Hydrogel “Affinity Trap” for microRNAs with a Self-Assembling Fluorescent “Split-Probe” to Monitor Their Expression and Degradation

The hydrogel "affinity trap" engineered here from peptides and nucleic acids into dynamic supramolecular structures offered the opportunity to measure physiological concentrations of tissue-specific microRNA expression and degradation, which are symptomatic for diseased cells and tissues. Hydrogel size-discriminating properties allowed to segregate microRNAs from complex biological media into a hydrogel matrix and entrap the target sequence via hybridization with a hydrogel-immobilized "capture" probe, where it could be detected through fluorescence quenching. We demonstrated the size-selective permeability of the hydrogel that provided a protective microenvironment for microRNAs and detection probes from cellular biological interference and afforded selective self-assembly and detection of oncogenic microRNA-21 (miR-21) in the presence of cell extracts, which is otherwise detrimental for detection in a gel-free solution. We were also able to monitor the degradation of unlabeled miR-21 by natural (RNase A and H) and synthetic (miR-21-RNase) ribonucleases and their synergistic actions, which could be potentially useful in the therapeutic knockdown of pathogenic RNAs.