Highly fluorescent morpholine naphthalimide deoxyuridine nucleotide for the detection of miRNA 24-3P through rolling circle amplification

Aggregation-Induced Emission Luminogen: Role in Biopsy for Precision Medicine

Biopsy, including tissue and liquid biopsy, offers comprehensive and real-time physiological and pathological information for disease detection, diagnosis, and monitoring. Fluorescent probes are frequently selected to obtain adequate information on pathological processes in a rapid and minimally invasive manner based on their advantages for biopsy. However, conventional fluorescent probes have been found to show aggregation-caused quenching (ACQ) properties, impeding greater progresses in this area. Since the discovery of aggregation-induced emission luminogen (AIEgen) have promoted rapid advancements in molecular bionanomaterials owing to their unique properties, including high quantum yield (QY) and signal-to-noise ratio (SNR), etc. This review seeks to present the latest advances in AIEgen-based biofluorescent probes for biopsy in real or artificial samples, and also the key properties of these AIE probes. This review is divided into: (i) tissue biopsy based on smart AIEgens, (ii) blood sample biopsy based on smart AIEgens, (iii) urine sample biopsy based on smart AIEgens, (iv) saliva sample biopsy based on smart AIEgens, (v) biopsy of other liquid samples based on smart AIEgens, and (vi) perspectives and conclusion. This review could provide additional guidance to motivate interest and bolster more innovative ideas for further exploring the applications of various smart AIEgens in precision medicine.

Blocker-dUThiophene poly tailing-based method for assessing methyl transferase activity

In this report, we present a method for the selective and sensitive detection of methyl transferase activity. The method uses a dsDNA probe that contains C3 spacers and is coupled with dUThioTP-TdT polymerase-based poly-tailing. The short dsDNA probe is designed with C3 spacers at both 3' ends to prevent any type of tailing reaction. However, the probe contains a methyl transferase recognition sequence that can methylate adenosines in the palindromic part of both strands. When a specific DpnI endonuclease is introduced, it selectively cleaves the dsDNA probe such that both strands are methylated, unblocking the probe into two separate dsDNA forms with exposed 3' OH groups. This makes the probe susceptible to tailing in the presence of a TdT tailing polymerase. The unblocked probe is then subjected to fluorescent dUThioTP-based tailing, which produces a strong fluorescent signal that indicates the presence of methyl transferase activity. In the absence of methyl transferase, the probe remains in the blocked state and does not undergo fluorescence. This method has a limit of detection of 0.049 U/mL with good selectivity and the potential for accurate MTase analysis.

Isothermal nucleic acid amplification and its uses in modern diagnostic technologies

Nucleic acids are prominent biomarkers for diagnosing infectious pathogens using nucleic acid amplification techniques (NAATs). PCR, a gold standard technique for amplifying nucleic acids, is widely used in scientific research and diagnosis. Efficient pathogen detection is a key to adequate food safety and hygiene. However, using bulky thermal cyclers and costly laboratory setup limits its uses in developing countries, including India. The isothermal amplification methods are exploited to develop miniaturized sensors against viruses, bacteria, fungi and other pathogenic organisms and have been applied for in situ diagnosis. Isothermal amplification techniques have been found suitable for POC techniques and follow WHO's ASSURED criteria. LAMP, NASBA, SDA, RCA and RPA are some of the isothermal amplification techniques which are preferable for POC diagnostics. Furthermore, methods such as WGA, CPA, HDA, EXPAR, SMART, SPIA and DAMP were introduced for even more accuracy and robustness. Using recombinant polymerases and other nucleic acid-modifying enzymes has dramatically broadened the detection range of target pathogens under the scanner. The coupling of isothermal amplification methods with advanced technologies such as CRISPR/Cas systems, fluorescence-based chemistries, microfluidics and paper-based sensors has significantly influenced the biosensing and diagnosis field. This review comprehensively analyzed isothermal nucleic acid amplification methods, emphasizing their advantages, disadvantages and limitations.

