Sensitive fluorescent detection of DNA methyltransferase using nicking endonuclease-mediated multiple primers-like rolling circle amplification

New G-Triplex DNA Dramatically Activates the Fluorescence of Thioflavin T and Acts as a Turn-On Fluorescent Sensor for Uracil-DNA Glycosylase Activity Detection

G-triplexes are G-rich oligonucleotides composed of three G-tracts and have absorbed much attention due to their potential biological functions and attractive performance in biosensing. Through the optimization of loop compositions, DNA lengths, and 5'-flanking bases of G-rich sequences, a new stable G-triplex sequence with 14 bases (G3-F15) was discovered to dramatically activate the fluorescence of Thioflavin T (ThT), a water-soluble fluorogenic dye. The fluorescence enhancement of ThT after binding with G3-F15 reached 3200 times, which was the strongest one by far among all of the G-rich sequences. The conformations of G3-F15 and G3-F15/ThT were studied by circular dichroism. The thermal stability measurements indicated that G3-F15 was a highly stable G-triplex structure. The conformations of G3-F15 and G3-F15/ThT in the presence of different metal cations were studied thoroughly by fluorescent spectroscopy, circular dichroism, and nuclear magnetic resonance. Furthermore, using the G3-F15/ThT complex as a fluorescent probe, a robust and simple turn-on fluorescent sensor for uracil-DNA glycosylase activity was developed. This study proposes a new systematic strategy to explore new functional G-rich sequences and their ligands, which will promote their applications in diagnosis, therapy, and biosensing.

Screening and Application of DNA Aptamers for Heparin-Binding Protein

Rapid detection of heparin-binding protein (HBP) is essential for timely intervention in sepsis cases. Current detection techniques are usually antibody-based immunological methods, which have certain problems, such as complexity and slow detection, and fall short in meeting the urgency of clinical needs. The application of an aptamer can address these concerns well. In this study, HBP-specific DNA aptamers were screened first. Among which, Apt-01, Apt-02, and Apt-13 had a high affinity for HBP, exhibiting impressive KD values of 3.42, 1.44, and 1.04 nmol/L, respectively. Then, the aptamer of HBP and its partially complementary primer probe were combined to form double-stranded DNA (dsDNA) and synthesize a circular DNA template. The template is complementary to the primer probe, but due to the presence of dsDNA, ExoIII cleaves C2-13 as an RCA primer probe, rendering the template unable to recognize the primer probe and preventing the RCA reaction from proceeding. When the target is present, it competes with the adapter for recognition and releases C2-13, exposing its 3' end. After initiating the RCA at room temperature and reacting with SYBR GreenII at 37 °C for 20 min, fluorescence changes can be observed and quantitatively analyzed at a 530 nm wavelength, achieving quantitative biological analysis. Apt-01 was used to develop a fluorescent biosensor for HBP detection, which exhibited a good linear range (0.01 nmol/L to 10 nmol/L) and detection limit (0.0056 nmol/L). This advancement holds the potential to lay a solid groundwork for pioneering sensitive and specific methods for HBP detection and to significantly enhance the diagnostic processes for sepsis.

Fluorogenic RNA Aptamer-Based Amplification and Transcription Strategy for Label-free Sensing of Methyltransferase Activity in Complex Matrixes

DNA methyltransferase is significant in cellular activities and gene expression, and its aberrant expression is closely linked to various cancers during initiation and progression. Currently, there is a great demand for reliable and label-free techniques for DNA methyltransferase evaluation in tumor diagnosis and cancer therapy. Herein, a low-background fluorescent RNA aptamer-based sensing approach for label-free quantification of cytosine-guanine (CpG) dinucleotides methyltransferase (M.SssI) is reported. The fluorogenic light-up RNA aptamers-based strategy exhibits high selectivity via restriction endonuclease, padlock-based recognition, and RNA transcription. By combining rolling circle amplification (RCA), and RNA transcription with fluorescence response of RNA aptamers of Spinach-dye compound, the proposed platform exhibited efficiently ultrahigh sensitivity toward M.SssI. Eventually, the detection can be achieved in a linear range of 0.02-100 U mL-1 with a detection limit of 1.6 × 10-3 U mL-1. Owing to these superior features, the method is further applied in serum samples spiked M.SssI, which delivers a recovery ranging from 92.0 to 107.0% and a relative standard deviation <7.0%, providing a promising and practical tool for determining M.SssI in complex biological matrices.

Identification and Quantification of Locus-Specific 8-Oxo-7,8-dihydroguanine in DNA at Ultrahigh Resolution Based on G-Triplex-Assisted Rolling Circle Amplification

Damage of reactive oxygen species to various molecules such as DNA has been related to many chronic and degenerative human diseases, aging, and even cancer. 8-Oxo-7,8-dihydroguanine (OG), the most significant oxidation product of guanine (G), has become a biomarker of oxidative stress as well as gene regulation. The positive effect of OG in activating transcription and the negative effect in inducing mutation are a double-edged sword; thus, site-specific quantification is helpful to quickly reveal the functional mechanism of OG at hotspots. Due to the possible biological effects of OG at extremely low abundance in the genome, the monitoring of OG is vulnerable to signal interference from a large amount of G. Herein, based on rolling circle amplification-induced G-triplex formation and Thioflavin T fluorescence enhancement, an ultrasensitive strategy for locus-specific OG quantification was constructed. Owing to the difference in the hydrogen-bonding pattern between OG and G, the nonspecific background signal of G sites was completely suppressed through enzymatic ligation of DNA probes and the triggered specificity of rolling circle amplification. After the signal amplification strategy was optimized, the high detection sensitivity of OG sites with an ultralow detection limit of 0.18 amol was achieved. Under the interference of G sites, as little as 0.05% of OG-containing DNA was first distinguished. This method was further used for qualitative and quantitative monitoring of locus-specific OG in genomic DNA under oxidative stress and identification of key OG sites with biological function.

