MicroRNA Detection Using a Double Molecular Beacon Approach: Distinguishing Between miRNA and Pre-miRNA

Biophysical characterization of microRNA mixtures based on Molecular Beacons

Diverse studies have shown a relationship between dysregulated microRNAs (miRNAs), including miRNA-29b and miRNA-9, and several diseases. So, it is hypothesized that miRNAs can be studied as potential agents to be exploited in biomedical applications, due to their ability to take part in gene expression regulation at a post-transcriptional level. Considering the possibility of using miRNAs, it is important to characterize and validate this bioproduct, structurally and functionally. The goal of this work is to optimize an assay that can detect and biophysically characterize a miRNA sample without interference from the respective precursor form, by using molecular beacons (MB). MBs are hairpin-shaped probes composed of nucleic acid labeled with a quencher at the 3' end and a fluorophore (reporter) at the 5' end. Here, MB loops were designed so MB-9-1 and MB-29-1 would be complementary to the miRNA-9-1-5p and the miRNA-29b-1-3p, respectively. The MBs designed in this work specifically identified each target miRNA, even in artificial mixtures or complex samples, and the obtained fluorescence was directly proportional to miRNA concentration. Even if the precursor forms (pre-miRNAs) were present in the samples, no significant signal was shown, allowing the distinction between both forms. The outcomes of this work confirm the MBs potential to assess and characterize miRNA samples to be exploited in biochemical, biophysical, or biomedical fields.

Confined DNA tetrahedral molecular sieve for size-selective electrochemiluminescence sensing

Size selectivity is crucial in highly accurate preparation of biosensors. Herein, we described an innovative electrochemiluminescence (ECL) sensing platform based on the confined DNA tetrahedral molecular sieve (DTMS) for size-selective recognition of nucleic acids and small biological molecule. Firstly, DNA template (T) was encapsulated into the inner cavity of DNA tetrahedral scaffold (DTS) and hybridized with quencher (Fc) labeled probe DNA to prepare DTMS, accordingly inducing Ru(bpy)32+ and Fc closely proximate, resulting the sensor in a "signal-off" state. Afterwards, target molecules entered the cavity of DTMS to realize the size-selective molecular recognition while prohibiting large molecules outside of the DTMS, resulting the sensor in a "signal-on" state due to the release of Fc. The rigid framework structure of DTS and the anchor of DNA probe inside the DTS effectively avoided the nuclease degradation of DNA probe, and nonspecific protein adsorption, making the sensor possess potential application prospect for size-selective molecular recognition in diagnostic analysis with high accuracy and specificity.

Integration of Isothermal Enzyme-Free Nucleic Acid Circuits for High-Performance Biosensing Applications

The isothermal enzyme-free nucleic acid amplification method plays an indispensable role in biosensing by virtue of its simple, robust, and highly efficient properties without the assistance of temperature cycling or/and enzymatic biocatalysis. Up to now, enzyme-free nucleic acid amplification has been extensively utilized for biological assays and has achieved the highly sensitive detection of various biological targets, including DNAs, RNAs, small molecules, proteins, and even cells. In this Review, the mechanisms of entropy-driven reaction, hybridization chain reaction, catalytic hairpin assembly and DNAzyme are concisely described and their recent application as biosensors is comprehensively summarized. Furthermore, the current problems and the developments of these DNA circuits are also discussed.

Visual and Electrochemical Detection of let-7a: A Tumor Suppressor and Biomarker

Let-7a, a type of low-expressed microRNAs in cancer cells, has been investigated as a promising biomarker and therapeutic target for tumor suppression. Developing simple and sensitive detection methods for let-7a is important for cancer diagnosis and treatment. In this work, the hybridization chain reaction (HCR) was initiated by let-7a via two hairpin primers (H1 and H2). After the HCR, the remaining hairpin H1 was further detected by lateral flow assay (LFA) and electrochemical impedance spectroscopy. For LFA, biotin-modified H1(bio-H1) and free H2 were used for HCR. With the decrease of let-7a concentration, the color of T line gradually increased. As for electrochemical methods, the H1'-AuNP-modified electrode was used for detection of bio-H1 based on the difference of impedance (ΔR_ct) detected without and with different concentrations of let-7a participating in the HCR. This method could detect let-7a in the range of 10.0 fM and 1.0 nM with detection limits of 4.2 fM.

