A label-free fluorescent molecular beacon based on DNA-Ag nanoclusters for the construction of versatile Biosensors

Ultrasensitive Electrochemiluminescence Biosensor Based on Efficient Signal Amplification of Copper Nanoclusters Induced by CaMnO3 for CD44 Trace Detection

Metal nanoclusters (Me NCs) have become a research hotspot in the field of electrochemiluminescence (ECL) sensing analysis. This is primarily attributed to their excellent luminescent properties and biocompatibility along with their easy synthesis and labeling characteristics. At present, the application of Me NCs in ECL mainly focuses on precious metals, whose high cost, to some extent, limits their widespread application. In this work, Cu NCs with cathode ECL emissions in persulfate (S2O82-) were prepared as signal probes using glutathione as ligands, which exhibited stable luminescence signals and high ECL efficiency. At the same time, CaMnO3 was introduced as a co-reaction promoter to increase the ECL responses of Cu NCs, thereby further expanding their application potential in biochemical analysis. Specifically, the reversible conversion of Mn3+/Mn4+ greatly promoted the generation of sulfate radicals (SO4•-), providing a guarantee for improving the luminescence signals of Cu NCs. Furthermore, a short peptide (NARKFYKGC) was introduced to enable the fixation of antibodies to specific targets, preventing the occupancy of antigen-binding sites (Fab fragments). Therefore, the sensitivity of the biosensor could be significantly enhanced by releasing additional Fab fragments. Considering the approaches discussed above, the constructed biosensor could achieve sensitive detection of CD44 over a broad range (10 fg/mL-100 ng/mL), with an ultralow detection limit of 3.55 fg/mL (S/N = 3), which had valuable implications for the application of nonprecious Me NCs in biosensing analysis.

Recent Developments on the Catalytic and Biosensing Applications of Porous Nanomaterials

Nanoscopic materials have demonstrated a versatile role in almost every emerging field of research. Nanomaterials have come to be one of the most important fields of advanced research today due to its controllable particle size in the nanoscale range, capacity to adopt diverse forms and morphologies, high surface area, and involvement of transition and non-transition metals. With the introduction of porosity, nanomaterials have become a more promising candidate than their bulk counterparts in catalysis, biomedicine, drug delivery, and other areas. This review intends to compile a self-contained set of papers related to new synthesis methods and versatile applications of porous nanomaterials that can give a realistic picture of current state-of-the-art research, especially for catalysis and sensor area. Especially, we cover various surface functionalization strategies by improving accessibility and mass transfer limitation of catalytic applications for wide variety of materials, including organic and inorganic materials (metals/metal oxides) with covalent porous organic (COFs) and inorganic (silica/carbon) frameworks, constituting solid backgrounds on porous materials.

Nanostructures for prevention, diagnosis, and treatment of viral respiratory infections: from influenza virus to SARS-CoV-2 variants

Viruses are a major cause of mortality and socio-economic downfall despite the plethora of biopharmaceuticals designed for their eradication. Conventional antiviral therapies are often ineffective. Live-attenuated vaccines can pose a safety risk due to the possibility of pathogen reversion, whereas inactivated viral vaccines and subunit vaccines do not generate robust and sustained immune responses. Recent studies have demonstrated the potential of strategies that combine nanotechnology concepts with the diagnosis, prevention, and treatment of viral infectious diseases. The present review provides a comprehensive introduction to the different strains of viruses involved in respiratory diseases and presents an overview of recent advances in the diagnosis and treatment of viral infections based on nanotechnology concepts and applications. Discussions in diagnostic/therapeutic nanotechnology-based approaches will be focused on H1N1 influenza, respiratory syncytial virus, human parainfluenza virus type 3 infections, as well as COVID-19 infections caused by the SARS-CoV-2 virus Delta variant and new emerging Omicron variant.

Iridium(III) solvent complex-based electrogenerated chemiluminescence and photoluminescence sensor array for the discrimination of bases in oligonucleotides

Development of rapid and sensitive method for the discrimination of bases in oligonucleotides is of great importance in clinical diagnosis. Here, we demonstrate the first case of single iridium(III) solvent complex-based electrogenerated chemiluminescence (ECL) and photoluminescence (PL) sensor array for the discrimination of bases in oligonucleotides. One iridium (III) solvent complex ([Ir(ppy)₂(DMSO)Cl], ppy = 2-phenylpyridine, probe 1) was designed as both ECL and PL probe while five bases (guanine, adenine, cytosine, thymine and uracil) were chosen as analytes. Two-element sensor array was built for the discrimination of five bases based on the fingerprint response of probe 1 to bases via coordination interactions. The combination of unique ECL and PL variations with principal component analysis was applied for the quantitative analysis of five bases in a linear range of 1.0 μM-10 μM and for the effective discrimination of individual base, the mixture of bases and oligonucleotides. Moreover, the sensor array was successfully applied to discriminate different mismatched ss-DNAs from HIV gene (a fully-matched ss-DNA), even at single-base difference. This work demonstrates that the sensor array using single iridium (III) solvent complex is a promising approach for the discrimination of bases with good sensitivity and simpleness in clinical diagnosis.

