Bioinspired Framework Nucleic Acid Capture Sensitively and Rapidly Resolving MicroRNAs Biomarkers in Living Cells

Abstract

Quantifying intracellular microRNA (miRNA) is essential for diagnosis and prognosis of diseases because of its importance to the development and progression of complex diseases. The challenge is to develop methods that enable multiplex miRNAs detection in ultralow amounts and over broad concentration ranges. Inspired by the “tentacles” of an octopus, herein, we present a framework nucleic acid (FNA) capture for sensitive, rapid, and multiplexed imaging of miRNAs cancer biomarkers in living cells. The programmable FNA is designed using three DNA triangular prism (DTP) nanostructures carrying two pairs of metastable catalytic hairpin assembled (CHA) probes, AS1411 aptamer, and pendent biotinylated DNA strand in different vertexes and is further assembled via streptavidin to form the multivalent DTP (SA-DTP). The SA-DTP system acts as an octopus that captures the target cancer miRNAs quickly and delivers them preferentially among DTPs’ “tentacles” in the SA-DTP system to produce strong, amplified fluorescence for detection. Precise multiplexed imaging of miRNA-155 and miRNA-21 cancer biomarkers’ aberrant expression and dynamic change in different cells demonstrates the feasibility of both monitoring disease progression and evaluating therapeutic efficacy.

3D DNA Scaffold-Assisted Dual Intramolecular Amplifications for Multiplexed and Sensitive MicroRNA Imaging in Living Cells

“…However, these liposome-based probe delivery methods can potentially lead to the use of toxic transfection reagents. Besides, traditional CHA and Dz reactions that occur via random free collision and interaction of the DNA reactants in solution are relatively low, resulting in the extension of sensing time and compromise of sensing sensitivity. − Therefore, the CHA amplification and Dz-powered nanomachine on gold nanoparticles via the Au–S bond for monitoring intracellular miRNAs with improved reaction kinetics have been designed. The confinement of the DNA sensing reactants on nanoparticles can significantly increase their local concentrations and collision efficiency, thereby leading to significantly enhanced reaction kinetics. − However, the intracellular thiol-containing biomolecules such as homocysteine, cysteine, and glutathione may destroy the Au–S bond and cause false-positive signals. − The design of nontoxic and stable probe delivery strategies with enhanced reaction kinetics is therefore highly desirable.…”

DNA nanostructure-based nucleic acid probes: construction and biological applications

“…To overcome the difficulty of transporting biological enzymes into living cells, some enzyme-free signal amplification techniques, such as the HCR, CHA and entropy-driven signal amplifier have been designed for intracellular signal amplification, and they are also demonstrated to work well for DNA nanostructure-mediated intracellular imaging analysis. Inspired by the tentacles of an octopus, Zhang et al 120 prepared a multivalent DNA triangular prism (DTP), which is assembled by linking three biotinylated DTPs by a streptavidin for sensitive, rapid and multiplexed imaging of miRNAs in living cells ( Fig. 8B ).…”

Shedding Light on DNA‐Based Nanoprobes for Live‐Cell MicroRNA Imaging

“…Dong et al proved that DNA triangular prism could protect the hairpin probe from protein interference and DNase I degradation during the delivery process. [25] Zhang et al constructed a DNA nanocage with encapsulated nanoprobes for specific recognition and response target molecules. It was accessible to small miRNA, while large endogenous nuclease and non-specific proteins was blocked outside the cage, leading to a better anti-degradation and anti-interference ability than the probes attached to the outside FNA.…”