Performing custom microRNA microarray experiments

Evaluation of probe-based ultra-sensitive detection of miRNA using a single-molecule fluorescence imaging method: miR-126 used as the model

This study proposed a new detection method of miRNA based on single-molecule fluorescence imaging, a method that has been successfully developed to measure the light signal of individual molecules labeled with proper fluorophores. We designed probes 1 and 2 to be labeled with Cy5 dye and BHQ2 quencher at the 3'terminals, respectively. Probe 1 consisted of two parts, the longer part complementary to miR-126 and the shorter part complementary to probe 2. After hybridization, miR-126 bound to probe 1 by replacing probe 2 and assembled into a double-stranded DNA with probe 1. The abundance of miR-126 was quantified by detecting image spots of Cy5 dye molecules from probe 1/miR-126 complexes. MiR-126 single-molecule imaging method showed high specificity and sensitivity for miR-126 with a detection limit of 50 fM. This method has good selectivity for miR-126 detection with 2.1-fold, 8.8-fold, and 26.9-41.3-fold higher than those of single-base mismatched miR-126, three-base mismatched miR-126 and non-complementary miRNAs (miR-221, miR-16, miR-143 and miR-141). The method to detect miR-126 was validated in breast cancer cell lines. Our single-molecule miRNA imaging showed high specificity and sensitivity for miRNAs. By changing the base pair sequence of the designed probes, our method would be able to detect different miRNAs.

A sensing system constructed by combining a structure-switchable molecular beacon with nicking-enhanced rolling circle amplification for highly sensitive miRNA detection

A novel amplification assay strategy is developed for the highly sensitive detection of miRNA-21 based on a combination of a structure-switchable molecular beacon with nicking-enhanced rolling circle amplification.

DNA Tetrahedron-Based MNAzyme for Sensitive Detection of microRNA with Elemental Tagging

Heterogeneous immunoassay based on magnetic separation is commonly used in inductively coupled plasma-mass spectrometry (ICP-MS)-based biomedical analysis with elemental labeling. However, the functionalized magnetic beads (MBs) often suffer from non-specific adsorption and random distribution of the functional probes. To overcome these problems, DNA tetrahedron (DT)-functionalized MBs were designed and further conjugated with substrate modified Au NPs (Sub-AuNP). Based on the prepared MB-DT-AuNP probes, an MB-DT based multicomponent nucleic acid enzyme (MNAzyme) system involving Au NPs as the elemental tags was proposed for highly sensitive quantification of miRNA-155 by ICP-MS. Target miRNA would trigger the assembly of MNAzyme, and Sub-AuNP would be cleaved from the MB-DT-AuNP probe, resulting in a cyclic amplification. Single-stranded DNA-functionalized MB (MB-ssDNA)-AuNP probes were prepared as well. Comparatively, the amount of Au NPs grafted onto MB-ssDNA-AuNP probes was higher than that grafted onto MB-DT-AuNP probes. Meanwhile, a higher signal-to-noise ratio was obtained by using MB-DT-AuNP probes over MB-ssDNA-AuNP probes in the MNAzyme system. Under the optimal experimental conditions, the limit of detection for target miRNA obtained by using MB-DT-AuNP probes was 1.15 pmol L^-1, improved by 23 times over that obtained by the use of MB-ssDNA-AuNP probes. The proposed MB-DT-MNAzyme-ICP-MS method was applied to the analysis of miRNA-155 in serum samples, and recoveries of 86.7-94.6% were obtained. This method is featured with high sensitivity, good specificity, and simple operation, showing a great application potential in biomedical analysis.

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.

MicroRNA detection at femtomolar concentrations with isothermal amplification and a biological nanopore

One of the greatest challenges faced by chemists and biologists is the detection of molecules at extremely low concentrations. This paper describes a method to detect ultra-low concentrations (1 femtomole) of nucleotides using isothermal amplification and a biological nanopore.

Methods and Techniques for miRNA Data Analysis

Genomic data analysis consists of techniques to analyze and extract information from genes. In particular, genome sequencing technologies allow to characterize genomic profiles and identify biomarkers and mutations that can be relevant for diagnosis and designing of clinical therapies. Studies often regard identification of genes related to inherited disorders, but recently mutations and phenotypes are considered both in diseases studies and drug designing as well as for biomarkers identification for early detection. Gene mutations are studied by comparing fold changes in a redundancy version of numeric and string representation of analyzed genes starting from macromolecules. This consists of studying often thousands of repetitions of gene representation and signatures identified by biological available instruments that starting from biological samples generate arrays of data representing nucleotides sequences representing known genes in an often not well-known sequence. High-performance platforms and optimized algorithms are required to manipulate gigabytes of raw data that are generated by the so far mentioned biological instruments, such as NGS (standing for Next-Generation Sequencing) as well as for microarray. Also, data analysis requires the use of several tools and databases that store gene targets as well as gene ontologies and gene-disease association. In this chapter we present an overview of available software platforms for genomic data analysis, as well as available databases with their query engines.