Ratiometric determination of human papillomavirus-16 DNA by using fluorescent DNA-templated silver nanoclusters and hairpin-blocked DNAzyme-assisted cascade amplification

Advancements in fluorescent nanobiosensors for HPV detection: from integrating nanomaterials to DNA nanotechnology

Human papillomavirus (HPV) is a leading cause of cervical cancer and other malignancies, necessitating the development of highly sensitive and specific detection tools. This review explores recent advancements in fluorescent nanobiosensors (FNBS) for HPV detection, focusing on the integration of nanomaterials and DNA nanotechnology, highlighting their contributions to improving sensitivity, specificity, and point-of-care (POC) usability. The review critically evaluates a range of nanomaterial-based FNBS, including those employing quantum and carbon dots, nanoclusters, nanosheets, and nanoparticles, discussing their underlying signal amplification mechanisms, target recognition strategies, and limitations related to toxicity, stability, and reproducibility. Furthermore, it examines the application of diverse DNA nanotechnology, such as DNA origami, DNAzyme, catalytic hairpin assembly (CHA), hybridization chain reaction (HCR), and DNA hydrogel in improving FNBS performance. It also addresses the current challenges in clinical translation, emphasizing the necessity for large-scale production methods and thorough clinical validation to ensure biosafety. It also outlines the potential of innovative technologies, such as CRISPR-Cas-based diagnostics and artificial intelligence, to further revolutionize HPV detection and enable accessible, cost-effective screening, particularly in resource-limited settings. This review provides a valuable resource for researchers and clinicians seeking to develop next-generation FNBS for improved HPV diagnostics and cervical cancer prevention.

PER-Based DNA Cube Captor for High Specific and Efficient SERS Detection of HPV

Early detection of human papillomavirus (HPV) is crucial for the treatment and prevention of some specific skin diseases and related cancers such as cervical cancer, anal cancer, penile cancer, etc. Herein, we designed a primer exchange reaction (PER)-based DNA cube captor (PDCC) to capture Raman molecular labeled DNA for high specificity and efficient detection of HPV. First, we converted the target into large amounts of single-stranded DNA based on PER. Second, the single-stranded DNA initiated catalytic hairpin assembly (CHA) reaction, facilitating the capture of Raman molecular labeled DNA onto the DNA cube nanostructures (DCNs). Then the DCNs were subsequently immobilized on gold hexagonal plates (GHPs) for Raman detection. Of note, the identification of the target by PER exhibits high specificity, as the PER reaction occurs exclusively when the target perfectly matches the PER hairpin. Moreover, the CHA reaction can occur on four sides of this structure, and the reaction efficiency is enhanced by the proximity effect. This work developed a device named PDCC that captured Raman molecular labeled DNA, which can realize highly sensitive detection of HPV-58. This DNA cube captor has a high reaction efficiency and specificity for HPV, which plays an indispensable role in diagnosis and treatment of related cancers.

Multifunctional Ethyl Violet@NH2-MIL-88B(Fe) Hybrids: CRISPR-Cas12a-Assisted PEC-FL-CL Triple-Mode Sensitive Detection of HPV-16

The multimode assay based on multiple response mechanisms has received great attention to effectively improve the accuracy of a sensing platform. However, multifunctional sensing materials for simultaneously satisfying the multiple-mode detections are still in shortage due to the incompatibility of the signal transduction mechanisms in different modes. Here, taking human papillomavirus 16 (HPV-16) DNA (TDNA) as the model due to its important role in cervical cancer, a novel multifunctional material, ethyl violet (EV)@NH2-MIL-88B(Fe) (ENM) hybrids, have been successfully prepared, which could simultaneously satisfy CRISPR-Cas12a-assisted photoelectrochemical (PEC)-fluorescent (FL)-colorimetric (CL) triple-mode detection of TDNA. Based on the TDNA-induced trans-cleavage ability of CRISPR-Cas12a and efficient separation of magnetic beads, ENM was obtained from the single-stranded DNA-surrounded streptavidin-modified magnetic beads-ENM (SMB-ssDNA-ENM) and decomposed by pyrophosphate to get free EV, 2-aminoterephthalic acid (NH2-BDC), and Fe3+. Thus, TDNA was sensitively detected based on the EV-enhanced PEC signal of SnS2 nanosheets (PEC mode), fluorescent signal of NH2-BDC (FL mode), and characteristic absorption peak at about 720 nm of Fe3+-induced Prussian blue (PB) (CL mode). The designed PEC-FL-CL triple-mode biosensing platform had good performance for the detection of TDNA with a wide linear range (0.1 fM-100 nM) and ultralow detection limits (0.07 fM for PEC, 0.03 fM for FL and 0.09 fM for CL). Additionally, the developed PEC-FL-CL triple-mode biosensing platform has great potential for applications in early disease diagnosis and bioanalysis, as it can be easily extended to other DNA assays through modification of the crRNA sequence within the CRISPR-Cas12a system.

