G-quadruplex based biosensor: A potential tool for SARS-CoV-2 detection

A FRET biosensor constructed using pH sensitive G-quadruplex DNA for detecting mitochondrial autophagy

Mitochondria are crucial powerhouses and central organelles for maintaining normal physiological activities in eukaryotic cells. The use of highly specific optical biosensors to monitor mitochondrial autophagy (mitophagy) is an important way for detecting mitochondrial abnormalities. Herein, we report a pH responsive G-quadruplex (G4) structure folded by the oligonucleotide named P24. P24 is composed of four GGCCTG repeating units, and the high guanine content allows it to form an antiparallel G4 topology at pH 4.5 (lysosomal pH). However, when pH increases to around 7.4 (mitochondrial pH), P24 further transforms into a double-stranded structure. Unlike most oligonucleotides that enter lysosomes, P24 highly targets mitochondria in live cells. These characteristics enable P24 to construct a pH responsive optical biosensor by linking a pair of fluorescence resonance energy transfer (FRET) fluorophores. The P24 based biosensor demonstrates reliable applications in detecting mitophagy in live cells.

A Novel Approach for Colorimetric Detection of Glyphosate in Food Based on a Split Aptamer Nanostructure and DNAzyme Activity

Glyphosate has become the most widely used herbicide worldwide in recent years. There are many concerns about toxicity and mutagenicity from long-term use of glyphosate in humans and animals. Therefore, the methods that can help in easy and quick detection of this chemical compound in food and water are critical. In this work, a biosensor was fabricated by combining the enzymatic properties of a specific DNA G-quadruplex and selectivity of a split aptamer to detect glyphosate in foods and water in a quick and simple colorimetric manner. The color change in this method is based on the oxidation of TMB by the G-quadruplex enzyme and the function of aptamer to trap glyphosate, which is visible to the naked eye in the presence and absence of the herbicide. The biosensor showed its high performance in various real samples of water and foods and provided a detection limit of 1.37 nM (R² = 0.9899) with a linear response range of 100 to 400 nM of glyphosate. This biosensor can provide an innovative, cheap and fast approach for the detection and monitoring of glyphosate in various foods and water.

Exploiting G-Quadruplex-DNA Damage as a Tool to Quantify Singlet Oxygen Production

G-Quadruplexes (G4s) are highly dynamic and polymorphic nucleic acid structures that can adopt a variety of conformations. When exposed to oxidative conditions, more specifically singlet oxygen, the guanosine nucleobases can be oxidized, which in turn can affect the conformation and folding of the G4. Based on this peculiar phenomenon, it is rationalized that G4s can serve as quantification sensors for the production of singlet oxygen. Here, a method for determining the quantum yield of singlet oxygen generation for visible as well as UV-light excited photosensitizers, using a short G4 DNA sequence, readily available from common DNA companies, as a biological and water-soluble probe, is presented.

Entangled World of DNA Quadruplex Folds

DNA quadruplexes participate in many biological functions. It takes up a variety of folds based on the sequence and environment. Here, a meticulous analysis of experimentally determined 437 quadruplex structures (433 PDBs) deposited in the PDB is carried out. The analysis reveals the modular representation of the quadruplex folds. Forty-eight unique quadruplex motifs (whose diversity arises out of the propeller, bulge, diagonal, and lateral loops that connect the quartets) are identified, leading to simple to complex inter/intramolecular quadruplex folds. The two-layered structural motifs are further classified into 33 continuous and 15 discontinuous motifs. While the continuous motifs can directly be extended to a quadruplex fold, the discontinuous motif requires an additional loop(s) to complete a fold, as illustrated here with examples. Similarly, higher-order quadruplex folds can also be represented by continuous or discontinuous motifs or their combinations. Such a modular representation of the quadruplex folds may assist in custom engineering of quadruplexes, designing motif-based drugs, and the prediction of the quadruplex structure. Furthermore, it could facilitate understanding of the role of quadruplexes in biological functions and diseases.

Enzyme-free and rapid colorimetric analysis of osteopontin via triple-helix aptamer probe coupled with catalytic hairpin assembly reaction

BACKGROUND

Osteopontin (OPN) is closely associated with tumorigenesis, growth, invasion, and immune escape and it serves as a plasma biomarker for hepatocellular carcinoma (HCC). Nevertheless, the accurate and rapid detection of low-abundance OPN still poses significant challenges. Currently, the majority of protein detection methods rely heavily on large precision instruments or involve complex procedures. Therefore, developing a simple, enzyme-free, rapid colorimetric analysis method with high sensitivity is imperative.

RESULTS

In this study, we have developed a portable colorimetric biosensor by integrating the triple-helix aptamer probe (THAP) and catalytic hairpin assembly (CHA) strategy, named as T-CHA. After binding to the OPN, the trigger probe can be released from THAP, then initiates the CHA reaction and outputs the signal through the formation of a G-quadruplex/Hemin DNAzyme with horseradish peroxidase-like activity. Consequently, this colorimetric sensor achieves visual free-labeled detection without additional fluorophore modification and allows for accurate quantification by measuring the optical density of the solution at 650 nm. Under optimal conditions, the logarithmic values of various OPN concentrations exhibit satisfactory linearity in the range of 5 pg mL-1 to 5 ng mL-1, with a detection limit of 2.04 pg mL-1. Compared with the widely used ELISA strategy, the proposed T-CHA strategy is rapid (∼105 min), highly sensitive, and cost-effective.

SIGNIFICANCE

The T-CHA strategy, leveraging the low background leakage of THAP and the high catalytic efficiency of CHA, has been successfully applied to the detection of OPN in plasma, demonstrating significant promise for the early diagnosis of HCC in point-of-care testing. Given the programmability of DNA and the universality of T-CHA, it can be readily modified for analyzing other useful tumor biomarkers.

Aptamer-based assembly systems for SARS-CoV-2 detection and therapeutics

Nucleic acid aptamers are oligonucleotide chains with molecular recognition properties. Compared with antibodies, aptamers show advantages given that they are readily produced via chemical synthesis and elicit minimal immunogenicity in biomedicine applications. Notably, aptamer-encoded nucleic acid assemblies further improve the binding affinity of aptamers with the targets due to their multivalent synergistic interactions. Specially, aptamers can be engineered with special topological arrangements in nucleic acid assemblies, which demonstrate spatial and valence matching towards antigens on viruses, thus showing potential in the detection and therapeutic applications of viruses. This review presents the recent progress on the aptamers explored for SARS-CoV-2 detection and infection treatment, wherein applications of aptamer-based assembly systems are introduced in detail. Screening methods and chemical modification strategies for aptamers are comprehensively summarized, and the types of aptamers employed against different target domains of SARS-CoV-2 are illustrated. The evolution of aptamer-based assembly systems for the detection and neutralization of SARS-CoV-2, as well as the construction principle and characteristics of aptamer-based DNA assemblies are demonstrated. The typically representative works are presented to demonstrate how to assemble aptamers rationally and elaborately for specific applications in SARS-CoV-2 diagnosis and neutralization. Finally, we provide deep insights into the current challenges and future perspectives towards aptamer-based nucleic acid assemblies for virus detection and neutralization in nanomedicine.

