High-Sensitive Assay of Nucleic Acid Using Tetrahedral DNA Probes and DNA Concatamers with a Surface-Enhanced Raman Scattering/Surface Plasmon Resonance Dual-Mode Biosensor Based on a Silver Nanorod-Covered Silver Nanohole Array

Tri-Mode CRISPR-Based Biosensor for miRNA Detection: Enhancing Clinical Diagnostics with Cross-Validation

In vitro diagnostics require the accurate detection of disease-associated target biomolecules at ultralow concentrations. A multimode sensing strategy is considered as a potential method for in vitro diagnosis because it allows cross-validation of test results through data complementation and self-calibration, and provides double confirmation. Here, we present a CRISPR/Cas12a-powered trimode biosensor (CPTMB) for ultrasensitive and reliable analysis of miRNA. Briefly, the presence of target miRNA initiates rolling circle extension-driven loop-mediated isothermal amplification (R-LAMP), which subsequently activates the trans-cleavage activity of CRISPR/Cas12a. Then, the hairpin probe (HP) biogate on nucleic acid-functionalized MB@Fe-MOF signal probe was degraded by Cas12a, leading to the release of methylene blue (MB) signal molecules encapsulated within Fe-MOF nanocarriers. Due to the capability of MB to generate output responses across three distinct modes: electrochemical (EC), fluorescence (FL), and ultraviolet-visible spectroscopy (UV-vis), a trimodal sensing system is achieved. Benefiting from the efficient signal amplification capabilities of R-LAMP and CRISPR/Cas12a, this strategy enables rapid detection of target miRNA at femtomolar levels within 70 min. Furthermore, the detection results across the three modes cross-validate one another, thereby enhancing the reliability of the analysis. More importantly, the platform has been successfully applied to miRNA analysis in real samples, and the detection results are in good agreement with those of the standard method RT-qPCR, indicating its great potential in the clinical diagnosis of early-stage cancer.

Advancements in functional tetrahedral DNA nanostructures for multi-biomarker biosensing: Applications in disease diagnosis, food safety, and environmental monitoring

Deoxyribonucleic acid (DNA) offers the fundamental building blocks for the precisely controlled assemblies due to its inherent self-assembly and programmability. The tetrahedral DNA nanostructure (TDN) stands out as a widely utilized nanostructure, attracting attention for its high biostability, excellent biocompatibility, and versatile modification sites. The capability of DNA tetrahedron to interact with various signal outputs makes it ideal for developing functional DNA nanostructures in biosensing platforms. This review highlights recent advancements in functional tetrahedral DNA nanostructures (FTDN) for various biomarkers monitoring, including nucleic acid, protein, mycotoxin, agent, and metal ion. Additionally, it discusses the potential of FTDN in the fields of disease diagnosis, food safety, and environmental monitoring. The review also introduces the application of FTDN-based biosensors for simultaneous identification of multiple biomarkers. Finally, challenges and prospects are addressed to provide guidance for the continued development of FTDN-based biosensing platforms.

Surface-Enhanced Raman Spectroscopy for Biomedical Applications: Recent Advances and Future Challenges

The year 2024 marks the 50th anniversary of the discovery of surface-enhanced Raman spectroscopy (SERS). Over recent years, SERS has experienced rapid development and became a critical tool in biomedicine with its unparalleled sensitivity and molecular specificity. This review summarizes the advancements and challenges in SERS substrates, nanotags, instrumentation, and spectral analysis for biomedical applications. We highlight the key developments in colloidal and solid SERS substrates, with an emphasis on surface chemistry, hotspot design, and 3D hydrogel plasmonic architectures. Additionally, we introduce recent innovations in SERS nanotags, including those with interior gaps, orthogonal Raman reporters, and near-infrared-II-responsive properties, along with biomimetic coatings. Emerging technologies such as optical tweezers, plasmonic nanopores, and wearable sensors have expanded SERS capabilities for single-cell and single-molecule analysis. Advances in spectral analysis, including signal digitalization, denoising, and deep learning algorithms, have improved the quantification of complex biological data. Finally, this review discusses SERS biomedical applications in nucleic acid detection, protein characterization, metabolite analysis, single-cell monitoring, and in vivo deep Raman spectroscopy, emphasizing its potential for liquid biopsy, metabolic phenotyping, and extracellular vesicle diagnostics. The review concludes with a perspective on clinical translation of SERS, addressing commercialization potentials and the challenges in deep tissue in vivo sensing and imaging.

