Aptamer-based surface-enhanced Raman scattering (SERS) sensor for thrombin based on supramolecular recognition, oriented assembly, and local field coupling

Construction and application of thrombin-activated fluorescence-SERS dual-mode optical nanoprobes

Thrombin (TB) plays a key role in the pathological and physiological coagulation of diseases. In this work, a TB-activated fluorescence-surface-enhanced Raman spectroscopy (SERS) dual-mode optical nanoprobe (MRAu) was constructed by linking rhodamine B (RB)-modified magnetic fluorescent nanospheres with AuNPs through TB-specific recognition peptides. In the presence of TB, the polypeptide substrate could specifically be cleaved by TB, resulting in the weakening of SERS hotspot effect and the reduction of Raman signal. Meanwhile, the fluorescence resonance energy transfer (FRET) system was destroyed, and the RB fluorescence signal originally quenched by AuNPs was recovered. Using MRAu, SERS and fluorescence methods were combined to extend the TB detection range to 1-150 pM, and the detection limit was as low as 0.35 pM. In addition, the ability to detect TB in human serum also verified the effectiveness and practicality of the nanoprobe. The probe was also successfully employed to evaluate the inhibitory effect against TB of active components in Panax notoginseng. This study provides a new technical means for the diagnosis and drug development of abnormal TB-related diseases.

Nanogold sol plasmon discattering assay for trace carbendazim in tea coupled aptamer with Au3+-glyoxal-carbon dot nanocatalytic reaction

Carbendazim (CBZ) is a broad-spectrum fungicide, which is toxic to mammals. Therefore, it is very necessary to establish a sensitive detection for food safety. An experiment found that CD_Fe exhibited excellent catalysis for the nano-indicator reaction of HAuCl₄-glyoxal to produce gold nanoparticles (AuNPs) and that the generated AuNPs have a very strong surface-enhanced Raman scattering (SERS) effect at 1613 cm^-1 in the presence of Victoria blue B molecular probes, and resonance Rayleigh scattering (RRS) signals at 370 nm. The aptamer (Apt) suppressed the catalysis of CD_Fe to cause the SERS and RRS signals decreasing. With the addition of CBZ, the specific Apt reaction occurred to restore the catalysis of CD_Fe, and resulting in a linear increase in the signals of RRS and SERS. As a result, this new nanocatalytic amplification indicator reaction was coupled with a specific Apt reaction of carbendazim (CBZ), to construct a new CD_Fe catalytic amplification-aptamer SERS/RRS discattering assay for ultratrace CBZ, which was used to analyze CBZ in tea samples with satisfactory results. In addition, this biosensoring platform can be also used to assay profenofos.

Aptamer-modified magnetic SERS substrate for label-based determination of cardiac troponin I

A sensitive label-based SERS strategy composed of magnetic bimetallic nanoparticles Fe₃O₄@Ag@Au, specific aptamer, and Bradford method was developed for the quantitative determination of cardiac troponin I (cTnI) in human serum. The prepared substrate with high magnetic character, signal enhancement, and uniformity exhibited significant Raman response. After the substrate was bound to the aptamer, the target protein cTnI was specifically captured, and it showed the Raman signal when the signal reporter Coomassie Brilliant Blue G-250 (CBBG) was supplied. The Raman signal intensity at 1621 cm^-1 showed a wide linear relationship with the log value of the cTnI concentration in the range 0.01 to 100 ng·mL^-1, and the estimated limit of detection (LOD) was 5.50 pg·mL^-1. The recovery and relative standard deviation (RSD) of the spike experiment in human serum samples were 92-115% and 7.4-12.7%, respectively.

The Role of Raman Spectroscopy Within Quantitative Metabolomics

Ninety-four years have passed since the discovery of the Raman effect, and there are currently more than 25 different types of Raman-based techniques. The past two decades have witnessed the blossoming of Raman spectroscopy as a powerful physicochemical technique with broad applications within the life sciences. In this review, we critique the use of Raman spectroscopy as a tool for quantitative metabolomics. We overview recent developments of Raman spectroscopy for identification and quantification of disease biomarkers in liquid biopsies, with a focus on the recent advances within surface-enhanced Raman scattering-based methods. Ultimately, we discuss the applications of imaging modalities based on Raman scattering as label-free methods to study the abundance and distribution of biomolecules in cells and tissues, including mammalian, algal, and bacterial cells.