Engineering of a DNAzyme-Based dimeric G-quadruplex rolling circle amplification for robust analysis of lead ion

Detecting heavy metal pollution, particularly lead ion (Pb2⁺) contamination, is imperative for safeguarding public health. In this study, we introduced an innovative approach by integrating DNAzyme with rolling circle amplification (RCA) to propose an amplification sensing method termed DNAzyme-based dimeric-G-quadruplex (dimer-G4) RCA. This sensing approach allows for precise and high-fidelity Pb2⁺ detection. Strategically, in the presence of Pb2⁺, the DNAzyme undergoes substrate strand (S-DNA) cleavage, liberating its enzyme strand (E-DNA) to prime isothermal amplification. This initiates the RCA process, producing numerous dimer-G-Quadruplexes (dimer-G4) as the signal reporting transducers. Compared to conventional strategies using monomeric G-quadruplex (mono-G4) as the reporting transducers, these dimer-G4 structures exhibit significantly enhanced fluorescence when bound with Thioflavin T (ThT), offering superior target signaling ability for even detection of Pb2⁺ at low concentration. Conversely, in the absence of Pb2⁺, the DNAzyme structure remains intact so that no primers can be produced to cause the RCA initiation. This nucleic acid amplification-based Pb2⁺ detection method combing with the high specificity of DNAzymes for Pb2⁺ recognition ensures highly sensitive detection of Pb2+ with a detection limit of 0.058 nM, providing a robust tool for food safety analysis and environmental monitoring.

Recent developments of (bio)-sensors for detection of main microbiological and non-biological pollutants in plastic bottled water samples: A critical review

The importance of water in all biological processes is undeniable. Ensuring access to clean and safe drinking water is crucial for maintaining sustainable water resources. To elaborate, the consumption of water of inadequate quality can have a repercussion on human health. Furthermore, according to the instability of tap water quality, the consumption rate of bottled water is increasing every day at the global level. Although most people believe bottled water is safe, it can also be contaminated by microbiological or chemical pollution, which can increase the risk of disease. Over the last decades, several conventional analytical tools applied to analyze the contamination of bottled water. On the other hand, some limitations restrict their application in this field. Therefore, biosensors, as emerging analytical method, attract tremendous attention for detection both microbial and chemical contamination of bottled water. Biosensors enjoy several facilities including selectivity, affordability, and sensitivity. In this review, the developed biosensors for analyzing contamination of bottled water were highlighted, as along with working strategies, pros and cons of studies. Challenges and prospects were also examined.

Cutting-edge biorecognition strategies to boost the detection performance of COVID-19 electrochemical biosensors: A review

Electrochemical biosensors are known for their high sensitivity, selectivity, and low cost. Recently, they have gained significant attention and became particularly important as promising tools for the detection of COVID-19 biomarkers, since they offer a rapid and accurate means of diagnosis. Biorecognition strategies are a crucial component of electrochemical biosensors and determine their specificity and sensitivity based on the interaction of biological molecules, such as antibodies, enzymes, and DNA, with target analytes (e.g., viral particles, proteins and genetic material) to create a measurable signal. Different biorecognition strategies have been developed to enhance the performance of electrochemical biosensors, including direct, competitive, and sandwich binding, alongside nucleic acid hybridization mechanisms and gene editing systems. In this review article, we present the different strategies used in electrochemical biosensors to target SARS-CoV-2 and other COVID-19 biomarkers, as well as explore the advantages and disadvantages of each strategy and highlight recent progress in this field. Additionally, we discuss the challenges associated with developing electrochemical biosensors for clinical COVID-19 diagnosis and their widespread commercialization.

A colorimetric tandem combination of CRISPR/Cas12a with dual functional hybridization chain reaction for ultra-sensitive detection of Mycobacterium bovis

Tuberculosis caused by Mycobacterium bovis poses a global infectious threat to humans and animals. Therefore, there is an urgent need to develop a sensitive, precise, and easy-to-readout strategy. Here, a novel tandem combination of a CRISPR/Cas12a system with dual HCR (denoted as CRISPR/Cas12a-D-HCR) was constructed for detecting Mycobacterium bovis. Based on the efficient trans-cleavage activity of the active CRISPR/Cas12a system, tandem-dsDNA with PAM sites was established using two flexible hairpins, providing multiple binding sites with CRISPR/Cas12a for further amplification. Furthermore, the activation of Cas12a initiated the second hybridization chain reaction (HCR), which integrated complete G-quadruplex sequences to assemble the hemin/G-quadruplex DNAzyme. With the addition of H2O2 and ABTS, a colorimetric signal readout strategy was achieved. Consequently, CRISPR/Cas12a-D-HCR achieved a satisfactory detection linear range from 20 aM to 50 fM, and the limit of detection was as low as 2.75 aM with single mismatched recognition capability, demonstrating good discrimination of different bacterial species. Notably, the practical application performance was verified via the standard addition method, with the recovery ranging from 96.0% to 105.2% and the relative standard deviations (RSD) ranging from 0.95% to 6.45%. The proposed CRISPR/Cas12a-D-HCR sensing system served as a promising application for accurate detection in food safety and agricultural fields.

Electrochemical Sensors and Biosensors for Identification of Viruses: A Critical Review

Due to their life cycle, viruses can disrupt the metabolism of their hosts, causing diseases. If we want to disrupt their life cycle, it is necessary to identify their presence. For this purpose, it is possible to use several molecular-biological and bioanalytical methods. The reference selection was performed based on electronic databases (2020-2023). This review focused on electrochemical methods with high sensitivity and selectivity (53% voltammetry/amperometry, 33% impedance, and 12% other methods) which showed their great potential for detecting various viruses. Moreover, the aforementioned electrochemical methods have considerable potential to be applicable for care-point use as they are portable due to their miniaturizability and fast speed analysis (minutes to hours), and are relatively easy to interpret. A total of 2011 articles were found, of which 86 original papers were subsequently evaluated (the majority of which are focused on human pathogens, whereas articles dealing with plant pathogens are in the minority). Thirty-two species of viruses were included in the evaluation. It was found that most of the examined research studies (77%) used nanotechnological modifications. Other ones performed immunological (52%) or genetic analyses (43%) for virus detection. 5% of the reports used peptides to increase the method's sensitivity. When evaluable, 65% of the research studies had LOD values in the order of ng or nM. The vast majority (79%) of the studies represent proof of concept and possibilities with low application potential and a high need of further research experimental work.