Rapid and ultrasensitive miRNA detection by combining endonuclease reactions in a rolling circle amplification (RCA)-based hairpin DNA fluorescent assay

MicroRNA (miRNA) sensing strategies employing rolling circle amplification (RCA) coupled with the hairpin DNA (HD) probe-mediated FRET assay have shown promise, but achieving rapid, sensitive, and specific detection of target miRNA remains a challenge in clinical diagnostics. Herein, we incorporate PstI endonuclease cleavage (PEC) into a conventional RCA-based HD probe FRET assay to develop an effective and feasible method. Long single-stranded RCA products are synthesized from miRNA-21 loaded on a circular dumbbell DNA, and the resultant RCA products self-assemble to generate long HD structures with double-stranded stem regions that are specifically recognized and cleaved by PstI endonucleases when incubated with PstI enzymes. This releases large amounts of short single-stranded DNA fragments that hybridize and open to the complementary loop-stem regions of HD probes labeled with FAM at one end and BHQ-1 at the other, resulting in a reduction in FRET efficiency. This assay achieves a 39.7 aM detection limit for target miRNA-21, approximately 37-fold higher than that of the conventional assay (1.5 fM). Moreover, quantitative detection is possible in a wide range from 1 aM to 1 pM within 90 min with high sequence specificity. We demonstrate the assay with the detection of target miRNA-21 in total RNA extracted from MCF-7 cancer cells.

Discrimination between Cancer Cells and DNA-Damaged Cells: Pre-miRNA Region Recognition Based on Hyperbranched Hybrid Chain Reaction Amplification for Simultaneous Sensitive Detection and Imaging of miRNA and Pre-miRNA

Herein, a novel region recognition of precursor microRNA (Pre-miRNA) based on hyperbranched hybrid chain reaction (HB-HCR) amplification was constructed to effectively eliminate the interference of Pre-miRNA to the mature microRNA (miRNA) by establishing the linear mapping relation between the two fluorescence signals produced by the miRNA sequence in the Pre-miRNA and Pre-miRNA residues to first realize simultaneous sensitive detection of Pre-miRNA and miRNA as well as highly sensitive imaging of intracellular Pre-miRNA and miRNA, which solves one main challenge of in vitro tumor disease diagnostics: inaccurate detection of tumor-induced miRNA changes. Impressively, this strategy easily distinguishes cancer cells from normal cells and DNA-damaged cells by the difference in miRNA and Pre-miRNA expression, which provides an innovative approach for accurate clinical diagnosis of cancer and precise treatment of prognosis.

Size-Discriminative DNA Nanocage Framework Enables Sensitive and High-Fidelity Imaging of Mature MicroRNA in Living Cells

Mature microRNAs (miRNAs) are closely associated with cell proliferation and differentiation, stress response, and carcinogenesis, and monitoring intracellular miRNAs can contribute to the studies of their regulatory roles and molecular mechanisms of disease progression. However, accurate and reliable detection of mature miRNAs in complex physiological environments encounters the challenge of undesired detection accuracy ascribed to the coexistence of their precursor microRNAs (pre-miRNAs) and degradation of sensing probes. Here, we demonstrate the synthesis of a new size-discriminative DNA nanocage framework (DNF) for the sensitive monitoring of mature miRNA-21 in living cells with high accuracy via cascaded toehold-mediated strand displacement reaction (TSDR) amplifications. The DNF is prepared by a simple self-assembly of six ssDNAs, and the signal probes are docked inside the DNF. Because of its rigid framework structure, the DNF shows enhanced enzyme stability. Upon entering cells, only the short target mature miRNA-21 sequences instead of the large-sized pre-miRNAs are allowed to be accommodated inside the cavity of the DNF owing to the size-discriminative capability of the DNF. The cascaded TSDR amplifications can thus be activated by the mature miRNA-21 together with endogenous ATP to result in magnified fluorescence for sensitive detection and selective discrimination of miRNA-21 from the interference pre-miRNAs. Our results indicate that the DNF probes can offer robust sensing means for detecting various intracellular mature miRNAs with high accuracy for disease diagnoses and biomedical studies.