Unnatural nucleotide-based rkDNA probe combined with graphene oxide for detection of alkaline phosphatase activity

In this study we developed a fluorescent double-stranded DNA, incorporating an unnatural dU^rk nucleotide, that we used as a probe for the detection of alkaline phosphatase (ALP) based on enzymatic cleavage of the non-fluorescent complementary strand. Primer extension performed using the unnatural nucleotide triphosphate dU^rkTP and the natural deoxynucleotide triphosphates dATP, dCTP, and dGTP provided a simple fluorescent DNA strand that hybridized with the 5́-monophosphate non-fluorescent complementary strand. When applying the 5́-phosphate recognition and cleavage properties of lambda exonuclease (λ-exo), this probe could bind to graphene oxide (GO) and quench the fluorescence (in the absence of ALP) or not bind to GO and retain its fluorescence (in the presence of ALP). We obtained strongly fluorescent DNA strands through simple incorporation of multiple A sites in the complementary sequence, thereby increasing the number of dU^rk residues during primer extension. This unnatural nucleotide-based rkDNA probing system exhibited high fluorescence differentiation for discriminating the status of ALP. This rkDNA-GO probing system appears to be a promising tool for monitoring the activity of disease-associated enzymes.

Modern Methods for Assessment of microRNAs

The review discusses modern methods for the quantitative and semi-quantitative analysis of miRNAs, which are small non-coding RNAs affecting numerous biological processes such as development, differentiation, metabolism, and immune response. miRNAs are considered as promising biomarkers in the diagnosis of various diseases.

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

In this study we developed a very simple and rapid miRNA 21 detection system using a novel quinolinium diethylamino salicylaldehyde (QnDESA) probe for sensing the 22AG hybrid G-quadruplex with a single-step rolling circle amplification (RCA) reaction. We synthesized a circular DNA padlock template containing a sequence complementary to the 22AG hybrid G-quadruplex, used SplintR ligase to ensure perfect hybridization with miRNA 21, applied this circular DNA and phi-29 DNA polymerase for tandem amplification of the 22AG hybrid G-quadruplex sequence, and then probed the product using QnDESA. This combination of RCA-G-quadruplex and QnDESA allowed the rapid (1 h) and simple one-pot detection of miRNA 21 based on a change in fluorescence. In addition, this system displayed high sensitivity (limit of detection: 1.37 fM) and selectivity. This probing system should also be useful for identifying a diverse range of DNA- and RNA-based biomarkers.

Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets

Detection and quantification of biotargets are important analytical tasks, which are solved using a wide range of various methods. In recent years, methods based on the isothermal amplification of nucleic acids (NAs) have been extensively developed. Among them, a special place is occupied by rolling circle amplification (RCA), which is used not only for the detection of a specific NA but also for the analysis of other biomolecules, and is also a versatile platform for the development of highly sensitive methods and convenient diagnostic devices. The present review reveals a number of methodical aspects of RCA-mediated analysis; in particular, the data on its key molecular participants are presented, the methods for increasing the efficiency and productivity of RCA are described, and different variants of reporter systems are briefly characterized. Differences in the techniques of RCA-mediated analysis of biotargets of various types are shown. Some examples of using different RCA variants for the solution of specific diagnostic problems are given.

Determination of miRNA derived from exosomes of prostate cancer via toehold-aided cyclic amplification combined with HRP enzyme catalysis and magnetic nanoparticles

MicroRNAs (miRNAs) play a significant role in tumorigenesis and tumor development. Exosomal microRNA-141 (miRNA-141, miR-141) has been reported to be overexpressed in prostate cancer (PCa) and has become a potential biomarker for the diagnosis of PCa. Herein, a novel fluorescent biosensor based on toehold-aided cyclic amplification combined with horseradish peroxidase (HRP) enzyme catalysis and magnetic nanoparticles (MNPs) was designed for determination of the exosomes-derived microRNA-141 (miRNA-141, miR-141). The synergy of HRP enzyme catalysis and toehold mediated strand display reaction (TSDR) increase the sensitivity of the method, and the good separation ability of MNPs ensures the specificity of the method. Therefore, under the optimized experimental conditions, the highly sensitive and specific detection of miRNA-141 can be realized, and the detection limit is as low as 10 fM. More importantly, the biosensor successfully determinates the exosomal miR-141 in the plasma of patients with PCa.