Importance of DNA nanotechnology for DNA methyltransferases in biosensing assays

DNA methylation is the process by which specific bases on a DNA sequence acquire methyl groups under the catalytic action of DNA methyltransferases (DNMT). Abnormal changes in the function of DNMT are important markers for cancers and other diseases; therefore, the detection of DNMT and the selection of its inhibitors are critical to biomedical research and clinical practice. DNA molecules can undergo intermolecular assembly to produce functional aggregates because of their inherently stable physical and chemical properties and unique structures. Conventional DNMT detection methods are cumbersome and complicated processes; therefore, it is necessary to develop biosensing technology based on the assembly of DNA nanostructures to achieve rapid analysis, simple operation, and high sensitivity. The design of the relevant program has been employed in life science, anticancer drug screening, and clinical diagnostics. In this review, we explore how DNA assembly, including 2D techniques like hybridization chain reaction (HCR), rolling circle amplification (RCA), catalytic hairpin assembly (CHA), and exponential isothermal amplified strand displacement reaction (EXPAR), as well as 3D structures such as DNA tetrahedra, G-quadruplexes, DNA hydrogels, and DNA origami, enhances DNMT detection. We highlight the benefits of these DNA nanostructure-based biosensing technologies for clinical use and critically examine the challenges of standardizing these methods. We aim to provide reference values for the application of these techniques in DNMT analysis and early cancer diagnosis and treatment, and to alert researchers to challenges in clinical application.

Leveraging Cas13a's trans-cleavage on RNA G-quadruplexes for amplification-free RNA detection

In this study, we investigated Cas13a's efficacy in trans-cleaving RNA G-quadruplexes (rG4s) as an alternative to ssRNA reporters in CRISPR-Cas13a diagnostics. Our findings demonstrate enhanced efficiency due to the structural arrangement of rG4s. Implementing a simplified CRISPR-Cas13a system based on rG4, we identified SARS-CoV-2 infections in 25 patient samples within 1 hour without target pre-amplification.

Processes triggered in guanine quadruplexes by direct absorption of UV radiation: From fundamental studies toward optoelectronic biosensors

Guanine quadruplexes (GQs) are four-stranded DNA/RNA structures exhibiting an important polymorphism. During the past two decades, their study by time-resolved spectroscopy, from femtoseconds to milliseconds, associated to computational methods, shed light on the primary processes occurring when they absorb UV radiation. Quite recently, their utilization in label-free and dye-free biosensors was explored by a few groups. In view of such developments, this review discusses the outcomes of the fundamental studies that could contribute to the design of future optoelectronic biosensors using fluorescence or charge carriers stemming directly from GQs, without mediation of other molecules, as it is the currently the case. It explains how the excited state relaxation influences both the fluorescence intensity and the efficiency of low-energy photoionization, occurring via a complex mechanism. The corresponding quantum yields, determined with excitation at 266/267 nm, fall in the range of (3.0-9.5) × 10-4 and (3.2-9.2) × 10-3 , respectively. These values, significantly higher than the corresponding values found for duplexes, depend strongly on certain structural factors (molecularity, metal cations, peripheral bases, number of tetrads …) which intervene in the relaxation process. Accordingly, these features can be tuned to optimize the desired signal.

Clinical Translation of Aptamers for COVID-19

The COVID-19 etiologic agent, SARS-CoV-2, continues to be one of the leading causes of death on a global scale. Although efficient methods for diagnosis and treatment of COVID-19 have been developed, new methods of battling SARS-CoV-2 variants and long COVID are still urgently needed. A number of aptamers have demonstrated tremendous potential to be developed into diagnostic and therapeutic agents for COVID-19. The translation of the aptamers for clinical uses, however, has been extremely slow. Overcoming the difficulties faced by aptamers would advance this technology toward clinical use for COVID-19 and other serious disorders.

Dual-Signal Mode Ratiometric Photoelectrochemical Sensor Based on G-Quadruplex Hole Transport for Rapid and Sensitive Detection of miRNA-210

For rapid and sensitive detection of miRNA-210, which is important for improving the reliability of clinical diagnosis of breast cancer, a dual-signal mode ratiometric photoelectrochemical (PEC) sensor based on a Au/GaN photoanode is proposed. First, a DNA probe was designed that could complement the target miRNA-210. Then, another G-rich DNA sequence was designed to mismatch the probe and form a double-stranded DNA (dsDNA). Upon addition of the target, the dsDNA unwinds from its binding site and releases G-rich single-stranded DNA. In the presence of Mg2+ and K+, this single-stranded DNA molecule spontaneously forms a G-quadruplex structure, facilitating the rapid transport of photogenerated holes, thereby increasing the photocurrent response of Au/GaN and enabling sensitive label-free detection of miRNA-210. By control of different pH values, a response signal was generated at pH 8, while a reference signal was produced at pH 5. The designed PEC system shows a high potential for the development of miRNA-210 detection. Ultimately, the response signal-to-reference signal ratio was used as the variable, and a broad linear span ranging from 10 fM to 1 nM (R2 = 0.993) has been exhibited, with a detection threshold of 3 fM (S/N = 3). The designed PEC platform shows potential for the development of other disease markers.

Biosensors for waterborne virus detection: Challenges and strategies

Waterborne viruses that can be harmful to human health pose significant challenges globally, affecting health care systems and the economy. Identifying these waterborne pathogens is essential for preventing diseases and protecting public health. However, handling complex samples such as human and wastewater can be challenging due to their dynamic and complex composition and the ultralow concentration of target analytes. This review presents a comprehensive overview of the latest breakthroughs in waterborne virus biosensors. It begins by highlighting several promising strategies that enhance the sensing performance of optical and electrochemical biosensors in human samples. These strategies include optimizing bioreceptor selection, transduction elements, signal amplification, and integrated sensing systems. Furthermore, the insights gained from biosensing waterborne viruses in human samples are applied to improve biosensing in wastewater, with a particular focus on sampling and sample pretreatment due to the dispersion characteristics of waterborne viruses in wastewater. This review suggests that implementing a comprehensive system that integrates the entire waterborne virus detection process with high-accuracy analysis could enhance virus monitoring. These findings provide valuable insights for improving the effectiveness of waterborne virus detection, which could have significant implications for public health and environmental management.