DNase I-assisted 2'-O-methyl molecular beacon for amplified detection of tumor exosomal microRNA-21

An end-modified 2'-O-methyl molecular beacon (eMB) with unique nuclease resistance was designed and prepared. The eMB can resist the enzymatic digestion by DNase I, which would otherwise occur upon the hybridization of the eMB with a complementary sequence. As a result, the coupling use of eMBs and DNase I allows highly sensitive detection of miRNA with a limit of detection (LOD) of 2.5 pM. The analytical strategy was further used for detection of tumor exosomal microRNA-21, and down to 0.86 μg mL^-1 A375 exosomes were detected. Overall, the present method can effectively quantify tumor-derived exosomes for cancer diagnosis.

Electrophoretic mobility shift as a molecular beacon-based readout for miRNA detection

MicroRNAs are short, non-coding RNA sequences involved in gene expression regulation. Quantification of miRNAs in biological fluids involves time consuming and laborious methods such as Northern blotting or PCR-based techniques. Molecular beacons (MB) are an attractive means for rapid detection of miRNAs, although the need for sophisticated readout methods limits their use in research and clinical settings. Here, we introduce a novel method based on delayed electrophoretic mobility, as a quantitative means for detection of miRNAs-MB hybridization. Upon hybridization with the target miRNAs, MB form a fluorescent duplex with reduced electrophoretic mobility, thus bypassing the need for additional staining. In addition to emission of light, the location of the fluorescent band on the gel acts as an orthogonal validation of the target identity, further confirming the specificity of binding. The limit of detection of this approach is approximately 100 pM, depending on the MB sequence. The method is sensitive enough to detect specific red blood cell miRNAs molecules in total RNA, with single nucleotide specificity. Altogether, we describe a rapid and affordable method that offers sensitive detection of single-stranded small DNA and RNA sequences.

A malachite green light-up aptasensor for the detection of theophylline

Biosensors are of interest for the quantitative detection of small molecules (metabolites, drugs and contaminants for instance). To this end, fluorescence is a widely used technique that is easily associated to aptamers. Light-up aptamers constitute a particular class of oligonucleotides that, specifically induce fluorescence emission when binding to cognate fluorogenic ligands such as malachite green (MG). We engineered a dual aptasensor for theophylline (Th) based on the combination of switching hairpin aptamers specific for MG on the one hand and for Th on the other hand, hence their names: malaswitch (Msw) and theoswitch (Thsw). The two aptaswitches form a loop-loop or kissing Msw-Thsw complex only in the presence of theophylline, allowing binding of MG, subsequently generating a fluorescent signal. The combination of the best Msw and Thsw variants, MswG12 and Thsw19.1, results in a 20-fold fluorescence enhancement of MG at saturating theophylline concentration. This aptasensor discriminates between theophylline and its analogues caffeine and theobromine. Kissing aptaswitches derived from light-up aptamers constitute a novel sensing device.

Size-selective DNA nanocage-based activatable CRISPR-Cas12a for sensitive and accurate detection of mature microRNA

The sensitive and accurate detection of mature miRNA without the signal interference by pre-miRNAs is highly important. Herein, a size-selective DNA nanocage-based activatable CRISPR/Cas12a system was developed to achieve this goal.

