Liquid Phase Interfacial Surface-Enhanced Raman Scattering Platform for Ratiometric Detection of MicroRNA 155

Surface-enhanced Raman scattering-based strategies for tumor markers detection: A review

The presence of malignant tumors poses a significant threat to people's life and well-being. As biochemical parameters indicate the occurrence and development of tumors, tumor markers play a pivotal role in early cancer detection, treatment, prognosis, efficient monitoring, and other aspects. Surface-enhanced Raman scattering (SERS) is considered a potent tool for the detection of tumor markers owing to its exceptional advantages encompassing high sensitivity, superior selectivity, rapid analysis speed, and photobleaching resistance nature. This review aims to provide a comprehensive understanding of SERS applications in the detection of tumor markers. Firstly, we introduce the SERS enhancement mechanism, classification of active substrates, and SERS detection techniques. Secondly, the latest research progress of in vitro SERS detection of different types of tumor markers in body fluids and the application of SERS imaging in biomedical imaging are highlighted in sections of the review. Finally, according to the current status of SERS detection of tumor markers, the challenges and problems of SERS in biomedical detection are discussed, and insights into future developments in SERS are offered.

Early Diagnosis of Triple-Negative Breast Cancer Based on Dual microRNA Detection Using a Well-Defined DNA Crown-Carbon Dots Structure as an Electrochemiluminescence Sensing Platform

Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer (BC). Thus, early detection and accurate diagnosis of this cancer are crucial for improving the survival rate of patients. Specific microRNAs (miRNAs) have been implicated in the occurrence, proliferation, and metastasis of TNBC. Addressing this need, our study developed a biosensor platform for early and accurate TNBC diagnosis by integrating electrochemiluminescence (ECL) technology with a DNA sensing strategy. Specifically, synthesized positively charged carbon dots (CDs) were used to neutralize the electrostatic repulsion between DNA strands and facilitate the assembly of DNA triangular prisms (DNA TP-CDs). Hairpins were then incorporated into the DNA TP-CDs to form the final DNA crown structure. The early TNBC biomarker, microRNA-93-3p (miR-93-3p), allowed for the binding between the DNA Crown and the DNA track on the electrode and initiated the ECL signal. Subsequently, microRNA-210 (miR-210) unlocked the DNA tripedal walker, and its movement on the DNA Crown eventually quenched the ECL signal, enabling accurate TNBC diagnosis and tumor stage assessment. Our proposed biosensor had satisfactory sensing efficiency due to the ordered DNA track and rapid-moving DNA walker. The data revealed a good linear relationship between the ECL signals and the logarithm of miRNA concentrations, with miR-93-3p having a detection limit of 31.04 aM and miR-210 having a detection limit of 7.69 aM. The biosensor also showed satisfactory performance in serum samples and cells. Taken together, this study hopes to provide ideas and applications for clinical diagnosis as well as the personalized treatment of TNBC.

SERS-based methods for the detection of genomic biomarkers of cancer

Genomic biomarkers of cancer are based on changes in nucleic acids, which include abnormal expression levels of some miRNAs, point mutations in DNA sequences, and altered levels of DNA methylation. The presence of tumor-related nucleic acids in body fluids (blood, saliva, or urine) makes it possible to achieve a non-invasive early-stage cancer diagnosis. Currently existing techniques for the discovery of nucleic acids require complex, time-consuming, costly assays and have limited multiplexing abilities. Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopy technique that is able to provide molecular specificity combined with trace sensitivity. SERS has gained research attention as a tool for the detection of nucleic acids because of its promising potential: label-free SERS can decrease the complexity of assays currently used with fluorescence-based detection due to the absence of the label, while labeled SERS may outperform the gold standard in terms of the multiplexing ability. The first papers about SERS-based methods for the measurement of genomic biomarkers were written in 2008, and since then, more than 150 papers have been published. The aim of this paper is to review and evaluate the proposed SERS-based methods in terms of their level of development and their potential for liquid biopsy application, as well as to contribute to their further evolution by attracting research attention to the field. This goal will be reached by grouping, on the basis of their experimental protocol, all the published manuscripts on the topic and evaluating each group in terms of its limit of detection and applicability to real body fluids. Thus, the methods are classified according to their working principles into five main groups, including capture-based, displacement-based, sandwich-based, enzyme-assisted, and specialized protocols.