The role of DNA nanotechnology in medical sensing

This paper explores how DNA nanotechnology enhances biosensors in medicine and pharmacology by taking advantage of the unique characteristics of DNA and the unique advantages of DNA origami technology. DNA origami allows the establishment of complex nanoobjects with precise size and complete molecular writability as well as the possibility of seamless integration and biocompatibility with biological systems. Utilizing this, the chemical denaturation of DNA chains allows for the combination of various functions, including organic fluorescence groups and photoreaction elements, etc. This has allowed DNA origami to become a transformative tool in biotechnology and other fields because of its versatility, use in innovative applications improving the design and function of biosensors, and potential to provide greater possibilities for early disease diagnosis and personalized medicine.

In Situ and In Vivo Evaluation of Multiplex Protein-Specific Glycosylation of Tumors with a Dual-SERS Encoding Strategy

A dual-SERS encoding strategy was designed for in situ and in vivo evaluation of multiplex protein-specific glycosylation of tumors. The dual-SERS encoding strategy consisted of two pairs of dual gold nanoprobes with different diameters of 10 and 30 nm, which were encoded with four different and distinguishable Raman signal molecules. The 10 and 30 nm gold nanoprobes (Au10 and Au30 probes, respectively) were further modified with lectins and aptamers to recognize the target glycans and proteins, respectively. After sequential binding to the target glycans and proteins, the adjacent Au10 and Au30 probes could emit strong surface-enhanced Raman scattering (SERS) signals to indicate the multiplex protein-specific glycosylation information on cells and in vivo, which can reveal in situ the distribution differences of different tumor markers in the central and marginal regions of tumors. This strategy has been successfully applied for in situ imaging and evaluation of the MUC1 and EpCAM-specific Sia and Gal/GalNAc information on cell surfaces and tumor xenografted mice, providing a convenient and powerful tool to study protein-specific glycosylation-related physiological and pathological mechanisms.

Characterization of SPR and cavity modes in one-dimensional (1D) gold nanograting chips: figure of merit analysis and implications for Raman signal enhancement

The optical properties of the 1D nanograting chip have been explored based on computational and experimental studies. Dispersion curve analysis demonstrates cavity and surface plasmon modes in the 1D nanograting chips with periods of 400 nm and 800 nm. In this grating period range, the cut-off period is at a grating period of 644 nm under excitation with a wavelength of 670 nm. Among the two investigated chips, the chip with a grating period of 800 nm is more promising for application as a dual-mode sensor based on SPR/Raman. By using the angle interrogation method, this chip has a figure of merit (FOM), which is 3.23 times higher than the 1D nanograting chip with a period of 400 nm. In the same system, Raman measurements have also been performed using Rhodamine 6 G (R6 G) as the standard material. The experimental results show that the Raman signal measured at the grating resonance angle shows higher intensity than the Raman measurement without Surface Plasmon Resonance (SPR) sensor. SPR-induced electromagnetic enhancement plays an important role in amplifying Raman signals in surface-enhanced Raman scattering (SERS) and this approach is very promising to be further developed to obtain sensors that are not only sensitive but also accurate.

Fabrication of high performance 2D flexible SERS substrate based on cellulose nanofibrils and its application for pesticide residue detection

Cellulose nanofibrils (CNFs) can serve as an efficient surface enhanced Raman scattering (SERS) platform for in situ detection of trace targets. In this study, a highly reproducible SERS platform based on TEMPO-oxidized CNFs (T-CNFs) was fabricated by the ion-exchange. Self-assembly of silver nanoparticles (AgNPs) was accomplished in only 120 s. The abundant carboxylate groups and good hydrophilicity of T-CNFs facilitated uniform and dense loading of AgNPs over the surface area. The obtained SERS substrate greatly enhanced the Raman signal of different pesticides, and the detection limits of thiram and thiabendazole were 5.81 × 10-8 M and 9.63 × 10-8 M, respectively. SERS substrate could produce homogeneous Raman-enhanced signals (relative standard deviation (RSD) = 6.59 %). In addition, due to the good flexibility, SERS substrate could collect and detect pesticide residues from the surface of apples. The intensities of Raman characteristic peak at 1384 cm-1 showed a good linear relationship with the analyte concentrations (0.96 ng/cm2-9600 ng/cm2). The constructed SERS substrate provided a theoretical basis for the preliminary rapid screening of hazardous chemical residues in food, which was of great value for the SERS technique to become a routine on-site analysis method for pesticide residues.

