Selective RNA binding and imaging with imidazopyrazine-based fluorescent molecule

We report the synthesis and characterization of novel imidazopyrazine-based fluorescent molecules 5a and 5b targeting RNA and DNA binding. Molecule 5b showed superior photophysical properties with stable fluorescence and high quantum yield in various solvents. UV-Vis and fluorescence spectroscopy revealed strong RNA binding with time-dependent fluorescence quenching and increasing absorbance, suggesting groove binding or it-it stacking interactions. Furthermore, agarose gel electrophoresis further confirmed selective RNA binding of 5b. Imaging studies demonstrated that 5b penetrated into viable MCF-7 cells and selectively stained RNA and retained fluorescence for up to 8 h under ambient conditions. These findings advance the study of RNA dynamics in living cells, highlighting the potential of 5b for RNA-specific bioimaging and sensing applications.