Photoelectrochemical aptasensing for thrombin based on exonuclease III-assisted recycling signal amplification and nanoceria enzymatic strategy

In the present work, a capture DNA (c-DNA) was immobilized on the TNA/g-C₃N₄ to develop a sensitive and selective TNA/g-C₃N₄/c-DNA photoelectrochemical aptasensor for determining thrombin. With the aid of the specific recognition of anti-thrombin aptamer towards thrombin, ingenious design of hairpin DNA, and exonuclease III-assisted recycling signal amplification, more nanoceria could be assembled on the TNA/g-C₃N₄/c-DNA to form TNA/g-C₃N₄/nanoceria in the presence of thrombin. Due to the oxidase-mimic catalytic efficiency of nanoceria and the oxygen consumption for glucose oxidation, the photoexcited electrons at the conduction band of g-C₃N₄ could be well transferred to that of TNA under visible light irradiation, resulting in the increase of the photocurrent of TNA/g-C₃N₄/nanoceria, and the increase value of photocurrent had a linear relationship with the concentration of thrombin under the optimal conditions. So, the constructed TNA/g-C₃N₄/c-DNA photoelectrochemical aptasensor exhibited a satisfactory quantitative range from 0.01 pM to 0.5 nM, low detection limit with 3.4 fM for thrombin determination, and was applied for the human serum analysis successfully with RSD of less than 4.8% and the recovery between 95% and 113%.

SERS-Based Aptasensor for Rapid Quantitative Detection of SARS-CoV-2

During the COVID-19 pandemic, the development of sensitive and rapid techniques for detection of viruses have become vital. Surface-enhanced Raman scattering (SERS) is an appropriate tool for new techniques due to its high sensitivity. SERS materials modified with short-structured oligonucleotides (DNA aptamers) provide specificity for SERS biosensors. Existing SERS-based aptasensors for rapid virus detection are either inapplicable for quantitative determination or have sophisticated and expensive construction and implementation. In this paper, we provide a SERS-aptasensor based on colloidal solutions which combines rapidity and specificity in quantitative determination of SARS-CoV-2 virus, discriminating it from the other respiratory viruses.

Aptamer-Based Detection of Circulating Targets for Precision Medicine

The past decade has witnessed ongoing progress in precision medicine to improve human health. As an emerging diagnostic technique, liquid biopsy can provide real-time, comprehensive, dynamic physiological and pathological information in a noninvasive manner, opening a new window for precision medicine. Liquid biopsy depends on the sensitive and reliable detection of circulating targets (e.g., cells, extracellular vesicles, proteins, microRNAs) from body fluids, the performance of which is largely governed by recognition ligands. Aptamers are single-stranded functional oligonucleotides, capable of folding into unique tertiary structures to bind to their targets with superior specificity and affinity. Their mature evolution procedure, facile modification, and affinity regulation, as well as versatile structural design and engineering, make aptamers ideal recognition ligands for liquid biopsy. In this review, we present a broad overview of aptamer-based liquid biopsy techniques for precision medicine. We begin with recent advances in aptamer selection, followed by a summary of state-of-the-art strategies for multivalent aptamer assembly and aptamer interface modification. We will further describe aptamer-based micro-/nanoisolation platforms, aptamer-enabled release methods, and aptamer-assisted signal amplification and detection strategies. Finally, we present our perspectives regarding the opportunities and challenges of aptamer-based liquid biopsy for precision medicine.

A review of aptamer-based SERS biosensors: Design strategies and applications

Surface-enhanced Raman spectroscopy, due to its high sensitivity, unique vibrational fingerprint identification of molecules and easy operation, has been extensively applied in different fields. Aptamers, being the unique single stranded DNA/RNA sequences that can specifically recognize and seize the target analytes, combined with Surface-enhanced Raman spectroscopy (SERS), can offer potent multiplex detection capacity with high specificity and sensitivity. In this review, we summarize and classify the general working strategies of different types of aptamer-based SERS biosensors with diversified protocols which either take aptamer conformational change as intrinsic reporter, or make use of various extrinsic Raman reporters in different sensor designs via on/off approach, sandwich-type and magnetic nanoparticles (NPs)-assisted approach, and catalytic reaction assisted approach with amplification of alternative Raman signals. The advantages, applications and perspectives of these aptamer-based SERS biosensors are also discussed.