Portable SERS biosensor based on aptamer-assisted catalytic hairpin assembly signal amplification for ultrasensitive detection of Staphylococcus aureus

Bacteria infections pose a serious threat to public health, and it is urgent to develop facile and accurate detection methods. To meet the important need, a potable and high-sensitive surface enhanced Raman scattering (SERS) biosensor based on aptamer recognition and catalytic hairpin assembly (CHA) signal amplification was proposed for point-of-care detection of Staphylococcus aureus (S. aureus). The SERS biosensor contains three parts: recognition probes, SERS sensing chip, and SERS tags. The feasibility of the strategy was verified by gel electrophoresis, and the one-step test route was optimized. The bacteria SERS biosensor has a good linear relationship ranging from 10 to 107 CFU mL-1 with high sensitivity low to 5 CFU mL-1, and shows excellent specificity, uniformity, and repeatability on S. aureus identification and enumeration, which can distinguish S. aureus from other bacteria. The SERS biosensor shows a good recovery rate (95.73 %-109.65 %) for testing S. aureus spiked in milk, and has good practicability for detecting S. aureus infected mouse wound, which provides a facile and reliable approach for detection of trace bacteria in the real samples.

Dual-Mode Sensing of Fe(III) Based on Etching Induced Modulation of Localized Surface Plasmon Resonance and Surface Enhanced Raman Spectroscopy

Convenient, rapid, highly sensitive and on-site iron determination is important for environmental safety and human health. We developed a sensing system for the detection of Fe(III) in water based on 7-mercapto-4-methylcoumarine (MMC)-stabilized silver-coated gold nanostars (GNS@Ag@MMC), exploiting a redox reaction between the Fe(III) cation and the silver shell of the nanoparticles, which causes a severe transformation of the nanomaterial structure, reverting it to pristine GNSs. This system works by simultaneously monitoring changes in the Localized Surface Plasmon Resonance (LSPR) and Surface-Enhanced Raman Spectroscopy (SERS) spectra as a function of added Fe(III). The proposed sensing system is able to detect the Fe(III) cation in the 1.0 × 10-5-1.5 × 10-4 M range, and its selectivity of the GNS@Ag@MMC sensor toward iron has been verified monitoring the LSPR and the SERS response to other cations with a clear selectivity toward Fe(III).

Accurate and reliable surface-enhanced Raman spectroscopy assay for early detection of SARS-CoV-2 RNA with exceptional sensitivity

This research proposes a highly sensitive and simple surface-enhanced Raman spectroscopy (SERS) assay for the detection of SARS-CoV-2 RNA using suitably designed probes specific for RdRp and N viral genes attached to a Raman marker. The sensitivity of the assay was optimized through precise adjustments to the conditions of immobilization and hybridization processes of the target RNA, including modifications to factors such as time and temperature. The assay achieved a remarkable sensitivity down to 58.39 copies/mL, comparable to or lower than the sensitivities reported for commercial fluorescent polymerase chain reaction (PCR) based methods. It has good selectivity in discriminating SARS-CoV-2 RNA against other respiratory viruses, respiratory syncytial virus (RSV), and influenza A virus. The reliability of the assay was validated by testing 24 clinical samples, including 12 positive samples with varying cycle threshold (Ct) values and 12 negative samples previously tested using real-time PCR. The assay consistently predicted true results that were in line with the PCR results for all samples. Furthermore, the assay demonstrated a notable limit of detection (LOD) of Ct (38 for RdRp gene and 37.5 for N-gene), indicating its capability to detect low concentrations of the target analyte and potentially facilitating early detection of the pathogen.

Nanoplasmonic Affinity Analysis System for Molecular Screening Based on Bright‐Field Imaging

Considering the improved detection of biological analytes for affinity analysis is highly desirable, a metasurface plasmon resonance (Meta‐SPR)‐based imaging system, incorporating a localized SPR sensing platform with different microfluidic systems and employing simple bright‐field imaging, is established in this study. This system enables low‐level analyte concentration analysis, ranging from 100 pm to 100 nm, with the real‐time removal of nonspecific binding signals within the same device field of view. Combined with microfluidic systems and microdroplet spotting, it is possible to automatically measure the kinetic curves of a sample at ten concentration gradients or detect the specific responses of multiple samples in a single experiment simultaneously. This system can inexpensively and conveniently achieve complex detection functions, demonstrating an innovative breakthrough in sensor detection.

