Quantitative Analysis of MicroRNA in Blood Serum with Protein-Facilitated Affinity Capillary Electrophoresis

3D walkable DNA gears for ultrasensitive detection of multiple microRNAs in lung cancer cell lysates

As a tumor biomarker with therapeutic application potential, microRNA (miRNA) was crucial for the accurate and sensitive detection of early-stage tumors. Herein, a unique three dimensional (3D) DNA nanomachine (DNM) was created, which was capable detecting lung cancer-related biomarkers miRNA-21, miRNA-205 and miRNA-125b in lung cancer cell lysates with extreme sensitivity. The 3D DNM was composed of DNA scissors and three flexible walkable DNA gears modified with various species of silver nanoclusters (AgNCs). Based on the flexibility of DNA scissors and the walkability of DNA gears, neighboring DNA gears closed the distance between different species of AgNCs by walking in the presence of targets, generating fluorescence resonance energy transfer (FRET) effect and emitting different kinds of fluorescence to complete the highly sensitive detection of single targets and multiple targets. The findings demonstrated that a linear model provided an excellent match for the association between fluorescence signal and target miRNAs. For miRNA-21, miRNA-205, and miRNA-125b, the limits of detection (LODs) (signal/noise = 3) were 4.2 pmol/L (pM), 6.3 pM, and 10.2 pM, respectively. Their recoveries in A549 cell lysate samples ranged from 95.3 to 108.8 % with relative standard deviations of 1.26 %-4.88 %. Satisfactorily, the 3D DNM displayed exceptional analytical performance with high sensitivity and stability, strong specificity and reproducibility, which was triumphantly employed to identify miRNAs in tumor cell lysates, providing a workable technique in creating adaptable nanostructure for dependable bioanalysis and clinical diagnosis of cancer biomarkers.

An unnatural enzyme with endonuclease activity towards small non-coding RNAs

Endonucleases are enzymes that cleave internal phosphodiester bonds within double-stranded DNA or RNA and are essential for biological functions. Herein, we use genetic code expansion to create an unnatural endonuclease that cleaves non-coding RNAs including short interfering RNA (siRNA) and microRNAs (miRNAs), a function that does not exist in nature. We introduce a metal-chelating unnatural amino acid, (2,2'-bipyridin-5-yl)alanine (BpyAla) to impart endonuclease activity to the viral suppressor of RNA silencing protein p19. Upon binding of copper, the mutant p19-T111BpyAla displays catalytic site-specific cleavage of siRNA and human miRNAs. Catalysis is confirmed using fluorescence polarization and fluorescence turn-on. Global miRNA profiling reveals that the engineered enzyme cleaves miRNAs in a human cell line. The therapeutic potential is demonstrated by targeting miR-122, a critical host factor for the hepatitis C virus (HCV). Unnatural endonuclease function is shown to deplete miR-122 levels with similar effects to an antagomir that reduces HCV levels therapeutically.

A rapid and simple method for simultaneous determination of three breast cancer related microRNAs based on magnetic nanoparticles modified with S9.6 antibody

Cancer progression is typically associated with the simultaneous changes of multiple microRNA (miR) levels. Therefore, simultaneous determination of multiple miR biomarkers exhibits great promise in early diagnosis of cancers. This research seeks to discuss a simple biosensing method for the ultrasensitive and specific detection of the three miRs related to the breast cancer based on S9.6 antibody coated magnetic beads, titanium phosphate nanospheres, and screen-printed carbon electrode. To prepare signaling probes, three hairpin DNAs (hDNAs) were labeled with three encoding titanium phosphate nanospheres with large quantities of different heavy metal ions (zinc, cadmium, lead), which have been utilized to discriminate the signals of three microRNA targets in relation with the corresponding heavy metal ions. After that, these hairpin structures hybridize with miR-21, miR-155 and miR-10b to form miR-21/hDNA1, miR-155/hDNA2 and miR-10b/hDNA3 complexes, which were captured by S9.6 antibodies (one anti-DNA/RNA antibody) pre-modified on magnetic bead surface. Therefore, the specific preconcentration of targets from complex matrixes can be carried out using magnetic actuation, increasing the sensitivity and specificity of the detection. The biosensor was suitably applied for direct and rapid detection of multiple microRNAs in real sample. It was observed that there were no significant differences between the results obtained by the suggested method and qRT-PCR as a reference method. So, this method makes an ultrasensitive novel platform for miRNAs expression profiling in clinical diagnosis and biomedical research.