DNA Hairpins and Stabilization of Gold Nanoparticles: Effect of Stem Length and Toehold Composition

This study investigates the effect of DNA hairpins on the stabilization of gold nanoparticles (AuNPs) against salt-induced aggregation (SIA) in label-free colorimetric biosensors. AuNPs were incubated with DNA hairpins of varying stem lengths and toehold sequences, followed by the addition of NaCl, before being subjected to ultraviolet-visible (UV-vis) measurement. Results showed that hairpins with longer stems generally provide better stabilization of AuNPs (18-bp >14-bp >10-bp). No improvement was observed for 14- and 18-bp hairpins with a toehold beyond 8A, which may be attributed to saturated adsorption of hairpins on the gold surface. For 14-bp hairpins with an 8-mer homopolymeric toehold, we observed a stabilization trend of A > C > G > T, similar to the reported trend of ssDNA. For variants containing ≥50% adenine as terminal bases, introducing cytosine or guanine as preceding bases could also result in strong stabilization. As the proportion of adenine decreases, variants with guanine or thymine provide less protection against SIA, especially for guanine-rich hairpins (≥6G) that could form G-quadruplexes. Such findings could serve as guidelines for researchers to design suitable DNA hairpins for label-free AuNP-based biosensors.

Ultra-sensitive and specific detection of pathogenic nucleic acids using composite-excited hyperfine plasma spectroscopy combs sensitized by Au nanoarrays functionalized with 2D Ta2C-MXene

Accurate and rapid screening techniques on a population scale are crucial for preventing and managing epidemics like COVID-19. The standard gold test for nucleic acids in pathogenic infections is primarily the reverse transcription polymerase chain reaction (RT-PCR). However, this method is not suitable for widespread screening due to its reliance on large-scale equipment and time-consuming extraction and amplification processes. Here, we developed a collaborative system that combines high-load hybridization probes targeting N and OFR1a with Au NPs@Ta2C-M modified gold-coated tilted fiber Bragg grating (TFBG) sensors to enable direct nucleic acid detection. Multiple activation sites of SARS-CoV-2 were saturable modified on the surface of a homogeneous arrayed AuNPs@Ta2C-M/Au structure based on a segmental modification approach. The combination of hybrid probe synergy and composite polarisation response in the excitation structure results in highly specific hybridization analysis and excellent signal transduction of trace target sequences. The system demonstrates excellent trace specificity, with a limit of detection of 0.2 pg/mL, and achieves a rapid response time of 1.5 min for clinical samples without amplification. The results showed high agreement with the RT-PCR test (Kappa index = 1). And the gradient-based detection of 10-in-1 mixed samples exhibits high-intensity interference immunity and excellent trace identification. Therefore, the proposed synergistic detection platform has a good tendency to curb the global spread of epidemics such as COVID-19.

Target-catalyzed self-assembled spherical G-quadruplex/hemin DNAzymes for highly sensitive colorimetric detection of microRNA in serum

The accurate and visual detection of circulating microRNA (miRNA) has attracted increasing interest due to its pivotal role in clinical disease diagnosis. Taking advantages of nucleic acid isothermal amplification and enzyme-catalyzed chromogenic reaction, here, a colorimetric sensing strategy was proposed for sensitive miRNA analysis. When the target miRNA was present, local catalytic hairpin assembly (CHA) would be triggered and proceed continuously to form dozens of double-stranded oligonucleotides with G-rich sticky ends on the gold nanoparticle, which could self-assemble into a spherical G-quadruplex (GQ)/hemin DNAzyme by binding with hemin and potassium ions. As a horseradish peroxidase-mimic, GQ/hemin DNAzyme could catalyze the redox reaction and color change of the substrates. Taking miRNA-21 as an example, the developed method exhibited satisfactory specificity as well as high sensitivity with a detection limit of 90.3 fM. Furthermore, the sensing platform has been successfully employed to detect miRNA-21 in spiked serum, providing a promising tool for early diagnosis of cancers.

Structurally diverse G-quadruplexes as the noncanonical nucleic acid drug target for live cell imaging and antibacterial study

The formation of G-quadruplex structures (G4s) in vitro from guanine (G)-rich nucleic acid sequences of DNA and RNA stabilized with monovalent cations, typically K⁺ and Na⁺, under physiological conditions, has been verified experimentally and some of them have high-resolution NMR or X-ray crystal structures; however, the biofunction of these special noncanonical secondary structures of nucleic acids has not been fully understood and their existence in vivo is still controversial at present. It is generally believed that the folding and unfolding of G4s in vivo is a transient process. Accumulating evidence has shown that G4s may play a role in the regulation of certain important cellular functions including telomere maintenance, replication, transcription and translation. Therefore, both DNA and RNA G4s of human cancer hallmark genes are recognized as the potential anticancer drug target for the investigation in cancer biology, chemical biology and drug discovery. The relationship between the sequence, structure and stability of G4s, the interaction of G4s with small molecules, and insights into the rational design of G4-selective binding ligands have been intensively studied over the decade. At present, some G4-ligands have achieved a new milestone and successfully entered the human clinical trials for anticancer therapy. Over the past few decades, numerous efforts have been devoted to anticancer therapy; however, G4s for molecular recognition and live cell imaging and for application as antibacterial agents and antibiofilms against antibiotic resistance have been obviously underexplored. The recent advances in G4-ligands in these areas are thus selected and discussed concentratedly in this article in order to shed light on the emerging role of G4s in chemical biology and therapeutic prospects against bacterial infections. In addition, the recently published molecular scaffolds for designing small ligands selectively targeting G4s in live cell imaging, bacterial biofilm imaging, and antibacterial studies are discussed. Furthermore, a number of underexplored G4-targets from the cytoplasmic membrane-associated DNA, the conserved promoter region of K. pneumoniae genomes, the RNA G4-sites in the transcriptome of E. coli and P. aeruginosa, and the mRNA G4-sites in the sequence for coding the vital bacterial FtsZ protein are highlighted to further explore in G4-drug development against human diseases.

Recent advances in applying G-quadruplex for SARS-CoV-2 targeting and diagnosis: A review

The coronavirus SARS-CoV-2 has caused a health care crisis all over the world since the end of 2019. Although vaccines and neutralizing antibodies have been developed, rapidly emerging variants usually display stronger immune escape ability and can better surpass vaccine protection. Therefore, it is still vital to find proper treatment strategies. To date, antiviral drugs against SARS-CoV-2 have mainly focused on proteases or polymerases. Notably, noncanonical nucleic acid structures called G-quadruplexes (G4s) have been identified in many viruses in recent years, and numerous G4 ligands have been developed. During this pandemic, literature on SARS-CoV-2 G4s is rapidly accumulating. Here, we first summarize the recent progress in the identification of SARS-CoV-2 G4s and their intervention by ligands. We then introduce the potential interacting proteins of SARS-CoV-2 G4s from both the virus and the host that may regulate G4 functions. The innovative strategy to use G4s as a diagnostic tool in SARS-CoV-2 detection is also reviewed. Finally, we discuss some key questions to be addressed in the future.