In situ growth of TiO2/Ti3C2 MXene Schottky heterojunction as a highly sensitive photoelectrochemical biosensor for DNA detection

In this work, a heterojunction composed of a TiO₂ nanosheet and layered Ti₃C₂ was synthesized by directly growing TiO₂ in Ti₃C₂ MXene. Compared with pure TiO₂, TiO₂/Ti₃C₂ composites had increased surface area, and a light absorption range that extended from ultraviolet to visible light, which greatly extended the life of photogenerated carriers. A photoelectrochemical biosensor for DNA detection was constructed based on the TiO₂/Ti₃C₂ heterogeneous structure, which was comprehensively studied based on photocurrent responses. In the absence of the target, the CdSe QDs were close to the surface of the electrode, resulting in enhanced sensitization and increased photocurrent. In the presence of the target, the photocurrent decreases due to the formation of rigid double strands with the probe DNA, which caused the CdSe QDs to be far away from the electrode surface. The sensor had stability and sensitivity for DNA detection in the range of 10 nM-10 fM, and the lower detection limit was 6 fM. Its outstanding characteristics also provided ideas for detecting various other target DNA for early diagnosis of various diseases.

Construction of rolling circle amplification products-based pure nucleic acid nanostructures for biomedical applications

Nucleic acid nanomaterials with good biocompatibility, biodegradability, and programmability have important applications in biomedical field. Nucleic acid nanomaterials are usually combined with some inorganic nanomaterials to improve their biological stability. However, undefined toxic side effects of composite nanocarriers hamper their application in vivo. As a nanotool capable of avoiding potential biotoxicity, nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in the field of biomedicine in recent years. Rolling circle amplification (RCA) is an isothermal enzymatic nucleic acid amplification technology for large-scale production of periodic DNA/RNA with pre-designed desirable structures and functions. RCA products with different functional parts can be customized by changing the sequence of the circular template, thereby generating complex multifunctional DNA nanostructures, such as DNA nanowire, nanoflower, origami, nanotube, nanoribbon, etc. More importantly, RCA products as nonnicked building blocks can enhance the biostability of DNA nanostructures, especially in vivo. These RCA products-based nucleic acid nanostructures can be used as scaffolds or nanocarriers to interact or load with metal nanoparticles, proteins, lipids, cationic polymers, therapeutic nucleic acids or drugs, etc. This paper reviews the assembly strategies of RCA based DNA nanostructures with different shape and their applications in biosensing, bioimaging and biomedicine. Finally, the development prospects of the nucleic acid nanomaterials in clinical diagnosis and treatment of diseases are described. STATEMENT OF SIGNIFICANCE: As a nanotool capable of avoiding potential biotoxicity, nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in the field of biomedicine in recent years. Rolling circle amplification (RCA) is an isothermal enzymatic nucleic acid amplification technology for large-scale production of periodic DNA/RNA with pre-designed desirable structures and functions. This paper reviews the construction of various shapes of pure nucleic acid nanomaterials based on RCA products and their applications in biosensing, bioimaging and biomedicine. This will promote the development of biocompatible DNA nanovehicles and their further application in living systems, including bioimaging, molecular detection, disease diagnosis and drug delivery, finally producing a significant impact in the field of nanotechnology and nanomedicine.

HpaII-assisted and linear amplification-enhanced isothermal exponential amplification fluorescent strategy for rapid and sensitive detection of DNA methyltransferase activity

The detection of methyltransferase (MTase) activity is of great significance in methylation-related disease diagnosis and drug screening. Herein, a HpaII-assisted and linear amplification-enhanced exponential amplification strategy is proposed for sensitive and label-free detection of M.SssI MTase activity. The P1 probe contains self-complementary sequence 5'-CTAGCCGGCTAG-3' at 3'-terminal. After denaturation and annealing, P1 probes hybridize with itself to generate P1 duplexes. M.SssI MTase induces methylation of cytosine at 5'-CG-3' in P1 duplexes, and thus, HpaII fails to cleave at 5'-CCGG-3' due to methylation sensitivity, leaving P1 duplex intact. Then, these intact P1 duplexes are extended along 3'-terminal through Vent (exo^-) DNA polymerase to generate dsDNA, which is recognized and nicked at the recognition sites by Nt.BstNBI, releasing two copies of primer X. Primer X hybridizes with X' at the amplification template T1 (X'-Y'-X') and then serves as primers to trigger the exponential amplification reaction (EXPAR). The point of inflection (POI) values of real-time fluorescence curves is linearly correlated with the logarithm of M.SssI MTase concentration in the range of 0.125 [Formula: see text] 8 U mL^-1 with a low detection limit of 0.034 U mL^-1. In the absence of M.SssI, P1 duplexes are cut by HpaII and separated into ssDNA under the executed temperature of EXPAR and thus unable to trigger the amplification. The strategy provides good selectivity against other types of MTases and protein and is able to detect M.SssI activity in human serum. Furthermore, the analytical method has the generality and can be extended to the analysis of other types of DNA MTases.

An ultrasensitive bunge bedstraw herb type DNA machine for absolute quantification of mRNA in single cell

Messenger ribonucleic acids (mRNAs) comprise a class of small nucleic acids carrying genetic information, which exhibit very important role in medical research and diagnosis. If only the mean mRNA expression levels of the mRNA population are considered in medical research, important information linking mRNA expression and cellular function may be lost. Single-cell analysis provides valuable insights into studying its heterogeneity, signaling, and stochastic gene expression. In this study, a "bunge bedstraw herb"-type DNA machine based on DNAzyme catalyzing coupled clamping hybrid chain reaction (c-HCR) is presented. In the DNA machine, a bunge bedstraw herb-type DNA structure was first formed by hybridizing a core junction scaffold cruciform probe to a hairpin probe that can trigger the c-HCR via a target molecule in four directions. This approach can reduce the detection limit of mRNA to 5 × 10^-15 M. Absolute quantification of survivin mRNA in individual cells was achieved using the DNA machine on a microfluidic chip electrophoresis platform. The reported method represents an unprecedented single-cell analysis platform for single-cell biology studies.

