A reverse transcription-free real-time PCR assay for rapid miRNAs quantification based on effects of base stacking

Reverse transcription-free digital-quantitative-PCR for microRNA analysis

MicroRNAs (miRNAs) are non-coding RNA sequences that regulate many biological processes and have become central targets of biomedical research. However, their naturally low abundances in biological samples necessitates the development of sensitive analytical techniques to conduct routine miRNA measurements in research laboratories. Digital PCR has the potential to meet this need because of its single-molecule detection capabilities, but PCR analyses of miRNAs are slowed by the ligation and reverse transcription steps first required to prepare samples. This report describes the development of a method to rapidly quantify miRNA in digital microwell arrays using base-stacking digital-quantitative-PCR (BS-dqPCR). BS-dqPCR expedites miRNA measurements by eliminating the need for ligation and reverse transcription steps, which reduces the time and cost compared to conventional miRNA PCR analyses. Under standard PCR thermocycling conditions, digital signals from miRNA samples were lower than expected, while signals from blanks were high. Therefore, a novel asymmetric thermocycling program was developed that maximized on-target signal from miRNA while minimizing non-specific amplification. The analytical response of BS-dqPCR was then evaluated over a range of miRNA concentrations. The digital PCR dimension increased in signal with increasing miRNA copy numbers. When the digital signal saturated, the quantitative PCR dimension readily discerned miRNA copy number differences. Overall, BS-dqPCR provides rapid, high-sensitivity measurements of miRNA over a wide dynamic range, which demonstrates its utility for routine miRNA analyses.

PNA-Based MicroRNA Detection Methodologies

MicroRNAs (miRNAs or miRs) are small noncoding RNAs involved in the fine regulation of post-transcriptional processes in the cell. The physiological levels of these short (20-22-mer) oligonucleotides are important for the homeostasis of the organism, and therefore dysregulation can lead to the onset of cancer and other pathologies. Their importance as biomarkers is constantly growing and, in this context, detection methods based on the hybridization to peptide nucleic acids (PNAs) are gaining their place in the spotlight. After a brief overview of their biogenesis, this review will discuss the significance of targeting miR, providing a wide range of PNA-based approaches to detect them at biologically significant concentrations, based on electrochemical, fluorescence and colorimetric assays.

Specific and relative detection of urinary microRNA signatures in bladder cancer for point-of-care diagnostics

We present a dual-isothermal cascade strategy assisted by a lateral flow peptide nucleic acid biosensor for point-of-care detection of urinary microRNAs without a temperature protocol and complex instruments. The proposed assay is expected to be of great promise for bladder cancer diagnosis and point-of-care diagnostics.

Quantification of microRNAs directly from body fluids using a base-stacking isothermal amplification method in a point-of-care device

MicroRNAs have been proposed to be a class of biomarkers of disease as expression levels are significantly altered in various tissues and body fluids when compared to healthy controls. As such, the detection and quantification of microRNAs is imperative. While many methods have been established for quantification of microRNAs, they typically rely on time consuming handling such as RNA extraction, purification, or ligation. Here we describe a novel method for quantification of microRNAs using direct amplification in body fluids without upstream sample preparation. Tested with a point-of-care device (termed Gene-Z), the presence of microRNA promotes base-stacking hybridization, and subsequent amplification between two universal strands. The base-stacking approach, which was achieved in <60 min, provided a sensitivity of 1.4 fmol per reaction. Tested in various percentages of whole blood, plasma, and faeces, precision (coefficient of variation = 2.6%) was maintained and comparable to amplification in pristine samples. Overall, the developed method represents a significant step towards rapid, one-step detection of microRNAs.