Size-selective molecular recognition based on a confined DNA molecular sieve using cavity-tunable framework nucleic acids

Size selectivity is an important mechanism for molecular recognition based on the size difference between targets and non-targets. However, rational design of an artificial size-selective molecular recognition system for biological targets in living cells remains challenging. Herein, we construct a DNA molecular sieve for size-selective molecular recognition to improve the biosensing selectivity in living cells. The system consists of functional nucleic acid probes (e.g., DNAzymes, aptamers and molecular beacons) encapsulated into the inner cavity of framework nucleic acid. Thus, small target molecules are able to enter the cavity for efficient molecular recognition, while large molecules are prohibited. The system not only effectively protect probes from nuclease degradation and nonspecific proteins binding, but also successfully realize size-selective discrimination between mature microRNA and precursor microRNA in living cells. Therefore, the DNA molecular sieve provides a simple, general, efficient and controllable approach for size-selective molecular recognition in biomedical studies and clinical diagnoses.

Size-selective discrimination is an issue in biosensing. Here, the authors report on a size selective DNA nanocage which excludes agents based on size and protects the probes against degradation, and demonstrate the discrimination between mature and precursor miRNA.

A Modified Magnified Analysis of Proteome (MAP) Method for Super-Resolution Cell Imaging that Retains Fluorescence

Biological systems consist of a variety of distinct cell types that form functional networks. Super-resolution imaging of individual cells is required for better understanding of these complex systems. Direct visualization of 3D subcellular and nano-scale structures in cells is helpful for the interpretation of biological interactions and system-level responses. Here we introduce a modified magnified analysis of proteome (MAP) method for cell super-resolution imaging (Cell-MAP) which preserves cell fluorescence. Cell-MAP expands cells more than four-fold while preserving their overall architecture and three-dimensional proteome organization after hydrogel embedding. In addition, Optimized-Cell-MAP completely preserves fluorescence and successfully allows for the observation of tagged small molecular probes containing peptides and microRNAs. Optimized-Cell-MAP further successfully applies to the study of structural characteristics and the identification of small molecules and organelles in mammalian cells. These results may give rise to many other applications related to the structural and molecular analysis of smaller assembled biological systems.

A sensitive and specific method for microRNA detection and in situ imaging based on a CRISPR–Cas9 modified catalytic hairpin assembly

We report here a method for the molecular detection of miRNAs in exosomes and imaging in living cells based on CRISPR–Cas9 and catalytic hairpin assembly.

A versatile luminescent resonance energy transfer (LRET)-based ratiometric upconversion nanoprobe for intracellular miRNA biosensing

A versatile LRET-based ratiometric (LBRU) nanoprobe of NaYF₄:Yb,Er@NaYF₄@NH₂–mSiO₂/rhodamine B/C-DNA sandwich-structured nanocomposites has been developed for intracellular miRNA biosensing.

Portable and Field-Ready Detection of Circulating MicroRNAs with Paper-Based Bioluminescent Sensing and Isothermal Amplification

We present a paper-based system that integrates bioluminescence resonance energy transfer (BRET) and isothermal amplification for the analysis of tumor-associated circulating microRNAs (miRNAs) in clinical serum samples. The analysis procedure could be easily accomplished with two pieces of functionalized paper and a low-cost smartphone-based device, which enables sequence-specific quantification of femtomolar miRNAs, without the need for tedious handling of aqueous reactions and operation of sophisticated equipment. Furthermore, the analytical performance of the proposed paper-based system was highly stable at room temperature, demonstrating its capability for cold-chain-free and remote deployment. These qualities highlight the practical utility of our method for the portable and field-ready miRNA diagnostic tests in resource-limited settings.

Recent advances on nanomaterials-based fluorimetric approaches for microRNAs detection

MicroRNAs are types of small single-stranded endogenous highly conserved non-coding RNAs, which play main regulatory functions in a wide range of cellular and physiological events, such as proliferation, differentiation, neoplastic transformation, and cell regeneration. Recent findings have proved a close association between microRNAs expression and the development of many diseases, indicating the importance of microRNAs as clinical biomarkers and targets for drug discovery. However, due to a number of prominent characteristics like small size, high sequence similarity and low abundance, sensitive and selective identification of microRNAs has rather been a hardship through routine traditional assays, including quantitative polymerase chain reaction, microarrays, and northern blotting analysis. More recently, the soaring progression in nanotechnology and fluorimetric methodologies in combination with nanomaterials have promised microRNAs detection with high sensitivity, efficiency and selectivity, excellent reproducibility and lower cost. Therefore, this review will represent an overview of latest advances in microRNAs detection through nanomaterials-based fluorescent methods, like gold nanoparticles, silver and copper nanoclusters, graphene oxide, and magnetic silicon nanoparticles.