Simple Detection of DNA Methyltransferase with an Integrated Padlock Probe

DNA methyltransferases (MTases) can be regarded as biomarkers, as demonstrated by many studies on genetic diseases. Many researchers have developed biosensors to detect the activity of DNA MTases, and nucleic acid amplification, which need other probe assistance, is often used to improve the sensitivity of DNA MTases. However, there is no integrated probe that incorporates substrates and template and primer for detecting DNA MTases activity. Herein, we first designed a padlock probe (PP) to detect DNA MTases, which combines target detection with rolling circle amplification (RCA) without purification or other probe assistance. As the substrate of MTase, the PP was methylated and defended against HpaII, lambda exonuclease, and ExoI cleavage, as well as digestion, by adding MTase and the undestroyed PP started RCA. Thus, the fluorescent signal was capable of being rapidly detected after adding SYBR^TM Gold to the RCA products. This method has a detection limit of approximately 0.0404 U/mL, and the linear range was 0.5–110 U/mL for M.SssI. Moreover, complex biological environment assays present prospects for possible application in intricacy environments. In addition, the designed detection system can also screen drugs or inhibitors for MTases.

Construction of an APE1-Mediated Cascade Signal Amplification Platform for Homogeneously Sensitive and Rapid Measurement of DNA Methyltransferase in Escherichia coli Cells

DNA methylation is an essential genomic epigenetic behavior in both eukaryotes and prokaryotes. Deregulation of DNA methyltransferase (Dam MTase) can change the DNA methylation level and cause various diseases. Herein, we develop an apurinic/apyrimidinic endonuclease 1 (APE1)-mediated cascade signal amplification platform for homogeneously sensitive and rapid measurement of Dam MTase in Escherichia coli cells. This assay involves a partial double-stranded DNA (dsDNA) substrate and two hairpin signal probes (HP1 and HP2) that are modified with Cy5 and BHQ2 at two ends, respectively. When Dam MTase is present, it methylates the dsDNA substrate, and subsequently, endonuclease DpnI cleaves the methylated substrate, yielding trigger probe 1. Hybridization of trigger probe 1 with HP1 forms a partial dsDNA containing an apurinic/apyrimidinic (AP) site, which is cleaved by APE1 to induce the cyclic cleavage of HP1 and the production of abundant trigger probe 2. Subsequent hybridization of trigger probe 2 with HP2 forms a partial dsDNA with an AP site, inducing the cyclic cleavage of HP2 by APE1. Consequently, cyclic cleavage of HP1 and HP2 induces the generation of abundant Cy5 molecules, which are easily measured by single-molecule imaging. This assay can be performed homogeneously and rapidly within 2 h, which is the shortest among the reported amplification-based assays. Moreover, it exhibits good selectivity and high sensitivity, and it can discriminate Dam MTase from other enzymes and screen inhibitors. Importantly, it can accurately measure the Dam MTase activity in serum and E. coli cells, with promising applications in clinical diagnosis and drug discovery.

Development of the DNA-based biosensors for high performance in detection of molecular biomarkers: More rapid, sensitive, and universal

The molecular biomarkers are molecules that are closely related to specific physiological states. Numerous molecular biomarkers have been identified as targets for disease diagnosis and biological research. To date, developing highly efficient probes for the precise detection of biomarkers has become an attractive research field which is very important for biological and biochemical studies. During the past decades, not only the small chemical probe molecules but also the biomacromolecules such as enzymes, antibodies, and nucleic acids have been introduced to construct of biosensor platform to achieve the detection of biomarkers in a highly specific and highly efficient way. Nevertheless, improving the performance of the biosensors, especially in clinical applications, is still in urgent demand in this field. A noteworthy example is the Corona Virus Disease 2019 (COVID-19) that breaks out globally in a short time in 2020. The COVID-19 was caused by the virus called SARS-CoV-2. Early diagnosis is very important to block the infection of the virus. Therefore, during these months scientists have developed dozens of methods to achieve rapid and sensitive detection of the virus. Nowadays some of these new methods have been applied for producing the commercial detection kit and help people against the disease worldwide. DNA-based biosensors are useful tools that have been widely applied in the detection of molecular biomarkers. The good stability, high specificity, and excellent biocompatibility make the DNA-based biosensors versatile in application both in vitro and in vivo. In this paper, we will review the major methods that emerged in recent years on the design of DNA-based biosensors and their applications. Moreover, we will also briefly discuss the possible future direction of DNA-based biosensors design. We believe this is helpful for people interested in not only the biosensor field but also in the field of analytical chemistry, DNA nanotechnology, biology, and disease diagnosis.

Recent advances in biological detection with rolling circle amplification: design strategy, biosensing mechanism, and practical applications

Rolling circle amplification (RCA) is a simple and isothermal DNA amplification technique that is used to generate thousands of repeating DNA sequences using circular templates under the catalysis of DNA polymerase.

Label-free fluorescence strategy for methyltransferase activity assay based on poly-thymine copper nanoclusters engineered by terminal deoxynucleotidyl transferase

The assay of detecting DNA methyltransferase activity has been identified as one of the central challenges in cancer diagnostics as DNA methylation is closely related to the diagnosis and treatment of tumors. In this study, a label-free fluorescence probe based on poly-thymine copper nanoclusters engineered by terminal deoxynucleotidyl transferase is proposed for methyltransferase activity assay. Taking advantage of the efficient polymerization extension reaction catalyzed by terminal deoxynucleotidyl transferase and the copper nanoclusters with large Stokes shift instead of labeling fluorescent dyes, the strategy exhibits a broader linear scope from 1 to 300 U mL^-1 with a detection limit of 0.176 U mL^-1. The economical method is specificity for M.SssI and also provides a convenient and high-throughput platform for screening the DNA methylation inhibitors, which displays a great potential for the practical applications of the drug development and clinical cancer diagnosis in the future.

