Engineering entropy-driven based multiple signal amplification strategy for visualized assay of miRNA by naked eye

Ultrasensitive fluorescence microRNA biosensor by coupling hybridization-initiated exonuclease I protection and tyramine signal amplification

Tyramine signal amplification (TSA) has made its mark in immunoassay due to its excellent signal amplification ability and short reaction time, but its application in nucleic acid detection is still very limited. Herein, an ultrasensitive microRNA (miRNA) biosensor by coupling hybridization-initiated exonuclease I (Exo I) protection and TSA strategy was established. Target miRNA is complementarily hybridized to the biotin-modified DNA probe to form a double strand, which protects the DNA probe from Exo I hydrolysis. Subsequently, horseradish peroxidase (HRP) is attached to the duplex via the biotin-streptavidin reaction and catalyzes the deposition of large amounts of biotin-tyramine in the presence of hydrogen peroxide (H2O2), followed by the conjugation of signal molecule streptavidin-phycoerythrin (SA-PE), which generates an intense fluorescence signal upon laser excitation. This method gave broad linearity in the range of 0.1 fM - 10 pM, yielding a detection limit as low as 74 aM. An increase in sensitivity of 4 orders of magnitude was observed compared to the miRNA detection without TSA amplification. This biosensor was successfully applied to the determination of miR-21 in breast cancer cells and human serum. By further design of specific DNA probes and coupling with the Luminex xMAP technology, it could be easily extended to multiplex miRNA assay, which possesses great application potential in clinical diagnosis.

An approach for state differentiation in nucleic acid circuits: Application to diagnostic DNA computing

BACKGROUND

Differentiating between different states in nucleic acid circuits is crucial for various biological applications. One approach, there is a requirement for complicated sequential summation, which can be excessive for practical purposes. By selectively labeling biologically significant states, this study tackles the issue and presents a more cost-effective and streamlined solution. The challenge is to efficiently distinguish between different states in a nucleic acid circuit.

RESULTS

An innovative method is introduced in this study to distinguish between states in a nucleic acid circuit, emphasizing the biologically relevant ones. The circuit comprises four DNA logic gates and two detection modules, one for determining fetal gender and the other for diagnosing X-linked genetic disorders. The primary module generates a G-quadruplex DNAzyme when activated by specific biomarkers, which leads to a distinct colorimetric signal. The secondary module responds to hemophilia and choroideremia biomarkers, generating one or two DNAzymes. The absence of female fetus indicators results in no DNAzyme or color change. The circuit can differentiate various fetal states by producing one to four active DNAzymes in response to male fetus biomarkers. A single-color solution for state differentiation is provided by this approach, which promises significant advancements in DNA computing and diagnostic applications.

SIGNIFICANCE

The innovative approach used in this study to distinguish states in nucleic acid circuits holds great significance. By selectively labeling biologically relevant states, circuit design is simplified and complexity is reduced. This advancement enables cost-effective and efficient diagnostic applications and contributes to DNA computing, providing a valuable solution to a fundamental problem.

Advances in Point-of-Care Testing of microRNAs Based on Portable Instruments and Visual Detection

MicroRNAs (miRNAs) are a class of small noncoding RNAs that are approximately 22 nt in length and regulate gene expression post-transcriptionally. miRNAs play a vital role in both physiological and pathological processes and are regarded as promising biomarkers for cancer, cardiovascular diseases, neurodegenerative diseases, and so on. Accurate detection of miRNA expression level in clinical samples is important for miRNA-guided diagnostics. However, the common miRNA detection approaches like RNA sequencing, qRT-PCR, and miRNA microarray are performed in a professional laboratory with complex intermediate steps and are time-consuming and costly, challenging the miRNA-guided diagnostics. Hence, sensitive, highly specific, rapid, and easy-to-use detection of miRNAs is crucial for clinical diagnosis based on miRNAs. With the advantages of being specific, sensitive, efficient, cost-saving, and easy to operate, point-of-care testing (POCT) has been widely used in the detection of miRNAs. For the first time, we mainly focus on summarizing the research progress in POCT of miRNAs based on portable instruments and visual readout methods. As widely available pocket-size portable instruments and visual detection play important roles in POCT, we provide an all-sided discussion of the principles of these methods and their main limitations and challenges, in order to provide a guide for the development of more accurate, specific, and sensitive POCT methods for miRNA detection.

MNAzymes and gold nanoparticles as isothermal signal amplification strategy for visual detection of miRNA

MicroRNAs (miRNAs) represent a class of small noncoding RNAs that are considered a novel emerging class of disease biomarkers in a variety of afflictions. Sensitive detection of miRNA is typically achieved using hybridization-based methods coupled with genetic amplification techniques. Although their sensitivity has improved, amplification techniques often present erroneous results due to their complexity. In addition, the use of these techniques is usually linked to the application of protein enzymes, the activity of which is dependent on the temperature and pH of the medium. To address these drawbacks, an alternative genetic enzyme for the highly sensitive detection of miRNAs is proposed in this work. Multicomponent nucleic acid enzymes (MNAzymes), coupled with the use of DNA-functionalized gold nanoparticles (AuNPs), were used in this study to develop an isothermal signal amplification strategy for visual genetic detection. miR146a, a biomarker of bovine mastitis present in milk, was selected as a model analyte. The developed methodology is easily carried out in 80 min at 50 °C, generating a low visual limit of detection of 250 pM based on the observation of a color change. The methodology was successfully applied to the detection of miR146a in raw cow milk samples.

