2-aminopurine probe in combination with catalyzed hairpin assembly signal amplification for simple and sensitive detection of microRNA

Structural Antagonism-Aided Conformational Regulation Enables an Aptamer-Loop G-Quadruplex Modular Sensor of β-Lactoglobulin

A simple, reliable method for identifying β-lactoglobulin (β-LG) in dairy products is needed to protect those with β-LG allergies. A common, practical strategy for target detection is designing simplified nucleic acid nanodevices by integrating functional components. This work presents a label-free modular β-LG aptasensor consisting of an aptamer-loop G-quadruplex (G4), the working conformation of which is regulated by conformational antagonism to ensure respective module functionality and the related signal transduction. The polymorphic conformations of the module-fused sequence are systematically characterized, and the cause is revealed as shifting antagonistic equilibrium. Combined with conformational folding dynamics, this helped regulate functional conformations by fine-tuning the sequences. Furthermore, the principle of specific β-LG detection by parallel G4 topology is examined as binding on the G4 aptamer loop by β-LG to reinforce the G4 topology and fluorescence. Finally, a label-free, assembly-free, succinct, and turn-on fluorescent aptasensor is established, achieving excellent sensitivity across five orders of magnitude, rapidly detecting β-LG within 22-min. This study provides a generalizable approach for the conformational regulation of module-fused G4 sequences and a reference model for creating simplified sensing devices for a variety of targets.

Biosensor model based on single hairpin structure for highly sensitive detection of multiple targets

Nowadays, due to the genetic information carried by nucleic acids, they can serve as a biomarker for the early diagnosis of diseases, including tumors and cardiovascular disease, among others, making genetic testing a hotspot of biomedicine. Therefore, we have designed a universal fluorescence biosensor that can detect multiple DNA sequences with good performance. In our designed biosensor, λ exonuclease is used due to its ability to digest double-stranded DNA from the phosphorylated 5'- end and promote the targeted cycle. The exonuclease is introduced into a DNA hairpin containing a target recognition sequence. Hence, with the target, λ exonuclease-assisted targeted recycling can be activated. The hydrolyzed DNA hairpin triggers a strand displacement reaction between the hairpin probe (H1) and F-Q double DNA strand (F-Q), increasing the distance between the fluorescent chain (F) and quenching chain (Q); thus the fluorescence signal is emitted. It is exciting that the detection limit of the biosensor is 300 fM, which is relatively low, and there is an excellent linear relationship between fluorescence intensity and target concentration. Moreover, the biosensor we designed has universal applicability in the detection of other genes, and the range of RSD is 1.28-2.45%. Hence, it has good application prospects and practical value in the early detection of some diseases and the design of fluorescent biosensors.

Signal Amplification-Based Biosensors and Application in RNA Tumor Markers

Tumor markers are important substances for assessing cancer development. In recent years, RNA tumor markers have attracted significant attention, and studies have shown that their abnormal expression of post-transcriptional regulatory genes is associated with tumor progression. Therefore, RNA tumor markers are considered as potential targets in clinical diagnosis and prognosis. Many studies show that biosensors have good application prospects in the field of medical diagnosis. The application of biosensors in RNA tumor markers is developing rapidly. These sensors have the advantages of high sensitivity, excellent selectivity, and convenience. However, the detection abundance of RNA tumor markers is low. In order to improve the detection sensitivity, researchers have developed a variety of signal amplification strategies to enhance the detection signal. In this review, after a brief introduction of the sensing principles and designs of different biosensing platforms, we will summarize the latest research progress of electrochemical, photoelectrochemical, and fluorescent biosensors based on signal amplification strategies for detecting RNA tumor markers. This review provides a high sensitivity and good selectivity sensing platform for early-stage cancer research. It provides a new idea for the development of accurate, sensitive, and convenient biological analysis in the future, which can be used for the early diagnosis and monitoring of cancer and contribute to the reduction in the mortality rate.

Development and validation of a PCR-free nucleic acid testing method for RNA viruses based on linear molecular beacon probes

Background

RNA viruses periodically trigger pandemics of severe human diseases, frequently causing enormous economic losses. Here, a nucleic acid extraction-free and amplification-free RNA virus testing probe was proposed for the sensitive and simple detection of classical swine fever virus (CSFV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), based on a double-stranded molecular beacon method. This RNA virus probe contains two base sequences—a recognition strand that binds to the specific domain of CSFV N2 or SARS-CoV-2 N, with a fluorophore (FAM) labeled at the 5′ end, and a complementary strand (CSFV-Probe B or SARS-CoV-2-Probe B), combined with a quencher (BHQ2) labeled at the 3′ end.

