Reprogrammable multiplexed detection of circulating oncomiRs using hybridization chain reaction

Abstract

In this study, we have coupled the DNA polymerization capability of hybridization chain reaction (HCR) with the plasmonic properties of gold nanoparticles to develop a reprogrammable and multiplexed detection of three circulating oncomiRs (miR-10b, miR-21 and miR-141) dysregulated in various disease states of breast cancer. We have demonstrated that by simply changing the initiator (label-free short single stranded DNA) content of the HCR, while keeping everything else unchanged, the same nanoparticle assembly can be reprogrammed for the detection of the target oncomiRs individually or simultaneously in all possible combinations. We have shown that as little as 20 femtomoles of each oncomiR can be detected visually without using any analytical instrument. Furthermore, we demonstrated that the target oncomiR can be detected in an RNA pool isolated from a liquid biopsy mimic of breast cancer.

Plasmonic molecular assays: Recent advances and applications for mobile health

“…Use of plasmonic nanoparticles as colorimetric reporters is a common strategy to enable sensitive and rapid readout with a simple instrument, or even with the naked eye. Au NP reporters have been used in many isothermal amplification methods including CEA [124][125][126], LAMP [127][128][129], RCA [130], HCR [131,132], CHA [133], and other DNA machinery [134,135]. Nano Res.…”

Low picomolar, instrument-free visual detection of mercury and silver ions using low-cost programmable nanoprobes

“…47 While AuNPs with low and/or short DNA coating density can aggregate under this high salt condition, DNA polymers anchored on the surface of the nanoparticles can protect the nanoparticles from aggregation by shielding this charge effect. To demonstrate the working principle of the assay the studies were performed separately for both metal ions (Fig.…”

“…The ∼13 nm sized AuNPs were functionalized with thiolated capture DNA probes (Cp Hg–Ag ) as described previously. 38,47 The resulting AuNP–Cp Hg–Ag was purified using centrifugation and re-suspended in an equal volume of nuclease-free water. The nanoparticles were characterized using a Cary 60 UV-Vis Spectrophotometer (Agilent Technologies Inc., USA).…”

“…1a, step 1). 42,46,47 However, in the presence of a specific short single stranded (ss) DNA (initiator = I) molecule the hairpins are activated and self-assemble to form a long double stranded (ds) DNA polymer. Briefly, the HCR process is as follows: the initiator (I) binds and opens the first hairpin (H1, Fig.…”

Label‐Free in Situ Monitoring of the DNA Hybridization Chain Reaction by Using Sequence‐Selective Minor‐Groove‐Binding Fluorophores

“…To overcome this problem, some label‐free methods of HCR detection, based on the use of fluorogenic DNA intercalators such as SYBR Green, Au nanoparticles, Ag nanoclusters, hemin/G‐quadruplex DNAzyme, or G‐quadruplex selective fluorescent probes, have been developed. These methods enable the detection of target DNA or RNA through fluorescence, chemiluminescence, or colorimetric changes by use of simple unmodified hairpin oligodeoxyribonucleotides (ODNs).…”