SPRi/SERS dual-mode biosensor based on ployA-DNA/ miRNA/AuNPs-enhanced probe sandwich structure for the detection of multiple miRNA biomarkers

MicroRNA (miRNA) has broad application prospects in the early detection of various cancers. In this work, a SPRi/SERS dual-mode biosensor was developed on the same gold chip by AuNPs as the reinforcing medium. High throughput and sensitivity detection of three typical cervical cancer markers miRNA21, miRNA124 and miRNA143 were achieved based on the sandwich structure of polyA blocks-DNA capture probe/target miRNA/AuNPs-assistant probe or SERS nanoprobes. AuNPs greatly improved the SPR response due to mass increase and more sensitive refractive index changes. Meanwhile, due to the LSPR effect of AuNPs, the signal of SERS nanoprobe can be amplified. The miRNAs were detected in serum to verify its practicality. SPRi achieved detection of three miRNAs simultaneously. LODs were 6.3 fM, 5.3 fM and 4.6 fM, respectively, and wide dynamic response range of 500 pM-10 nM. While SERS assay ensured high sensitivity with LODs as low as 1 fM, 0.8 fM and 1.2 fM, respectively, and with the recoveries in the range of 90.0 %-100.2 %. The redundant detection signals of the two modes can provide more reliable data to prevent false positive or false negative detection, and have great application prospects in detection of cancer-related nucleic acids in early stage of disease.

A fluorescence and SERS dual-mode sensing on tetracycline antibiotics based on Ag@NH2-MIL-101(Al) nanoprobe

Antibiotic residues are becoming more and more concern due to the increasingly serious resistance from bacteria to organism. On-site and accurate evaluation on antibiotics is necessary and urgent to effectively solve such public issue. To provide point-of-care-test (POCT) ideas for antibiotic accurate evaluation, a fluorescence (FL)-surface-enhanced Raman scattering (SERS) dual-mode detection of tetracycline antibiotic (TCs) was realized for the first time. Based on the inner filter effect in Ag@NH2-MIL-101(Al) nanoprobe, the fluorescence quenching was induced and the SERS signal was swiftly turn on through π-π interaction and hydrogen bonding in the presence of TCs. This FL-SERS dual mode sensor displayed excellent detection limits (FL in ∼10-3 ppm, SERS in ∼10-5 ppm), and achieved a reliable detection of TCs in honey with a recovery rate of 84.45%-112.08%. This method combines the advantages of FL and SERS detection, meanwhile, two techniques verified against each other to achieve highly sensitive and specific FL-SERS dual-mode sensor for TCs. We believe that such antibody-or aptamer-independent FL and SERS complementary nanoprobe can be applied to fast, direct and multiple sensing in environment and food hazards.

Unraveling the Dynamics of SARS-CoV-2 Mutations: Insights from Surface Plasmon Resonance Biosensor Kinetics

Surface Plasmon Resonance (SPR) technology is known to be a powerful tool for studying biomolecular interactions because it offers real-time and label-free multiparameter analysis with high sensitivity. This article summarizes the results that have been obtained from the use of SPR technology in studying the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations. This paper will begin by introducing the working principle of SPR and the kinetic parameters of the sensorgram, which include the association rate constant (ka), dissociation rate constant (kd), equilibrium association constant (KA), and equilibrium dissociation constant (KD). At the end of the paper, we will summarize the kinetic data on the interaction between angiotensin-converting enzyme 2 (ACE2) and SARS-CoV-2 obtained from the results of SPR signal analysis. ACE2 is a material that mediates virus entry. Therefore, understanding the kinetic changes between ACE2 and SARS-CoV-2 caused by the mutation will provide beneficial information for drug discovery, vaccine development, and other therapeutic purposes.

Unveiling practical considerations for reliable and standardized SERS measurements: lessons from a comprehensive review of oblique angle deposition-fabricated silver nanorod array substrates

Recently, there has been an exponential growth in the number of publications focusing on surface-enhanced Raman scattering (SERS), primarily driven by advancements in nanotechnology and the increasing demand for chemical and biological detection. While many of these publications have focused on the development of new substrates and detection-based applications, there is a noticeable lack of attention given to various practical issues related to SERS measurements and detection. This review aims to fill this gap by utilizing silver nanorod (AgNR) SERS substrates fabricated through the oblique angle deposition method as an illustrative example. The review highlights and addresses a range of practical issues associated with SERS measurements and detection. These include the optimization of SERS substrates in terms of morphology and structural design, considerations for measurement configurations such as polarization and the incident angle of the excitation laser, and exploration of enhancement mechanisms encompassing both intrinsic properties induced by the structure and materials, as well as extrinsic factors arising from wetting/dewetting phenomena and analyte size. The manufacturing and storage aspects of SERS substrates, including scalable fabrication techniques, contamination control, cleaning procedures, and appropriate storage methods, are also discussed. Furthermore, the review delves into device design considerations, such as well arrays, flow cells, and fiber probes, and explores various sample preparation methods such as drop-cast and immersion. Measurement issues, including the effect of excitation laser wavelength and power, as well as the influence of buffer, are thoroughly examined. Additionally, the review discusses spectral analysis techniques, encompassing baseline removal, chemometric analysis, and machine learning approaches. The wide range of AgNR-based applications of SERS, across various fields, is also explored. Throughout the comprehensive review, key lessons learned from collective findings are outlined and analyzed, particularly in the context of detailed SERS measurements and standardization. The review also provides insights into future challenges and perspectives in the field of SERS. It is our hope that this comprehensive review will serve as a valuable reference for researchers seeking to embark on in-depth studies and applications involving their own SERS substrates.