Detection of average methylation level of specific genes by binary-probe hybridization

We developed a simple and highly-selective method for 5-methylcytosine detection of specific gene sequence based on binary-probe DNA hybridization. The sequence complementary to the target was designed into two probes, and each fragment of binary probes bound to a relatively short sequence of the target, which made it sensitive to the base mismatches introduced by bisulfite treatment. The advantages of a low detection limit of methylation abundance of 0.1% for the fully methylated target and high sensitivity of 10 pM have been proved by the successful design of binary-probe hybridization. The successful design of the binary probes makes it possible to quantify the average methylation levels of five CpG sites. Thirty-two DNA strands containing 5, 4, 3, 2, 1 and 0 CpG sites were successfully analyzed with the same pair of binary probes. The higher the average methylation level of the target was, the higher the degree of the hybridization reaction. Based on the simple construction of the binary-probe hybridization, the developed biosensor exhibited signals proportional to the average methylation level of the vimentin gene and could evaluate the average methylation level of artificial mixtures. Furthermore, the method has been used to detect vimentin methylation in a genomic context with good specificity, which indicated its potential in the pre-diagnosis of methylation related disease.

Ultra-sensitive detection of DNA N6-adenine methyltransferase based on a 3D tetrahedral fluorescence scaffold assisted by symmetrical double-ring dumbbells

DNA methylation is an epigenetic modification that plays a vital role in X chromosome inactivation, genome imprinting, and gene expression. DNA methyltransferase establishes and maintains a stable methylation state in genomic DNA. Efficient and specific DNA methyltransferase testing is essential for the early diagnosis and treatment of cancer. In this study, we designed an ultra-sensitive fluorescent biosensor, based on a 3D tetrahedral fluorescent scaffold assisted by symmetrical double-ring dumbbells, for the detection of DNA-[N 6-adenine]-methyltransferase (Dam MTase). Double-stranded DNA was methylated by Dam MTase and then digested by DpnI to form two identical dumbbell rings. The 3D tetrahedral fluorescent scaffold was synthesized from four oligonucleotide chains containing hairpins. When the sheared dumbbells reacted with the 3D tetrahedral fluorescent scaffold, the hairpins opened and a fluorescence signal could be detected. The strategy was successful over a wide detection range, from 0.002 to 100 U mL^-1 Dam MTase, and the lowest detection limit was 0.00036 U mL^-1. Control experiments with M.SssI methyltransferase and HpaII methylation restriction endonuclease confirmed the specificity of the method. Experiments with spiked human serum and the 5-fluorouracil inhibitor proved the suitability of the method for early cancer diagnosis.

'Plug and play' microelectrode assisted with Y-motif-mediated primer-free cyclic signal amplification for sensitive quantitation of DNA methyltransferase activity

DNA methyltransferase (MTase), modulating the level of genomic DNA methylation, harbors both a pharmacological target for clinical therapy and a potential biomarker for genetic disorders and tumorigenesis. Typical homogeneous electrochemical approaches, employing solution phase probes, have been considered simple, efficient, and economical method, yet these architectures usually require electroactive molecules labeling, rely on weak electrostatic adsorption interaction, and possess low sensitivity. For circumventing the above drawbacks, herein, we devise a 'plug and play' microelectrode featuring microminiaturization, rapid response time and enhanced mass transport to quantify MTase activity through monitoring the variation of diffusion current of methylene blue (MB) induced by the less-mobile G-quadruplex framework. By coupling the unique signal-transduction approach with Y-motif-mediated primer-free cyclic signal amplification (YPCSA), the miniaturized biosensor possesses low detection limit (down to 2.5 × 10^-4 U mL^-1), high specificity, good stability and satisfying reusability, and has been successfully applied to the screening of MTase inhibitors, holding great potential in clinical diagnosis and pharmacological research.

Multifunctional electrochemical biosensor with "tetrahedral tripods" assisted multiple tandem hairpins assembly for ultra-sensitive detection of target DNA

Nucleic acids are genetic materials in the human body that play important roles in storing, copying, and transmitting genetic information. Abnormal nucleic acid sequences, base mutations, and genetic changes often lead to cancer and other diseases. Meanwhile, methylated DNA is one of the main epigenetic modifications, which is considered to be an excellent biomarker in the early detection, prognosis, and treatment of cancers. Therefore, a multifunctional electrochemical biosensor was constructed with sturdy tetrahedral tripods, which assisted multiple tandem hairpins through base complementary pairing and effective ultra-sensitive detection of targets (DNA, microRNA, and methylated DNA). In the experiments, experimental conditions were optimized, and different DNA concentrations in serum were detected to verify the sensitivity of the biosensor and the feasibility of this protocol. In addition, microRNA and DNA methylation were detected through different designs of tetrahedral tripods (TTs) that capture probes to prove the superiority of this scheme. A sturdy pyramid structure of TTs extremely enhanced the capture efficiency of targets. The targets triggered the one-step isothermal multi-tandem amplification reaction by incubating multiple hairpin assemblies. To our knowledge, a combination of two parts, which greatly reduced background interference and decreased non-specific substance interference, has appeared for the first time in this paper. Moreover, the load area of electrochemical substances was significantly increased than that in previous studies. This greatly increased the detection range and detection limit of targets. The electrochemical signal responses were generated in freely diffusing hexaammineruthenium(iii) chloride (RuHex). RuHex could adhere to the DNA phosphate backbone by a powerful electrostatic attraction, causing increased current responses.

Schematic illustration of the fabricated electrochemical biosensor. TTs assisted multiple tandem hairpins assembly for ultra-sensitive detection of target DNA.