On-chip miRNA extraction platforms: recent technological advances and implications for next generation point-of-care nucleic acid tests

Circulating microRNAs (or miRNAs) in bodily fluids, are increasingly being highlighted as promising diagnostic and predictive biomarkers for a broad range of pathologies. Although nucleic acid sensors have been developed that can detect minute concentrations of biomarkers with high sensitivity and sequence specificity, their robustness is often compromised by sample collection and processing prior to analysis. Such steps either (i) involve complex, multi-step procedures and toxic chemicals unsuitable for incorporation into portable devices or (ii) are inefficient and non-standardised therefore affecting the reliability/reproducibility of the test. The development of point-of-care nucleic acid tests based on the detection of miRNAs is therefore highly dependent on the development of an automated, on-chip, sample processing platform that would enable extraction or pre-purification of the biological specimen prior to reaching the sensing platform. In this review we categorise and critically discuss the most promising technologies that have been developed to facilitate the transition of nucleic acid tests based on miRNA detection from bench to bedside.

A rapid and reliable CE-LIF method for the quantitative analysis of miRNA-497 in plasma and organs and its application to a pharmacokinetic and biodistribution study

MicroRNAs (miRNAs) are involved in the pathogenesis of many human diseases, and various miRNAs have been reported and developed as therapeutic candidates for treating various diseases. Various miRNA and carrier modification systems have been investigated for effective systemic miRNA delivery to cells, organs, and tissues of interest. Consequently, effective and reliable analytical methods of miRNAs are required for evaluating the pharmacokinetics and biodistribution of miRNAs as therapeutic candidates. The capillary electrophoresis with laser-induced fluorescence (CE-LIF) method has been recently reported as a promising and relatively rapidly developing tool with the potential to provide highly sensitive and specific analysis of biological molecules including miRNAs. Here, the CE-LIF method was used for application in the pharmacokinetic and distribution studies of miRNA-497 as a model miRNA for a lung target; miRNA-497 hybridized with 6-FAM-labeled DNA probes were separated using CE-LIF and detected within 6 min without any interference. This method showed a wide calibration range of 1.0-50 nM and 0.1-50 nM for plasma and the four organs, liver, spleen, lung, and kidney, respectively, with acceptable precision and accuracy. Using CE-LIF, the miRNA-497 level was evaluated in rat plasma and organs after intravenously administering 1 mg ml-1 of a miRNA-497 mimic. Hence, miRNA-497 displayed a relatively short half-life of 1.76 h and was delivered to the lungs but mainly accumulated in the liver and spleen. This study evaluated the pharmacokinetics and biodistribution of the miRNA-497 mimic using CE-LIF for the first time and suggested the need for further studies to extend the half-life and conduct lung-targeted delivery of miRNA-497.

MicroRNAs in ovarian cancer and recent advances in the development of microRNA-based biosensors

Ovarian cancer is the most aggressive of all gynaecological malignancies and is the leading cause of cancer-associated mortality worldwide.

