Large-Stokes-shift-based folded DNA probing systems targeting DNA and miRNA 21 with signal amplification

Updated review of advances in microRNAs and complex diseases: experimental results, databases, webservers and data fusion

MicroRNAs (miRNAs) are gene regulators involved in the pathogenesis of complex diseases such as cancers, and thus serve as potential diagnostic markers and therapeutic targets. The prerequisite for designing effective miRNA therapies is accurate discovery of miRNA-disease associations (MDAs), which has attracted substantial research interests during the last 15 years, as reflected by more than 55 000 related entries available on PubMed. Abundant experimental data gathered from the wealth of literature could effectively support the development of computational models for predicting novel associations. In 2017, Chen et al. published the first-ever comprehensive review on MDA prediction, presenting various relevant databases, 20 representative computational models, and suggestions for building more powerful ones. In the current review, as the continuation of the previous study, we revisit miRNA biogenesis, detection techniques and functions; summarize recent experimental findings related to common miRNA-associated diseases; introduce recent updates of miRNA-relevant databases and novel database releases since 2017, present mainstream webservers and new webserver releases since 2017 and finally elaborate on how fusion of diverse data sources has contributed to accurate MDA prediction.

A persistent luminescence resonance energy transfer-based molecular beacon probe for the highly sensitive detection of microRNA in biological samples

Herein, a time-resolved luminescence resonance energy transfer (TR-LRET) molecular beacon (MB) probe employing persistent luminescence nanoparticles (PLNPs) as the energy donors was first constructed, and further designed for microRNA21 (miR21) sensing. This probe (named as PLNPs-MB) was facilely fabricated by covalent bioconjugation between poly-(acrylic acid) (PAA) modified near-infrared (NIR) emissive PLNPs i.e. ZnGa₂O₄:Cr³⁺ and functionalized MB oligonucleotide (5'-NH₂ and 3'-BHQ3). Accordingly, PLNPs and BHQ3 were in close proximity to each other, leading to the occurrence of LRET and obvious persistent luminescence (PL) quenching. In the presence of miR21, loop of the PLNP-MB was hybridized, accompanying BHQ3 away from PLNPs and the restraint of LRET process. As a result, PL of the PLNPs was recovered, which built the foundation of miR21 quantification. The probe provided a linear response range from 0.1 to 10 nM for miR21 detection. Quantification limit of this probe was competitive and about 1-2 orders of magnitude lower than that of other reported MB probes for nucleic acid. Moreover, the proposed probe was successfully adopted for miR21 detection in biological fluids (human serum, cell extraction). This work also provided a sensitive detection nanoplatform for other targets through modifying diverse MBs onto the surface of PLNPs.

Rapid and highly sensitive hairpin structure-mediated colorimetric detection of miRNA

Herein, we report a novel hairpin structure-mediated diagnostic method for the simple and rapid colorimetric detection of miRNA through the sensing of pyrophosphate. When the hairpin structure of the template DNA (h-Probe) was hybridized with the primer, the DNA primer extension mediated by nPfu special enzyme was blocked. However, this h-Probe was extended using nPfu special enzyme, upon the structural change of the template DNA, from a hairpin to a linear structure, in the presence of the target miRNA. The miRNA-hybridized template DNA sequence was cleaved by a duplex-specific nuclease (DSN), which cleaved the DNA from the RNA-DNA hybrid, thereby allowing the target miRNA to be recycled. Primer extension using nPfu special enzyme produced pyrophosphate when nucleotide triphosphate was incorporated into the DNA; this pyrophosphate was sensed in terms of a color change, from pink to colorless, when using pp Probe, a probe developed previously by our group. This novel system for the colorimetric detection of target miRNA operated with high sensitivity (LOD = 132 aM) and selectivity, with the whole detection process requiring only 30 min. Furthermore, this system could also detect miRNA fluorimetrically with similar sensitivity (LOD = 105 aM), highlighting the dual-sensing properties of pp Probe. This unique, extremely simple, and rapid system for the detection of miRNA through a highly sensitive color change would presumably be useful in applications requiring point-of-care detection.

Highly fluorescent morpholine naphthalimide deoxyuridine nucleotide for the detection of miRNA 24-3P through rolling circle amplification

In this study we synthesized the nucleotide dUrkTP, a highly fluorescent naphthalimide deoxyuridine triphosphate that undergoes aggregation-induced emission (AIE). We incorporated and extended dUrkTP during the primer extension of DNA mediated by DNA polymerase, and also in the rolling circle amplification of DNA mediated by Phi29 polymerase. Accordingly, we could use this fluorescent nucleotide for the detection of microRNA 24-3P, a biomarker of porcine reproductive and respiratory syndrome virus. The direct labeling system obtained during rolling circle DNA amplification exhibited increased fluorescence, due to AIE of the dUrkTP residue upon gel formation, thereby allowing the detection of miRNA 24-3P. This direct labeling system facilitated the simple and inexpensive detection of miRNA 24-3P with high sensitivity (limit of detection: 3.58 fM) and selectivity.

rkDNA-graphene oxide as a simple probe for the rapid detection of miRNA21

In this study we developed a novel diagnostic tool for the detection of miRNA21, based on the fluorescent nucleotide morpholine naphthalimide deoxyuridine (dUrkTP). We incorporated dUrkTP into DNA through primer extension to obtain rkDNA displaying high fluorescence. We then used lambda exonuclease, a specific nuclease for 3́-monophosphate-containing DNA, to separate rkDNA from its complementary sequence. The fluorescence of the free rkDNA was quenched dramatically upon interacting with graphene oxide (GO). Our rkDNA-GO fluorescence probing system exhibited high sensitivity and selectivity for the detection of miRNA21. This inexpensive probing system, employing simple primer extension and exonuclease degradation, required only 30 min to detect its target miRNA. This strategy appears suitable for the detection of diverse types of miRNA.

Propargylamine-selective dual fluorescence turn-on method for post-synthetic labeling of DNA

We have developed a propargylamine-selective dual fluorescence turn-on system, using ylidenemalononitrile enamines, for post-synthetic DNA labeling, allowing the direct monitoring of DNA using dual emission in living cells.

Research advances in the detection of miRNA

MicroRNAs (miRNAs) are a family of endogenous, small (approximately 22 nucleotides in length), noncoding, functional RNAs. With the development of molecular biology, the research of miRNA biological function has attracted significant interest, as abnormal miRNA expression is identified to contribute to serious human diseases such as cancers. Traditional methods for miRNA detection do not meet current demands. In particular, nanomaterial-based methods, nucleic acid amplification-based methods such as rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP), strand-displacement amplification (SDA) and some enzyme-free amplifications have been employed widely for the highly sensitive detection of miRNA. MiRNA functional research and clinical diagnostics have been accelerated by these new techniques. Herein, we summarize and discuss the recent progress in the development of miRNA detection methods and new applications. This review will provide guidelines for the development of follow-up miRNA detection methods with high sensitivity and specificity, and applicability to disease diagnosis and therapy.