Locking-to-unlocking system is an efficient strategy to design DNA/silver nanoclusters (AgNCs) probe for human miRNAs

Abstract

MicroRNAs (miRNAs), small non-coding RNA molecules, are important biomarkers for research and medical purposes. Here, we describe the development of a fast and simple method using highly fluorescent oligonucleotide-silver nanocluster probes (DNA/AgNCs) to efficiently detect specific miRNAs. Due to the great sequence diversity of miRNAs in humans and other organisms, a uniform strategy for miRNA detection is attractive. The concept presented is an oligonucleotide-based locking-to-unlocking system that can be endowed with miRNA complementarity while maintaining the same secondary structure. The locking-to-unlocking system is based on fold-back anchored DNA templates that consist of a cytosine-rich loop for AgNCs stabilization, an miRNA recognition site and an overlap region for hairpin stabilization. When an miRNA is recognized, fluorescence in the visible region is specifically extinguished in a concentration-dependent manner. Here, the exact composition of the fold-back anchor for the locking-to-unlocking system has been systematically optimized, balancing propensity for loop-structure formation, encapsulation of emissive AgNCs and target sensitivity. It is demonstrated that the applied strategy successfully can detect a number of cancer related miRNAs in RNA extracts from human cancer cell lines.

FASTmiR: an RNA-based sensor for in vitro quantification and live-cell localization of small RNAs

“…Similar to DNA/AgNC miRNA sensors ( 48 ), our method is faster and easier than traditional miRNA quantification methods. The northern blot assay requires a long, labor-intensive protocol handling radioactive probes (radiolabeled) or expensive DIG-labeled LNA probes.…”

“…Furthermore, it could be used to estimate the average absolute concentrations of miRNAs in cells. This approach has been used previously for DNA/AgNC miRNA sensors ( 48 ), and here we used a similar approach to estimate 33 723–38 541 copies of miR122 per Huh7 cell. Our estimation is similar but higher than the previously reported copy number of miR122 in a Huh7 (∼16 000 copies), which was estimated by an RNase protection assay ( 39 ).…”

Control and optical mapping of mechanical transitions in polymer networks and DNA-based soft materials

“…One of the most widely used motifs is the molecular beacon [36] (Fig. 2c) Cytosine-rich sequences can be selected which stabilize silver nanoclusters, hence triggering their fluorescent emission [37] (Fig. 2d).…”

“…Reproduced with permission from refs. [2] (Copyright 2017 American Chemical Society), [36] (Copyright 1999 NationalAcademy of Sciences),[37] and[38].field of mechanochromic materials, which display an optical response to mechanical stimuli[39]. The optical signal can come from changes in absorption, emission or reflection of light, as the result of variations in the chemical or physical properties of the material and its integrated features.…”

Preparation and characterization of solid DNA silver nanoclusters with superior aerobic and thermal stability

“…[9][10][11] Nowadays, different noble metal (such as Ag, Au, Pt, and Cu) NCs have been reported. 6,12 Among these metal clusters, DNA-stabilized silver nanoclusters (DNA AgNCs) have received particular attention because they are highly biocompatible and have been applied in the detection of DNA/ RNA, [13][14][15][16][17][18] sensing of small molecules 19 and bioimaging [20][21][22] studies. Recent studies have indicated that the emission color of AgNCs is controlled by multiple factors, including the number of silver atoms, 23 the shape of silver clusters, 24 the oxidization states of the silver atom, 25,26 the conformation of deoxyribose 27 and the silver-base interaction.…”