A Fluorescence Enhancement Sensor Based on Silver Nanoclusters Protected by Rich-G-DNA for ATP Detection

In this study, a turn-on fluorescence sensor for the detection of adenosine 5'-triphosphate (ATP) was developed and tested using ATP-DNA2-Ag NCs. The results showed that the fluorescence of ATP-DNA2-Ag NCs was significantly enhanced with the addition of ATP. The fluorescence enhancement was a result of the specific binding activity of the ATP aptamer and ATP, which caused G-rich sequences to approach the dark DNA-Ag NCs, owing to the alteration in ATP aptamer conformation. The proposed sensor demonstrated a good linear range of 18-42 mM and a limit of detection (LOD) of 2.8 μM. The sensor's features include sensitivity, selectivity, and simple operation. In addition, the proposed sensor successfully measured ATP in 100-fold diluted fetal bovine serum.

Simultaneous detection of CaMV35S and NOS using fluorescence sensors with dual-emission silver nanoclusters and catalytic hairpin amplification strategy

A dual-emission fluorescent biosensing method was developed for simultaneous determination of CaMV35S and NOS in genetically modified (GM) plants. Two designed hairpin DNA (H1, H2) sequences were used as templates to synthesize H1-AgNCs (λex = 570 nm, λem = 625 nm) and H2-AgNCs (λex = 470 nm, λem = 555 nm). By using H1-AgNCs and H2-AgNCs as dual-signal tags, combined with signal amplification strategy of magnetic separation to reduce background signal and an enzyme-free catalytic hairpin assembly (CHA) signal amplification strategy, a novel multi-target fluorescent biosensor was fabricated to detect multiple targets based on FRET between signal tags (donors) and magnetic Fe3O4 modified graphene oxide (Fe3O4@GO, acceptors). In the presence of the target NOS and CaMV35S, the hairpin structures of H1 and H2 can be opened respectively, and the exposed sequences will hybridize with the G-rich hairpin sequences HP1 and HP2 respectively, displacing the target sequences to participate in the next round of CHA cycle. Meanwhile, H1-HP1 and H2-HP2 double-stranded DNA sequences (dsDNA) were formed, resulting in the desorption of dsDNA from the surface of Fe3O4@GO due to weak π-π interaction between dsDNA and Fe3O4@GO and leading to the fluorescence recovery of AgNCs. Under optimal conditions, the linear ranges of this fluorescence sensor were 5 ~ 300 nmol L-1 for NOS and 5 ~ 200 nmol L-1 CaMV35S, and the LODs were 0.14 nmol L-1 and 0.18 nmol L-1, respectively. In addition, the fluorescence sensor has good selectivity for the detection of NOS and CaMV35S in GM soybean samples, showing the potential applications in GM screening.

Fluorescence Sensors for the Detection of L-Histidine Based on Silver Nanoclusters Modulated by Copper Ions

In this study, Cu2+ modulated silver nanoclusters were constructed for the turn-on, label-free detection of L-histidine. Six Ag NCs protected by oligonucleotides (DNA-Ag NCs) were tested in a series of experiments. Finally, A-DAN-Ag NCs were chosen as the best candidate due to their excellent fluorescent properties. The fluorescence of A-DAN-Ag NCs was quenched using Cu2+ through energy or electron transfer. However, quenched fluorescence could be restored dramatically in the presence of L-histidine due to Cu2+ liberation from A-DAN-Ag NCs and because of the chelation between the imidazole group of L-histidine and Cu2+. The proposed sensor exhibited high selectivity towards L-histidine over other amino acids, with a limit of detection (LOD) of 0.096 μM ranging from 0 to 8 μM. The proposed sensor succeeded in detecting L-histidine in diluted human urine. Therefore, the sensor has promising practical applications in biological systems.

Turn-on fluorescent nanoprobe for ATP detection based on DNA-templated silver nanoclusters

A turn-on fluorescence nanoprobe was constructed for the determination of adenosine 5'-triphosphate (ATP) based on DNA-templated silver nanoclusters (DNA-AgNCs). The significant enhancement fluorescence intensity of DNA-AgNCs in the presence of ATP is due to the high special binding affinity between ATP and the aptamer, resulting in the environment of DNA-AgNCs with darkish fluorescence lying at one terminus of DNA slightly altering owing to the change of ATP aptamer conformation. A good linear range runs from 9 to 24 mM with a satisfactory detection limit of 3 μM. Furthermore, the proposed nanoprobe exhibited good performance for ATP detection in diluted fetal bovine serum.