Target-Catalyzed Self-Assembly of DNA-Streptavidin Nanogel for Enzyme-Free miRNA Assay

Rapid, sensitive, specific, and user-friendly microRNA (miRNA) assays are in high demand for point-of-care diagnosis. Target-catalyzed toehold-mediated strand displacement (TMSD) has received increasing attention as an enzyme-free molecular tool for DNA detection. However, the application of TMSD to miRNA targets is challenging because relatively weak DNA/RNA hybridization leads to failure in the subtle kinetic control of multiple hybridization steps. Here, a simple method is presented for miRNA assay based on the one-pot self-assembly of Y-shaped DNAs with streptavidin via an miRNA-catalyzed TMSD cascade reaction. A single miRNA catalyzes the opening cycle of DNA hairpin loops to generate multiple Y-shaped DNAs carrying biotin and a quencher at the end of their arms. Introducing a single base-pair mismatch near the toehold facilitates RNA-triggered strand displacement while barely disturbing nonspecific reactions. The Y-shaped DNAs are self-assembled with fluorescently labeled streptavidin (sAv), which produces nanoscale DNA-sAv nanogel particles mediating efficient Förster resonance energy transfer in their 3D network. The enhancing effect dramatically reduces the detection limit from the nanomolar level to the picomolar level. This work proves that TMSD-based DNA nanogel with a base-pair mismatch incorporated to a hairpin structure is a promising approach towards sensitive and accurate miRNA assay.

DNA Templated Silver Nanoclusters for Bioanalytical Applications: A Review

Due to their unique programmability, biocompatibility, photostability and high fluorescent quantum yield, DNA templated silver nanoclusters (DNA Ag NCs) have attracted increasing attention for bioanalytical application. This review summarizes the recent developments in fluorescence properties of DNA templated Ag NCs, as well as their applications in bioanalysis. Finally, we herein discuss some current challenges in bioanalytical applications, to promote developments of DNA Ag NCs in biochemical analysis.

Comparison between various biosensor methods for human T-lymphotropic virus-1 (HTLV-1) detection

Due to the drawback of traditional and current diagnostic methods including serological and molecular assays, the development of the rapid and free-PCR techniques can be an alternative technique for the human T-cell lymphotropic virus (HTLV-1) DNA detection sequences. On the other hand, early detection of HTLV-1 prevents two dangerous diseases including Adult T-cell leukemia/lymphoma and HTLV-1 Associated Myelopathy/Tropical Spastic Paraparesis. The biosensor-based methods are sensitive techniques that can provide new opportunities to detect infectious diseases, particularly in the early stage. This study provides a comparative view among recently designed biosensors for the detection of HTLV-1.

A Review on the Development of Gold and Silver Nanoparticles-Based Biosensor as a Detection Strategy of Emerging and Pathogenic RNA Virus

The emergence of highly pathogenic and deadly human coronaviruses, namely SARS-CoV and MERS-CoV within the past two decades and currently SARS-CoV-2, have resulted in millions of human death across the world. In addition, other human viral diseases, such as mosquito borne-viral diseases and blood-borne viruses, also contribute to a higher risk of death in severe cases. To date, there is no specific drug or medicine available to cure these human viral diseases. Therefore, the early and rapid detection without compromising the test accuracy is required in order to provide a suitable treatment for the containment of the diseases. Recently, nanomaterials-based biosensors have attracted enormous interest due to their biological activities and unique sensing properties, which enable the detection of analytes such as nucleic acid (DNA or RNA), aptamers, and proteins in clinical samples. In addition, the advances of nanotechnologies also enable the development of miniaturized detection systems for point-of-care (POC) biosensors, which could be a new strategy for detecting human viral diseases. The detection of virus-specific genes by using single-stranded DNA (ssDNA) probes has become a particular interest due to their higher sensitivity and specificity compared to immunological methods based on antibody or antigen for early diagnosis of viral infection. Hence, this review has been developed to provide an overview of the current development of nanoparticles-based biosensors that target pathogenic RNA viruses, toward a robust and effective detection strategy of the existing or newly emerging human viral diseases such as SARS-CoV-2. This review emphasizes the nanoparticles-based biosensors developed using noble metals such as gold (Au) and silver (Ag) by virtue of their powerful characteristics as a signal amplifier or enhancer in the detection of nucleic acid. In addition, this review provides a broad knowledge with respect to several analytical methods involved in the development of nanoparticles-based biosensors for the detection of viral nucleic acid using both optical and electrochemical techniques.