A highly sensitive and robust electrochemical biosensor for microRNA detection based on PNA-DNA hetero-three-way junction formation and target-recycling catalytic hairpin assembly amplification

Robust and sensitive methods for the detection of microRNAs (miRNAs) are crucial in the clinical diagnosis of cancers. In this study, a novel electrochemical biosensor with high sensitivity for miRNA-21 detection is developed, which relies on the formation of a peptide nucleic acid (PNA)-DNA hetero-three-way junction (H3WJ) and target-recycling catalytic hairpin assembly (CHA) amplification. The electroneutral PNA probes are initially immobilized onto a gold electrode to construct the sensor. Upon introduction of miRNA-21, target-recycling CHA is initiated, resulting in abundant double-stranded CHA products. Subsequently, association between the PNA probes and these products leads to the formation of PNA-DNA H3WJs. Consequently, the electrode surface is densely populated with numerous electroactive Ferrocene (Fc) groups, resulting in a significantly amplified current response for highly sensitive detection of miRNA-21 at concentrations as low as 0.15 fM. This approach demonstrates remarkable specificity towards target miRNAs and can be utilized for quantitative monitoring of miRNA-21 expression in human cancer cells. More importantly, the sensor exhibits exceptional stability and shows a significant reduction in background noise during miRNA detection, making this method a highly promising sensing platform for monitoring various miRNA biomarkers to facilitate the diagnosis of diverse cancers.

A ratiometric SERS sensor with one signal probe for ultrasensitive and quantitative monitoring of serum xanthine

Xanthine can be converted into uric acid, and a high concentration of xanthine in the human body can cause many diseases. Therefore, it is important to develop a sensitive, simple, and reliable approach for measuring xanthine in biological liquids. Hence, a ratiometric surface-enhanced Raman spectroscopy (SERS) sensing strategy with one signal probe was exploited for reliable, sensitive, and quantitative monitoring of serum xanthine. 3-Mercaptophenylboronic acid (3-MPBA) was used as a typical reference with a Raman peak at 996 cm-1. First, 3-MPBA was bound to gold nanoflowers@silica (GNFs@Si) through Au-S bonds. Xanthine oxidase (XOD) catalyzed the oxidation of xanthine into H2O2 on GNFs@Si. Afterward, the obtained H2O2 further reduced 3-MPBA to 3-hydroxythiophenol (3-HTP) accompanied by the emergence of a new Raman peak at 883 cm-1. Meanwhile, the Raman intensity at 996 cm-1 remained constant. Therefore, the ratio of I883/I996 increased with the increasing of xanthine concentration, thus realizing quantitative detection of xanthine. As a result, a ratiometric SERS sensor for the detection of xanthine was proposed with a detection limit of 5.7 nM for xanthine. The novel ratiometric SERS sensor provides a new direction for analyzing other biomolecules with high sensitivity and reliability.

Quantification of Multiplex miRNAs by Mass Spectrometry with Duplex-Specific Nuclease-Mediated Amplification

Early quantification of multiplex biomarkers such as microRNAs (miRNAs) is critical during disease pathologic development and therapy. To tackle challenges of low abundance and multiplexing, we herein report a mass-encoded biosensing approach with duplex-specific nuclease (DSN) mediated signal amplification. Magnetic Fe3O4 cores are coated with small gold nanoparticles (AuNPs), which are applied to achieve facile DNA immobilization subsequent separation. This biosensor integrates multiple mass reporters corresponding to different targets (five miRNAs as examples). Due to the excellent resolution of mass spectrometry, these targets can be successfully distinguished in a single spectrum. Wide detection ranges from 10 fM to 1 nM are achieved, and the limits of detection are estimated to be 10 fM. High selectivity is promised due to the enzyme activity of DSN, and practical application in human serum samples performs satisfactorily. The number of targets to be tested can be further expanded by designing different specific mass tags in theory. Therefore, the proposed method can be utilized as an important and valuable tool to quantify multiplex miRNAs for disease screening as well as biomedical investigations.

A novel detection of MicroRNA based on homogeneous electrochemical sensor with enzyme-assisted signal amplification

Rapid and sensitive detection of microRNAs is of great importance in biological researches and cancer diagnosis. Herein, we proposed a novel homogeneous electrochemical sensor to detect microRNA-21 (miRNA-21) using functionalized magnetic nanoparticles combined with enzyme-assisted signal amplification. The biotinylated capture probe (CP) labeled magnetic nanoparticles can capture miRNA-21 and introduce streptavidin-conjugated hydroxyapatite (HAP) nanoparticles. In the presence of miRNA-21, hybridization between RNA and DNA results in the formation of RNA/DNA duplexes, and then duplex-specific nuclease (DSN) cleave the duplexes to digest the capture chain and release the miRNA-21 in a loop. Meanwhile, the HAP nanoparticles strip from the magnetic nanoparticles and electrochemical signal by the reaction of HAP with molybdate is changed. The current variation before and after incubation with miRNA-21 is linearly correlated with the miRNA-21 concentration between 1 aM and 1 pM with a low detection limit (LOD) of 0.27 aM. Remarkably, the expression of miRNA-21 in human serum and different cell lysate was successfully performed, which fully demonstrates the great practical potentials in biomedical diagnostics and clinical therapeutics.