Visual and label-free ASFV and PCV2 detection by CRISPR-Cas12a combined with G-quadruplex

African swine fever (ASF) and postweaning multisystemic wasting syndrome (PMWS) are acute infectious diseases caused by the African swine fever virus (ASFV) and porcine circovirus type 2 (PCV2). At present, there are no effective vaccines for the prevention of ASFV. PMWS, which is harmful to the domestic and even the world pig industry, is difficult to cure and has a high mortality. So, developing simple, inexpensive, and accurate analytical methods to detect and effectively diagnose ASFV and PCV2 can be conducive to avoid ASFV and PCV2 infection. CRISPR has become a potentially rapid diagnostic tool due to recent discoveries of the trans-cleavage properties of CRISPR type V effectors. Herein, we report the visual detection based on CRISPR-Cas12a (cpf1), which is more convenient than fluorescence detection. Through in vitro cleavage target DNA activation, Cas12a can trans-cleavage ssDNA G-quadruplex. TMB/H2O2 and Hemin cannot be catalyzed by cleavaged G-DNA to produce green color products. This protocol is useful for the detection of ASFV and PCV2 with high sensitivity. This method can enable the development of visual and label-free ASFV and PCV2 detection and can be carried out in the field without relying on instruments or power. This method can complete nucleic acid detection at 37 °C without using other instruments or energy. Our research has expanded the application of Cas12a and laid the foundation for the field's rapid detection of viral nucleic acid in future.

Recent Developments in G-Quadruplex Binding Ligands and Specific Beacons on Smart Fluorescent Sensor for Targeting Metal Ions and Biological Analytes

The G-quadruplex structure is crucial in several biological processes, including DNA replication, transcription, and genomic maintenance. G-quadruplex-based fluorescent probes have recently gained popularity because of their ease of use, low cost, excellent selectivity, and sensitivity. This review summarizes the latest applications of G-quadruplex structures as detectors of genome-wide, enantioselective catalysts, disease therapeutics, promising drug targets, and smart fluorescence probes. In every section, sensing of G-quadruplex and employing G4 for the detection of other analytes were introduced, respectively. Since the discovery of the G-quadruplex structure, several studies have been conducted to investigate its conformations, biological potential, stability, reactivity, selectivity for chemical modification, and optical properties. The formation mechanism and advancements for detecting different metal ions (Na⁺, K⁺, Ag⁺, Tl⁺, Cu⁺/Cu²⁺, Hg²⁺, and Pb²⁺) and biomolecules (AMP, ATP, DNA/RNA, microRNA, thrombin, T4 PNK, RNase H, ALP, CEA, lipocalin 1, and UDG) using fluorescent sensors based on G-quadruplex modification, such as dye labels, artificial nucleobase moieties, dye complexes, intercalating dyes, and bioconjugated nanomaterials (AgNCs, GO, QDs, CDs, and MOF) is described herein. To investigate these extremely efficient responsive agents for diagnostic and therapeutic applications in medicine, fluorescence sensors based on G-quadruplexes have also been employed as a quantitative visualization technique.

Developing a DNA logic gate nanosensing platform for the detection of acetamiprid

This paper reports a novel fluorescence and colorimetric dual-signal-output DNA aptamer based sensor for the detection of acetamiprid residue. Acetamiprid is a new systemic broad-spectrum insecticide with high insecticidal efficiency that is widely used worldwide, but there is a risk of adverse neurological reactions in humans and animals. The dual-mode output principle designed in this paper, consisting of a fluorescence signal and colorimetric signal, is based on the relevant reaction of the special domain of a G-quadruplex, bidding farewell to a classical single-signal output, with a target-recognition cycle used to complete signal amplification through a hybridization chain reaction. Upgraded detection sensitivity and the qualitative and semi-quantitative detection of acetamiprid are achieved based on the fluorescence signal output and visual discrimination observations during colorimetric experiments. This model was applied to the determination of acetamiprid residue in fruits and vegetables. The dual-detection platform further reduced systematic error, with a detection limit of 27.7 pM. When applied in a comparative detection study using three different pesticides, the system shows excellent discrimination specificity and it performs well in actual sample detection and has a fast response time. Designing DNA logic gates that operate in the presence of targets and molecular-switch-based detection platforms also involves the intersection of biology and computational modeling, providing new ideas for biological platforms.

A Framework for Biosensors Assisted by Multiphoton Effects and Machine Learning

The ability to interpret information through automatic sensors is one of the most important pillars of modern technology. In particular, the potential of biosensors has been used to evaluate biological information of living organisms, and to detect danger or predict urgent situations in a battlefield, as in the invasion of SARS-CoV-2 in this era. This work is devoted to describing a panoramic overview of optical biosensors that can be improved by the assistance of nonlinear optics and machine learning methods. Optical biosensors have demonstrated their effectiveness in detecting a diverse range of viruses. Specifically, the SARS-CoV-2 virus has generated disturbance all over the world, and biosensors have emerged as a key for providing an analysis based on physical and chemical phenomena. In this perspective, we highlight how multiphoton interactions can be responsible for an enhancement in sensibility exhibited by biosensors. The nonlinear optical effects open up a series of options to expand the applications of optical biosensors. Nonlinearities together with computer tools are suitable for the identification of complex low-dimensional agents. Machine learning methods can approximate functions to reveal patterns in the detection of dynamic objects in the human body and determine viruses, harmful entities, or strange kinetics in cells.

State-of-the-Art Smart and Intelligent Nanobiosensors for SARS-CoV-2 Diagnosis

The novel coronavirus appeared to be a milder infection initially, but the unexpected outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), commonly called COVID-19, was transmitted all over the world in late 2019 and caused a pandemic. Human health has been disastrously affected by SARS-CoV-2, which is still evolving and causing more serious concerns, leading to the innumerable loss of lives. Thus, this review provides an outline of SARS-CoV-2, of the traditional tools to diagnose SARS-CoV-2, and of the role of emerging nanomaterials with unique properties for fabricating biosensor devices to diagnose SARS-CoV-2. Smart and intelligent nanomaterial-enabled biosensors (nanobiosensors) have already proven their utility for the diagnosis of several viral infections, as various detection strategies based on nanobiosensor devices are already present, and several other methods are also being investigated by researchers for the determination of SARS-CoV-2 disease; however, considerably more is undetermined and yet to be explored. Hence, this review highlights the utility of various nanobiosensor devices for SARS-CoV-2 determination. Further, it also emphasizes the future outlook of nanobiosensing technologies for SARS-CoV-2 diagnosis.