A signal-enhanced and sensitive lateral flow aptasensor for the rapid detection of PDGF-BB

Platelet-derived growth factor BB (PDGF-BB) is a potential biomarker of tumor angiogenesis. For the first time, we developed a highly sensitive aptasensor for PDGF-BB with an enhanced test line signal by using two different gold nanoparticles (AuNPs). Herein, we describe a highly sensitive biosensor for PDGF-BB detection that combines biotinylated aptamer on a sample pad and poly thymine-Cy3-AuNP-monoclonal antibody complexes against PDGF-BB immobilized on conjugate pad A. Streptavidin (SA) and rabbit anti-mouse polyclonal antibody were also immobilized in the nitrocellulose membrane at the test and control zones, respectively. When the target PDGF-BB protein was added, it first bound the aptamer, and later the monoclonal antibody to form a biotinylated complex that was captured by SA, resulting in a visual red line on the test zone. In addition, to enhance the sensitivity, another monoclonal antibody against Cy3 was conjugated on AuNP B and immobilized on conjugate pad B to form a AuNPs (A&B)-antibody-(PDGF-BB-Cy3)-aptamer-biotin-SA complex on the test line when a loading buffer was subsequently added. This approach showed a linear response to PDGF-BB from 3 ng mL⁻¹ to 300 ng mL⁻¹ with a limit of detection as low as 1 ng mL⁻¹ obtained in 10 minutes. Our biosensor displayed results through red lines readable by the naked eye. Interestingly, our approach has been successfully applied for real sample verification, proving its applicability for cancer monitoring and diagnosis.

Platelet-derived growth factor BB (PDGF-BB) is a potential biomarker of tumor angiogenesis.

Indirect surface-enhanced Raman scattering assay of insulin-like growth factor 2 receptor protein by combining the aptamer modified gold substrate and silver nanoprobes

An indirect aptamer-based SERS assay for insulin-like growth factor 2 receptor (IGF-IIR) protein was developed. The gold substrate and silver nanoparticles (AgNPs) were employed simultaneously to achieve double enhancement for SERS signals. Firstly, the five commercial SERS substrates including Enspectr, Ocean-Au, Ocean-AG, Ocean-SP and Q-SERS substrates were evaluated using 4-mercaptobenzoic acid (4-MBA). The Q-SERS substrate was selected based on low relative standard deviation (RSD, 8.6%) and high enhancement factor (EF, 8.7*10⁵), using a 785 nm laser. The aptamer for IGF-IIR protein was designed to include two sequences: one grafted on gold substrate to specifically capture the IGF-IIR protein and a second one forming a 3' sticky bridge to capture SERS nanotags. The SERS nanotag was composed by AgNPs (20 nm), 4-MBA and DNA probes that can hybridize with the aptamer. Due to the steric-hindrance effect, when the aptamer doesn't combine with IGF-IIR protein, it only can capture the SERS nanotags. Therefore, there was a negative correlation between the concentration of IGF-IIR protein and the intensity of 4-MBA at 1076 cm^-1. The detection limit reached to 141.2 fM and linear range was from 10 pM to 1 μM. The SERS aptasensor also exhibits a high reproducibility with an average RSD of 4.5%. The interference test was conducted with other four proteins to verify the accuracy of measuring. The study provides an approach to quantitative determination of proteins based on specific recognition and nucleic acid hybridization of aptamers, to establish sandwich structure for SERS enhancement. Graphical abstractSchematic representation of surface-enhanced Raman scattering (SERS) assay on insulin-like growth factor 2 receptor (IGF-IIR) protein by combining the aptamer modified gold substrate and 4-mercaptobenzoic acid (4-MBA) and DNA probe modified silver nanoparticles.

Present and Future of Surface-Enhanced Raman Scattering

The discovery of the enhancement of Raman scattering by molecules adsorbed on nanostructured metal surfaces is a landmark in the history of spectroscopic and analytical techniques. Significant experimental and theoretical effort has been directed toward understanding the surface-enhanced Raman scattering (SERS) effect and demonstrating its potential in various types of ultrasensitive sensing applications in a wide variety of fields. In the 45 years since its discovery, SERS has blossomed into a rich area of research and technology, but additional efforts are still needed before it can be routinely used analytically and in commercial products. In this Review, prominent authors from around the world joined together to summarize the state of the art in understanding and using SERS and to predict what can be expected in the near future in terms of research, applications, and technological development. This Review is dedicated to SERS pioneer and our coauthor, the late Prof. Richard Van Duyne, whom we lost during the preparation of this article.

Research advances of DNA aptasensors for foodborne pathogen detection

Aptamers, referring to single-stranded DNA or RNA molecules can specifically recognize and bind to their targets. Based on their excellent specificity, sensitivity, high affinity, and simplicity of modification, aptamers offer great potential for pathogen detection and biomolecular screening. This article reviews aptamer screening technologies and aptamer application technologies, including gold-nanoparticle lateral flow assays, fluorescence assays, electrochemical assays, colorimetric assays, and surface-enhanced Raman assays, in the detection of foodborne pathogens. Although notable progress (more rapid, sensitive, and accurate) has been achieved in the field, challenges and drawbacks in their applications still remain to be overcome.

