Design of oligonucleotide-capped mesoporous silica nanoparticles for the detection of miRNA-145 by duplex and triplex formation

Abstract

The development of new strategies to detect microRNAs (miRNAS) has become an important challenge in the biomedical field. We report herein the use of oligonucleotide-gated silica nanoparticles for the detection of miRNA-145. In the proposed design, mesoporous silica nanoparticles (MSNs) are loaded with a fluorescent reporter (rhodamine B) and pores are blocked by specific DNA oligonucleotides. The opening of the gated system and dye delivery is selectively controlled by DNA-miRNA recognition. Moreover, the use of DNA capture probes able to form duplex or triplex structures between target miRNA and the complementary oligonucleotides has been studied. By this simple procedure a limit of detection as low as 0.25 pM was found for miRNA. The method was successfully applied to detect miRNA-145 in serum samples, which demonstrates the high potential of these capped materials to detect miRNA for diagnostic purposes.

Overview of the Evolution of Silica-Based Chromo-Fluorogenic Nanosensors

“…The applications of gated materials in recognition protocols have attracted great attention and systems similar to that described above for the detection of acetylcholine [58], endotoxin [59], miRNA-145 [60], glutathione [61], nitroaromatic explosives [62,63,64,65], borate [66], and glucose [67] were recently described.…”

Parallel Clamps and Polypurine Hairpins (PPRH) for Gene Silencing and Triplex‐Affinity Capture: Design, Synthesis, and Use

“…They also represent a tool to validate genes in proliferation and cancer (Villalobos et al., ), and can be used to target genes related to resistance (de Almagro, Coma, Noé, & Ciudad, ), as chemosensitizers (de Almagro, Mencia, Noé, & Ciudad, ), and in immunotherapy (Bener et al., ; Medina Enríquez, Félix, Ciudad, & Noé, ). Several examples of PPRHs for the inhibition of gene expression have been described (Ciudad et al., ; Félix, Ciudad, & Noé, ; Rodriguez et al., ; Rodríguez et al., ; Solé et al., ), as well as for the capture of miRNA (Ribes et al., ) and double‐stranded DNA for the analysis of DNA methylation status (Huertas et al., ).…”

“…PolyPurine Reverse Hoogsteen (PPRH) technology is often used for targeting single‐ and double‐stranded nucleic acid sequences (Villalobos et al., ). Several examples of PPRHs for the inhibition of gene expression (Ciudad, Rodríguez, Villalobos, Félix, & Noé, ; Coma, Noé, Eritja, & Ciudad, ; Solé, Delagoutte, Ciudad, Noé, & Alberti, ), as well as for capture of miRNA (Ribes et al., ) and double‐stranded DNA for the analysis of DNA methylation status (Huertas et al., ), have been previously described.…”

Simple Endotoxin Detection Using Polymyxin‐B‐Gated Nanoparticles

“…However, in the presence of the analyte, the pores open due to the interaction of the analyte with the capping ensemble leading to cargo release. [21][22][23][24][25][26] One of the advantages of these solids is the potential existence of amplification features as few analyte molecules may trigger gate opening, and induce the release of a high amount of entrapped dye molecules. Given our interest in exploring the potential use of gated nanomaterials in sensing protocols, we report herein a new nanodevice based on mesoporous silica nanoparticles (MSNs) functionalized with carboxylate moieties and capped with the cationic peptide polymyxin B for the selective and sensitive detection of endotoxin.…”