Electrochemical nano-genosensor for highly sensitive detection of miR-21 biomarker based on SWCNT-grafted dendritic Au nanostructure for early detection of prostate cancer

MicroRNAs (miRNAs) appear as a novel reliable candidate in biomarkers for early diagnosis of cancer. Due to their roles in various types of cancer, their potential as a diagnostic biomarker is getting more attention. Here, a novel electrochemical biosensor for detection of miR-21 was demonstrated, through combining the advantages of electrochemical methods and nanomaterials with the selectivity of oligonucleotides, based on thiolated receptor probe-functionalized dendritic gold nanostructures (den-Au) via the self-assembly monolayer (SAM) process which grafted on the single-wall carbon nanotubes (SWCNTs) platform on the surface of the fluorine-doped tin oxide (FTO) electrode. Cadmium ions (Cd²⁺) were used as signal units and also signal amplification substance which labeled before on miR-21 target. The oxidation signal of Cd²⁺ as a signal unit was measured by differential pulse voltammetry (DPV) technique that had a very wide linear relationship with the concentration of miR-21 target (0.01 fmol L^-1 to 1 μmol L^-1) and low experimental detection limit of 0.01 fmol L^-1. Furthermore, fabricated biosensor showed acceptable performance in human serum samples and also good selectivity indiscriminate between the complementary target and non-complementary one, so this nano-genosensor can clinically be used for prostate cancer diagnosis through the detection of miR-21 in human serum samples.

Site-Specific Cross-Linking of a p19 Viral Suppressor of RNA Silencing Protein and Its RNA Targets Using an Expanded Genetic Code

The p19 viral suppressor of RNA silencing protein has useful applications in biotechnology due to its high affinity for binding to small RNAs such as small interfering RNAs (siRNAs). Also, its applications for the study and modulation of microRNAs are actively expanding. Here we demonstrate the successful site-specific incorporation of a photoactivatable unnatural amino acid, p-azido-l-phenylalanine (AzF), for cross-linking to RNA substrates into the p19 sequence. Incorporation of AzF was performed at three positions in the protein near the RNA binding site: K67, R115, and T111. Incorporation of AzF at position T111 of p19 did not affect the binding affinity of p19 for siRNAs and also showed nanomolar affinity for human microRNA miR-122. The affinity was less favorable with AzF incorporation at two other positions, suggesting the sensitivity of placement of the unnatural amino acid. Exposure of the T111AzF in complex with either siRNA or miRNA to ultraviolet light resulted in cross-linking of the protein with the RNA, but no cross-linking could be detected with the wild-type protein. Our results demonstrate that p19-T111AzF can be used for detection of small RNAs, including human miR-122, with high sensitivity and to irreversibly sequester these RNAs through covalent photo-cross-linking.

Avenues Toward microRNA Detection In Vitro: A Review of Technical Advances and Challenges

Over the decades, the biological role of microRNAs (miRNAs) in the post-transcriptional regulation of gene expression has been discovered in many cancer types, thus initiating the tremendous expectation of their application as biomarkers in the diagnosis, prognosis, and treatment of cancer. Hence, the development of efficient miRNA detection methods in vitro is in high demand. Extensive efforts have been made based on the intrinsic properties of miRNAs, such as low expression levels, high sequence homology, and short length, to develop novel in vitro miRNA detection methods with high accuracy, low cost, practicality, and multiplexity at point-of-care settings. In this review, we mainly summarized the newly developed in vitro miRNA detection methods classified by three key elements, including biological recognition elements, additional micro-/nano-materials and signal transduction/readout elements, their current challenges and further applications are also discussed.