Cooperative Amplification of Au@FeCo as Mimetic Catalytic Nanozymes and Bicycled Hairpin Assembly for Ultrasensitive Electrochemical Biosensing

Exploring the cooperative amplification of peroxidase-like metal nanocomposites and cycled hairpin assembly is intriguing for sensitive bioanalysis. Herein, we report the first design of a unique electrochemical biosensor based on mimicking Au@FeCo nanozymes and bicycled hairpin assembly (BHA) for synergistic signal amplification. By loading the enzyme-like FeCo alloy in Au nanoparticles (AuNPs), the as-synthesized Au@FeCo hybrids display great improvement of electronic conductivity and active surface area and excellent mimic catalase activity to H₂O₂ decomposition into ^•OH radicals. The immobilization of Au@FeCo in an electrode sensing interface is stabilized via the resulting electrodeposition in HAuCl₄ while efficiently accelerating the electron transfer of electroactive ferrocene (Fc). Upon the immobilization of a helping hairpin (HH) via Au-S bonds, a specific DNA trigger (T*) is introduced to activate BHA operation through competitive strand displacement reactions among recognizing hairpin (RH), signaling hairpin (SH), and HH. T* and RH are rationally released to catalyze two cycles, in which the transient depletion of dsDNA intermediates rapidly drives the progressive hairpin assemblies to output more products SH·HH. Thus, the efficient amplification of Au@FeCo mimic catalase activity combined with BHA leads to a significantly increased current signal of Fc dependent on miRNA-21 analogous to T*, thereby directing the creation of a highly sensitive electrochemical biosensor having applicable potential in actual samples.

The self-powered electrochemical biosensing platform with multi-amplification strategy for ultrasensitive detection of microRNA-155

A self-powered biosensor (SPB) was constructed for the ultra-sensitive detection of microRNA-155 (miR-155) by combining a capacitor/enzymatic biofuel cell (EBFC), a strategy of rolling circle amplification (RCA) and a digital multimeter (DMM). The experimental results show that the sensitivity of the assembled EBFC-SPB can reach 15.85 μA/pM with the action of matching capacitor, which is 513% of that without capacitor (3.09 μA/pM). This achieves the first signal amplification. Furthermore, when the target miR-155 triggers RCA, electrons are continuous generated and flow to the biocathode through the external circuit to catalyze the reduction of oxygen and release [Ru(NH₃)₆]³⁺ electron acceptor. This achieves the second signal amplification. Finally, DMM is used to convert the signal into instantaneous current and amplify it for real-time reading. This achieves the third signal amplification. Therefore, the limit of detection (LOD) of the developed biosensor is as low as 0.17 fM (S/N = 3), and the linear range is between 0.5 fM and 10,000 fM, indicating that the EBFC-SPB has a broad application prospect for cancer marker of miR-155 with ultrasensitive detection.

Microcontact printing of gold nanoparticle at three-phase interface as flexible substrate for SERS detection of MicroRNA

The rigidity of traditional solid-state surface-enhanced Raman spectroscopy (SERS) substrate hampers their application in the curved structure for nonplanar surface test and in-situ detection. Traditionally, the flexible Raman substrates are often prepared by transferring printing of patterned nanoparticles on the flexible materials such as polymer, paper, etc. However，the replicate patterns are often produced by high-cost instruments. In this study, a low-cost and flexible SERS substrate is prepared by using a microcontact printing technology to transfer three-phase-assembled nanoparticles on a polydimethylsiloxane film, which can stabilize the assembled nanoparticles. Combining with the endonuclease Nt.BbvCI assisted amplification method, a SERS biosensor is constructed for microRNA 21 (miRNA 21) assay. This platform presents a wide dynamic range (100 fM ∼1 nM), achieving a fabulous sensitivity with limit of detection of 11.96 fM for miRNA 21. Furthermore, after being bent 90° for 50 times, the Raman intensity of the flexible substrate shows a negligible change. This versatile flexible substrate exhibits considerable potential for SERS analysis, which also opens a new avenue for preparing flexible devices.