A two-fold SPR-SERS sensor utilizing gold nanoparticles and graphene thin membrane as a spacer in a 3D composite structure

Localized surface plasmonic resonance (LSPR) biosensing using optical fibers has gained popularity due to its label-free approach and high sensitivity to changes in the nanoparticle surface's local index of refraction. However, improving sensitivity remains a challenge. In this study, a two-step approach was employed to fabricate a composite structure using gold nanoparticles and monolayer graphene (Gr-AuNPs). The combination of AuNPs and graphene membrane demonstrated high potential for Surface-enhanced Raman scattering (SERS) and surface plasmonic resonance (SPR) fiber sensors. The Gr-AuNPs sensor successfully detected R6G molecules with a low detection limit of 10-12 M, indicating promising SERS activity. Numerical simulations confirmed that the graphene generated densely hot spots in the nanogap region between plasmonic layers. It's interesting that the proposed SPR-SERS Sensor can detect both glucose and thiram. This demonstrates the sensors practicality and can help with a basic environmental need to find leftover pesticides in the soil. The combination of SPR-SERS dual-mode detection provides more options for detecting and verifying data, increasing the precision and repeatability of experiments.

Plasmonic Nanostructure Biosensors: A Review

Plasmonic nanostructure biosensors based on metal are a powerful tool in the biosensing field. Surface plasmon resonance (SPR) can be classified into localized surface plasmon resonance (LSPR) and propagating surface plasmon polariton (PSPP), based on the transmission mode. Initially, the physical principles of LSPR and PSPP are elaborated. In what follows, the recent development of the biosensors related to SPR principle is summarized. For clarity, they are categorized into three groups according to the sensing principle: (i) inherent resonance-based biosensors, which are sensitive to the refractive index changes of the surroundings; (ii) plasmon nanoruler biosensors in which the distances of the nanostructure can be changed by biomolecules at the nanoscale; and (iii) surface-enhanced Raman scattering biosensors in which the nanostructure serves as an amplifier for Raman scattering signals. Moreover, the advanced application of single-molecule detection is discussed in terms of metal nanoparticle and nanopore structures. The review concludes by providing perspectives on the future development of plasmonic nanostructure biosensors.

CRISPR/Cas12a-Powered EC/FL Dual-Mode Controlled-Release Homogeneous Biosensor for Ultrasensitive and Cross-Validated Detection of Messenger Ribonucleic Acid

Accurate detection of cancer-associated mRNAs is beneficial to early diagnosis and potential treatment of cancer. Herein, for the first time, we developed a novel CRISPR/Cas12a-powered electrochemical/fluorescent (EC/FL) dual-mode controlled-release homogeneous biosensor for mRNA detection. A functionalized ssDNA P2-capped Fe3O4-NH2 loaded with methylene blue (P2@MB-Fe3O4-NH2) was synthesized as the signal probe, while survivin mRNA was chosen as the target RNA. In the presence of the target mRNA, the nicking endonuclease-mediated rolling circle amplification (NEM-RCA) was triggered to produce significant amounts of ssDNA, activating the collateral activity of Cas12a toward the surrounding single-stranded DNA. Thus, the ssDNA P1 completely complementary to ssDNA P2 was cleaved, resulting in that the ssDNA P2 bio-gate on Fe3O4-NH2 could not be opened due to electrostatic interactions. As a result, there was no or only a little MB in the supernatant after magnetic separation, and the measured EC/FL signal was exceedingly weak. On the contrary, the ssDNA P2 bio-gate was opened, enabling MB to be released into the supernatant, and generating an obvious EC/FL signal. Benefiting from the accuracy of EC/FL dual-mode cross-verification, high amplification efficiency, high specificity of NEM-RCA and CRISPR/Cas12a, and high loading of mesoporous Fe3O4-NH2 on signal molecules, the strategy shows aM-level sensitivity and single-base mismatch specificity. More importantly, the practical applicability of this dual-mode strategy was confirmed by mRNA quantification in complex serum environments and tumor cell lysates, providing a new way for developing a powerful disease diagnosis tool.

Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection

Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.