Results

Using linear molecular beacon probe technology, the detection limit of the RNA virus probe corresponding to CSFV and SARS-CoV-2 were as low as 0.28 nM and 0.24 nM, respectively. After CSFV E2 and SARS-CoV-2 N genes were transfected into corresponding host cells, the monitoring of RNA virus probes showed that fluorescence signals were dramatically enhanced in a concentration- and time-dependent manner. These results were supported by those of quantitative (qRT-PCR) and visualization (confocal microscopy) analyses. Furthermore, CSF-positive swine samples and simulated SARS-CoV-2 infected mouse samples were used to demonstrate their applicability for different distributions of viral nucleic acids in series tissues.

Conclusions

The proposed RNA virus probe could be used as a PCR-free, cost-effective, and rapid point-of-care (POC) diagnostic platform for target RNA virus detection, holding great potential for the convenient monitoring of different RNA viruses for early mass virus screening.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12951-022-01470-1.

A persistent luminescence resonance energy transfer-based molecular beacon probe for the highly sensitive detection of microRNA in biological samples

Herein, a time-resolved luminescence resonance energy transfer (TR-LRET) molecular beacon (MB) probe employing persistent luminescence nanoparticles (PLNPs) as the energy donors was first constructed, and further designed for microRNA21 (miR21) sensing. This probe (named as PLNPs-MB) was facilely fabricated by covalent bioconjugation between poly-(acrylic acid) (PAA) modified near-infrared (NIR) emissive PLNPs i.e. ZnGa₂O₄:Cr³⁺ and functionalized MB oligonucleotide (5'-NH₂ and 3'-BHQ3). Accordingly, PLNPs and BHQ3 were in close proximity to each other, leading to the occurrence of LRET and obvious persistent luminescence (PL) quenching. In the presence of miR21, loop of the PLNP-MB was hybridized, accompanying BHQ3 away from PLNPs and the restraint of LRET process. As a result, PL of the PLNPs was recovered, which built the foundation of miR21 quantification. The probe provided a linear response range from 0.1 to 10 nM for miR21 detection. Quantification limit of this probe was competitive and about 1-2 orders of magnitude lower than that of other reported MB probes for nucleic acid. Moreover, the proposed probe was successfully adopted for miR21 detection in biological fluids (human serum, cell extraction). This work also provided a sensitive detection nanoplatform for other targets through modifying diverse MBs onto the surface of PLNPs.

Full liberation of 2-Aminopurine with nucleases digestion for highly sensitive biosensing

2-Aminopurine (2-AP), a fluorescent isomer of adenine, is a popular fluorescent tag for DNA-based biosensors. The fluorescence of 2-AP is highly dependent on its microenvironment, i.e., almost non-fluorescent and merely fluorescent in dsDNA and ssDNA, respectively, but can be greatly brightened as mononucleotide. In most 2-AP-based biosensors, DNA transformation from dsDNA to ssDNA was employed, while selective digestion of 2-AP-labeled DNA with nucleases represents an appealing approach for improving the biosensor sensitivity. However, some detailed fundamental information, such as the reason for nuclease digestion, the influence of the labeling site, neighboring bases, or the label number of 2-AP for final signal output, are still largely unknown, which greatly limits the utility of 2-AP-based biosensors. In this work, using both steady- and excited-state fluorescence (lifetime), we demonstrated that nuclease digestion resulted in almost full liberation of 2-AP mononucleotides, and was free from labeling site and neighboring bases. Furthermore, we also found that nuclease digestion could lead to multiplexed sensitivity from increasing number of 2-AP labelling, but was not achievable for the conventional biosensors without full liberation of 2-AP. Considering the popularity of 2-AP in biosensing and other related applications, the above obtained information in sensitivity boosting is fundamentally important for future design of 2-AP-based biosensors.

Fluorescence nucleobase analogue-based strategy with high signal-to-noise ratio for ultrasensitive detection of food poisoning bacteria

We developed a simple and ultrasensitive strategy for the identification of foodborne pathogens utilizing a fluorescent nucleobase analogue [2-aminopurine (2-AP)]-containing split G-quadruplex that binds blocker DNA. Compared to a previous strategy that did not use blocker DNA, this strategy showed a significant increase in the signal-to-noise ratio-by approximately 300%-owing to the displacement of the blocker DNA by the target DNA that induces the formation of an active G-quadruplex structure, thereby leading to a substantial increase in the 2-AP fluorescence signal. The proposed strategy was rationally combined with polymerase chain reaction, which resulted in the successful determination of genomic DNA (within the range of 10-106 copies) derived from the food poisoning bacterium Escherichia coli, with a limit of detection of 5.2 copies and high selectivity. In addition, the practical applicability of this method was demonstrated by analyzing E. coli-spiked lettuce samples.