The role of electrochemical biosensors in SARS-CoV-2 detection: a bibliometrics-based analysis and review

The global pandemic of COVID-19, which began in late 2019, has resulted in extremely high morbidity and severe mortality worldwide, with important implications for human health, international trade, and national politics. Severe acute respiratory syndrome coronavirus (SARS-CoV-2) is the primary pathogen causing COVID-19. Analytical chemistry played an important role in this global epidemic event, and detection of SARS-CoV-2 even became a part of daily life. Analytical chemists have devoted much effort and enthusiasm to this event, and different analytical techniques have shown very rapid development. Electrochemical biosensors are highly efficient, sensitive, and cost-effective and have been used to detect many highly pathogenic viruses long before this event. However, another fact is that electrochemical biosensors are not the technology of choice for most detection applications. This review describes for the first time the role played by electrochemical biosensors in SARS-CoV-2 detection from a bibliometric perspective. This paper analyzed 254 relevant research papers up to June 2022. The contributions of different countries and institutions to this topic were analyzed. Keyword analysis was used to explore different methodological attempts of electrochemical detection techniques. More importantly, we are trying to find an answer to the question: do electrochemical biosensors have the potential to become a genuinely employable detection technology in an outbreak of infectious disease?

SARS-CoV-2 spike protein detection using slightly tapered no-core fiber-based optical transducer

The label-free detection of SARS-CoV-2 spike protein is demonstrated by using slightly tapered no-core fiber (ST-NCF) functionalized with ACE2. In the fabricated sensor head, abrupt changes in the mode-field diameter at the interfaces between single-mode fiber and no-core fiber excite multi-guided modes and facilitate multi-mode interference (MMI). Its slightly tapered region causes the MMI to be more sensitive to the refractive index (RI) modulation of the surrounding medium. The transmission minimum of the MMI spectrum was selected as a sensor indicator. The sensor surface was functionalized with ACE2 bioreceptors through the pretreatment process. The ACE2-immobilized ST-NCF sensor head was exposed to the samples of SARS-CoV-2 spike protein with concentrations ranging from 1 to 10⁴ ng/mL. With increasing sample concentration, we observed that the indicator dip moved towards a longer wavelength region. The observed spectral shifts are attributed to localized RI modulations at the sensor surface, which are induced by selective bioaffinity binding between ACE2 and SARS-CoV-2 spike protein. Also, we confirmed the capability of the sensor head as an effective and simple optical probe for detecting antigen protein samples by applying saliva solution used as a measurement buffer. Moreover, we compared its detection sensitivity to SARS-CoV-2 and MERS-CoV spike protein to examine its cross-reactivity. In particular, we proved the reproducibility of the bioassay protocol adopted here by employing the ST-NCF sensor head reconstructed with ACE2. Our ST-NCF transducer is expected to be beneficially utilized as a low-cost and portable biosensing platform for the rapid detection of SARS-CoV-2 spike protein.

Single-molecule displacement assay reveals strong binding of polyvalent dendrimer ligands to telomeric G-quadruplex

Binding between a ligand and a receptor is a fundamental step in many natural or synthetic processes. In biosensing, a tight binding with a small dissociation constant (Kd) between the probe and analyte can lead to superior specificity and sensitivity. Owing to their capability of evaluating competitors, displacement assays have been used to estimate Kd at the ensemble average level. At the more sensitive single-molecule level, displacement assays are yet to be established. Here, we developed a single-molecule displacement assay (smDA) in an optical tweezers instrument and used this innovation to evaluate the binding of the L2H2-6OTD ligands to human telomeric DNA G-quadruplexes. After measuring Kd of linear and dendrimer L2H2-6OTD ligands, we found that dendrimer ligands have enhanced binding affinity to the G-quadruplexes due to their polyvalent geometry. This increased binding affinity enhanced inhibition of telomerase elongation on a telomere template in a Telomerase Repeated Amplification Protocol (TRAP). Our experiments demonstrate that the smDA approach can efficiently evaluate binding processes in chemical and biological processes.

Development of Fluorescent Aptasensors Based on G-Quadruplex Quenching Ability for Ochratoxin A and Potassium Ions Detection

G-quadruplexes have received significant attention in aptasensing due to their structural polymorphisms and unique binding properties. In this work, we exploited the fluorescence-quenching properties of G-quadruplex to develop a simple, fast, and sensitive platform for fluorescence detection of ochratoxin A (OTA) and potassium ions (K+) with a label-free fluorophore and quencher strategy. The quenching ability of G-quadruplex was confirmed during the recognition process after the formation of the G-quadruplex structure and the quenching of the labeled fluorescein fluorophore (FAM). The fluorescence-quenching mechanism was studied by introducing specific ligands of G-quadruplex to enhance the quenching effect, to show that this phenomenon is due to photo-induced electron transfer. The proposed fluorescence sensor based on G-quadruplex quenching showed excellent selectivity with a low detection limit of 0.19 nM and 0.24 µM for OTA and K+, respectively. Moreover, we demonstrated that our detection method enables accurate concentration determination of real samples with the prospect of practical application. Therefore, G-quadruplexes can be excellent candidates as quenchers, and the strategy implemented in the study can be extended to an aptasensor with G-quadruplex.

Recent Advances in DNA Nanotechnology for Plasmonic Biosensor Construction

Since 2010, DNA nanotechnology has advanced rapidly, helping overcome limitations in the use of DNA solely as genetic material. DNA nanotechnology has thus helped develop a new method for the construction of biosensors. Among bioprobe materials for biosensors, nucleic acids have shown several advantages. First, it has a complementary sequence for hybridizing the target gene. Second, DNA has various functionalities, such as DNAzymes, DNA junctions or aptamers, because of its unique folded structures with specific sequences. Third, functional groups, such as thiols, amines, or other fluorophores, can easily be introduced into DNA at the 5′ or 3′ end. Finally, DNA can easily be tailored by making junctions or origami structures; these unique structures extend the DNA arm and create a multi-functional bioprobe. Meanwhile, nanomaterials have also been used to advance plasmonic biosensor technologies. Nanomaterials provide various biosensing platforms with high sensitivity and selectivity. Several plasmonic biosensor types have been fabricated, such as surface plasmons, and Raman-based or metal-enhanced biosensors. Introducing DNA nanotechnology to plasmonic biosensors has brought in sight new horizons in the fields of biosensors and nanobiotechnology. This review discusses the recent progress of DNA nanotechnology-based plasmonic biosensors.