Elemental Mass Spectrometry and Fluorescence Dual-Mode Strategy for Ultrasensitive Label-Free Detection of HBV DNA

This work reported a simple and ultrasensitive label-free method for the detection of hepatitis B virus (HBV) DNA by combining hyperbranched rolling circle amplification (HRCA) with dual-mode detection by inductively coupled plasma mass spectrometry (ICP-MS) and fluorescence using ruthenium complex [Ru(bpy)₂dppz]²⁺ (bpy = 2,2'-bipyridine, dppz = dipyrido [3,2-a:2',3'-c] phenazine) as a dual functional probe. An HBV DNA-initiated HRCA system was designed to realize the highly efficient amplification of HBV DNA with the generation of a mass of dsDNA. Also, the [Ru(bpy)₂dppz]²⁺ probe was then added to intercalate into the dsDNA products, resulting in strong fluorescence recovery of the probe for fluorescence detection. Meanwhile, using a biotin-modified primer in HRCA, the dsDNA-[Ru(bpy)₂dppz]²⁺ complexes could be captured by the avidin-coated 96-well plates, and the captured [Ru(bpy)₂dppz]²⁺ probe was later desorbed by acid for ICP-MS detection. The linear range of the proposed method was 3.5-200 amol L^-1 and the limit of detection (LOD) was 1 amol L^-1 for ICP-MS detection, while the linear range was 20-500 amol L^-1 and the LOD was 9.6 amol L^-1 for fluorescence detection. The developed method was applied to human serum sample analysis, and the analytical results coincided very well with those obtained by the real-time polymerase chain reaction (PCR) method. The developed dual-mode label-free detection method was ultrasensitive, simple, and accurate, showing great potential for therapeutic monitoring of HBV infection.

Dual-Channel Logic Gates Operating on the Chemopalette ssDNA-Ag NCs/GO Nanocomposites

In this work, we demonstrate that the emission wavelength and intensity of silver nanoclusters (Ag NCs) can be facilely tuned by the configuration transformation from the adsorption of Ag NCs to the graphene oxide (GO) surface to the desorption of Ag NCs from GO. Bicolor Ag NCs tethering the complementary sequence of influenza A virus genes are prepared, named green-emitting G-Ag NCs-CH5N1 (530 nm) and red-emitting R-Ag NCs-CH1N1 (589 nm). As for the high affinity of the complementary fragment of genes to GO, the adsorption of Ag NCs to GO leads to the formation of G-Ag NCs-CH5N1/GO and R-Ag NCs-CH1N1/GO nanocomposites, leading to fluorescent quenching due to energy transfer. By conjugating complementary sequences as capturing probes for targets, the formation of genes/Ag NC duplex-stranded structures results in the desorption of Ag NCs from GO, activating the fluorescence signal. More interestingly, compared with sole single-stranded DNA-templated fluorescent Ag NCs (ssDNA-Ag NCs), the activatable emission wavelength of the G-Ag NCs-CH5N1/H5N1 complex exhibits a notable red shift (555 nm) with a 49% recovery rate, while that of the R-Ag NCs-CH1N1/H1N1 complex shows a distinct blue shift (569 nm) with a 200% recovery rate. Via target-responsive configuration transformation of Ag NCs/GO hybrid materials, the emission wavelength and intensity of Ag NCs are effectively regulated. Based on the output changes according to different input combinations, novel dual-channel logic gates for multiplex simultaneous detection are developed by using the tunable color and intensity of ssDNA-Ag NCs. Our observation may open a new path for multiplex analysis in a facile and rapid way combining the logic gate strategy.