A quencher-free 2-aminopurine modified hairpin aptasensor for ultrasensitive detection of Ochratoxin A

A sensitive, efficient and quencher-free fluorescence aptasensor to detect Ochratoxin A (OTA) based on aptamer, 2-aminopurine (2AP) labeled Oligonucleotide sequence, as well as exonuclease I (Exo I) activity was developed. In which the aptamer specific to OTA was modified into a hairpin structure, and 8 bases at the 3' ends are exposed (H); also, 2AP is embedded in the oligonucleotide complementary to the 8 bases (2AP-probe).The detection principle based on 2AP-probe could be bonded to its complementary sequence and quenches the fluorescence of 2AP; The aptamer has a stronger affinity for the target than its complementary sequence; Exo I can dissociate single-stranded DNA and has little effect on double-stranded DNA as well as folded DNA. In the absence of OTA, the fluorescence of 2AP is quenched due to the complementary pairing of H and 2AP-probe; in the presence of OTA, H selective binding target is detached from 2AP-probe, and the fluorescence of 2AP is slightly restored. Moreover, when the Exo I is added to the detection system, 2AP-probe is dissociated by the Exo I to release the free 2AP, and the fluorescence of the system is further enhanced thereby realizing the detection of OTA. The detection limit of the aptasensor was low as 0.03 nM with a linear range of 0.5-100 nM. Moreover, the aptasensor has good selectivity and practicability and also has good potential in realizing the detection of toxic and harmful substances in food complex matrices.

Triple-Input Molecular AND Logic Gates for Sensitive Detection of Multiple miRNAs

Abnormal miRNA expressions are closely related to the occurrence and development of cancers. It is of great significance to monitor miRNA expression levels for early diagnosis and therapy of the diseases. This study presents two independent colorimetric strategies for simultaneously monitoring multiple miRNAs based on cross-linking or non-cross-linking aggregations of gold nanoparticles (AuNPs). By introducing a Y shaped DNA structure and two types of DNA modified AuNPs, a triple-input DNA AND logic gate is facilely developed with the cross-linking aggregation of AuNPs as the signal output. To improve the sensitivity and shorten reaction time, the logic gate is modified by further employing a three DNA strands formed duplex and hybridization chain reaction. Non-cross-linking aggregation of AuNPs is used to evaluate the concentration of initial miRNA inputs. This strategy does not require DNA modification of AuNPs and ultrahigh sensitivity is achieved with the amplification of hybridization chain reaction. The present work may provide powerful tools for multiple miRNAs diagnostics and inspire further development of DNA based logic gates.

Cationic copolymer-chaperoned DNAzyme sensor for microRNA detection

Multi-component nucleic acid enzymes (MNAzymes) are allosteric deoxyribozymes that are activated upon binding of a specific nucleic acid effector. MNAzyme activity is limited due to an insufficient assembly of the MNAzyme and its turnover. In this work, we describe the successful improvement of MNAzyme reactivity and selectivity by addition of cationic copolymers, which exhibit nucleic acid chaperone-like activity. The copolymer allowed a 210-fold increase in signal activity and a 95-fold increase in the signal-to-background selectivity of MNAzymes constructed for microRNA (miRNA) detection. The selectivity of the MNAzyme for homologous miRNAs was demonstrated in a multiplex format in which isothermal reactions of two different MNAzymes were performed. In addition, the copolymer permitted miRNA detections even in the presence of a ribonuclease which is ubiquitous in environments, indicating the protective effect of the copolymer against ribonucleases.

Applications of Catalytic Hairpin Assembly Reaction in Biosensing

Nucleic acids are considered as perfect programmable materials for cascade signal amplification and not merely as genetic information carriers. Among them, catalytic hairpin assembly (CHA), an enzyme-free, high-efficiency, and isothermal amplification method, is a typical example. A typical CHA reaction is initiated by single-stranded analytes, and substrate hairpins are successively opened, resulting in thermodynamically stable duplexes. CHA circuits, which were first proposed in 2008, present dozens of systems today. Through in-depth research on mechanisms, the CHA circuits have been continuously enriched with diverse reaction systems and improved analytical performance. After a short time, the CHA reaction can realize exponential amplification under isothermal conditions. Under certain conditions, the CHA reaction can even achieve 600 000-fold signal amplification. Owing to its promising versatility, CHA is able to be applied for analysis of various markers in vitro and in living cells. Also, CHA is integrated with nanomaterials and other molecular biotechnologies to produce diverse readouts. Herein, the varied CHA mechanisms, hairpin designs, and reaction conditions are introduced in detail. Additionally, biosensors based on CHA are presented. Finally, challenges and the outlook of CHA development are considered.