Rapid and highly sensitive hairpin structure-mediated colorimetric detection of miRNA

Herein, we report a novel hairpin structure-mediated diagnostic method for the simple and rapid colorimetric detection of miRNA through the sensing of pyrophosphate. When the hairpin structure of the template DNA (h-Probe) was hybridized with the primer, the DNA primer extension mediated by nPfu special enzyme was blocked. However, this h-Probe was extended using nPfu special enzyme, upon the structural change of the template DNA, from a hairpin to a linear structure, in the presence of the target miRNA. The miRNA-hybridized template DNA sequence was cleaved by a duplex-specific nuclease (DSN), which cleaved the DNA from the RNA-DNA hybrid, thereby allowing the target miRNA to be recycled. Primer extension using nPfu special enzyme produced pyrophosphate when nucleotide triphosphate was incorporated into the DNA; this pyrophosphate was sensed in terms of a color change, from pink to colorless, when using pp Probe, a probe developed previously by our group. This novel system for the colorimetric detection of target miRNA operated with high sensitivity (LOD = 132 aM) and selectivity, with the whole detection process requiring only 30 min. Furthermore, this system could also detect miRNA fluorimetrically with similar sensitivity (LOD = 105 aM), highlighting the dual-sensing properties of pp Probe. This unique, extremely simple, and rapid system for the detection of miRNA through a highly sensitive color change would presumably be useful in applications requiring point-of-care detection.

Polymerase-mediated synthesis of p-vinylaniline-coupled fluorescent DNA for the sensing of nucleolin protein-c-myc G-quadruplex interactions

In this paper we report the synthesis of two deoxyuridine derivatives (dUCN2, dUPy)-featuring p-vinylaniline-based fluorophores linked through a propargyl unit at the 5' position-that function as molecular rotors. This probing system proved to be useful for the sensing of gene regulation arising from interactions between this G-quadruplex and nucleolin.

Combined recombinase polymerase amplification/rkDNA-graphene oxide probing system for detection of SARS-CoV-2

The development of rapid, highly sensitive, and selective methods for the diagnosis of infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) should help to prevent the spread of this pandemic virus. In this study, we combined recombinase polymerase amplification (RPA), as a means of isothermal DNA amplification, with an rkDNA-graphene oxide (GO) probe system to allow the rapid detection of SARS-CoV-2 with high sensitivity and selectivity. We used in situ enzymatic synthesis to prepare an rkDNA probe that was complementary to an RPA-amplified sequence of the target N-gene of SARS-CoV-2. The fluorescence of this rkDNA was perfectly quenched in the presence of GO. When the quenched rkDNA-GO system was added to the RPA-amplified sequence of the target SARS-CoV-2, the fluorescence recovered dramatically. The combined RPA/rkDNA-GO system exhibited extremely high selectivity (discrimination factor: 17.2) and sensitivity (LOD = 6.0 aM) for the detection of SARS-CoV-2. The total processing time was only 1.6 h. This combined RPA/rkDNA-GO system appears to be a very efficient and simple method for the point-of-care detection of SARS-CoV-2.

rkDNA-graphene oxide as a simple probe for the rapid detection of miRNA21

In this study we developed a novel diagnostic tool for the detection of miRNA21, based on the fluorescent nucleotide morpholine naphthalimide deoxyuridine (dUrkTP). We incorporated dUrkTP into DNA through primer extension to obtain rkDNA displaying high fluorescence. We then used lambda exonuclease, a specific nuclease for 3́-monophosphate-containing DNA, to separate rkDNA from its complementary sequence. The fluorescence of the free rkDNA was quenched dramatically upon interacting with graphene oxide (GO). Our rkDNA-GO fluorescence probing system exhibited high sensitivity and selectivity for the detection of miRNA21. This inexpensive probing system, employing simple primer extension and exonuclease degradation, required only 30 min to detect its target miRNA. This strategy appears suitable for the detection of diverse types of miRNA.