A novel disease-associated nucleic acid sensing platform based on split DNA-scaffolded sliver nanocluster

Disease-associated nucleic acids, such as DNAs and miRNAs, are important biomarkers for the diagnosis, prognosis and treatment guidance of human diseases. Therefore, the accurate and sensitive detection of nucleic acid is of great significance for the early diagnosis of diseases. DNA-scaffolded silver nanocluster (DNA-Ag NC) is a new type of probe with good photostability and low toxicity that has been widely used in biomedical analysis. In this work, a new universal sensing platform based on target triggered labeling luminescent DNA-Ag NC for disease-related nucleic acids detection was constructed. The assembled split DNA fragment pair (C₄AC₄T and C₃GT₄) could be used as a template to develop a bright green fluorescent Ag NC. According to this phenomenon, we devised two probe sequences DNA 1 and DNA 2, which could hybridize to the same one target and contained a different split fragment of Ag NC' scaffold. The target compelled the split fragments close to each other through base pairing with DNA 1 and DNA 2, thus quantification of the target could be achieved through measuring green fluorescence of Ag NC that produced by assembled scaffold in ternary hybrid products. We applied this platform successfully for miR-362, a potential biomarker of inflammatory bowel diseases (IBD), or HIV-related DNA (hDNA) detection, achieving the detection limits of 6.5 nM and 1.7 nM, respectively. Both of the assays showed excellent reproducibility, selectivity and potential applications in human serum samples. In summary, an economic and convenient universal platform was developed for disease-associated nucleic acid detection.

Base amount-dependent fluorescence enhancement for the assay of vascular endothelial growth factor 165 in human serum using hairpin DNA-silver nanoclusters and oxidized carbon nanoparticles

A base amount-dependent fluorescence enhancement-based strategy is put forward to determine vascular endothelial growth factor 165 (VEGF₁₆₅) in human serum by the use of hairpin DNA-silver nanoclusters (hDNA-AgNCs) and oxidized carbon nanoparticles (CNPs). The hDNA-AgNCs aptasensing probe consists of AgNCs-contained hairpin loop (that generates a fluorescence signal), hairpin stem (that makes the structure stable), and the terminal aptamer 1 (that recognizes the target together with aptamer 2). It has been demonstrated that the fluorescence intensity of hDNA-AgNCs is ~ 3-fold stronger than that of single-stranded DNA-AgNCs (ssDNA-AgNCs), and hDNA-AgNCs have a strong dependence of fluorescence enhancement on the base amount in hairpin stem and loop. Upon the addition of oxidized CNPs, the terminal aptamer 1 of hDNA-AgNCs can adsorb onto the surface of oxidized CNPs via π-π stacking, and the fluorescence of hDNA-AgNCs (with excitation/emission maxima at 490/567 nm) is quenched via fluorescence resonance energy transfer (FRET). When aptamer 2 and VEGF₁₆₅ are subsequently added, aptamer 1, VEGF₁₆₅, and aptamer 2 reassemble into an intact tertiary structure, and the fluorescence is recovered because hDNA-AgNCs are far away from the surface of oxidized CNPs and the FRET efficiency decreases. Under the optimized conditions, the aptasensing probe can selectively assay VEGF₁₆₅ with a detection limit of 14 pM. The results provide a label-free and sensitive method to monitor VEGF₁₆₅ in human serum. Schematic representation of the strong dependence of fluorescence enhancement on base amount in stem and loop of hairpin DNA-silver nanoclusters. The probe can be used to assay vascular endothelial growth factor 165 (VEGF₁₆₅) and give a judgment whether human serum VEGF₁₆₅ is at a normal or abnormal level for clinical diagnosis.

Nanotechnology based strategies for HIV-1 and HTLV-1 retroviruses gene detection

Early detection of retroviruses including human T-cell lymphotropic virus and human immunodeficiency virus in the human body is indispensable to prevent retroviral infection propagation and improve clinical treatment. Until now, diverse techniques have been employed for the early detection of viruses. Traditional methods are time-consuming, resource-intensive, and laborious performing. Therefore, designing and constructing a selective and sensitive diagnosis system to detect serious diseases is highly demanded. Genetic detection with high sensitivity has striking significance for the early detection and remedy of disparate pathogenic diseases. The nucleic acid biosensors are based on the identification of specific DNA sequences in biological samples. Nanotechnology has an important impact on the development of sensitive biosensors. Different kinds of nanomaterials include nanoparticles, nanoclusters, quantum dots, carbon nanotubes, nanocomposites, etc., with different properties have been used to improve the performance of biosensors. Recently, DNA nanobiosensors are developed to provide simple, fast, selective, low-cost, and sensitive detection of infectious diseases. In this paper, the research progresses of nano genosensors for the detection of HIV-1 and HTLV-1 viruses, based on electrochemical, optical, and photoelectrochemical platforms are overviewed.