Sensitively distinguishing intracellular precursor and mature microRNA abundance

Mature microRNAs (miRNAs) produced from precursor microRNAs (pre-miRNAs) by the RNase Dicer have showed significant potential for cancer diagnosis and prognosis due to their key regulatory roles in various pathological processes. However, discriminatory detection of low-abundance miRNAs and pre-miRNAs remains a key challenge since the mature sequence is also present in the pre-miRNA forms. Herein, we report a novel cascade reaction to sensitively distinguish miRNAs versus pre-miRNAs in living cells based on two pairs of programmable hairpin oligonucleotide probes with a simple sequence design. The programmable hairpin probes can metastably coexist until the introduction of miRNAs or pre-miRNAs, which can trigger a specific hybridization chain reaction (HCR), respectively, leading to the self-assembly of nicked DNA duplex structures and a remarkable specific fluorescence intensity increase. The system can readily and sensitively assess the miRNA or pre-miRNA abundance in a homogeneous solution. The intracellular miRNA and pre-miRNA expression level assessment in different living cells is realized. Thus, we provide a novel investigation tool for discriminatorily and accurately assessing miRNA and pre-miRNA abundance, which could be useful for the biomedical application of miRNAs.

Accurate detection of intracellular microRNAs using functional Mo2C quantum dots nanoprobe

A functionalized Mo₂C quantum dots nanoprobe was developed for accurate detection of intracellular mature microRNAs.

A sensitive RNA chaperone assay using induced RNA annealing by duplex specific nuclease for amplification

The hybridization of two complementary RNAs in single cells depends on their complementary sequences and secondary structures, and is usual inefficient at the low concentrations. The bacterial RNA chaperone Hfq increases the rate of base pairing hybridization of mRNA, and stabilizes sRNA-mRNA duplexes. However, The RNA chaperone Hfq accelerates the RNA annealing between two complementary pair RNAs with a still unknown mechanism. So the sensitivity assay of Hfq induced RNA annealing is very important. By using a 2-OMe-RNA modified molecular beacon as a reporter, which can be specificity cleavage by DSN, we observed the amplification reaction kinetics (κ_rea) is 0.16 s^-1. Our results showed that the Hfq hexamer directly induced the RNA annealing, and DSN aided the ultra-sensitivity assay reaction with 0.18 fM Hfq/RNA1/MB1.

Catalytic hairpin assembly gel assay for multiple and sensitive microRNA detection

As important modulators of gene expression, microRNAs (miRNAs) have been identified as promising biomarkers with powerful predictive value in diagnosis and prognosis for several diseases, especially for cancers. Here we report a facile, multiple and sensitive miRNA detection method that uses conventional gel electrophoresis and catalytic hairpin assembly (CHA) system without any complex nanomaterials or enzymatic amplification. Methods: In this study, three pairs of hairpin probes are rationally designed with thermodynamically and kinetically preferable feasibility for the CHA process. In the present of target miRNA, the stem of the corresponding hairpin detection probe (HDP) will be unfolded and expose the concealed domain. The corresponding hairpin assistant probe (HAP) then replaces the hybridized target miRNA to form specific HDP/HAP complexes and releases miRNA based on thermodynamically driven entropy gain process, and the released miRNA triggers the next recycle to produce tremendous corresponding HDP/HAP complexes. Results: The results showed that the CHA gel assay can detect miRNA at fM levels and shows good capability of discriminating miRNA family members and base-mismatched miRNAs. It is able to analyze miRNAs extracted from cell lysates, which are consistent with the results of conventional polymerase chain reaction (PCR) method. Depending on the length of the designed hairpin probes, the CHA gel assay consisting of different hairpin probes effectively discriminated and simultaneously detected multiple miRNAs in homogenous solution and miRNAs extracted from cell lysates. Conclusion: The work highlights the practical use of a conventional gel electrophoresis for sensitive interesting nucleic acid sequences detection.