Bifunctional Y-shaped probe combined with dual amplification for colorimetric sensing and molecular logic operation of two miRNAs

The abnormal expression of miRNA is closely related to various human diseases. In particular, the sensitivity detection of miRNA expression level is of great significance for the early diagnosis and prognosis of cancer. In this paper, we designed a Y-shaped DNA probe, using miRNA-21 and miRNA-141 as the dual input signals of AND logic gate. By combining with EXO III assisted target recycle and DNA hybridization chain reaction (HCR), we have realized dual signal amplification for detection of two miRNAs. In short, the Y-shaped DNA probe consists of two parts: the miRNA target binding region and the HCR initiator. When the two miRNAs are present at the same time, the target binding region specifically recognizes the target to generate two circulators, and then the HCR initiator is released. The EXO III specific cleavage two circulator, and release the target again which achieves the first step of signal amplification. After that, HCR was started by the split initiator generated in the first stage of continuous cycle, and the second step of signal amplification was realized. Thanks to the sensitive color change of gold nanoparticles in response to salt, we achieved ultra-high sensitivity for visual detection of miRNA-21 and miRNA-141. Under optimal conditions, the detection limit of both miRNA is 3 pM and the linear range is 10 pM to 0.4 nM. The method we designed could be applied in early detection and diagnosis of cancer.

Wheel drive-based DNA sensing system for highly specific and rapid one-step detection of MiRNAs at the attomolar level

With the use of DNA as building blocks, a variety of microRNA amplification-based sensing systems have been developed. Nevertheless, ultrasensitive, selective and rapid detection of microRNAs with a high signal-to-background ratio and point mutation discrimination ability remains a challenge. Herein, we propose a novel wheel drive-based DNA sensing system (NWDS) based on a self-assembled, self-quenched nanoprobe (SQP) to conduct highly specific and ultrasensitive one-step measurement of microRNAs. In this work, a signalling recognition DNA hairpin (DH) sequence with a self-complementary stem domain of 14 base pairs was used, which contained three functional regions, namely a recognition region for the target miRNA-21, a sticky region with 9 complementary nucleotides to the 3'terminus of a DNA wheel (DW) and a region for the hybridization with a quenching DNA primer (DP). The SQP was ingeniously self-assembled at room temperature by the DH and DP, which was capable of eliminating unwanted background signals. MiRNA-21 was employed as a target model to specifically activate the SQP, leading to specific hybridization between the HP and DW. With the assistance of a polymerase, an SQP-based wheel driving took place to induce hybridization/polymerization displacement cycles, initiating target recycling and DP displacement. As a result, a large amount of the newly formed hybrid SQP/DW accumulated to generate a substantially enhanced fluorescence signal. In this way, the newly proposed NWDS exhibits ultrasensitivity with a detection limit of 5.62 aM across a wide linear dynamic response range up to 200 nM, excellent selectivity with the capability to discriminate homologous miRNAs and one-base, two-base and three-base mismatched sequences, and an outstanding analytical performance in complex systems. In addition, the significant simultaneous advantages of one-step operation, rapid detection within 15 min and a high signal-to-background ratio of 26 offer a unique opportunity to promote the early diagnosis of cancer-related diseases and molecular biological analysis.

Programming the dynamic range of nanobiosensors with engineering poly-adenine-mediated spherical nucleic acid

Spherical nucleic acid (SNA) conjugates consisting of gold cores functionalized with a densely packed DNA shells are of great significance in the field of medical detection and intracellular imaging. Especially, poly adenine (polyA)-mediated SNAs can improve the controllability and reproducibility of DNA assembly on the nanointerface, showing the tunable hybridization ability. However, due to the physics of single-site binding, the biosensor based on SNA usually exhibits a dynamic range spanning a fixed 81-fold change in target concentration, which limits its application in disease monitoring. To address this problem, we report a tri-block DNA-based approach to assemble SNA for nucleic acid detection based on structure-switching mechanism with programmable dynamic range. The tri-block DNA is a FAM-labeled stem-loop structure, which contains three blocks: polyA block as an anchoring block for tunable surface density, stem block with different GC base pair content for varying the structure stability, and the fixed loop block for target recognition. We find that varying the polyA block, the reaction temperature, and the GC base pair, SNA shows different target binding affinity and detection limit but with normally 81-fold dynamic range. We can extend the dynamic range to 1000-fold by using the combination of two SNAs with different affinity, and narrow the dynamic range to 5-fold by sequestration mechanism. Furthermore, the tunable SNA enables sensitive detection of mRNA in cells. Given its tunable dynamic range, such nanobiosensor based on SNA offers new possibility for various biomedical and clinical applications.