Precision medicine, bioanalytics and nanomaterials: toward a new generation of personalized portable diagnostics

The customization of disease treatment focused on genetic, environmental and lifestyle factors of individual patients, including tailored medical decisions and treatments, is identified as precision medicine. This approach involves the combination of various aspects such as the collection and processing of a large amount of data, the selection of optimized and personalized drug dosage for each patient and the development of selective and reliable analytical tools for the monitoring of clinical, genetic and environmental parameters. In this context, miniaturized, compact and ultrasensitive bioanalytical devices play a crucial role for achieving the goals of personalized medicine. In this review, the latest analytical technologies suitable for providing portable and easy-to-use diagnostic tools in clinical settings will be discussed, highlighting new opportunities arising from nanotechnologies, offering peculiar perspectives and opportunities for precision medicine.

Noble Metal Nanostructured Materials for Chemical and Biosensing Systems

Nanomaterials with unique physical and chemical properties have attracted extensive attention of scientific research and will play an increasingly important role in the future development of science and technology. With the gradual deepening of research, noble metal nanomaterials have been applied in the fields of new energy materials, photoelectric information storage, and nano-enhanced catalysis due to their unique optical, electrical and catalytic properties. Nanostructured materials formed by noble metal elements (Au, Ag, etc.) exhibit remarkable photoelectric properties, good stability and low biotoxicity, which received extensive attention in chemical and biological sensing field and achieved significant research progress. In this paper, the research on the synthesis, modification and sensing application of the existing noble metal nanomaterials is reviewed in detail, which provides a theoretical guidance for further research on the functional properties of such nanostructured materials and their applications of other nanofields.

HIV biosensors for early diagnosis of infection: The intertwine of nanotechnology with sensing strategies

Human immunodeficiency virus (HIV) is a lentivirus that leads to acquired immunodeficiency syndrome (AIDS). With increasing awareness of AIDS emerging as a global public health threat, different HIV testing kits have been developed to detect antibodies (Ab) directed toward different parts of HIV. A great limitation of these tests is that they can not detect HIV antibodies during early virus infection. Therefore, to overcome this challenge, a wide range of biosensors have been developed for early diagnosis of HIV infection. A significant amount of these studies have been focused on the application of nanomaterials for improving the sensitivity and accuracy of the sensing methods. Following an introduction into this field, a first section of this review covers the synthesis and applicability of such nanomaterials as metal nanoparticles (NPs), quantum dots (QDs), carbon-based nanomaterials and metal nanoclusters (NCs). A second larger section covers the latest developments concerning nanomaterial-based biosensors for HIV diagnosis, with paying a special attention to the determination of CD4⁺ cells as a hall mark of HIV infection, HIV gene, HIV p24 core protein, HIV p17 peptide, HIV-1 virus-like particles (VLPs) and HIV related enzymes, particularly those that are passed on from the virus to the CD⁴⁺ T lymphocytes and are necessary for viral reproduction within the host cell. These studies are described in detail along with their diverse principles/mechanisms (e.g. electrochemistry, fluorescence, electromagnetic-piezoelectric, surface plasmon resonance (SPR), surface enhanced Raman spectroscopy (SERS) and colorimetry). Despite the significant progress in HIV biosensing in the last years, there is a great need for the development of point-of-care (POC) technologies which are affordable, robust, easy to use, portable, and possessing sufficient quantitative accuracy to enable clinical decision making. In the final section, the focus is on the portable sensing devices as a new standard of POC and personalized diagnostics.

Enzyme-free fluorescence microarray for determination of hepatitis B virus DNA based on silver nanoparticle aggregates-assisted signal amplification

In this study, we designed a fluorescence enhancement strategy based on silver nanoparticle (AgNP) aggregates for the detection of hepatitis B virus DNA sequences. AgNPs were functioned with recognition probes (Cy3-probe) and hybrid probes (Oligomer-A and Oligomer-B). The presence of target DNA mediated the formation of sandwich complexes between the immobilized capture probes and the functionalized AgNPs, which was followed by hybridization-induced formation of AgNP aggregates. The fluorescent intensity could be extremely amplified by both the increasing number of fluorophores and metal enhanced fluorescence (MEF) effect. Under optimal conditions, this method achieved a detection limit of 50 fM which was 1560-fold lower than that of un-enhanced fluorescent assays. It was illustrated that the HBV DNA concentrations ranging from 100 fM to 10 nM had a good log-linear correlation with the corresponding fluorescent intensity (R = 0.991). Moreover, this method had high specificity both for distinguishing single-base mismatches and identifying target DNA under the interference of genomic DNA. This fluorescent microarray had high-throughput analytical potential and could apply to many other disease diagnoses.

