPR systems, outlines current technical challenges, and highlights future directions for improving the implementation of this innovative technology in microalgal biotechnology.

Carbon dots (CDs) are gaining significant attention as multifunctional nanomaterials due to their optical properties, aqueous dispersibility, redox activity, and overall biocompatibility. This review presents a critical overview of the recent advances concerning the application of CDs in nucleic acid-centered diagnostics, with a specific focus on oxidative DNA damage. The use of CDs for the detection of oxidative DNA damage biomarkers, such as 8-oxo-2′-deoxyguanosine (8-oxo-dG), and their potential roles as fluorescent probes in environments related to oxidative stress is discussed in detail. The relationship between surface functionalization and biological performance is examined, highlighting how physicochemical properties dictate both the beneficial and adverse biological responses to CDs. Remarkably, CDs can act as antioxidants, mitigating oxidative damage, or as pro-oxidants, inducing cytotoxic effects, an ambivalent behavior that can be strategically harnessed for cytoprotection or selective tumor cell killing. Overall, this review outlines how CDs can contribute to the development of precision tools for studying oxidative environments affecting nucleic acids, with important implications for both diagnostics and redox-based therapeutic strategies of human diseases.

A study on the amino acid‐mediated intramolecular cyclization of diketoaldehyde 2 to form bicyclic ketocarbaldehyde 1, a potentially useful intermediate in the synthesis of some polycyclic diterpenes, is hereafter presented. This cyclization exhibits a peculiar enantio‐selectivity if compared to similar intramolecular cyclizations due to its product being the (S)‐enantiomer when using d‐amino acids. Our findings reveal that the transformation proceeds through two irreversible steps: the cyclization and the subsequent dehydration process. The reaction enantiomeric excess (e.e.) was optimized by systematically varying the amino acids, solvents, and acids used. Aldol intermediates were successfully isolated. The structure of the most abundant one was confirmed by X‐ray analysis, which supported the proposed reaction mechanism. NMR and MS were employed to monitor in real‐time the formation and the evolution of these intermediates. This approach allowed us to detect the key species that contribute to the enantioselectivity and yield of the final product. Additionally, the transition state energies associated with the formation of the eight possible aldol intermediates were examined through computational studies, further elucidating the mechanistic pathway of this enantioselective cyclization.

Carbon dots (CDs) represent an emerging class of nanomaterials that combine outstanding photoluminescent properties with low toxicity and excellent biocompatibility. These unique features have garnered significant interest for potential applications in sensing as well as nanovectors for bioactive compounds. Within this context, the possibility of synthesizing chiral carbon dots (CCDs) has paved the way for a plethora of bioapplications in their interaction with chiral biomolecules. In this study we report the synthesis and characterization of CCDs with opposite chiralities and their selective interaction with nucleic acids. A systematic study on their interaction with different oligonucleotides (ODNs) using UV‐vis, photoluminescence, and circular dichroism analyses highlighted how the chiral surface of the CCDs induces distinct spectroscopic responses in CCDs‐ODN conjugates. These findings establish the foundation for innovative applications of CCDs as nanosensors and nanocarriers for nucleic acids. Additionally, the antioxidant properties of CCDs were investigated, highlighting their dual potential as both sensing and preservative nanomaterials for genetic material. Our results suggest significant implications for the development of chiral‐specific diagnostic tools, drug delivery systems, and therapeutic agents. Furthermore, these properties open new avenues for the use of CCDs in antibiotic residue detection, fluorescence imaging, and photodynamic therapy.

In recent years, nucleic acids have emerged as powerful biomaterials, revolutionizing the field of biomedicine. This review explores the multifaceted applications of nucleic acids, focusing on their pivotal role in various biomedical applications. Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), possess unique properties such as molecular recognition ability, programmability, and ease of synthesis, making them versatile tools in biosensing and for gene regulation, drug delivery, and targeted therapy. Their compatibility with chemical modifications enhances their binding affinity and resistance to degradation, elevating their effectiveness in targeted applications. Additionally, nucleic acids have found utility as self-assembling building blocks, leading to the creation of nanostructures whose high order underpins their enhanced biological stability and affects the cellular uptake efficiency. Furthermore, this review delves into the significant role of oligonucleotides (ODNs) as indispensable tools for biological studies and biomarker discovery. ODNs, short sequences of nucleic acids, have been instrumental in unraveling complex biological mechanisms. They serve as probes for studying gene expression, protein interactions, and cellular pathways, providing invaluable insights into fundamental biological processes. By examining the synergistic interplay between nucleic acids as powerful biomaterials and ODNs as indispensable tools for biological studies and biomarkers, this review highlights the transformative impact of these molecules on biomedical research. Their versatile applications not only deepen our understanding of biological systems but also are the driving force for innovation in diagnostics and therapeutics, ultimately advancing the field of biomedicine.

We examined the reaction of hydroxyl radicals (HO^•) and sulfate radical anions (SO₄^•−), which is generated by ionizing radiation in aqueous solutions under anoxic conditions, with an alternating GC doubled-stranded oligodeoxynucleotide (ds-ODN), i.e., the palindromic 5′-d(GCGCGC)-3′. In particular, the optical spectra of the intermediate species and associated kinetic data in the range of ns to ms were obtained via pulse radiolysis. Computational studies by means of density functional theory (DFT) for structural and time-dependent DFT for spectroscopic features were performed on 5′-d(GCGC)-3′. Comprehensively, our results suggest the addition of HO^• to the G:C pair moiety, affording the [8-HO-G:C]^• detectable adduct. The previous reported spectra of one-electron oxidation of a variety of ds-ODN were assigned to [G(-H⁺):C]^• after deprotonation. Regarding 5′-d(GCGCGC)-3′ ds-ODN, the spectrum at 800 ns has a completely different spectral shape and kinetic behavior. By means of calculations, we assigned the species to [G:C/C:G]^•+, in which the electron hole is predicted to be delocalized on the two stacked base pairs. This transient species was further hydrated to afford the [8-HO-G:C]^• detectable adduct. These remarkable findings suggest that the double-stranded alternating GC sequences allow for a new type of electron hole stabilization via delocalization over the whole sequence or part of it.