Structural insights into interactions between viral suppressor of RNA silencing protein p19 mutants and small RNAs

Viral suppressors of RNA silencing (VSRSs) are a diverse group of viral proteins that have evolved to disrupt eukaryotic RNA silencing pathways, thereby contributing to viral pathogenicity. The p19 protein is a VSRS that selectively binds to short interfering RNAs (siRNAs) over microRNAs (miRNAs). Mutational analysis has identified single amino acid substitutions that reverse this selectivity through new high-affinity interactions with human miR-122. Herein, we report crystal structures of complexed p19-T111S (2.6 Å), p19-T111H (2.3 Å) and wild-type p19 protein (2.2 Å) from the Carnation Italian ringspot virus with small interfering RNA (siRNA) ligands. Structural comparisons reveal that these mutations do not lead to major changes in p19 architecture, but instead promote subtle rearrangement of residues and solvent molecules along the p19 midline. These observations suggest p19 uses many small interactions to distinguish siRNAs from miRNAs and perturbing these interactions can create p19 variants with novel RNA-recognition properties. DATABASE: Model data are deposited in the PDB database under the accession numbers 6BJG, 6BJH and 6BJV.

Separation and determination of microRNAs by high-speed capillary sieving electrophoresis

In this work, high-speed capillary sieving electrophoresis with laser-induced fluorescence detection was applied to simultaneously determine three microRNAs. A developed manual sample introduction device for the high-speed capillary electrophoresis system was applied to perform sample injection. Strategies, including field-amplified sample injection and electrokinetic injection, were studied to improve the detection sensitivity. Under the optimal conditions, the limit of detection for DNA-159 could be lowered to 5.10 × 10^-12  mol/L. In order to achieve enough separation resolution, two DNA probes were designed to have extra sequences that acted as the drag tails. Under the optimized conditions, the three DNA probes and the complexes of microRNA-156, microRNA-159, and microRNA-166 could be completely separated within 3.2 min in background electrolyte (pH 8.7) containing 2.0% m/m polyvinyl pyrrolidone and 0.4% m/m hydroxyethyl cellulose. The limits of detection for the three microRNAs were 0.051, 0.11, and 0.25 nmol/L, respectively. Then the method was applied to analyze the microRNAs spiked in the samples extracted from banana leaves. The recoveries ranged from 114.3 to 121.1% (n = 3). The results showed that the method developed in this work was an effective means for microRNA assay.

Sandwich DNA Hybridization Fluorescence Resonance Energy-Transfer Strategy for miR-122 Detection by Core-Shell Upconversion Nanoparticles

An upconversion nanoparticle (UCNP)-based fluorescence resonance energy-transfer (FRET) strategy is normally restricted by the complicated preparations, low energy-transfer efficiency, and the challenge on improving specificity. Herein, simple DNA-functionalized UCNPs were designed as energy donors for constructing a FRET-based probe to detect the liver-specific microRNA 122 (miR-122). To improve FRET efficiency, UCNPs were constructed with confined core-shell structures, in which emitting ions were precisely located in the thin shell to make them close enough to external energy acceptors. Subsequently, capture DNA was simply functionalized on the outer surface of UCNPs based on ligand exchange that contributed to shortening the energy-transfer distance without extra modification. To gain high specificity, the donor-to-acceptor distance of FRET was controlled by a sandwich DNA hybridization structure using two shorter DNAs with designed complementary sequences (capture DNA and dye-labeled report DNA) to capture the longer target of miR-122. Therefore, the sensitive detection of miR-122 was achieved based on the decreased signals of UCNPs and the increased signals of the dye labeled on reported DNA. With good biocompatibility, this method has been further applied to cancer cell imaging and in vivo imaging, which opened up a new avenue to the sensitive detection and imaging of microRNA in biological systems.

Preparation of a Surface-functionalized Power-free PDMS Microchip for MicroRNA Detection Utilizing Electron Beam-induced Graft Polymerization

We propose an easy microchannel surface functionalization method for a poly(dimethylsiloxane) (PDMS) microchip that utilizes electron beam-induced graft polymerization (EIGP) as a platform for microchip-based biomarker analysis. Unlike other grafting techniques, EIGP enables rapid surface modification of PDMS without initiator immobilization. The grafted microchip is preservable, and can be easily functionalized for versatile applications. In this study, the surface-functionalized power-free microchip (SF-PF microchip) was used for the detection of microRNA (miRNA), which is a biomarker for many serious diseases. The EIGP enables high-density three-dimensional probe DNA immobilization, resulting in rapid and sensitive miRNA detection on the portable SF-PF microchip. The limit of detection was 0.8 pM, the required sample volume was 0.5 μL, and the analysis time was 15 min. The SF-PF microchip will be a versatile platform for microchip-based point-of-care diagnosis.