DNA concatemer-silver nanoparticles as a signal probe for electrochemical prostate-specific antigen detection

A ultrasensitive electrochemical detection of prostate-specific antigen was reported based on hybridization chain reaction amplifying silver nanoparticles response signal.

Double G-quadruplexes in a copper nanoparticle based fluorescent probe for determination of HIV genes

A DNA-templated copper nanoparticle (CuNP) probe has been developed for the determination of the human immunodeficiency virus oligonucleotide (HIV-DNA). The function of the probe relies on affinity binding-induced DNA hybridization associated with the use of double G-quadruplexes. Double-stranded DNA (dsDNA) with poly(AT-TA) bases was used as a template for synthesis of dsDNA-CuNPs. These have weak fluorescence. In the next step, two G-rich sequences that are linked to both sides of the ds-DNA are locked by HIV complementary DNA (cDNA). If HIV-DNA is introduced, it will hybridize with cDNA, thereby transforming the two G-rich sequences into G-quadruplexes. This enhances the fluorescence of the adjacent dsDNA-CuNPs. Fluorescence increases linearly in the 1 to 200 and 250-1000 nM HIV-DNA concentration range, and the detection limit is 13 pM. This enzyme-free fluorometric assay is time-saving, easily operated, and therefore has large potential in biosensing because it may be extended to various other DNA targets. Graphic abstract Double-strand DNA-templated copper nanoparticles (DNA-CuNPs) have weak fluorescence. When Human Immunodeficiency Virus oligonucleotide (HIV-DNA) is added, it completely hybridized with HIV complementary DNA (cDNA). As a result, the two exposed G-rich sequences are transformed into G-quadruplexes, and an apparent increase in the fluorescence intensity can be observed. (AA: ascorbic acid).

A genosensor for detection of HTLV-I based on photoluminescence quenching of fluorescent carbon dots in presence of iron magnetic nanoparticle-capped Au

Carbon dots and Fe₃O₄@Au were synthesized to develop a new biosensor to detect DNA target. We investigated the photoluminescence property of carbon dots (CDs) in the presence of Fe₃O₄-capped Au (Fe₃O₄@Au). Firstly, we designed two dedicated probes for unique long sequence region of human T-lymphotropic virus type 1 genome. One of the probes was covalently bound to the CDs. In the absence of target, CDs-probe was adsorbed on the surface of Fe₃O₄@Au through two possible mechanisms, leading to quenching the fluorescence emission of CDs. The fluorescence emission of CDs was recovered in the presence of target since double-stranded DNA cannot adsorb on the Fe₃O₄@Au. Also, Fe₃O₄@Au can adsorb the unhybridized oligonucleotides and improves the accuracy of detection. The specificity of the proposed biosensor was confirmed by BLAST search and assessed by exposing the biosensor to other virus targets. The experimental detection limit of the biosensor was below 10 nM with linear range from 10 to 320 nM.

Detecting transcription factors with allosteric DNA-Silver nanocluster switches

Sensitive and efficient detection of protein markers, such as transcription factors (TFs), is an important issue in postgenomic era. In this paper, we report a DNA nanodevice, allosteric DNA-silver nanocluster switches (AgSwitches), for TFs detection. The mechanism of this nanodevice is based on the binding-induced allostery whereby the binding between AgSwitches and TFs alters the conformation of AgSwitches. This alteration brings DNA-silver nanocluster (DNA-AgNCs) and guanine-rich enhancer sequences (GRS) into close proximity, generating fluorescent enhancement for quantifications. Our results revealed that the sequence design of AgSwitches can be rationally optimized according to stimulated free energy, and we demonstrated that this method can not only be used for detecting TFs in nuclear extracts of cells, but also be developed as a tool for screening inhibitors of TFs. Overall, this work expanded the category allosteric DNA nanodevices by first introducing DNA-AgNCs into this area, and the obtained method was efficient for TFs-related investigations.