Advanced technologies towards improved HPV diagnostics

Persistent infection with high-risk types of human papillomaviruses (HPV) is a major cause of cervical cancer, and an important factor in other malignancies, for example, head and neck cancer. Despite recent progress in screening and vaccination, the incidence and mortality are still relatively high, especially in low-income countries. The mortality and financial burden associated with the treatment could be decreased if a simple, rapid, and inexpensive technology for HPV testing becomes available, targeting individuals for further monitoring with increased risk of developing cancer. Commercial HPV tests available in the market are often relatively expensive, time-consuming, and require sophisticated instrumentation, which limits their more widespread utilization. To address these challenges, novel technologies are being implemented also for HPV diagnostics that include for example, isothermal amplification techniques, lateral flow assays, CRISPR-Cas-based systems, as well as microfluidics, paperfluidics and lab-on-a-chip devices, ideal for point-of-care testing in decentralized settings. In this review, we first evaluate current commercial HPV tests, followed by a description of advanced technologies, explanation of their principles, critical evaluation of their strengths and weaknesses, and suggestions for their possible implementation into medical diagnostics.

HCR/DNAzyme-triggered cascaded feedback cycle amplification for self-powered dual-photoelectrode detection of femtomolar HPV16

For high-performance dual-photoelectrode assay, developing a pair of photoactive materials with well-matched band structure and the design of a powerful sensing strategy are highly desirable. Herein, the Zn-TBAPy pyrene-based MOF and BiVO4/Ti3C2 Schottky junction were employed as photocathode and photoanode to form an efficient dual-photoelectrode system. The integration of the cascaded hybridization chain reaction (HCR)/DNAzyme-assisted feedback amplification with DNA walker-mediated cycle amplification strategy realizes femtomolar HPV16 dual-photoelectrode bioassay. Through the activation of the HCR cascaded with the DNAzyme system in the presence of HPV16, plentiful HPV16 analogs are generated that leads to exponential positive feedback signal amplification. Meanwhile on the Zn-TBAPy photocathode, the NDNA hybridizes with the bipedal DNA walker followed by circular cleavage by Nb.BbvCI NEase, producing a dramatically enhanced PEC readout. The achieved ultralow detection limit of 0.57 fM and a wide linear range of 10-6 nM-103 nM showcase the excellent performance of the developed dual-photoelectrode system.

Rapid and portable bunyavirus SFTSV RNA testing utilizing catalytic hairpin assembly coupled with lateral flow immunoassay

Severe fever with thrombocytopenia syndrome (SFTS) is a prevalent, life-threatening, emergent infectious disease. Currently, reverse transcription-polymerase chain reaction is the gold standard for diagnosing SFTS virus (SFTSV) infection, which requires sophisticated equipment and professional personnel that are frequently unavailable in most SFTS endemic rural areas. Here, we reported a simple, rapid nucleic acid amplification system that combined the catalytic hairpin assembly (CHA) with a lateral flow immunoassay (LFIA) strip-based detection method for SFTSV detection. The detection of SFTSV RNA could be realized by generation of H1-H2 hybrid duplexes labeled with biotin and digoxin, which subsequently added to the LFIA test strips containing streptavidin conjugated with Alexa Fluor 647 as well as anti-digoxin antibodies. Our CHA-based LFIA assay offered high amplification efficiency and specificity with a detection limit of 1 aM. Crucially, this method enabled stable detection of 500 copies/mL of SFTSV within 30 min using clinical serum samples. Therefore, our CHA-based LFIA approach provided a potential useful tool to facilitate early and precise diagnosis of SFTS patients in poorly resourced SFTS endemic areas.IMPORTANCESevere fever with thrombocytopenia syndrome (SFTS) is an emerging and potentially fatal infectious disease prevalent in China. Here we report a simple, rapid nucleic acid amplification system, the catalytic hairpin assembly (CHA) in conjunction with a lateral flow immunoassay (LFIA) strip-based detection method for SFTS virus detection, which demonstrated high amplification efficiency and specificity with limit of detection of 1 aM. Most importantly, we also validate our CHA-based LFIA assay using the clinical serum samples, which was fully compatible with reverse transcription-PCR results. Therefore, our strategy provides a potential useful tool to facilitate early and precise diagnosis of SFTS patients especially in poorly resourced SFTS endemic areas.