Nonamplification Multiplexed Assay of Endonucleases and DNA Methyltransferases by Colocalized Particle Counting

Restriction endonucleases (ENases) and DNA methyltransferases (MTases) are important enzymes in biological processes, and detection of ENases/MTases activity is significant for biological and pharmaceutical studies. However, available nonamplification methods with a versatile design, desirable sensitivity, and signal production mode of unbiased quantification toward multiple nucleases are rare. By combining deliberately designed hairpin DNA probes with the colocalized particle counting technique, we present a nonamplification, separation-free method for multiplexed detection of ENases and MTases. In the presence of target ENases, the hairpin DNA is cleaved and the resulting DNA sequence forms a sandwich structure to tie two different-colored fluorescent microbeads together to generate a colocalization signal that can be easily detected using a standard fluorescence microscope. The multiplexed assay is realized via different color combinations. For the assay of methyltransferase, methylation by MTases prevents cleavage of the hairpin by the corresponding ENase, leading to decreased colocalization events. Three ENases can be simultaneously detected with high selectivity, minimal cross-talk, and detection limits of (4.1-6.4) × 10^-4 U/mL, and the corresponding MTase activity can be measured without a change of the probe design. The potential for practical application is evaluated with human serum samples and different ENase and MTase inhibitors with satisfactory results. The proposed method is separation-free, unbiased toward multiple targets, and easy to implement, and the strategy has the potential to be extended to other targets.

COVID-19 Pandemic: Review of Contemporary and Forthcoming Detection Tools

Recent severe acute respiratory syndrome 2 (SARS-CoV-2) known as COVID-19, presents a deadly challenge to the global healthcare system of developing and developed countries, exposing the limitations of health facilities preparedness for emerging infectious disease pandemic. Opportune detection, confinement, and early treatment of infected cases present the first step in combating COVID-19. In this review, we elaborate on various COVID-19 diagnostic tools that are available or under investigation. Consequently, cell culture, followed by an indirect fluorescent antibody, is one of the most accurate methods for detecting SARS-CoV-2 infection. However, restrictions imposed by the regulatory authorities prevented its general use and implementation. Diagnosis via radiologic imaging and reverse transcriptase PCR assay is frequently employed, considered as standard procedures, whereas isothermal amplification methods are currently on the verge of clinical introduction. Notably, techniques such as CRISPR-Cas and microfluidics have added new dimensions to the SARS-CoV-2 diagnosis. Furthermore, commonly used immunoassays such as enzyme-linked immunosorbent assay (ELISA), lateral flow immunoassay (LFIA), neutralization assay, and the chemiluminescent assay can also be used for early detection and surveillance of SARS-CoV-2 infection. Finally, advancement in the next generation sequencing (NGS) and metagenomic analysis are smoothing the viral detection further in this global challenge.

Rolling Circle Replication for Biosensing, Bioimaging, and Biomedicine

Rolling circle replication (RCR), including rolling circle amplification (RCA) and rolling circle transcription (RCT), is an isothermal enzymatic reaction. Because of its high amplification efficiency, RCR is a powerful biosensing tool for detecting biomolecules. In recent years, RCR has also been extended to the field of bioimaging to better understand biological pathways. Furthermore, RCR provides a simple technique to design and generate DNA/RNA structures with unique advantages in delivering drugs and enhanced targeting ability. In this review, we introduce the fundamentals of RCR and describe the most recent advances in RCR-based detection methods and delivery vehicles for biosensing, bioimaging, and biomedicine. Finally, some challenges and further opportunities of RCR-based biotechnology are discussed.

Ultrasensitive Detection of 17β-Estradiol (E2) Based on Multistep Isothermal Amplification

17β-Estradiol (E2) can cause an adverse effect on the human endocrine system even at the nanomolar level. Measurements of very low levels of E2 remain a critical challenge due to insufficient sensitivity. In this study, a multistep isothermal amplification fluorescence strategy was constructed, which could realize the exponential amplification of target E2. Specifically, strand displacement reaction (SDA), rolling circle amplification (RCA), and multiprimed rolling circle amplification (MRCA) were combined in a series to quantify trace complementary strand of E2 (cDNA). The E2 aptamer and cDNA were hybridized and modified on the magnetic beads. E2 could bind to its aptamer and cause the release of the cDNA. Then, cDNA would combine with the template DNA, initiating the SDA-RCA-MRCA. The molecular beacons, possessing low background signal, whose fluorescence was quenched in the state of chain folding, could be specifically recognized by the long single-stranded DNA (L-ssDNA) generated by the multistep isothermal amplification triggered by cDNA, and then the fluorescence of the molecular beacons could be restored. Therefore, the E2 could be quantitatively detected by the recovery fluorescence intensity. The fluorescence value showed a good linear relationship with the concentration of E2 in the range of 0.001836-183.6 nM, and the limit of detection (LOD) was as low as 63.09 fM. In addition, the recovery rates of this method spiked in milk and water were 80.8-107.0%, respectively. This method has the advantage of multistep isothermal amplification to obtain abundant fluorescence signals, which may provide a new possibility for highly sensitive detection of other small-molecule targets.

New insight into G-quadruplexes; diagnosis application in cancer

Biochemical properties and flexibility of nitrogenous bases allow DNA to fold into higher-order structures. Among different DNA secondary structure, G-quadruplexes (tetrapelexes-G4) - which are formed in guanine rich sequences - have gained more attention because of their biological significance, therapeutic intervention, and application in molecular device and biosensor. G4-quadruplex studies categorize into three main fields, in vivo, in vitro, and in silico. The in vitro field includes G4 synthetic oligonucleotides. This review focuses on the G-quadruplex synthetic aptamers structure features and considers the applicability of G4-aptamers for cancer biomarkers detection. Various biosensing methods will be reviewed based on G-quadruplex aptamers for cancer detection.