A label-free fluorescent adenosine triphosphate biosensor via overhanging aptamer-triggered enzyme protection and target recycling amplification

Herein, a label-free fluorescent adenosine triphosphate (ATP) aptasensor is fabricated with a DNA hairpin and an overhanging aptamer. In the presence of ATP, the overhanging sequences of the aptamer may form preferred substrates of exo III, and thus trigger the enzyme-assisted amplification, which results in the release of G-rich sequences. Free G-rich sequences subsequently generate an enhanced flourescent signal by binding with thioflavin T. However, if ATP is absent, the overhanging sequence can induce steric hindrance and protect the DNA hairpin against the digestion of exo III, significantly reducing the noise of this biosensor. Accordingly, the signal-to-noise ratio of the sensing system is greatly improved, which ensures the desirable analytical performance of the proposed aptasensor both in pure samples and real samples.

Logic circuit controlled multi-responsive branched DNA scaffolds

A logic circuit controlled multi-responsive sensing platform built on a three-way DNA junction (TWJ) is reported. It enabled the construction of novel fluorescent sensing platforms responsive to any target out of HIV gene, ATP and pH value, and furthermore were logically regulated by two other targets and then behaved as different logic circuits, which consist of two tandem AND gates or cascaded NAND and INH gates by varying the positions of the fluorescent tags.

A Thioflavin T-induced G-Quadruplex Fluorescent Biosensor for Target DNA Detection

The detection of disease-related DNA is of great significance for early and accurate diagnosis and therapy. In this work, we successfully achieved the sensitive detection of target DNA based on a thioflavin T (ThT)-induced G-quadruplex fluorescent biosensor. ThT, a water-soluble fluorescent dye, can induce G-rich sequences to form G-quadruplexes and obtain an obviously enhanced fluorescence. In this work, it was employed to construct a biosensor for the detection of HIV. When the target HIV existed, the hairpin DNA probes would be opened in succession and release the completely exposed G-rich sequence to combine with ThT. The simple and rapid biosensor performed satisfactory selectivity; it also exhibited sensitivity with a detection limit of 2.4 nM. With good performance in human serum, we believe that this optical biosensor has the potential to be applied to the practical detection of target DNA.

Quantum Dot Fullerene-Based Molecular Beacon Nanosensors for Rapid, Highly Sensitive Nucleic Acid Detection

Spherical fullerene (C₆₀) can quench the fluorescence of a quantum dot (QD) through energy-transfer and charge-transfer processes, with the quenching efficiency regulated by the number of proximate C₆₀ on each QD. With the quenching property and its small size compared with other nanoparticle-based quenchers, it is advantageous to group a QD reporter and multiple C₆₀-labeled oligonucleotide probes to construct a molecular beacon (MB) probe for sensitive, robust nucleic acid detection. We demonstrated a rapid, high-sensitivity DNA detection method using the nanosensors composed of QD-C₆₀-based MBs carried by magnetic nanoparticles. The assay was accelerated by first dispersing the nanosensors in analytes for highly efficient DNA capture resulting from short-distance three-dimensional diffusion of targets to the sensor surface and then concentrating the nanosensors to a substrate by magnetic force to amplify the fluorescence signal for target quantification. The enhanced mass transport enabled a rapid detection (<10 min) with a small sample volume (1-10 μL). The high signal-to-noise ratio produced by the QD-C₆₀ pairs and magnetic concentration yielded a detection limit of 100 fM (∼10⁶ target DNA copies for a 10 μL analyte). The rapid, sensitive, label-free detection method will benefit the applications in point-of-care molecular diagnostic technologies.

A universal split spinach aptamer (USSA) for nucleic acid analysis and DNA computation

We demonstrate how a single universal spinach aptamer (USSA) probe can be used to detect multiple (potentially any) nucleic acid sequences. USSA can be used for cost-efficient and highly selective analysis of even folded DNA and RNA analytes, as well as for the readout of outputs of DNA logic circuits.

DNA metallization: principles, methods, structures, and applications

This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.

Nucleic acid probe based on DNA-templated silver nanoclusters for turn-on fluorescence detection of tumor suppressor gene p53

In this paper, we construct a fluorescence nucleic acid probe based on DNA-templated silver nanoclusters (DNA-Ag NCs) for the detection of the p53 gene. The fluorescence biosensing of the “turn-on” model is successfully implemented as a result of the target-triggered configurational change in the hairpin DNA probe and the synthesis of fluorescent Ag NCs. With this biosensor, the limit of detection (LOD) for the p53 gene is 3.57 nM and the linear range is 250–2500 nM in phosphate buffer solution, while a LOD of 6.06 nM in the linear range of 250–2500 nM is obtained in 1% diluted fetal calf serum. So this probe, with its advantages of specificity, practical application, easy operation and low cost, will have favourable development prospects in biological sensing and imaging.