Analysis of microRNA and modified oligonucleotides with the use of ultra high performance liquid chromatography coupled with mass spectrometry

The present study highlights the application of ultra high performance liquid chromatography coupled with mass spectrometry for the selective separation and sensitive quantification of microRNAs and modified phosphorothioate oligonucleotide. The Central Composite Design was used for comprehensive optimization of mass spectrometer parameters (for tandem mass spectrometer and quadrupole-time-of-flight mass spectrometer). Ion pair chromatography was used in order to separate the studied compounds. Furthermore, the optimization of concentration of ion pair reagents in the mobile phase was done with respect to mass spectrometry sensitivity and liquid chromatography separation. The greatest sensitivity for studied compounds was determined for the mixture of 100 mM hexafluoroisopropanol, 5 mM N,N-dimethylbutylamine and methanol. This mobile phase also provided the best separation results in the shortest time for two of the four columns used in the study. Finally, the Hypersil GOLD aQ was selected for routine analysis of microRNA and modified phosphorothioate oligonucleotide in serum samples. These compounds were extracted from the sample with the use of combined liquid-liquid and solid phase extraction. The method developed during the study was then applied for the qualitative and quantitative analysis with limits od quantification equal to 49-63 nM.

Hybridization conditions of oligonucleotide-capped gold nanoparticles for SPR sensing of microRNA

MicroRNA (miRNA) sensing, especially the miRNA-200 family, is increasingly targeted for cancer diagnostics. As the sensing schemes often rely on nanoparticles functionalized with a specific oligonucleotide, we investigate the hydribization conditions using the common case of surface plasmon resonance (SPR) sensing of miRNA and a gold nanoparticle (Au NP) competitor. In this type of assays, the Au NPs compete with the microRNA to bind the capture probe immobilized on the gold surface. In our study, we simplify and improve the detection procedure by adopting 11-mercaptoundecanoic acid (11-MUA) as linker to the gold surface, not only omitting the blocking step of 6-mercapto-1-hexanol (MCH), but also increasing the probe density. We report that the response in our SPR sensing studies increased with the size of Au NPs according to the plasmon ruler equation, but the larger AuNPs of 32 nm lacked colloidal stability. In addition, decreasing the ratio of oligonucleotide to Au NPs and the addition of polyethylene glycol (PEG) to hybridization buffer also favored a better response in SPR sensing of miRNA. The optimization led to an improved detection sensitivity in our competition method and a detection limit as low as 500 pM for miRNA-200b without amplification of miRNA and use of other amplification schemes.

An improvement of miRNA extraction efficiency in human plasma

MicroRNAs (miRNAs) are short noncoding RNA molecules that control the expression of mRNAs associated with various biological processes. Therefore, deregulated miRNAs play important roles in the pathogenesis of diseases. Numerous studies are aimed at discovering biomarkers of diseases or determining miRNA functions by monitoring circulating miRNAs in various biological sources such as plasma and urine. However, the analysis of miRNA in such fluids presents problems related to accuracy and reproducibility because of their low levels in biological fluids. Therefore, better extraction kits and more sensitive detection systems have been developed for improved and reproducible analysis of circulating miRNAs. However, new extraction methods are also needed to improve the yield of miRNAs for their reliable analysis from biological fluids. The combination of yeast transfer RNA (tRNA) and glycogen as carrier molecules and incubation durations were optimized to maximize extraction efficiency. The extraction recovery using a combination of yeast tRNA and glycogen was approximately threefold more than that by using glycogen or yeast tRNA alone. In addition, reproducible and accurate analysis of miRNAs can be carried out after extraction using a combination of yeast tRNA and glycogen without an impact on plasma components. Graphical abstract Steps of miRNA extraction in plasma.