Recent Advances in the DNA-Mediated Multi-Mode Analytical Methods for Biological Samples

DNA-mediated nanotechnology has become a research hot spot in recent decades and is widely used in the field of biosensing analysis due to its distinctive properties of precise programmability, easy synthesis and high stability. Multi-mode analytical methods can provide sensitive, accurate and complementary analytical information by merging two or more detection techniques with higher analytical throughput and efficiency. Currently, the development of DNA-mediated multi-mode analytical methods by integrating DNA-mediated nanotechnology with multi-mode analytical methods has been proved to be an effective assay for greatly enhancing the selectivity, sensitivity and accuracy, as well as detection throughput, for complex biological analysis. In this paper, the recent progress in the preparation of typical DNA-mediated multi-mode probes is reviewed from the aspect of deoxyribozyme, aptamer, templated-DNA and G-quadruplex-mediated strategies. Then, the advances in DNA-mediated multi-mode analytical methods for biological samples are summarized in detail. Moreover, the corresponding current applications for biomarker analysis, bioimaging analysis and biological monitoring are introduced. Finally, a proper summary is given and future prospective trends are discussed, hopefully providing useful information to the readers in this research field.

Contractile Hairpin DNA-Mediated Dual-Mode Strategy for Simultaneous Quantification of Lactoferrin and Iron Ion by Surface-Enhanced Raman Scattering and Fluorescence Analysis

DNA-mediated self-assembly technology with good sensitivity and affinity ability has been rapidly developed in the field of probe sensing. The efficient and accurate quantification of lactoferrin (Lac) and iron ions (Fe³⁺) in human serum and milk samples by the probe sensing method can provide useful clues for human health and early diagnosis of anemia. In this paper, contractile hairpin DNA-mediated dual-mode probes of Fe₃O₄/Ag-ZIF8/graphitic quantum dot (Fe₃O₄/Ag-ZIF8/GQD) NPs were prepared to realize the simultaneous quantification of Lac by surface-enhanced Raman scattering (SERS) and Fe³⁺ by fluorescence (FL). In the presence of targets, these dual-mode probes would be triggered by the recognition of aptamer and release GQDs to produce FL response. Meanwhile, the complementary DNA began to shrink and form a new hairpin structure on the surface of Fe₃O₄/Ag, which produced hot spots and generated a good SERS response. Thus, the proposed dual-mode analytical strategy possessed excellent selectivity, sensitivity, and accuracy due to the dual-mode switchable signals from "off" to "on" in SERS mode and from "on" to "off" in FL mode. Under the optimized conditions, a good linear range was obtained in the range of 0.5-100.0 μg/L for Lac and 0.01-5.0 μmol/L for Fe³⁺ and with detection limits of 0.14 μg/L and 3.8 nmol/L, respectively. Finally, the contractile hairpin DNA-mediated SERS-FL dual-mode probes were successfully applied in the simultaneous quantification of iron ion and Lac in human serum and milk samples.

Ultrasensitive detection of SARS-CoV-2 S protein with aptamers biosensor based on surface-enhanced Raman scattering

A rapid and accurate diagnostic modality is essential to prevent the spread of SARS-CoV-2. In this study, we proposed a SARS-CoV-2 detection sensor based on surface-enhanced Raman scattering (SERS) to achieve rapid and ultrasensitive detection. The sensor utilized spike protein deoxyribonucleic acid aptamers with strong affinity as the recognition entity to achieve high specificity. The spherical cocktail aptamers-gold nanoparticles (SCAP) SERS substrate was used as the base and Au nanoparticles modified with the Raman reporter molecule that resonates with the excitation light and spike protein aptamers were used as the SERS nanoprobe. The SCAP substrate and SERS nanoprobes were used to target and capture the SARS-CoV-2 S protein to form a sandwich structure on the Au film substrate, which can generate ultra-strong "hot spots" to achieve ultrasensitive detection. Analysis of SARS-CoV-2 S protein was performed by monitoring changes in SERS peak intensity on a SCAP SERS substrate-based detection platform. This assay detects S protein with a LOD of less than 0.7 fg mL^-1 and pseudovirus as low as 0.8 TU mL^-1 in about 12 min. The results of the simulated oropharyngeal swab system in this study indicated the possibility of it being used for clinical detection, providing a potential option for rapid and accurate diagnosis and more effective control of SARS-CoV-2 transmission.