RNA-Cleaving DNAzyme-Based Amplification Strategies for Biosensing and Therapy

Since their first discovery in 1994, DNAzymes have been extensively applied in biosensing and therapy that act as recognition elements and signal generators with the outstanding properties of good stability, simple synthesis, and high sensitivity. One subset, RNA-cleaving DNAzymes, is widely employed for diverse applications, including as reporters capable of transmitting detectable signals. In this review, the recent advances of RNA-cleaving DNAzyme-based amplification strategies in scaled-up biosensing are focused, the application in diagnosis and disease treatment are also discussed. Two major types of RNA-cleaving DNAzyme-based amplification strategies are highlighted, namely direct response amplification strategies and combinational response amplification strategies. The direct response amplification strategies refer to those based on novel designed single-stranded DNAzyme, and the combinational response amplification strategies mainly include two-part assembled DNAzyme, cascade reactions, CHA/HCR/RCA, DNA walker, CRISPR-Cas12a and aptamer. Finally, the current status of DNAzymes, the challenges, and the prospects of DNAzyme-based biosensors are presented.

Recent advances of catalytic hairpin assembly and its application in bioimaging and biomedicine

Catalytic hairpin assembly (CHA) appears to be a particularly appealing nucleic acid circuit because of its powerful amplification capability, simple protocols, and enzyme-free and isothermal conditions, and can combine with various signal output modes for the biosensing of various analytes. Especially in the last five years, vast CHA related studies have sprung up. With the deep exploration of the CHA mechanism, some novel and excellent CHA strategies have been proposed; meanwhile the CHA cascade strategies with various amplification techniques further improve the analysis performance. Furthermore, diverse CHA based biosensors have been tactfully engineered and extensively employed in imaging applications in living cells and in vivo ascribed to its gentle reaction, efficient amplification and universality. Hence, we present a comprehensive and systematic summary of the progress in CHA and its application in bioimaging and biomedicine to date. At first, we introduced the mechanism and diversification of CHA in detail, including the newly developed CHA and its ingenious combination with a variety of other technologies. Concurrently, we summarized the latest application progress of different CHA strategies in bioimaging and biomedicine, highlighting the merits and drawbacks of representative approaches. Finally, we put forward some views on the challenges and prospects of CHA in bioimaging and biomedicine in the future.

Internal heating method of loop-mediated isothermal amplification for detection of HPV-6 DNA

Loop-mediated isothermal amplification (LAMP) is a promising diagnostic tool for genetic amplification, which is known for its rapid process, simple operation, high amplification efficiency, and excellent sensitivity. However, most of the existing heating methods are external for completion of molecular amplification with possibility of contamination of specimens. The present research provided an internal heating method for LAMP using magnetic nanoparticles (MNPs), which is called nano-LAMP. Near-infrared light with an excitation wavelength of 808 nm was employed as the heating source; hydroxy naphthol blue (HNB) was used as an indicator to conduct methodological research. We demonstrate that the best temperature was controlled at a working power of 2 W and 4.8 µg/µL concentration of nanoparticles. The lowest limit for the detection of HPV by the nano-LAMP method is 10² copies/mL, which was confirmed by a gel electrophoresis assay. In the feasibility investigation of validated clinical samples, all 10 positive HPV-6 specimens amplified by nano-LAMP were consistent with conventional LAMP methods. Therefore, the nano-LAMP detection method using internal heating of MNPs may bring a new vision to the exploration of thermostatic detection in the future.

One-Pot Identification of BCR/ABLp210 Transcript Isoforms Based on Nanocluster Beacon

The BCR/ABL^p210 fusion gene is a classic biomarker of chronic myeloid leukemia, which can be divided into e13a2 and e14a2 isoforms according to different breakpoints. These two isoforms showed distinct differences in clinical manifestation, treatment effect, and prognosis risk. Herein, a strategy based on nanocluster beacon (NCB) fluorescence was developed to identify the e13a2 and e14a2 isoforms in one-pot. Because the fluorescence of AgNCs can be activated when they are placed in proximity to the corresponding enhancer sequences, thymine-rich (T-rich) or guanine-rich (G-rich). In this work, we explored an ideal DNA-AgNCs template as an excellent molecular reporter with a high signal-to-noise ratio. After recognition with the corresponding isoforms, the AgNCs can be pulled closer to the T-rich or G-rich sequences to form a three-way junction structure and generate fluorescence with corresponding wavelengths. Therefore, by distinguishing the corresponding wavelengths of AgNCs, we successfully identified two isoforms in one tube with the limitation of 16 pM for e13a2 and 9 pM for e14a2. Moreover, this strategy also realized isoform identification in leukemia cells and newly diagnosed CML patients within 40 min, which provides a powerful tool to distinguish fusion gene subtypes at the same time.