“Turn-on” fluorescence detection for p53 gene based on target-triggered opening of hairpin DNA probe and synthesis of DNA-Ag NCs.

A molecular beacon based on DNA-templated silver nanoclusters for the highly sensitive and selective multiplexed detection of virulence genes

In this work, we develop a fluorescent molecular beacon based on the DNA-templated silver nanoclusters (DNA-Ag NCs). The skillfully designed molecular beacon can be conveniently used for detection of diverse virulence genes as long as the corresponding recognition sequences are embedded. Importantly, the constructed detection system allows simultaneous detection of multiple nucleic acids, which is attributed to non-overlapping emission spectra of the as-synthesized silver nanoclusters. Based on the target-induced fluorescence enhancement, three infectious disease-related genes HIV, H1N1, and H5N1 are detected, and the corresponding detection limits are 3.53, 0.12 and 3.95nM, respectively. This design allows specific, versatile and simultaneous detection of diverse targets with easy operation and low cost.

Nanomaterial-based biosensors for detection of pathogenic virus

Viruses are real menace to human safety that cause devastating viral disease. The high prevalence of these diseases is due to improper detecting tools. Therefore, there is a remarkable demand to identify viruses in a fast, selective and accurate way. Several biosensors have been designed and commercialized for detection of pathogenic viruses. However, they present many challenges. Nanotechnology overcomes these challenges and performs direct detection of molecular targets in real time. In this overview, studies concerning nanotechnology-based biosensors for pathogenic virus detection have been summarized, paying special attention to biosensors based on graphene oxide, silica, carbon nanotubes, gold, silver, zinc oxide and magnetic nanoparticles, which could pave the way to detect viral diseases and provide healthy life for infected patients.

Self-Assembled Ti4+@Biospore Microspheres for Sensitive DNA Analysis

Ti⁴⁺ can be chemically adsorbed and assembled on the surface of the modified spore to form highly monodispersed Ti⁴⁺@spore microspheres. Moreover, we for the first time found that these biomicrospheres exhibit differential affinities toward ssDNA and dsDNA. As a principle-of-proof, we exploited the self-assembled Ti⁴⁺@spore microspheres for a hybridization analysis. Interestingly, in the hybridization analysis, residual ssDNA probes are selectively adsorbed on Ti⁴⁺@spore microspheres at pH 5.0 and then removed via centrifugation. By taking advantage of this property, the signal-to-noise ratio for DNA analysis was considerably increased by reducing the noise caused by the residual ssDNA probes. The proposed method features easy operation, high specificity, and sensitivity and thus exhibits potential for further applications on DNA biosensing.

Selectivity enhancements in gel-based DNA-nanoparticle assays by membrane-induced isotachophoresis: thermodynamics versus kinetics

Selectivity against mutant nontargets with a few mismatches remains challenging in nucleic acid sensing. Sensitivity enhancement by analyte concentration does not improve selectivity because it affects targets and nontargets equally. Hydrodynamic or electrical shear enhanced selectivity is often accompanied by substantial losses in target signals, thereby leading to poor limits of detection. We introduce a platform based on depletion isotachophoresis in agarose gel generated by an ion-selective membrane that allows both selectivity and sensitivity enhancement with a two-step assay involving concentration polarization at an ion-selective membrane. By concentrating both the targets and probe-functionalized nanoparticles by ion enrichment at the membrane, the effective thermodynamic dissociation constant is lowered from 40 nM to below 500 pM, and the detection limit is 10 pM as reported previously. A dynamically optimized ion depletion front is then generated from the membrane with a high electrical shear force to selectively and irreversibly dehybridize nontargets. The optimized selectivity against a two-mismatch nontarget (in a 35-base pairing sequence) is shown to be better than the thermodynamic equilibrium selectivity by more than a hundred-fold, such that there is no detectable signal from the two-mismatch nontarget. We offer empirical evidence that irreversible cooperative dehybridization plays an important role in this kinetic selectivity enhancement and that mismatch location controls the optimum selectivity even when there is little change in the corresponding thermodynamic dissociation constant.

A new AgNC fluorescence regulation mechanism caused by coiled DNA and its applications in constructing molecular beacons with low background and large signal enhancement

A AgNC fluorescence interference strategy caused by a coiled DNA sequence (A) and its applications in target DNA detection (B).

MoS2-DNA and MoS2 based sensors

MoS₂, a family member of transition-metal dichalcogenides, has shown highly attractive superiority for detection arising from its unique physical and chemical properties.