A novel cascade signal amplification strategy integrating CRISPR/Cas13a and branched hybridization chain reaction for ultra-sensitive and specific SERS detection of disease-related nucleic acids

The molecular diagnosis of disease by high-sensitively and specifically detecting extremely trace amounts of nucleic acid biomarkers in biological samples is still a great challenge, and the powerful sensing strategy has become an urgent need for basic researches and clinical applications. Herein, a novel one-pot cascade signal amplification strategy (Cas13a-bHCR) integrating CRISPR/Cas13a system (Cas13a) and branched hybridization chain reaction (bHCR) was proposed for ultra-highly sensitive and specific SERS assay of disease-related nucleic acids on SERS-active silver nanorods sensing chips. The Cas13a-bHCR based SERS assay of gastric cancer-related miRNA-106a (miR-106a) can be achieved within 60 min and output significantly enhanced SERS signal due to the multiple signal amplification, which possesses a good linear calibration curve from 10 aM to 1 nM with the limit of detection (LOD) low to 8.55 aM for detecting gastric cancer-related miR-106a in human serum. The Cas13a-bHCR based SERS sensing also shows good specificity, uniformity, repeatability and reliability, and has good practicability for detection of miR-106a in clinical samples, which can provide a potential powerful tool for SERS detection of disease-related nucleic acids and promise brighter prospects in the field of clinical diagnosis of early disease.

Non-enzymatic signal amplification-powered point-of-care SERS sensor for rapid and ultra-sensitive assay of SARS-CoV-2 RNA

The development of rapid and ultra-sensitive detection technology of SARS-CoV-2 RNA for shortening the diagnostic window and achieving early detection of virus infections is a huge challenge to the efficient prevention and control of COVID-19. Herein, a novel ultra-sensitive surface-enhanced Raman spectroscopy (SERS) sensor powered by non-enzymatic signal amplification is proposed for rapid and reliable assay of SARS-CoV-2 RNA based on SERS-active silver nanorods (AgNRs) sensing chips and a specially designed smart unlocking-mediated target recycling signal amplification strategy. The SERS sensing was carried out by a one-pot hybridization of the lock probes (LPs), hairpin DNAs and SERS tags with SARS-CoV-2 RNA samples on an arrayed SERS sensing chip to achieve the recognition of SARS-CoV-2 RNA, the execution of nuclease-free unlocking-mediated target recycling signal amplification, and the combination of SERS tags to generate SERS signal. The SERS sensor for SARS-CoV-2 RNA can be achieved within 50 min with an ultra-high sensitivity low to 51.38 copies/mL, and has good selectivity in discriminating SARS-CoV-2 RNA against other respiratory viruses in representative clinical samples, which is well adapted for rapid, ultra-sensitive, multi-channel and point-of-care testing of viral nucleic acids, and is expected to achieve detection of SARS-CoV-2 infection in earlier detection windows for efficient COVID-19 prevention and control.

A flap endonuclease 1-assisted universal viral nucleic acid sensing system using surface-enhanced Raman scattering

Flap endonuclease 1 recognizes a specific DNA structure and cleaves Raman tag-labeled probe molecules in a target-specific manner. With SERS-based sensing, the developed detection approach produces sensitive, quantitative, and multiplexable signals.

SPR/SERS dual-mode plasmonic biosensor via catalytic hairpin assembly-induced AuNP network

Highly sensitive and reliable detection of disease-related nucleic acids is still a big challenge in liquid biopsy because of their homologous sequences and low abundance. Herein, a novel surface plasmon resonance/surface-enhanced Raman scattering (SPR/SERS) dual-mode plasmonic biosensor based on catalytic hairpin assembly (CHA)-induced Au nanoparticle (AuNP) network was proposed for highly sensitive and reliable detection of cancer-related miRNA-652. The biosensor includes capture DNA-functionalized AuNPs (Probe 1), H1 and 4-mercaptobenzoic acid (4-MBA) co-modified AuNPs (Probe 2), and 6-carboxyl-Xrhodamine (ROX)-labeled H2 (fuel strands). The Probe 1-Probe 2 networks were formed via the target-triggered CHA reactions, which resulted in the color change of dark-field microscopy (DFM) images and enhanced SERS effect. The SPR sensing was achieved by extracting the integral optical density of dark-field color in DFM images, and the SERS sensing was realized by the ratiometric SERS signals of ROX and internal standards 4-MBA molecules. After characterizing the feasibility and optimality of the sensing strategy, the good performance of biosensors on sensitivity, specificity and uniformity was approved. The practicability of biosensors was confirmed by detecting miRNA-652 in human serum, and both the SPR and SERS assays showed good linear calibration curves and low limit of detections (LODs) of 42.5 fM and 2.91 fM, respectively, with the recovery in the range of 94.67-111.4%. These two modes show complementary advantages, and the combined SPR/SERS dual-mode can provide more options for detection and double check the results to improve the accuracy and reliability of assays, which holds a great application prospect for cancer-related nucleic acids detection in early disease stage.