Bioactive hybrid metal-organic framework (MOF)-based nanosensors for optical detection of recombinant SARS-CoV-2 spike antigen

Fast, efficient, and accurate detection of SARS-CoV-2 spike antigen is pivotal to control the spread and reduce the mortality of COVID-19. Nevertheless, the sensitivity of available nanobiosensors to detect recombinant SARS-CoV-2 spike antigen seems insufficient. As a proof-of-concept, MOF-5/CoNi₂S₄ is developed as a low-cost, safe, and bioactive hybrid nanostructure via the one-pot high-gravity protocol. Then, the porphyrin, H₂TMP, was attached to the surface of the synthesized nanomaterial to increase the porosity for efficient detection of recombinant SARS-CoV-2 spike antigen. AFM results approved roughness in different ranges, including 0.54 to 0.74 μm and 0.78 to ≈0.80 μm, showing good physical interactions with the recombinant SARS-CoV-2 spike antigen. MTT assay was performed and compared to the conventional synthesis methods, including hydrothermal, solvothermal, and microwave-assisted methods. The synthesized nanodevices demonstrated above 88% relative cell viability after 24 h and even 48 h of treatment. Besides, the ability of the synthesized nanomaterials to detect the recombinant SARS-CoV-2 spike antigen was investigated, with a detection limit of 5 nM. The in-situ synthesized nanoplatforms exhibited low cytotoxicity, high biocompatibility, and appropriate tunability. The fabricated nanosystems seem promising for future surveys as potential platforms to be integrated into biosensors.

Novel Detection Method for Circulating EGFR Tumor DNA Using Gravitationally Condensed Gold Nanoparticles and Catalytic Walker DNA

The detection of circulating tumor DNA is a major challenge in liquid biopsies for cancer. Conventionally, quantitative polymerase chain reactions or next-generation sequencing are used to detect circulating tumor DNA; however, these techniques require significant expertise, and are expensive. Owing to the increasing demand for a simple diagnostic method and constant monitoring of cancer, a cost-effective detection technique that can be conducted by non-experts is required. The aim of this study was to detect the circulating tumor DNA containing the epidermal growth factor receptor (EGFR) exon 19 deletion, which frequently occurs in lung cancer. By applying walker DNA to a catalytic hairpin assembly and using the differential dispersibility of gold nanoparticles, we detected EGFR exon 19 deletion mutant #2 DNA associated with lung cancer. Our sensing platform exhibited a limit of detection of 38.5 aM and a selectivity of 0.1% for EGFR exon 19 wild-type DNA. Moreover, we tested and compared EGFR exon 19 deletion mutants #1 and #3 to evaluate the effect of base pair mismatches on the performance of the said technique.

Electrochemical biosensors for the detection of SARS-CoV-2 pathogen and protein biomarkers

Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV CoV-2) pathogen and protein biomarkers can improve the diagnosis accuracy for Coronavirus disease 2019 (COVID-19). Electrochemical biosensors have attracted extensive attention in the scientific community because of their simple design, fast response, good portability, high sensitivity and high selectivity. In this review, we summarized the progress in the electrochemical detection of COVID-19 pathogen and SARS-CoV-2 biomarkers, including SARS-CoV-2 spike protein and nucleocapsid protein and their antibodies.

Chaperone Copolymer Assisted G-Quadruplex-Based Signal Amplification Assay for Highly Sensitive Detection of VEGF

Vascular endothelial growth factor (VEGF) is a critical biomarker in the angiogenesis of several cancers. Nowadays, novel approaches to rapid, sensitive, and reliable VEGF detection are urgently required for early cancer diagnosis. Cationic comb-type copolymer, poly(L-lysine)-graft-dextran (PLL-g-Dex) accelerates DNA hybridization and chain exchange reaction while stabilizing the DNA assembly structure. In this work, we examined the chaperone activity of PLL-g-Dex to assist G-quadruplex-based fluorescent DNA biosensors for sensitive detection of VEGF. This convenient and effective strategy is based on chitosan hydrogel, c-myc, Thioflavin T (ThT), VEGF aptamer, and its partially complementary strand. The results show that chaperone copolymer PLL-g-Dex significantly promotes the accumulation of G-quadruplex and assembles into G-wires, allowing an effective signal amplification. Using this method, the detection limit of VEGF was as low as 23 pM, better than many previous works on aptamer-based VEGF detection. This chaperone copolymer-assisted signal amplification strategy has potential applications in the highly sensitive detection of target proteins, even including viruses.

Nucleic Acids as Biotools at the Interface between Chemistry and Nanomedicine in the COVID-19 Era

The recent development of mRNA vaccines against the SARS-CoV-2 infection has turned the spotlight on the potential of nucleic acids as innovative prophylactic agents and as diagnostic and therapeutic tools. Until now, their use has been severely limited by their reduced half-life in the biological environment and the difficulties related to their transport to target cells. These limiting aspects can now be overcome by resorting to chemical modifications in the drug and using appropriate nanocarriers, respectively. Oligonucleotides can interact with complementary sequences of nucleic acid targets, forming stable complexes and determining their loss of function. An alternative strategy uses nucleic acid aptamers that, like the antibodies, bind to specific proteins to modulate their activity. In this review, the authors will examine the recent literature on nucleic acids-based strategies in the COVID-19 era, focusing the attention on their applications for the prophylaxis of COVID-19, but also on antisense- and aptamer-based strategies directed to the diagnosis and therapy of the coronavirus pandemic.

Validation of circular dichroic spectroscopy of synthetic oligonucleotide PS2.M for K + concentration measurements

The single-stranded synthetic oligonucleotide PS2.M is known to provide a basis for developing sensors since it tends to fold into structures called G-quadruplexes (G4) having characteristic topology and orientation with probabilities that depend on the chemical environment. The presence and concentration of cation species are among the key factors that determine the outcome of such a process. PS2.M and other aptamers have been used in several applications in conjunction with various probes, such as hemin, at the cost of increased technical complexity and applicability limitations. We instead validated the application limits of Circular Dichroic spectroscopy (CD) as only measurement method to assay PS2.M asK + sensor in a variety of solutions having different chemical complexity. The tested solutions range from simple NaCl and KCl solutions to chemically complex solutions like DMEM-Dulbecco's Modified Eagle Medium-which is widely used in a biological laboratory. PS2.M was also evaluated in solutions of KHCO 3 and D-ribose (K:D-rib), an antioxidant potassium compound, to compare its response to the simple KCl solution case. Our findings show that, within specific concentration applicability ranges, CD spectra can estimate theK + concentration in the examined water solutions even at high Na + concentrations with respect toK + and in the presence of antioxidant molecules.