Amplification-based method for microRNA detection

Over the last two decades, the study of miRNAs has attracted tremendous attention since they regulate gene expression post-transcriptionally and have been demonstrated to be dysregulated in many diseases. Detection methods with higher sensitivity, specificity and selectivity between precursors and mature microRNAs are urgently needed and widely studied. This review gave an overview of the amplification-based technologies including traditional methods, current modified methods and the cross-platforms of them combined with other techniques. Many progresses were found in the modified amplification-based microRNA detection methods, while traditional platforms could not be replaced until now. Several sample-specific normalizers had been validated, suggesting that the different normalizers should be established for different sample types and the combination of several normalizers might be more appropriate than a single universal normalizer. This systematic overview would be useful to provide comprehensive information for subsequent related studies and could reduce the un-necessary repetition in the future.

A universal real-time PCR assay for rapid quantification of microRNAs via the enhancement of base-stacking hybridization

Via the base-stacking hybridization strategy, we have developed a universal, one-step real-time quantitative PCR assay for sensitive and selective detection of microRNAs. This proposed assay has several intrinsic features including rapid response, low cost, simple handling procedures, etc.

Rapid and reliable microRNA detection by stacking hybridization on electrochemiluminescent chip system

MicroRNAs play pivotal roles in many fundamental aspects of life. Because microRNAs have the characteristics of small size, similar sequence, and low abundance, it is challenging to identify microRNAs rapidly and specifically with high sensitivity. Herein, we developed an electrochemiluminescent (ECL) chip system for microRNA detection based on base-stacking hybridization and magnetic microparticle enrichment technology. In the designed system, the integration of the microfluidic system with ECL detection made it easy to assemble the multiple assay steps and allowed the construction of a device that is convenient to carry. A limit of detection of 1fmol was achieved with this assay. The proposed direct optical microRNA detection technique demonstrated an acceptable sensitivity combined with the advantages of reliability and rapidity.

Electrochemical determination of microRNA-21 based on bio bar code and hemin/G-quadruplet DNAenzyme

A simple and novel microRNA (miRNA) biosensor was developed using DNA-Au bio bar code (DNA-Au) and G-quadruplex-based DNAenzyme. DNA-Au increased the amount of miRNA-21 participating in hybridization. Hemin/G-quadruplex DNAenzyme significantly improved the catalysis of H(2)O(2) by oxidation of hydroquinone, resulting in an obvious reduction current of benzoquinone for miRNA-21 indirect detection. Under optimum conditions, the linear relationship between miRNA-21 concentration and reduction response was obtained with the detection limit of 0.006 pM, which showed a good sensitivity. Besides, selectivity of the biosensor was investigated by detecting the base mismatched miRNAs. This proposed method was further applied to detect miRNA-21 extracted from human hepatocarcinoma BEL-7402 cells and human mastocarcinoma MCF-7 cells. The influence of bisphenol A (BPA) on the expression of miRNA-21 in cells was also investigated. The biosensor performs well in practical applications, which suggests it may provide a new platform for gene diagnosis.

Aptamer-based colorimetric detection of platelet-derived growth factor using unmodified gold nanoparticles

We developed a simple method for the detection of platelet-derived growth factors (PDGFs) based on base stacking effect coupled with an unmodified gold nanoparticle (AuNP) indicator. In the absence of a target, an aptamer probe and a capture probe stably co-exist in a solution, as it is difficult to sustain an interaction between both these probes due to the short 8bp duplex. However, when a target protein binds to the aptamer probe, the strong base stacking effect can lead to a favorable and stable interaction between the aptamer and capture probes. Hence, the capture probe dissociates from the AuNP surfaces, inducing AuNP aggregation. Compared with other AuNP-based aptasensors for PDGFs, using this base stacking effect can overcome a structured-aptamer method's limitation of requiring thiolated-aptamer-modified AuNPs. Under optimal detection conditions, this label-free colorimetric sensor could detect PDGFs down to 6nM with high selectivity in the presence of other interferring proteins. This simple detection approach provides viable methods for a structured-aptamer sensing protocol.

Ultrasensitive quantification of mature microRNAs by real-time PCR based on ligation of a ribonucleotide-modified DNA probe

It was first demonstrated that the DNA probe modified with ribonucleotides can be efficiently ligated by using miRNA as the template. With PCR amplification of the ligated DNA probe, as low as 0.2 fM target miRNAs can be detected with high specificity.