"Dual-Signal-On" Integrated-Type Biosensor for Portable Detection of miRNA: Cas12a-Induced Photoelectrochemistry and Fluorescence Strategy

The abnormal expression of microRNA (miRNA) can affect the RNA transcription and protein translation, leading to tumor progression and metastasis. Currently, the accurate detection of aberrant expression of miRNA, particularly using a portable detection system, remains a great challenge. Herein, a novel dual-mode biosensor with high sensitivity and robustness for miR-21 detection was developed based on the cis-cleavage and trans-cleavage activities of Cas12a. miRNA can be combined with hairpin DNA-horseradish peroxidase anchored on a CdS/g-C₃N₄/B-TiO₂ photoelectrode, thus the nonenzymatic amplification was triggered to form numerous HRP-modified double-stranded DNA (HRP-dsDNA). Then, HRP-dsDNA can be specifically recognized and efficiently cis-cleaved by Cas12a nucleases to detach HRP from the substrate, while the remaining HRP on HRP-dsDNA can catalyze 4-chloro-1-naphthol (4-CN) to form biocatalytic precipitation (BCP) on the surface of the photoelectrode, and thus the photocurrent can be changed. Meanwhile, the trans-cleavage ability of Cas12a was activated, and nonspecifically degrade the FQ-reporter and a significant fluorescence signal can be generated. Such two different kinds of signals with independent transmission paths can mutually support to improve the performance of the detection platform. Besides, a portable device was constructed for the point-of-care (POC) detection of miR-21. Moreover, the dual-mode detection platform can be easily expanded for the specific detection of other types of biomarkers by changing the sequence of hairpin DNA, thereby promoting the establishment of POC detection for early cancer diagnosis.

CRISPR-/Cas12a-Mediated Liposome-Amplified Strategy for the Surface-Enhanced Raman Scattering and Naked-Eye Detection of Nucleic Acid and Application to Food Authenticity Screening

Surface-enhanced Raman scattering (SERS) has been recognized as a powerful tool for biosensors due to the ultrahigh sensitivity and unique fingerprint information. However, there are some limitations in trace target nucleic acid detection for the restricted signal-transducing and amplification strategies. Inspired by CRISPR/Cas12a with specific target DNA-activated collateral single-strand DNA (ssDNA) cleavage activity and liposome with signal molecule-loading properties, we first proposed a sensitive SERS-based on-site nucleic acid detection strategy mediated by CRISPR/Cas12a with trans-cleavage activity on ssDNA linkers utilized to capture liposomes. Liposomes loading two kinds of signal molecules, 4-nitrothiophenol (4-NTP) and cysteine, could achieve the dual-mode detection of target DNA with SERS and naked eye, respectively. The promptly amplified signals were initiated by the triggered breakdown of signal molecule-loaded liposomes. Emancipated 4-NTP, a biological-silent Raman reporter, would achieve highly selective and sensitive SERS measurement. Released cysteine induced the aggregation of plasmonic gold nanoparticles, leading to an obvious red to blue colorimetric shift to realize portable naked-eye detection. With this strategy, target nucleic acid concentration was dexterously converted into SERS and visualization signals and could be detected as low as 100 aM and 10 pM, respectively. The approach was also successfully applied to determine meat adulteration, achieving the detection of a low adulteration ratio in the complicated food matrix. We anticipate that this strategy will not only be regarded as a universal platform for the on-site detection of food authenticity but also broaden SERS application for the accurate determination of diverse biomarkers.

Establishment of a reliable scheme for obtaining highly stable SERS signal of biological serum

As a rapid and non-destructive biological serum detection method, SERS technology was widely used in the screening and medical diagnosis of various diseases by combining the analysis of serum SERS spectrum and multivariate statistical algorithm. Because of the high complexity of serum components and the variability of SERS spectra, which often resulted in the phenomenon that the SERS spectrum of the same biological serum was significantly different due to the different test conditions. In this experiment, through the dilution treatment of the serum and the systematic test of the serum of all concentration gradients with lasers of wavelength of 785, 633 and 532 nm, the most suitable conditions for detecting the serum were investigated. The experimental results showed that only when the serum is diluted to low concentration (10 ppm), the SERS spectrum with high reproducibility and stability could be obtained, furthermore, the low concentration serum had weak tolerance to laser, and 532 nm laser was not suitable for serum detection. In this paper, a set of test scheme for obtaining highly stable serum SERS spectra was established by using high-performance gold nanoparticles (Au NPs) as the active substrate of SERS. Through comparative analysis of SERS spectrum of serum of normal people and cervical cancer, the reliability of the established low-concentration serum test program was verified, as well as its great potential advantages in disease screening and diagnosis.