Fluorescent DNA-templated silver nanoclusters for highly sensitive detection of D-penicillamine

Herein, fluorescent DNA-templated silver nanoclusters (DNA-AgNCs) with red emission were synthesized and utilized as novel probe to detect D-penicillamine (D-Pen) for the first time. D-Pen molecules contain a thiol which can combine with Ag to form a non-fluorescent ground state complex, inducing the aggregation of DNA-AgNCs followed by the fluorescence quenching. The quenching mechanism is well-studied and found to be a static quenching process. This method can detect D-Pen in the range of 0.025-0.7 μM with the detection limit as low as 8 nM, which is 1-3 orders of magnitude more sensitive than those based on other fluorescent nanoprobes. More importantly, the preparation procedure for DNA-AgNCs is fast and without the requirement of heavy metal ions. Thus, this detection strategy is time-saving and eco-friendly. Satisfactory recoveries have been acquired for monitoring D-Pen in human serum samples and pharmaceutical samples owing to the high sensitivity.

A ratiometric fluorescence assay for bleomycin based on dual-emissive chameleon DNA-templated silver nanoclusters

The authors design dual-emissive DNA-templated silver nanoclusters (DNA-AgNCs) for ratiometric fluorescence sensing bleomycin (BLM) for the first time. A hairpin probe containing two different C-rich DNA templates at two terminals is used to synthesize chameleon DNA-AgNCs, which possess two emission peaks when they are in close proximity. A strong emission is founded at 622 nm (λex = 570 nm) while a weak one is located at 572 nm (λex = 504 nm). Meanwhile, the loop of this probe contains the scission site (5'-GC-3') of BLM. The loop can be cleaved into two parts by BLM-Fe(II) complex, inducing the two DNA-AgNCs away from each other. The fluorescence intensity at 572 nm and 622 nm increases and decreases, respectively. Such chameleon DNA-AgNCs exhibit an obvious fluorescence discoloration from orange to yellow. Therefore, a sensitive ratiometric fluorescent strategy for BLM detection has been proposed with the detection limit of 67 pM. Finally, this ratiometric method is used to detect BLM in serum samples.

Development of dual-emission cluster of Ag atoms for genetically modified organisms detection

A DNA-silver nanocluster with two distinct emissions is devised, in which this unique modality has been exploited to develop a novel nanosensor for transgenic DNA detection. TEM and fluorescence analysis revealed the formation of Ag nanoclusters with a size of around 2 nm, which exhibit dual-emissions at 550 nm (green) and 630 nm (red). Moreover, in the presence of the target sequence (CaMV 35S promoter) from the transgenic plant, the nanoclusters showed an enhancement in the green emission and a reduction in the red emission. This property provided a ratiometric-sensing platform which lacks unavoidable noises. The ratio of green to red fluorescence emission (G/R) of the nanoclusters exhibited a linear relation with the target concentration in the range 10 to 1000 nM. However, the control DNA did not affect this ratio, which clearly confirmed the selective response of the designed nanosensor. This sensing platform had a detection limit of 1.5 nM and identified the DNA of transgenic soybeans within a short time. The mechanistic evaluation of the nanoclusters further revealed the role of protonated cytosine bases in the dual emission behavior. Finally, unique features of the designed nanosensor may improve the current approaches for the development and manufacturing of GMO detection tools.

Label-free probes using DNA-templated silver nanoclusters as versatile reporters

DNA-templated silver nanoclusters (DNA-AgNCs) have demonstrated pervasive applications in analytical chemistry recently. As a way of signal output in DNA-based detection methods, DNA-AgNCs have prominent advantages: first, the recognition and synthesizing sequences are naturally integrated in one DNA probe without any chemical modification or connection; second, the emissive wavelength of DNA-AgNCs can be adjusted in a wide range by employing different sequences; third, DNA-AgNCs can be utilized for producing not only fluorescence, also electrochemiluminescence and electrochemical signals. Besides, they also show potential applications for cell imaging, and are considered to be one of the most ideal nanomaterials for in-vivo imaging due to their ultra-small particle size. In this review, a brief and comprehensive introduction of DNA-AgNCs is firstly given, then label-free probes using DNA-AgNCs are classified and summarized, lastly concluding perspectives are provided on the defects and application potentials.