Fluorescence-SERS dual-mode for sensing histamine on specific binding histamine-derivative and gold nanoparticles

Histamine (His) is used as an indicator of seafood quality, but it can be toxic at high intakes. A fluorescence (FL)-surface-enhanced Raman scattering (SERS) dual-mode assay system has been developed for His detection. The His detection method was established based on the specific binding capacity of gold nanoparticles (AuNPs) for the FL derivative of His and o-phthalaldehyde (OPA). In this strategy, His reacted with the OPA to form a Schiff base product (O-His) along with a change in FL and SERS activities. The usual nature of AuNPs could display a significant role both enhancement of SERS and quenching of FL signals. The current investigation displayed a good selectivity toward His over all other biogenic amines. Under the optimized analytical conditions, the SERS and FL intensity of the system were linearly proportional to the His concentration in the range of 0.05-4.5 mg/L and 1-20 mg/L with a detection limit of 0.04 mg/L and 0.32 mg/L, respectively. Moreover, the proposed method was successfully applied for His determination in seafood with promising results.

DNAzyme signal amplification based on Au@Ag core-shell nanorods for highly sensitive SERS sensing miRNA-21

Here, we developed a surface-enhanced Raman scattering (SERS) sensor based on functionalized Au@Ag core-shell nanorods (Au@Ag NRs) and cascade DNAzyme amplifier (CSA) for sensitive and accurate determination of microRNA-21 (miRNA-21). The as-prepared SERS nanoprobes were composed of a thiol-modification hairpin probe (HP2)-functionalized Au@Ag NRs and hairpin DNAzyme (HP1-Dz). Compared with original gold nanorods, the silver shell caused an enhancement of plasmonic properties, resulting in a significant enhancement of Raman signals. In the presence of target miRNAs, the hairpin construction of HP1-Dz changed due to DNA/RNA hybridization; subsequently, the DNAzyme-catalyzed cleaving process changed, and the Raman signals of the SERS nanoprobes gradually "turned off" with time elapse because of the dissociation of the Raman reporter from the surface of Au@Ag NRs. Hence, based on this principle, the proposed SERS sensor exhibited good linearity in the range 0.5 fM to 10 nM for miRNA-21 detection with a detection limit (LOD) of 0.5 fM. The proposed SERS platform has potential application in quantitative and precise detection of miRNA-21 in human serum.

Simultaneous Imaging of Dual microRNAs in Cancer Cells through Catalytic Hairpin Assembly on a DNA Tetrahedron

Accurate detection and imaging of tumor-related microRNA (miRNA) in living cells hold great promise for early cancer diagnosis and prognosis. One of the challenges is to develop methods that enable the identification of multiple miRNAs simultaneously to further improve the detection accuracy. Herein, a simultaneous detection and imaging method of two miRNAs was established by using a programmable designed DNA tetrahedron nanostructure (DTN) probe that includes a nucleolin aptamer (AS1411), two miRNA capture strands, and two pairs of metastable catalytic hairpins at different vertexes. The DTN probe exhibited enhanced tumor cell recognition ability, excellent stability and biocompatibility, and fast miRNA recognition and reaction kinetics. It was found that the DTN probe could specifically enter tumor cells, in which the capture strand could hybridize with miRNAs and initiate the catalytic hairpin assembly (CHA) only when the overexpressed miR-21 and miR-155 existed simultaneously, resulting in a distinct fluorescence resonance energy transfer signal and demonstrating the feasibility of this method for tumor diagnosis.

Engineering an Au nanostar-based liquid phase interfacial ratiometric SERS platform with programmable entropy-driven DNA circuits to detect protein biomarkers in clinical samples

Developing sensing platforms that simultaneously integrate high sensitivity and accuracy has been a promising but challenging task for the detection of protein biomarkers in clinical samples. Herein, we engineered an Au nanostar-based liquid phase interfacial ratiometric SERS platform with programmable entropy-driven DNA circuits to detect the protein biomarker Mucin 1 (MUC1) in clinical samples.

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.