Recent advances in signal amplification strategy based on oligonucleotide and nanomaterials for microRNA detection-a review

MicroRNAs (MiRNAs) play multiple crucial regulating roles in cell which can regulate one third of protein-coding genes. MiRNAs participate in the developmental and physiological processes of human body, while their aberrant adjustment will be more likely to trigger diseases such as cancers, kidney disease, central nervous system diseases, cardiovascular diseases, diabetes, viral infections and so on. What's worse, for the detection of miRNAs, their small size, high sequence similarity, low abundance and difficult extraction from cells impose great challenges in the analysis. Hence, it's necessary to fabricate accurate and sensitive biosensing platform for miRNAs detection. Up to now, researchers have developed many signal-amplification strategies for miRNAs detection, including hybridization chain reaction, nuclease amplification, rolling circle amplification, catalyzed hairpin assembly amplification and nanomaterials based amplification. These methods are typical, feasible and frequently used. In this review, we retrospect recent advances in signal amplification strategies for detecting miRNAs and point out the pros and cons of them. Furthermore, further prospects and promising developments of the signal-amplification strategies for detecting miRNAs are proposed.

Evaluation of inhibition of miRNA expression induced by anti-miRNA oligonucleotides

MicroRNAs (miRNAs) are short RNA molecules that control the expression of mRNAs associated with various biological processes. Therefore, deregulated miRNAs play an important role in the pathogenesis of diseases. Numerous studies aimed at developing novel miRNA-based drugs or determining miRNA functions have been conducted by inhibiting miRNAs using anti-miRNA oligonucleotides (AMOs), which inhibit the function by hybridizing with miRNA. To increase the binding affinity and specificity to target miRNA, AMOs with various chemical modifications have been developed. Evaluating the potency of these various types of AMOs is an essential step in their development. In this study, we developed a capillary electrophoresis with laser-induced fluorescence (CE-LIF) method to evaluate the potency of AMOs by measuring changes in miRNA levels with fluorescence-labeled ssDNA probes using AMO-miR-23a, which inhibits miR-23a related to lung cancer. In order to eliminate interference by excess AMOs during hybridization of the ssDNA probe with the miR-23a, the concentration of the ssDNA probe was optimized. This newly developed method was used to compare the potency of two different modified AMOs. The data were supported by the results of a luciferase assay. This study demonstrated that CE-LIF analysis could be used to accurately evaluate AMO potency in biological samples.

A Novel p19 Fusion Protein as a Delivery Agent for Short-interfering RNAs

RNA interference (RNAi) is the biological mechanism that allows targeted gene knockdown through the addition of exogenous short-interfering RNAs (siRNAs) to cells and organisms. RNAi has revolutionized cell biology and holds enormous potential for human therapy. One of the major challenges facing RNAi as a therapy is achieving efficient and nontoxic delivery of siRNAs into the cell cytoplasm, since their highly anionic character precludes their passage across the cell membrane unaided. Herein, we report a novel fusion protein between the tombusviral p19 protein, which binds siRNAs with picomolar affinity, and the “TAT” peptide (RKKRRQRRRR), which is derived from the transactivator of transcription (TAT) protein of the human immunodeficiency virus and acts as a cell-penetrating peptide. We demonstrate that this fusion protein, 2x-p19-TAT, delivers siRNAs into the cytoplasm of human hepatoma cells where they elicit potent and sustained gene knockdown activity without toxic effects.

