Influence of core extension and side chain nature in targeting G-quadruplex structures with perylene monoimide derivatives

Rationally Designed G-Quadruplex Selective "Turn-On" NIR Fluorescent Probe with Large Stokes Shift for Nucleic Acid Research-Based Applications

Guanine-rich DNA/RNA sequences can form Hoogsteen bonds to adopt noncanonical secondary structures called G-quadruplexes, and these have been associated with diverse cellular processes. There has been considerable research interest in the design of G4-interacting ligands for cellular probing of the G4 structure and understanding its associated biological function. Most of the fluorescent G4 ligands either do not have significant selectivity over other nucleic acid structures, have high Stokes shift, or are not in the near-infrared (NIR) region, which limits its cellular visualization. The current work involves the rational design and synthesis of NIR fluorescent probes comprising a (Z)-1-methyl-2-((3-methylbenzo[d]thiazol-2(3H)-ylidene)methyl)quinolin-1-ium scaffold. Among the designed molecules, 4a exhibited far-red fluorescence (λmax = 680 nm) with large Stokes shift (∼182 nm) upon selective binding to human telomeric G-quadruplexes. The dye 4a does not disturb the conformation and stability of G-quadruplexes, thereby making it suitable for nucleic acid research based applications. Interestingly, 4a showed remarkable selectivity over single- and double-stranded structures in contrast to a commercially available quadruplex binding probe, Thiazole orange (TO). The molecular docking studies indicate that 4a binds at the groove region of the telomeric DNA G-quadruplex through π-π stacking interactions with the quinoline and amine-substituted phenyl ring and with the phosphate backbone through anion-π interactions with the benzothiazole ring. The designed molecule 4a has interesting photophysical properties, cell permeability, and biocompatibility with minimal cytotoxicity. Fluorescence imaging studies in live HeLa cells showed that probe 4a binds to the transient population of the DNA G-quadruplex in the nucleus and RNA quadruplexes in the cytoplasm. In brief, G-quadruplex NIR fluorescent probe 4a with a higher signal/noise ratio has significant potential for cellular imaging studies and thus opens avenues to decipher the biological pathways for better understanding of G-quadruplex biology.

G-quadruplex ligands as therapeutic agents against cancer, neurological disorders and viral infections

G-quadruplexes (G4s) within the human genome have undergone extensive molecular investigation, with a strong focus on telomeres, gene promoters and repetitive regulatory sequences. G4s play central roles in regulating essential biological processes, including telomere maintenance, replication, transcription and translation. Targeting these molecular processes with G4-binding ligands holds substantial therapeutic potential in anticancer treatments and has also shown promise in treating neurological, skeletal and muscular disorders. The presence of G4s in bacterial and viral genomes also suggests that G4-binding ligands could be a critical tool in fighting infections. This review provides an overview of the progress and applications of G4-binding ligands, their proposed mechanisms of action, challenges faced and prospects for their utilization in anticancer treatments, neurological disorders and antiviral activities.

Recent Advances in Applications of Fluorescent Perylenediimide and Perylenemonoimide Dyes in Bioimaging, Photothermal and Photodynamic Therapy

The emblematic perylenediimide (PDI) motif which was initially used as a simple dye has undergone incredible development in recent decades. The increasing power of synthetic organic chemistry has allowed it to decorate PDIs to achieve highly functional dyes. As these PDI derivatives combine thermal, chemical and photostability, with an additional high absorption coefficient and near-unity fluorescence quantum yield, they have been widely studied for applications in materials science, particularly in photovoltaics. Although PDIs have always been in the spotlight, their asymmetric counterparts, perylenemonoimide (PMI) analogues, are now experiencing a resurgence of interest with new efforts to create architectures with equally exciting properties. Namely, their exceptional fluorescence properties have recently been used to develop novel systems for applications in bioimaging, biosensing and photodynamic therapy. This review covers the state of the art in the synthesis, photophysical characterizations and recently reported applications demonstrating the versatility of these two sister PDI and PMI compounds. The objective is to show that after well-known applications in materials science, the emerging trends in the use of PDI- and PMI-based derivatives concern very specific biomedicinal applications including drug delivery, diagnostics and theranostics.