Affordable small molecules as promising fluorescent labels for biomolecules: application in RNA-FISH probes

Abstract

Fluorescent labels play a vital role in a wide range of contemporary scientific techniques, including direct and indirect immunochemistry, fluorescence microscopy, histochemistry, flow cytometry, and fluorescence in situ hybridization (FISH). Small fluorescent labels provide substantial practical advantages by allowing multiple fluorophores to be conjugated to a single biomolecule, thereby enhancing fluorescence signal optimization. Widely used fluorescent labels are often too costly for routine applications and typically exhibit small Stokes shifts, limiting their practical utility. In this study, we report three novel small molecules as promising fluorescent labels for biomolecules, synthesized via an efficient, straightforward, and cost-effective approach. Additionally, we assess the fluorescence properties of the three new small molecules as potential fluorescent labels for biomolecules. Six novel fluorescent oligonucleotide probes were synthesized, including three targeting the rRNA region of eukaryotic cells (EUK516) and three targeting the rRNA region of prokaryotic cells (EUB338). The synthesized fluorescent probes were evaluated using microorganisms from the culture collection of the Laboratory of Biodegradation and Biotechnology at the HERCULES Laboratory, University of Évora. The probes demonstrated effective performance in RNA-FISH applications, highlighting the potential of these new small molecules for biomolecule labeling and bioimaging.