DNA Structure-Stabilized Liquid-Liquid Self-Assembled Ordered Au Nanoparticle Interface for Sensitive Detection of MiRNA 155

Au nanoparticles (Au NPs) can be self-assembled in a bottom-up orderly manner at the oil-water interface, which is widely used as SERS platforms, but the stability of the Au NP interface needs to be improved due to shaking or shifting and the Brownian motion. The DNA structure with unique sequence specificity, excellent programmability, and flexible end-group modification capability owns good potential to precisely control the plasmonic structure's distance. In this study, a large area of the SERS substrate is obtained from the DNA structure-stabilized self-assembled ordered Au NPs on the cyclohexane-water interface. Combining with the exonuclease III (exo III)-assisted DNA recycling amplification strategy, we construct a liquid-phase SERS biosensor for efficient detection of microRNA 155 (miRNA 155). Compared with the traditional randomly assembled Au NPs on the two-phase interface, the SERS signal is significantly enhanced and more stable. The detection limit of the SERS biosensor for miRNA 155 reached 1.45 fmol/L, which has a very wide linear range (100 fmol/L-5 nmol/L). This work gives an efficient approach to stabilize the self-assembly Au NPs on the liquid-liquid interface, which can broaden the application of SERS analysis.

Surface-enhanced Raman scattering holography chip for rapid, sensitive and multiplexed detection of human breast cancer-associated MicroRNAs in clinical samples

MicroRNAs (miRNAs) are promising biomarkers for the early diagnosis of breast cancer. Yet, simultaneous achievement of rapid, sensitive and accurate detection of diverse miRNAs in clinical samples is still challenging due to the low abundance of miRNAs and the complex procedures of RNA extraction and separation. Herein, we develop an innovative three-dimensional (3D) surface-enhanced Raman scattering (SERS) holography sensing strategy for rapid, sensitive and multiplexed detection of human breast cancer-associated miRNAs. To establish a proof of concept, nine kinds of human breast cancer-associated miRNAs are isothermally amplified by Exonuclease (Exo) III enzyme, and the products could be spatially separated to corresponding sensing region on silicon SERS substrates. Each region has been modified with corresponding hairpin DNA probes, which are used to identify and quantify the miRNAs. Different DNA probes are labeled with different Raman reporters, which serve as "SERS tags" to incorporate spectroscopic information into computer-generated 3D SERS hologram within ~9 min. We demonstrate that 3D SERS holography chip not only achieves an ultrahigh sensitivity down to ~1 aM but also feature a high correlation with RT-qPCR in the detection of nine miRNAs in 30 clinical serum samples. This work provides a feasible tool to improve the diagnosis of breast cancer.

Dual-Mode SERS and Electrochemical Detection of miRNA Based on Popcorn-like Gold Nanofilms and Toehold-Mediated Strand Displacement Amplification Reaction

MicroRNA (miRNA) has emerged as one of the ideal target biomarker analytes for cancer detection because its abnormal expression is closely related to the occurrence of many cancers. In this work, we combined three-dimensional (3D) popcorn-like gold nanofilms as novel surface-enhanced Raman scattering (SERS)-electrochemistry active substrates with toehold-mediated strand displacement reactions (TSDRs) to construct a DNA molecular machine for SERS-electrochemistry dual-mode detection of miRNA. 3D popcorn-like spatial structures generated more active "hot spots" and thus enhanced the sensitivity of SERS and electrochemical signals. Besides, the TSDRs showed high sequence-dependence and high specificity. The addition of target miRNA will trigger the molecular machine to perform two TSDRs in the presence of signal DNA strands modified by R6G (R6G-DNA), thus achieving an enzyme-free amplification detection of miRNA with a low limit of detection of 0.12 fM (for the SERS method) and 2.2 fM (for the electrochemical method). This biosensor can also serve as a universally amplified and sensitive detection platform for monitoring different biomarkers, such as cancer-related DNA, messenger RNA, or miRNA molecules, with high selectivity by changing the corresponding probe sequence.

Self-assembly of colloidal nanoparticles into 2D arrays at water-oil interfaces: rational construction of stable SERS substrates with accessible enhancing surfaces and tailored plasmonic response

Self-assembly at water-oil interfaces has been shown to be a cheap, convenient and efficient route to obtain densely packed layers of plasmonic nanoparticles which have small interparticle distances. This creates highly plasmonically active materials that can be used to give strong SERS enhancement and whose structure means that they are well suited to creating the highly stable, reproducible and uniform substrates that are needed to allow routine and accurate quantitative SERS measurements. A variety of methods have been developed to induce nanoparticle self-assembly at water-oil interfaces, fine tune the surface chemistry and adjust the position of the nanoparticles at the interface but only some of these are compatible with eventual use in SERS, where it is important that target molecules can access the active surface unimpeded. Similarly, it is useful to transform liquid plasmonic arrays into easy-to-handle free-standing solid films but these can only be used as solid SERS substrates if the process leaves the surface nanoparticles exposed. Here, we review the progress made in these research areas and discuss how these developments may lead towards achieving rational construction of tailored SERS substrates for sensitive and quantitative SERS analysis.