Achieving Single-Nucleotide Specificity in Direct Quantitative Analysis of Multiple MicroRNAs (DQAMmiR)

Direct quantitative analysis of multiple miRNAs (DQAMmiR) utilizes CE with fluorescence detection for fast, accurate, and sensitive quantitation of multiple miRNAs. Here we report on achieving single-nucleotide specificity and, thus, overcoming a principle obstacle on the way of DQAMmiR becoming a practical miRNA analysis tool. In general, sequence specificity is reached by raising the temperature to the level at which the probe-miRNA hybrids with mismatches melt while the matches remain intact. This elevated temperature is used as the hybridization temperature. Practical implementation of this apparently trivial approach in DQAMmiR has two major challenges. First, melting temperatures of all mismatched hybrids should be similar to each other and should not reach the melting temperature of any of the matched hybrids. Second, the elevated hybridization temperature should not deteriorate CE separation of the hybrids from the excess probes and the hybrids from each other. The second problem is further complicated by the reliance of separation in DQAMmiR on single-strand DNA binding protein (SSB) whose native structure and binding properties may be drastically affected by the elevated temperature. These problems were solved by two approaches. First, locked nucleic acid (LNA) bases were incorporated into the probes to normalize the melting temperatures of all target miRNA hybrids allowing for a single hybridization temperature; binding of SSB was not affected by LNA bases. Second, a dual-temperature CE was developed in which separation started with a high capillary temperature required for proper hybridization and continued at a low capillary temperature required for quality electrophoretic separation of the hybrids from excess probes and the hybrids from each other. The developed approach was sufficiently robust to allow its integration with sample preconcentration by isotachophoresis to achieve a limit of detection below 10 pM.

A novel membrane with heterogeneously functionalized nanocrystal layers performing blood separation and sensing synchronously

A novel membrane can synchronously perform blood separation and sensing for serum extraction and analysis of various physiological indexes.

MicroRNAs: biogenesis, roles for carcinogenesis and as potential biomarkers for cancer diagnosis and prognosis

MicroRNAs (miRNAs) are short non-coding RNAs of 20-24 nucleotides that play important roles in carcinogenesis. Accordingly, miRNAs control numerous cancer-relevant biological events such as cell proliferation, cell cycle control, metabolism and apoptosis. In this review, we summarize the current knowledge and concepts concerning the biogenesis of miRNAs, miRNA roles in cancer and their potential as biomarkers for cancer diagnosis and prognosis including the regulation of key cancer-related pathways, such as cell cycle control and miRNA dysregulation. Moreover, microRNA molecules are already receiving the attention of world researchers as therapeutic targets and agents. Therefore, in-depth knowledge of microRNAs has the potential not only to identify their roles in cancer, but also to exploit them as potential biomarkers for cancer diagnosis and identify therapeutic targets for new drug discovery.

Suppressing RNA silencing with small molecules and the viral suppressor of RNA silencing protein p19

RNA silencing is a gene regulatory and host defense mechanism whereby small RNA molecules are engaged by Argonaute (AGO) proteins, which facilitate gene knockdown of complementary mRNA targets. Small molecule inhibitors of AGO represent a convenient method for reversing this effect and have applications in human therapy and biotechnology. Viral suppressors of RNA silencing, such as p19, can also be used to suppress the pathway. Here we assess the compatibility of these two approaches, by examining whether synthetic inhibitors of AGO would inhibit p19-siRNA interactions. We observe that aurintricarboxylic acid (ATA) is a potent inhibitor of p19's ability to bind siRNA (IC50 = 0.43 μM), oxidopamine does not inhibit p19:siRNA interactions, and suramin is a mild inhibitor of p19:siRNA interactions (IC50 = 430 μM). We observe that p19 and suramin are compatible inhibitors of RNA silencing in human hepatoma cells. Our data suggests that at least some inhibitors of AGO may be used in combination with p19 to inhibit RNA silencing at different points in the pathway.

