Catalytic hairpin assembled polymeric tetrahedral DNA frameworks for MicroRNA imaging in live cells

Dynamic DNA nanodevices-based assembly is currently well developed for a broad range of analytical applications. However, some problems persist, such as false positives, nuclease digestions, and exclusive interferences with single signal in complex cellular environment. Herein, we have established a method for imaging cellular miR-155, where it induced assembly of two tetrahedral DNA frameworks (TDFs), TDF-1 and TDF-2, both of which had four fluorescence modified hairpins (Cy3 for TDF-1 and Cy5 for TDF-2, respectively) at each angle, into polymeric tetrahedral DNA frameworks (PTDFs). The formation of PTDFs was greatly dependent on miR-155 overexpressed in breast cancer cells since miR-155 drove catalytic hairpin assembly (CHA) reaction by opening the hairpins at the vertices of TDF-1 to hybridize with TDF-2. Upon the completion of hybridization, the miR-155 was released, starting the next cycle of the CHA reaction. Measurements of atomic force microscopy (AFM) and Förster resonance energy transfer (FRET) showed that the formation of PTDFs occurred owing to the multivalent assembly of TDF-1 and TDF-2. By utilizing the formation of PTDFs, miR-155 was detected in a linear range from 0.5 nM to 30 nM with a 0.35 nM limit of determination, enabling the successful imaging of endogenous miR-155 in live cells through the FRET signal from Cy3 to Cy5. These studies demonstrated that this method significantly strengthened the resistance nuclease to digestion and stable ability with exclusive interference.