Exonuclease III-assisted fluorometric aptasensor for the carcinoembryonic antigen using graphene oxide and 2-aminopurine

A reliable fluorometric assay is described for the determination carcinoembryonic antigen (CEA) using exonuclease III (Exo III) and a 2-aminopurine binding aptamer. In the absence of CEA, dsDNA is degraded by Exo III, and free 2-AP (which has a blue fluorescence with excitation/emission maxima of 310/365 nm) is released. Strong fluorescence is generated after addition of graphene oxide (GO) to the solution. However, the 2-AP modified DNA (T2) cannot be degraded in the presence of CEA by Exo III due to the interaction between CEA and aptamer T1. Hence, only weak fluorescence can be detected after addition of GO. In this system, CEA can be quantified in the 0.05 - 2 ng·mL^-1 concentration range with a detection limit of 30 pg·mL^-1 (at S/N = 3). The method was successfully applied to analyze serum samples for CEA. Graphical Abstract An exonuclease III-assisted fluorometric aptasensor has been developed for the detection of carcinoembryonic antigen using graphene oxide and 2-aminopurine.

The use of a 2-aminopurine-containing split G-quadruplex for sequence-specific DNA detection

A simple, sequence-specific DNA detection method, utilizing a fluorescent 2-aminopurine (2-AP) nucleobase analogue-containing split G-quadruplex as the key detection component, is described. In the sensor, the 2-AP-containing G-quadruplex is split into two segments and linked to a target-specific overhang sequence. The separate G-quadruplex sequences form an active G-quadruplex structure only in the presence of a complementary target DNA, which leads to a significant increase in the intensity of fluorescence from the 2-AP fluorophore. This simple, one-step, homogenous assay was successfully employed to detect target DNA with a high selectivity. In addition, the practical applicability of the detection method was demonstrated by its use in analyzing target DNAs in human serum. To the best of our knowledge, this is the first time that an investigation was carried out in which a fluorescent nucleobase analogue was incorporated into a split G-quadruplex structure and this structure was utilized as the foundation for a specific DNA sensor.

Improving the Signal-to-Background Ratio during Catalytic Hairpin Assembly through Both-End-Blocked DNAzyme

Catalyzed hairpin assembly (CHA) is an important DNA engineering tool for a variety of applications such as DNA nanotechnology and biosensing. Here we report a hairpin-type of both-end-blocked DNAzyme to improve the signal-to-background ratio during the CHA process. In the design, the DNAzyme activity can be blocked efficiently via locking both ends of the G-rich DNAzyme sequence in the loop and stem (blocking efficiency = 96%) and can be easily recovered during the CHA process (activation efficiency = 94%). The both-end-blocked DNAzyme is by far the most sensitive optical detection mode for monitoring the CHA process that can be used for determination of 0.05 fmol miRNA-21. The fabricated CHA-DNAzyme sensing system was also able to discriminate miRNA-21 from single-/three-base mismatch miRNA-21. The feasibility of real application was also tested via detection of miRNA-21 levels in tumor cell samples. Therefore, the sensing system with the advantages of convenience, high sensitivity, and selectivity is an appealing strategy for miRNA detection.

Single polydiacetylene microtube waveguide platform for discriminating microRNA-215 expression levels in clinical gastric cancerous, paracancerous and normal tissues

MicroRNAs (miRNAs) have emerged as novel biomarkers for human early-phase cancer diagnosis and disease prevention recently. Herein, we reported a novel miRNA-215 targeting biosensor, which was based on single polydiacetylene (PDA) microtube waveguide system integrated with sandwich-type hybridization design and condensing enrichment effect. The target miRNA could be captured by oligonucleotides conjugated on the surface of PDA microtube and Au nanorod (AuNR) respectively, resulting in the out-coupled fluorescence of PDA microtube quenching. In this strategy, the formation of a sandwich structure, as a result of co-hybridization of the target miRNA, enabled simplified preparation process, enhanced reaction efficiency, and increased recyclability and stability of the platform. Based on condensing enrichment effect, the co-hybridization reaction could be enriched on the surface of microtube and the proposed platform could easily achieve highly sensitive detection of miRNA-215 in one step. Remarkably, this platform could be directly applied to discriminate the miRNA-215 expression levels in clinical gastric cancerous, paracancerous and normal tissues samples. This assay offers a simple and convenient method for miRNA quantification in clinical samples, even with the potential for invasive, portable equipment for early clinical diagnosis of diseases.

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.