Protein detection based on rolling circle amplification sensors

Rolling circle amplification (RCA) is an isothermal process under the action of DNA polymerases. Large-scale DNA templates have been generated using RCA for target detection. Some signal amplification strategies including optical sensors and electrochemical sensors based on RCA have been applied to achieve sensitive detection. Sensors based on RCA have attracted increasing interest. Advances in RCA-based sensors for protein detection are reviewed in this paper. The advantages and detection mechanisms of sensors based on RCA are revealed and discussed. Finally, possible challenges and future perspectives are also outlined.

Recent advances in rolling circle amplification-based biosensing strategies-A review

Rolling circle amplification (RCA) is an efficient enzymatic isothermal reaction that using circular probe as a template to generate long tandem single-stranded DNA or RNA products under the initiation of short DNA or RNA primers. As a simplified derivative of natural rolling circle replication which synthesizes copies of circular nucleic acids molecules such as plasmids, RCA amplifies the circular template rapidly without thermal cycling and finds various applications in molecular biology. Compared with other amplification strategies, RCA has many obvious advantages. Firstly, because of the strict complementarity required in ligation of a padlock probe, it endows the RCA reaction with high specificity and can even be utilized to distinguish single base mismatches. Secondly, through the introduction of multiple primers, exponential amplification can be achieved easily and leads to a good sensitivity. Thirdly, RCA products can be customized by manipulating circular templates to generate functional nucleic acids such as aptamer, DNAzymes and restriction enzyme sites. Moreover, the RCA has good biocompatibility and is especially suitable for in situ detection. Therefore, RCA has attracted considerable attention as an efficient and potential tool for highly sensitive detection of biomarkers. Herein, we comprehensively introduce the fundamental principles of RCA technology, summarize it from three aspects including initiation mode, amplification mode and signal output mode, and discuss the recent application of RCA-based biosensor in this review.

Cytosine-5 methylation-directed construction of a Au nanoparticle-based nanosensor for simultaneous detection of multiple DNA methyltransferases at the single-molecule level

DNA methylation at cytosine/guanine dinucleotide islands (CpGIs) is the most prominent epigenetic modification in prokaryotic and eukaryotic genomes. DNA methyltransferases (MTases) are responsible for genomic methylation, and their aberrant activities are closely associated with various diseases including cancers. However, the specific and sensitive detection of multiple DNA MTases has remained a great challenge due to the specificity of the methylase substrate and the rareness of methylation-sensitive restriction endonuclease species. Here, we demonstrate for the first time the cytosine-5 methylation-directed construction of a Au nanoparticle (AuNP)-based nanosensor for simultaneous detection of multiple DNA MTases at the single-molecule level. We used the methyl-directed endonuclease GlaI to cleave the site-specific 5-methylcytosine (5-mC). In the presence of CpG and GpC MTases (i.e., M.SssI and M.CviPI), their hairpin substrates are methylated at cytosine-5 to form the catalytic substrates for GlaI, respectively, followed by simultaneous cleavage by GlaI to yield two capture probes. These two capture probes can hybridize with the Cy5/Cy3-signal probes which are assembled on the AuNPs, respectively, to form the double-stranded DNAs (dsDNAs). Each dsDNA with a guanine ribonucleotide can act as the catalytic substrate for ribonuclease (RNase HII), inducing recycling cleavage of signal probes to liberate large numbers of Cy5 and Cy3 molecules from the AuNPs. The released Cy5 and Cy3 molecules can be simply quantified by total internal reflection fluorescence (TIRF)-based single-molecule imaging for simultaneous measurement of M.SssI and M.CviPI MTase activities. This method exhibits good specificity and high sensitivity with a detection limit of 2.01 × 10-3 U mL-1 for M.SssI MTase and 3.39 × 10-3 U mL-1 for M.CviPI MTase, and it can be further applied for discriminating different kinds of DNA MTases, screening potential inhibitors, and measuring DNA MTase activities in human serum and cell lysate samples, holding great potential in biomedical research, clinical diagnosis, drug discovery and cancer therapeutics.

Homogeneous circle-to-circle amplification for real-time optomagnetic detection of SARS-CoV-2 RdRp coding sequence

Circle-to-circle amplification (C2CA) is a specific and precise cascade nucleic acid amplification method consisting of more than one round of padlock probe ligation and rolling circle amplification (RCA). Although C2CA provides a high amplification efficiency with a negligible increase of false-positive risk, it contains several step-by-step operation processes. We herein demonstrate a homogeneous and isothermal nucleic acid quantification strategy based on C2CA and optomagnetic analysis of magnetic nanoparticle (MNP) assembly. The proposed homogeneous circle-to-circle amplification eliminates the need for additional monomerization and ligation steps after the first round of RCA, and combines two amplification rounds in a one-pot reaction. The second round of RCA produces amplicon coils that anneal to detection probes grafted onto MNPs, resulting in MNP assembly that can be detected in real-time using an optomagnetic sensor. The proposed methodology was applied for the detection of a synthetic complementary DNA of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2, also known as 2019-nCoV) RdRp (RNA-dependent RNA polymerase) coding sequence, achieving a detection limit of 0.4 fM with a dynamic detection range of 3 orders of magnitude and a total assay time of ca. 100 min. A mathematical model was set up and validated to predict the assay performance. Moreover, the proposed method was specific to distinguish SARS-CoV and SARS-CoV-2 sequences with high similarity.