Supplementary Information

The online version supplementary material available at 10.1140/epjp/s13360-022-02581-2.

G-quadruplex based biosensors for the detection of food contaminants

G-quadruplex (G4) is a very interesting DNA structure, commonly associated with cancer and its treatment. With flexible binding ability, G4 has been extended as a significant component in biosensors. On account of its simple operation, high sensitivity and low cost, G4-based biosensors have attracted considerable interest for the detection of food contaminants. In this review, research published in recent 5 years is collated from a principle perspective, that is target recognition and signal transduction. Contaminants with G4 binding capacity are illustrated, emerging G4-based biosensors including colorimetric, electrochemical and fluorescent sensors are also elaborated. The current review indicates that G4 has provided an efficient and effective solution for the rapid detection of food contaminants. A distinctive feature of G4 as recognition unit is the simple composition, but the selectivity is still unsatisfactory. As signal reporter, G4/hemin DNAzyme has not only achieved amplified signals, but also enabled visualized detection, which offers great potential for on-site measurement. With improved selectivity and visualized signal, the combination of aptamer and G4 seems to be an ideal strategy. This promising combination should be developed for the real-time monitor of multiple contaminants in food matrix.

A Novel SELEX Based on Immobilizing Libraries Enables Screening of Saxitoxin Aptamers for BLI Aptasensor Applications

Saxitoxin (STX) is one of the potent marine biotoxins that has high rate of lethality. However, there are no effective treatments at present, and the existing detection methods need to be further explored because of ethical problems or technical limitations. In this work, oligonucleotide aptamers toward STX were screened based on immobilizing libraries on Immobilized Metal-Chelate (IMC), such as Ni-NTA Sepharose, and the IMC-SELEX was conducted by the G-quadruplex library and the random library, respectively. Aptamer 45e (from the G-quadruplex library) and aptamer 75a were obtained after optimization, and aptamer 45e turned out to have a higher affinity toward STX. Furthermore, it was found that the hydrogen bonding and the van der Waals forces (VDW) played major roles in the high efficiency and specificity between STX and 45e by means of molecular docking and dynamics simulation. Based on this, aptamer 45e-1 with the Kd value of 19 nM was obtained by further optimization, which was then used to construct a simple, label-free and real-time optical BLI aptasensor for the detection of STX. This aptasensor showed good reproducibility and stability. In summary, with the advantages of screening aptamers of high efficiency and specificity toward the targets, the proposed IMC-SELEX provides a promising screening strategy for discovering aptamers, which could be used as the potential molecular recognition elements in the fields of biomedicine, food safety and environmental monitoring.

Label free detection of auramine O by G-quadruplex-based fluorescent turn-on strategy

Auramine o (AO) is a synthetic dye used in paper and textile industries. Although it has been an unauthorized food additive in many countries due to its toxic and carcinogenic possibility, its illegal uses have been detected in certain food products such as pasta, semolina and spices and also in pharmaceuticals. The presence of AO in food products should be monitored, therefore, to minimize the negative health effects on consumers. In this study, a simple, highly sensitive and selective label free detection method was investigated for AO by G-quadruplex-based fluorescent turn-on strategy. The optimum fluorescent detection assay was achieved with a specific G-quadruplex DNA sequence, c-myc, at 400 nM in Tris-HCl buffer at pH 7.4. The linearity of fluorescence intensity depending on AO concentration ranged from 0 to 0.07 µM and LOD and LOQ were 3 nM and 10 nM, respectively. The G-quadruplex-based detection assay was highly specific for AO as compared to other two synthetic food colorings and successfully applied to determine AO in pasta, bulgur and curry powder with recoveries in the range from 70.33% to 106.49%. This G-quadruplex-based label free detection assay has a significant potential to be used in the detection of AO in food products.

Engineering DNA G-quadruplex assembly for label-free detection of Ochratoxin A in colorimetric and fluorescent dual modes

Colorimetric and fluorescent methods for Ochratoxin A (OTA) detection are convenient and well received. However, the pigments and autofluorescence originated from food matrices often interfere with detection signals. We have developed a strategy with colorimetric and fluorescent dual modes to solve this challenge. In the colorimetric mode, OTA aptamer (AP9) was assembled into a DNA triple-helix switch with a specially designed signal-amplifying sequence. The OTA-induced G-quadruplex (G4) of AP9 would open the switch and release the signal-amplifying sequence for colorimetric signal amplification. The G4 structures of AP9 were further utilized to combine with the fluorogenic dye ThT for fluorescent mode. By skillfully engineering DNA G4 assembly for signal amplification, there was no need for any DNA amplification or nanomaterials labeling. Detections could be carried out in a wide temperature range (22-37 ℃) and finished rapidly (colorimetric mode, 60 min; fluorescent mode, 15 min). Broad linear ranges (colorimetric mode, 10-1.5 ×10³ μg/kg; fluorescent mode, 0.05-1.0 ×10³ μg/kg) were achieved. The limit of detection for colorimetric and fluorescent modes were 4 μg/kg and 0.01 μg/kg, respectively. The two modes have been successfully applied to detect OTA in samples with intrinsic pigments and autofluorescence, showing their applicability and reliability.

ONQUADRO: a database of experimentally determined quadruplex structures

ONQUADRO is an advanced database system that supports the study of the structures of canonical and non-canonical quadruplexes. It combines a relational database that collects comprehensive information on tetrads, quadruplexes, and G4-helices; programs to compute structure parameters and visualise the data; scripts for statistical analysis; automatic updates and newsletter modules; and a web application that provides a user interface. The database is a self-updating resource, with new information arriving once a week. The preliminary data are downloaded from the Protein Data Bank, processed, annotated, and completed. As of August 2021, ONQUADRO contains 1,661 tetrads, 518 quadruplexes, and 30 G4-helices found in 467 experimentally determined 3D structures of nucleic acids. Users can view and download their description: sequence, secondary structure (dot-bracket, classical diagram, arc diagram), tertiary structure (ball-and-stick, surface or vdw-ball model, layer diagram), planarity, twist, rise, chi angle (value and type), loop characteristics, strand directionality, metal ions, ONZ, and Webba da Silva classification (the latter by loop topology and tetrad combination), origin structure ID, assembly ID, experimental method, and molecule type. The database is freely available at https://onquadro.cs.put.poznan.pl/. It can be used on both desktop computers and mobile devices.

Fluorescence detection of the human angiotensinogen protein by the G-quadruplex aptamer

Schematic diagram of AGT detection by a G-quadruplex based fluorescent biosensor.