Visualization of Long Noncoding RNA MEG3 in Living Cells by a Triple-Helix-Powered 3D Catcher

Visual imaging of long noncoding RNA (lncRNA) MEG3, a newfound regulator of transactivation and tumor growth suppression, is conducive to unlock the secrets of MEG3 in some important biological processes. Here, for the first time, we designed a DNA tetrahedron-based three-dimensional (3D) catcher for imaging cytoplasmic lncRNA MEG3 in living cells. The 3D catcher is composed of a triple-helix-forming dsDNA with capacity to bind the 5'-end GA-rich domain of the lncRNA MEG3 and four hairpin-shaped antisense sequences toward contiguous domain on MEG3. Once ingested by the cell, the 3D catcher quickly captures lncRNA MEG3 via forming a DNA-RNA triple-helix structure and triggering the hybridization-based string disassembly of the catcher. Concomitantly, the quenched hairpin is opened and the fluorescent signal undergoes lighting on conversion. Ascribed to the triple-helix-induced "domino effect," the disassembly reaction time is greatly shorter than the reaction with the inability to form a triple helix. The 3D catcher allows detection of long-chain targets as long as 129 nucleotide (129 nt) with a detection limit of 0.36 nM and distinguishes endogenous lncRNA MEG3 fragments in living cells between hepatoma cells and normal hepatocytes, which provides a reliable strategy for monitoring endogenous long fragment nucleic acid biomarkers in early clinical lesion diagnoses.