Multiplexed detection of nucleic acids using 19F NMR chemical shift changes based on DNA photo-cross-linking of 3-vinylcarbazole derivatives

The detection methodology for nucleic acids is a useful tool for the analysis of biological systems and diagnosis of diseases. We demonstrated the feasibility of the detection of any nucleic acids based on large chemical shifts via ultrafast DNA photo-cross-linking and the effects of substitution by 3-vinylcarbazole derivatives. These chemical shifts enable the sequence-specific detection of any strand using hybridization chain reaction.

HMG-box transcription factor 1: a positive regulator of the G1/S transition through the Cyclin-CDK-CDKI molecular network in nasopharyngeal carcinoma

HMG-box transcription factor 1 (HBP1) has been reported to be a tumor suppressor in diverse malignant carcinomas. However, our findings provide a conclusion that HBP1 plays a novel role in facilitating nasopharyngeal carcinoma (NPC) growth. The Kaplan-Meier analysis indicates that high expression HBP1 and low miR-29c expression both are negatively correlated with the overall survival rates of NPC patients. HBP1 knockdown inhibits cellular proliferation and growth, and arrested cells in G1 phase rather than affected cell apoptosis via flow cytometry (FCM) analysis. Mechanistically, HBP1 induces the expression of CCND1 and CCND3 levels by binding to their promoters, and binds to CDK4, CDK6 and p16^INK4A promoters while not affects their expression levels. CCND1 and CCND3 promote CCND1-CDK4, CCND3-CDK6, and CDK2-CCNE1 complex formation, thus, E2F-1 and DP-1 are activated to accelerate the G1/S transition in the cell cycle. MiR-29c is down-regulated and correlated with NPC tumorigenesis and progression. Luciferase assays confirms that miR-29c binds to the 3' untranslated region (3'-UTR) of HBP1. Introduction of pre-miR-29c decreased HBP1 mRNA and protein levels. Therefore, the high endogenous HBP1 expression might be attributed to the low levels of endogenous miR-29c in NPC. In addition, HBP1 knockdown and miR-29c agomir administration both decrease xenograft growth in nude mice in vivo. It is firstly reported that HBP1 knockdown inhibited the proliferation and metastasis of NPC, which indicates that HBP1 functions as a non-tumor suppressor gene in NPC. This study provides a novel potential target for the prevention of and therapies for NPC.

Decrease in Lymphoid Specific Helicase and 5-hydroxymethylcytosine Is Associated with Metastasis and Genome Instability

DNA methylation is an important epigenetic modification as a hallmark in cancer. Conversion of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) by ten-eleven translocation (TET) family enzymes plays an important biological role in embryonic stem cells, development, aging and disease. Lymphoid specific helicase (LSH), a chromatin remodeling factor, is regarded as a reader of 5-hmC. Recent reports show that the level of 5-hmC is altered in various types of cancers. However, the change in 5-hmC levels in cancer and associated metastasis is not well defined. We report that the level of 5-hmC was decreased in metastatic tissues of nasopharyngeal carcinoma, breast cancer, and colon cancer relative to that in non-metastasis tumor tissues. Furthermore, our data show that TET2, but not TET3, interacted with LSH, whereas LSH increased TET2 expression through silencing miR-26b-5p and miR-29c-5p. Finally, LSH promoted genome stability by silencing satellite expression by affecting 5-hmC levels in pericentromeric satellite repeats, and LSH was resistant to cisplatin-induced DNA damage. Our data indicate that 5-hmC might serve as a metastasis marker for cancer and that the decreased expression of LSH is likely one of the mechanisms of genome instability underlying 5-hmC loss in cancer.