Selective profiling of non-canonical nucleic acid structures via size-discriminative supramolecular probes

Abstract: Nucleic acids can form diverse non-canonical structures, such as G-quadruplexes (G4s) and i-motifs (iMs), which are critical in biological processes and disease pathways. This study presents an innovative probe design strategy based on groove size differences, leading to the development of BT-Cy-1, a supramolecular cyanine probe optimized by fine-tuning dimer "thickness". BT-Cy-1 demonstrated high sensitivity in detecting structural transitions and variations in G4s and iMs, even in complex environments with excess dsDNA. Applied to clinical blood samples, it revealed significant differences in RNA G4 and iM levels between liver cancer patients and healthy individuals, marking the first report of altered iM levels in clinical samples. This work highlights a novel approach for precise nucleic acid structural profiling, offering insights into their biological significance and potential in disease diagnostics.