Highly sensitive, selective, and rapid detection of miRNA-21 using an RCA/G-quadruplex/QnDESA probing system

SplintR ligation-triggered in-situ rolling circle amplification on magnetic bead for accurate detection of circulating microRNAs

The circulating microRNAs (miRNAs), endogenous noncoding RNAs, post-transcriptionally participate in multiple processes during cell growth and development. Moreover, dysregulation of miRNAs expression is intricately associated with cancer. Currently, challenges of high homology, sequence similarity, and low abundance encountered in the detection of target miRNAs in complex samples need to be addressed. Biosensors established for miRNAs detection suffer from limitations in terms of sensitivity, specificity and high cost. Herein, a miRNA detection method based on in-situ RCA on magnetic bead catalyzed by SplintR ligase was proposed to achieve high sensitivity and high specificity. The following steps are included: (1) formation of P1-P2-miRNA double-stranded complex under catalyzation of SplintR ligase, and the release of P1-P2 single strand under denaturation; (2) enrichment of P1-P2 single chain by streptavidin-modified magnetic beads (SM-MB); (3) in situ RCA on surface of magnetic beads; (4) fluorescence detection. After optimization of experimental conditions, miRNA-155 detection with improved sensitivity and specificity was achieved. The detection limit was low to 36.39 fM, and one-base mismatch discrimination was demonstrated. Also, the clinical practicability for circulating miRNA-155 detection was preliminarily validated in human serum samples.

One-pot isothermal CRISPR/Dx system for specific and sensitive detection of microRNA

MicroRNA (miRNA) is a promising biomarker for the early diagnosis of pancreatic cancer. To enable sensitive and reliable miRNA detection, we have developed a one-pot isothermal CRISPR/Dx detection system by combining rolling circle amplification (RCA) and CRISPR/Cas12a. RCA and CRISPR/Cas12a reactions are carried out in a single closed tube, bypassing the transferring step. We demonstrate the feasibility of our one-pot CRISPR/Dx system in detecting pancreatic cancer by targeting miR-25, miR-191, miR-205, and miR-1246. When applied to fluorescence- and lateral flow strip paper-based detection platforms, our one-pot CRISPR/Dx system detects synthetic miR-25 at a LOD of 6.60 fM and 500 fM, respectively. It has high targeting specificity, as shown by its ability to discriminate miR-25 with a single-base mutation and highly homologous miRNA species. It is also successfully generalized to detect other pancreatic cancer-associated miRNAs, including miR-191, miR-205, and miR-1246. Importantly, our one-pot CRISPR/Dx system enables specific and sensitive detection of endogenous miR-25 in the human pancreatic cancer cell line PANC-1. We have successfully developed a one-pot isothermal CRISPR/Dx system for detecting miRNA with high specificity and sensitivity. It is highly flexible and economical, as a common crRNA can detect different miRNAs and only requires minor modifications to the locking padlock probe. Therefore, it can potentially be translated into clinical settings and POCT for the diagnosis of various human cancers.

CRISPR-Cas13a-Triggered DNAzyme Signal Amplification-Based Colorimetric miRNA Detection Method and Its Application in Evaluating the Anxiety

The development of a bio-sensing strategy based on CRISPR/Cas that is exceptionally sensitive is crucial for the identification of trace molecules. Colorimetric miRNA detection utilizing CRISPR/Cas13a-triggered DNAzyme signal amplification was described in this article. The developed strategy was implemented for miRNA-21 detection as a proof of concept. The cleavage activity of Cas13a was triggered when the target molecule bonded to the Cas13a-crRNA complex and cleaved uracil ribonucleotides (rU) in the substrate probe. As a consequence, the S chain was liberated from the T chain that had been modified on magnetic beads (MB). The G-rich sections were then exposed when the catalytic hairpin assembly between the H1 and H2 probes was activated by the released T@MB. G-rich section can fold into G-quadruplex. By catalyzing the formation of green ABTS3- via HRP-mimicking G-quadruplex/hemin complexes, colorimetric measurements of miRNA can be achieved visually through DNAzyme-mediated signal amplification. The method demonstrated a low limit of detection of 27 fM and a high selectivity towards target miRNA eventually. As a result, the developed strategy provides a clinical application platform for the detection of miRNAs that is both ultrasensitive and extremely specific.

I-motif sensor for the fluorometric detection of Monkeypox

In this study, we developed an isothermal fluorometric diagnostic method for DNA virus-generating disorders such as Mpox. Our results showed that the release of a large number of protons during multiplex-LAMP markedly lowered the pH level, which transformed the retinoblastoma (Rb) linear ssDNA into i-motifs. Consequently, thiazole orange (TO; a fluorometric probe sensitive to the i-motif) boosted the signal-on fluorescence because of its ability to bind selectively to i-motifs. This multiplex-LAMP/i-motif-TO system enabled simultaneous detection aimed at numerous potential targets with remarkable sensitivity (1.47 pg per mL) and efficiency (30 minutes). Our method is expected to enable DNA-virus-related diseases to be efficiently and accurately assessed.

Dual amplification-based ultrasensitive and highly selective colorimetric detection of miRNA

In this study, we combined a Pradeep Kumar (PK)-probe with a ligation-transcription-ramified RCA (LTR) dual-amplification system for the isothermal colorimetric detection of miRNA 25-3P, where the PK-probe transformed from its pink color to colorless in the presence of the amplification byproduct pyrophosphate (PPi), thereby allowing the simple naked-eye qualitative detection of the miRNA. Through this double-amplification strategy, the limit of detection reached as low as 91.4 aM-quite extraordinary sensitivity for a colorimetric miRNA detection system based on absorbance readings. Our detection system also operated with high specificity, the result of using two different target-selective ligation steps (linear DNA ligation and circular DNA ligation) mediated by SplintR ligase, and so could discriminate single-mismatched from perfectly matched target sequences. We suspect that this ultrasensitive and selective PK-probe/LTR dual-amplification system should be a great colorimetric diagnostic for the detection of any miRNA with high efficiency.

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.

22AG G-quadruplex RNA/QnMorpholine-mediated fluorimetric detection of miR-21

Herein we report a simple ligation/transcription-mediated system, using a 22AG G-quadruplex RNA secondary structure and a fluorescence-inducing QnMorpholine probe, for the detection of miR-21. In the presence of the target miR-21, two oligonucleotide probes (promoter and reporter) were ligated, thereby transcribing the 22AG RNA sequence, a complement of the reporter probe. In contrast, in the absence of this target-induced ligation, the reporter complement could not be transcribed to produce the 22AG RNA sequence. Subsequent addition of the QnMorpholine probe resulted in binding with the 22AG G-quadruplex RNA, thereby generating high fluorescence; no fluorescence occurred in the absence of this secondary structure. Hence, the presence of miR-21 was evidenced by a target-induced high-intensity signal. This simple one-pot fluorimetric system, which could detect miR-21 of up to 3.08 femtomolar in less than 30 min, holds promise as a diagnostic tool for selective and sensitive miRNA detection.