Sensitive acid phosphatase assay based on light-activated specific oxidase mimic activity

Acid phosphatase (ACP) is a key marker in the diagnosis of many diseases. However, exploiting a simple and sensitive sensor for the real-time quantitative analysis of ACP is still challenging. Herein, we attempted to develop a sensitive colorimetric sensing strategy for the detection of ACP based on light-activated oxidase mimic property of carbon dots (CDs). The synthesized CDs were proved to be capable of intrinsic light-activated oxidase mimic activity, which could generate reactive oxygen species to oxidize chromogenic substrate under ultraviolet light stimulation. Interestingly, this light-activated oxidase mimic behavior would be effectively suppressed by the antioxidant ascorbic acid (AA), a product from the hydrolysis of 2-phospho-L-ascorbic acid trisodium (AAP) mediated by ACP. Based on the above property, a facile and sensitive colorimetric sensing method for ACP was developed. Under the optimal conditions, the linear range for ACP 0.1-5.5 U/L, and the detection limit was 0.056 U/L. Compared with conventional nanozyme based ACP assay systems, the catalytic activity of light-activated nanozyme could be conveniently regulated by switching the light on and off, which made it easier to precisely control the extent of the reaction and ensured the accuracy of the assay. In addition, the proposed sensing system would be readout directly by the naked eye or smartphone-based RGB analysis system, and have been successfully applied to analyze diluted in diluted fetal bovine serum and urine samples spiked with ACP. All these results indicated that this approach holds good promise for future applications in clinical analysis and point-of-care (POC) biosensor platforms.

DNA-functionalized gold nanoparticles: Modification, characterization, and biomedical applications

With the development of technologies based on gold nanoparticles (AuNPs), bare AuNPs cannot meet the increasing requirements of biomedical applications. Modifications with different functional ligands are usually needed. DNA is not only the main genetic material, but also a good biological material, which has excellent biocompatibility, facile design, and accurate identification. DNA is a perfect ligand candidate for AuNPs, which can make up for the shortcoming of bare AuNPs. DNA-modified AuNPs (DNA-AuNPs) have exciting features and bright prospects in many fields, which have been intensively investigated in the past decade. In this review, we summarize the various approaches for the immobilization of DNA strands on the surface of AuNPs. Representative studies for biomedical applications based on DNA-AuNPs are also discussed. Finally, we present the challenges and future directions.

Ratiometric Fluorescence Detection of Colorectal Cancer-Associated Exosomal miR-92a-3p with DSN-Assisted Signal Amplification by a MWCNTs@Au NCs Nanoplatform

The detection of miRNA shows great promise in disease diagnosis. In this work, a ratiometric fluorescent biosensor based on multi-walled carbon nanotubes@gold nanoclusters (MWCNTs@Au NCs) and duplex-specific nuclease (DSN)-assisted signal amplification was fabricated for miRNA detection. Colorectal cancer (CRC)-associated miR-92a-3p extracted from exosomes was selected as the target. MWCNTs@Au NCs performs the dual functions of fluorescence quencher and internal fluorescence reference. In the absence of miR-92a-3p, an Atto-425-modified single-stranded DNA probe is adsorbed on MWCNTs@Au NCs, resulting in the quenching of Atto-425. In the presence of miR-92a-3p, the duplex is formed by hybridization of the probe and miR-92a-3p and leaves the MWCNTs@Au NCs, resulting in the fluorescence recovery of Atto-425. DSN can cleave the probe and result in the release of miR-92a-3p. The released miR-92a-3p can hybridize with other probes to form a signal amplification cycle. The fluorescence of MWCNTs@Au NCs remains stable and constitutes a ratiometric fluorescence system with that of Atto-425. A detection concentration interval of 0.1–10 pM and a limit of detection of 31 fM was obtained under optimized measurement conditions. In addition, the accuracy of the biosensor was validated by detecting the concentration of miR-92a-3p extracted from clinical exosome samples.

An intramolecular DNAzyme-based amplification for miRNA analysis with improving reaction kinetics and high sensitivity

Sensitive, specific and rapid methods for detecting microRNAs (miRNAs) play critical roles in disease diagnosis and therapy. Enzyme-free amplification techniques based on DNAzyme assembly have recently been developed for the highly specific miRNA analysis. However, traditional DNAzyme-based assembly (free DNAzyme) amplifiers is mainly dependent on the target-induced split DNAzyme fragments to assemble into activated DNAzyme structures, which have made a compromise between the sensitivity and specificity due to the random diffusion of dissociative probes in a bulk solution with poor kinetics. Herein, based on a rationally designed DNA probe, we developed an intramolecular DNAzyme assembly (intra-DNAzyme) method to overcome these challenges. The miR-373 is used as model analyte for our current proof-of-concept experiments. Compared with the free-DNAzyme method, our method showed significantly improved analytical performance in terms of dynamic range, assay sensitivity and speed. This method can detect miR-373 specifically with a detection limit as low as 4.3 fM, which is about 83.7 times lower than the previous free-DNAzyme method. This intra-DNAzyme strategy would be of great value in both basic research and clinical diagnosis.