Probing interaction of a fluorescent ligand with HIV TAR RNA

A Light-Up Strategy with Aggregation-Induced Emission for Identification of HIV-I RNA-Binding Small Molecules

“…It has been reported that these six aminoglycoside ligands have a strong binding affinity with the RNA, 10,22 and they all showed a relatively high replacement rate for all two RNA constructs in our system. In contrast, the four unreported molecules had a lower replacement rate, demonstrating that, at a concentration of 10 μM, the competition effect between these four ligands and RNA was weak.…”

“…On the contrary, captopril and estazolam were less effective in binding even at high concentrations (fluorescence spectra were shown in Figure S7). We previously reported that ligands binding to TAR RNA at the Tat binding site should meet three conditions: an aromatic or heteroaromatic moiety, a cationic residue, and a linker in their structure . Captopril and estazolam tested here apparently do not meet these conditions, and that probably explained why they hardly bind to the RNAs.…”

“…We previously reported that ligands binding to TAR RNA at the Tat binding site should meet three conditions: an aromatic or heteroaromatic moiety, a cationic residue, and a linker in their structure. 22 Captopril and estazolam tested here apparently do not meet these conditions, and that probably explained why they hardly bind to the RNAs. The binding affinities were estimated using the CD 50 value (dosage of competitor ligands required for displacement of 50% of peptides from a preformed RNA−peptide complex).…”

“…Fluorescence methods, especially the direct-labeling strategy, are usually employed to identify RNA-binding small molecules in drug screenings. ,− However, most fluorescent dyes have poor light stability, severe photobleaching, or high background signals. In addition, the direct-labeling method may alter the interaction surface of proteins or RNAs and hamper the binding affinity in consequence. , On the other hand, fluorescent indicator displacement assay can also be used to identify the small molecule ligands that disrupt the formation of the RNA–protein complex. , Although this method can avoid covalent modification, it asks for fluorescent indicators that bind to RNA and the optical properties need to be modulated before and after binding, which is not readily available most of the time. To achieve better fluorescent performance, fluorescent nanomaterials are engaged in the competitive displacement assays for screening of RNA-binding molecules. − …”

“…20,21 On the other hand, fluorescent indicator displacement assay can also be used to identify the small molecule ligands that disrupt the formation of the RNA−protein complex. 11,22 Although this method can avoid covalent modification, it asks for fluorescent indicators that bind to RNA and the optical properties need to be modulated before and after binding, which is not readily available most of the time. performance, fluorescent nanomaterials are engaged in the competitive displacement assays for screening of RNA-binding molecules.…”