Nicking-assisted on-loop and off-loop enzymatic cascade amplification for optomagnetic detection of a highly conserved dengue virus sequence

Applications of conventional linear ligation-rolling circle amplification (RCA) are restricted by the sophisticated operation steps and unsatisfactory picomolar-level detection limits. We herein demonstrate an RCA-based cascade amplification reaction that converts a side-reaction to secondary amplification, which improves the detection limit and simplifies the operation compared to linear ligation-RCA assays. The proposed nicking-assisted enzymatic cascade amplification (NECA) comprises an on-loop amplification reaction using circular templates to generate intermediate amplicons, and an off-loop amplification reaction using intermediate amplicons as primers for end amplicons. The whole NECA reaction is homogeneous and isothermal. Amplicons anneal to detection probes that are grafted onto magnetic nanoparticles (MNPs), such that MNP clusters form and can be detected in real-time using optomagnetic measurements. The optomagnetic sensor detects the presence and size increase of MNP clusters by optical transmission measurements in an oscillating magnetic field. A detection limit of 2 fM was achieved with a total assay time of ca. 70 min. By combining optomagnetic readouts of signal phase lag and hydrodynamic size increase of MNPs, NECA-based target quantification provided a wide dynamic detection range of ca. 4.5 orders of magnitude. Moreover, the specificity and the serum detection capability of the proposed method were investigated.

Circular Nucleic Acids: Discovery, Functions and Applications

Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.

Construction of a single quantum dot nanosensor with the capability of sensing methylcytosine sites for sensitive quantification of methyltransferase

CpG island methylation plays an important role in diverse biological processes including the regulation of imprinted genes, X chromosome inactivation, and tumor suppressor gene silencing in human cancer. Due to the dependence of DNA methylation on DNA methyltransferase (MTase) activity, DNA MTases have become the potential targets in anticancer therapy. Herein we demonstrate for the first time the construction of a single quantum dot (QD) nanosensor with the capability of sensing methylcytosine sites for sensitive quantification of M.SssI CpG methyltransferase (M.SssI MTase). We design a biotin-/phosphate-modified double-stranded DNA (dsDNA) substrate with a 5'-G-C-G-mC-3'/3'-mC-G-mC-G-5' site for sensing M.SssI MTase. In the presence of M.SssI MTase, the methylation-responsive sequence of the dsDNA substrate is methylated and cleaved by GlaI endonuclease, producing two dsDNA fragments with a free 3'-OH terminus. In the presence of terminal deoxynucleotidyl transferase (TdT), multiple Cy5-dATPs can be sequentially added to the free 3'-OH terminus of dsDNA fragments to obtain biotin-/multiple Cy5-labeled dsDNAs. The resultant biotin-/multiple Cy5-labeled dsDNAs can assemble on the surface of the streptavidin-coated QD to obtain a QD-dsDNA-Cy5 nanostructure in which the fluorescence resonance energy transfer (FRET) from the QD to Cy5 can occur. The emission of Cy5 can be simply quantified by single-molecule detection. By the integration of sensing methylcytosine sites and enzymatic polymerization, the sensitivity of this nanosensor has been significantly enhanced. This nanosensor can detect as low as 2.1 × 10-7 U μL-1 M.SssI MTase with good selectivity against other cytosine MTases, and it can be further applied for the screening of MTase inhibitors and complex biological sample analysis, holding great potential in clinical diagnosis and drug discovery.

Dual-signal amplification strategy: Universal asymmetric tailing-PCR triggered rolling circle amplification assay for fluorescent detection of Cronobacter spp. in milk

Cronobacter spp. are important opportunistic foodborne pathogens in powdered infant formula that cause many serious diseases in neonates and infants. In this study, a novel assay based on dual signal amplification strategy was developed by coupling asymmetric tailing PCR (AT-PCR) with rolling circle amplification (RCA) for the detection of Cronobacter spp. in milk. The tailing single-stranded DNA was generated through AT-PCR and used to initiate RCA, generating tandem repetitive G-quadruplex sequences. In the presence of the fluorescence dye thioflavin T that could intercalate into the G-quadruplex structures, the fluorescence signal was detected with a microplate reader. The AT-PCR coupled with RCA assay was specific for Cronobacter spp. detection because of the highly specific primers chosen for the AT-PCR. The limits of detection were 4.3 × 10¹ cfu/mL in pure culture and 4.5 × 10² cfu/mL in spiked milk, respectively. The fixed sequences designed in the hairpin DNA allowed this AT-PCR coupled with RCA assay to serve as a universal platform for the detection of other pathogens by modifying the specificity of the PCR primers.

A portable oligonucleotide-based microfluidic device for the detection of VEGF165 in a three-step suspended-droplet mode

Vascular endothelial growth factor (VEGF165), an important glycosylated protein from the VEGF family, is a type of signal protein highly associated with the development and progression of cancers. In this work, we designed a G-quadruplex-based aptasensing platform for the sensitive and selective detection of VEGF165 in aqueous solution and red blood cell solution. A long-lived phosphorescence iridium(iii) complex (1) with promising photophysical properties and a large Stokes shift was chosen as a selective G-quadruplex probe. The platform could achieve a limit of detection (LOD) down to the picomolar level using a conventional fluorometer. Furthermore, we successfully applied the platform to a three-step suspended droplet (SD)-based microfluidic device for the monitoring of VEGF165. In contrast to the channel-based and digital microfluidic chips, SD-based chips allow easy introduction of liquid samples, valve-free manipulation of multiple reaction steps and flexible volume range. Importantly, polypropylene (PP), a hydrophobic and thermally stable material, was chosen as a substrate to fabricate the chip for the SD-based microfluidic device. The PP-based chip allows the combination of superhydrophobic force, gravity and surface tension for effective driving of the suspended droplet throughout the channel without reverse migration. After assembling all the major components, including a UV lamp, a rotatable chip holder, a filter and a camera into the portable device, we successfully demonstrated the applicability of the device to detect VEGF165 in aqueous solution with a LOD of 0.33 nM at a signal-to-noise ratio (S/N) of 3 and a linear range of 1-100 nM.

Three-dimensional DNA nanostructures to improve the hyperbranched hybridization chain reaction

Nonenzymatic nucleic acid amplification techniques (e.g. the hybridization chain reaction, HCR) have shown promising potential for amplified detection of biomarkers.