Electron transfer mediated electrochemical biosensor for microRNAs detection based on metal ion functionalized titanium phosphate nanospheres at attomole level

MicroRNAs (miRNAs) have emerged as new candidates as diagnostic and prognostic biomarkers for the detection of a wide variety of cancers; thus, sensitive and selective detection of microRNAs is significant for early-phase cancer diagnosis and disease prevention. A novel and simple electrochemical miRNA biosensor was developed using Cd(2+)-modified titanium phosphate nanoparticles as signal unit, two DNA as capture probes, and Ru(NH3)6(3+) as electron transfer mediator. Large quantities of cadmium ions were mounted in titanium phosphate spheres to output the electrochemical signal. Because of the presence of Ru(NH3)6(3+) molecules that interacted with DNA base-pairs as electron wire, the electrochemical signal significantly increased more than 5 times. This approach achieved a wide dynamic linear range from 1.0 aM to 10.0 pM with an ultralow limit detection of 0.76 aM, exerting a substantial enhancement in sensitivity. Moreover, the proposed biosensor was sufficiently selective to discriminate the target miRNAs from homologous miRNAs and could be used for rapid and direct analysis of miRNAs in human serum. Therefore, this strategy provides a new and ultrasensitive platform for miRNA expression profiling in biomedical research and clinical diagnosis.

MicroRNA Detection: Current Technology and Research Strategies

The relatively new field of microRNA (miR) has experienced rapid growth in methodology associated with its detection and bioanalysis as well as with its role in -omics research, clinical diagnostics, and new therapeutic strategies. The breadth of this area of research and the seemingly exponential increase in number of publications on the subject can present scientists new to the field with a daunting amount of information to evaluate. This review aims to provide a collective overview of miR detection methods by relating conventional, established techniques [such as quantitative reverse transcription polymerase chain reaction (RT-qPCR), microarray, and Northern blotting (NB)] and relatively recent advancements [such as next-generation sequencing (NGS), highly sensitive biosensors, and computational prediction of microRNA/targets] to common miR research strategies. This should guide interested readers toward a more focused study of miR research and the surrounding technology.

A photoluminescent biosensor based on long-range self-assembled DNA cascades and upconversion nanoparticles for the detection of breast cancer-associated circulating microRNA in serum samples

A photoluminescent biosensor was developed for the detection of microRNA (miRNA) combined signal amplification of long-range self-assembled DNA cascades with upconversion nanoparticles.

Capillary electrophoresis methods for microRNAs assays: a review

MicroRNAs (miRNAs) are short noncoding RNAs that conduct important roles in many cellular processes such as development, proliferation, differentiation, and apoptosis. In particular, circulating miRNAs have been proposed as biomarkers for cancer, diabetes, cardiovascular disease, and other illnesses. Therefore, determination of miRNA expression levels in various biofluids is important for the investigation of biological processes in health and disease and for discovering their potential as new biomarkers and drug targets. Capillary electrophoresis (CE) is emerging as a useful analytical tool for analyzing miRNA because of its simple sample preparation steps and efficient resolution of a diverse size range of compounds. In particular, CE with laser-induced fluorescence detection is a promising and relatively rapidly developing tool with the potential to provide high sensitivity and specificity in the analysis of miRNAs. This paper covers a short overview of the recent developments and applications of CE systems in miRNA studies in biological and biomedical areas.

Nanotechnology-based strategies for the detection and quantification of microRNA

MicroRNAs (miRNAs) are important regulators of gene expression, and many pathological conditions, including cancer, are characterized by altered miRNA expression levels. Therefore, accurate and sensitive quantification of miRNAs may result in correct disease diagnosis establishing these small noncoding RNA transcripts as valuable biomarkers. Aiming at overcoming some limitations of conventional quantification strategies, nanotechnology is currently providing numerous significant alternatives to miRNA sensing. In this review an up-to-date account of nanotechnology-based strategies for miRNA detection and quantification is given. The topics covered are: nanoparticle-based approaches in solution, sensing based on nanostructured surfaces, combined nanoparticle/surface sensing approaches, and single-molecule approaches.