Nonenzymatic nucleic acid amplification techniques (e.g. the hybridization chain reaction, HCR) have shown promising potential for amplified detection of biomarkers. However, the traditional HCR occurs through random diffusion of DNA hairpins, making the kinetics and efficiency quite low. By assembling DNA hairpins at the vertexes of tetrahedral DNA nanostructures (TDNs), the reaction kinetics of the HCR is greatly accelerated due to the synergetic contributions of multiple reaction orientations, increased collision probability and enhanced local concentrations. The proposed quadrivalent TDN (qTDN)-mediated hyperbranched HCR has a ∼70-fold faster reaction rate than the traditional HCR. The approximately 76% fluorescence resonance energy transfer (FRET) efficiency obtained is the highest in the reported DNA-based FRET sensing systems as far as we know. Moreover, qTDNs modified by hairpins can easily load drugs, freely traverse plasma membranes and be rapidly cross-linked via the target-triggered HCR in live cells. The reduced freedom of movement as a result of the large crosslinked structure might constrain the hyperbranched HCR in a confined environment, thus making it a promising candidate for in situ imaging and photodynamic therapy. Hence, we present a paradigm of perfect integration of DNA nanotechnology with nucleic acid amplification, thus paving a promising way to the improved performance of nucleic acid amplification techniques and their wider application.

Sensitive fluorescent detection of Listeria monocytogenes by combining a universal asymmetric polymerase chain reaction with rolling circle amplification

A new, facile, low-cost, and highly sensitive method for detection of Listeria monocytogenes involving a combination of asymmetric polymerase chain reaction (aPCR) and rolling circle amplification (RCA) had been developed. The aPCR-RCA processes were not new but components of the processes made the assay useful. Twenty-one thymine (21-T) tagged forward primer generated universal twenty-one adenine (21-A) aPCR amplicons after aPCR amplification. A poly-T sequence dumbbell-like RCA template was produced through the blunt-end ligation activity of T4 DNA ligase. After the mixture of aPCR amplicons and dumbbell-like RCA template, the RCA reaction would initiate when the addition of phi29 DNA polymerase, then a large number of G-quadruplex sequences were produced which allowed the intercalation of Thioflavin T (3,6-dimethyl-2-(4-dimethylaminophenyl) benzo-thiazolium cation, THT) for easy fluorescence detection. Under the optimal conditions, the assay showed a limit of detection (LOD) of 4.8 × 10¹ CFU/mL in pure culture and 4.0 × 10² CFU/g in spiked lettuce homogenates. By changing the aPCR primer, the aPCR-RCA method developed in this study had a potential to detect other bacteria without the design an RCA template for each bacterium.

An integrated-molecular-beacon based multiple exponential strand displacement amplification strategy for ultrasensitive detection of DNA methyltransferase activity

DNA methylation is a significant epigenetic mechanism involving processes of transferring a methyl group onto cytosine or adenine. Such DNA modification catalyzed by methyltransferase (MTase) plays important roles in the modulation of gene expression and other cellular activities. Herein, we develop a simple and sensitive biosensing platform for the detection of DNA MTase activity by using only two oligonucleotides. The fluorophore labeled molecular beacon (MB) can be methylated by MTase and subsequently cleaved by endonuclease DpnI at the stem, giving a shortened MB. The shortened MB can then hybridize with a primer DNA, initiating a cycle of strand displacement amplification (SDA) reactions. The obtained SDA products can unfold new MB and initiate another cycle of SDA reaction. Therefore, continuous enlargement of SDA and exponential amplification of the fluorescence signal are achieved. Because the triple functions of substrate, template and probe are elegantly integrated in one oligonucleotide, only two oligonucleotides are necessary for multiple amplification cycles, which not only reduces the complexity of the system, but also overcomes the laborious and cumbersome operation that is always a challenge in conventional methods. This platform exhibits an extremely low limit of detection of 3.3 × 10-6 U mL-1, which is the lowest to our knowledge. The proposed MTase-sensing platform was also demonstrated to perform well in a real-time monitoring mode, which can achieve a further simplified and high-throughput detection. The sensing strategy might be extended to the activity detection of other enzymes, thus showing great application potential in bioanalysis and clinical diagnosis.

A new DNA sensor system for specific and quantitative detection of mycobacteria

In the current study, we describe a novel DNA sensor system for specific and quantitative detection of mycobacteria, which is the causative agent of tuberculosis. Detection is achieved by using the enzymatic activity of the mycobacterial encoded enzyme topoisomerase IA (TOP1A) as a biomarker. The presented work is the first to describe how the catalytic activities of a member of the type IA family of topoisomerases can be exploited for specific detection of bacteria. The principle for detection relies on a solid support anchored DNA substrate with dual functions namely: (1) the ability to isolate mycobacterial TOP1A from crude samples and (2) the ability to be converted into a closed DNA circle upon reaction with the isolated enzyme. The DNA circle can act as a template for rolling circle amplification generating a tandem repeat product that can be visualized at the single molecule level by fluorescent labelling. This reaction scheme ensures specific, sensitive, and quantitative detection of the mycobacteria TOP1A biomarker as demonstrated by the use of purified mycobacterial TOP1A and extracts from an array of non-mycobacteria and mycobacteria species. When combined with mycobacteriophage induced lysis as a novel way of effective yet gentle extraction of the cellular content from the model Mycobacterium smegmatis, the DNA sensor system allowed detection of mycobacteria in small volumes of cell suspensions. Moreover, it was possible to detect M. smegmatis added to human saliva. Depending on the composition of the sample, we were able to detect 0.6 or 0.9 million colony forming units (CFU) per mL of mycobacteria, which is within the range of clinically relevant infection numbers. We, therefore, believe that the presented assay, which relies on techniques that can be adapted to limited resource settings, may be the first step towards the development of a new point-of-care diagnostic test for tuberculosis.