Functionalized Gold Nanoparticles as Biosensors for Monitoring Cellular Uptake and Localization in Normal and Tumor Prostatic Cells

In the present contribution the fabrication and characterization of functionalized gold nanospheres of uniform shape and controlled size is reported. These nano-objects are intended to be used as Surface Enhanced Raman Spectroscopy (SERS) sensors for in-vitro cellular uptake and localization. Thiophenol was used as molecular reporter and was bound to the Au surface by a chemisorption process in aqueous solution. The obtained colloidal solution was highly stable and no aggregation of the single nanospheres into larger clusters was observed. The nanoparticles were incubated in human prostatic cells with the aim of developing a robust, SERS-based method to differentiate normal and tumor cell lines. SERS imaging experiments showed that tumor cells uptake considerably larger amounts of nanoparticles in comparison to normal cells (up to 950% more); significant differences were also observed in the uptake kinetics. This largely different behaviour might be exploited in diagnostic and therapeutic applications.

Analysis of Biomolecules Based on the Surface Enhanced Raman Spectroscopy

Analyzing biomolecules is essential for disease diagnostics, food safety inspection, environmental monitoring and pharmaceutical development. Surface-enhanced Raman spectroscopy (SERS) is a powerful tool for detecting biomolecules due to its high sensitivity, rapidness and specificity in identifying molecular structures. This review focuses on the SERS analysis of biomolecules originated from humans, animals, plants and microorganisms, combined with nanomaterials as SERS substrates and nanotags. Recent advances in SERS detection of target molecules were summarized with different detection strategies including label-free and label-mediated types. This comprehensive and critical summary of SERS analysis of biomolecules might help researchers from different scientific backgrounds spark new ideas and proposals.

A chemiluminescence aptasensor for thrombin detection based on aptamer-conjugated and hemin/G-quadruplex DNAzyme signal-amplified carbon fiber composite

In this work, a highly sensitive and selective chemiluminescence (CL) aptasensor was prepared for thrombin (THR) detection based on aptamer-conjugated and hemin/G-quadruplex DNAzyme signal-amplified carbon fiber composite (HG-DNAzyme/T-Apt/SiO₂@GO@CF). Initially, SiO₂@GO@CF was successfully prepared and characterized by Scanning Electron Microscopy (SEM), X-ray Diffraction (XRD) and Fourier Transform Infrared Spectroscopy (FT-IR). Thrombin aptamer (T-Apt) as an identification element and simulated enzyme - hemin/G-quadruplex DNAzyme (HG-DNAzyme) as a signal-amplified material, were applied in the CL aptasensor. Then, the immobilization properties of SiO₂@GO@CF and adsorption properties of T-Apt/SiO₂@GO@CF were studied. Lastly, HG-DNAzyme/T-Apt/SiO₂@GO@CF was applied in construction of the CL aptasensor. When THR existed, HG-DNAzyme was desorbed from the surface of T-Apt/SiO₂@GO@CF and catalyzed the CL system of luminol-H₂O₂. Under optimized CL conditions, THR was measured with the linear concentration range of 1.5 × 10^-14 to 2.5 × 10^-11 moL/L and the detection limit of 6.3 × 10^-15 moL/L (3δ). The proposed CL aptasensor was used to the determination of THR in human serum samples and recoveries ranged from 99.0% to 102.4%. Those satisfactory results illustrated the CL aptasensor could achieve highly sensitive and selective detection of THR and revealed potential application in practical samples.

Facing Challenges in Real-Life Application of Surface-Enhanced Raman Scattering: Design and Nanofabrication of Surface-Enhanced Raman Scattering Substrates for Rapid Field Test of Food Contaminants

Surface-enhanced Raman scattering (SERS) is capable of detecting a single molecule with high specificity and has become a promising technique for rapid chemical analysis of agricultural products and foods. With a deeper understanding of the SERS effect and advances in nanofabrication technology, SERS is now on the edge of going out of the laboratory and becoming a sophisticated analytical tool to fulfill various real-world tasks. This review focuses on the challenges that SERS has met in this progress, such as how to obtain a reliable SERS signal, improve the sensitivity and specificity in a complex sample matrix, develop simple and user-friendly practical sensing approach, reduce the running cost, etc. This review highlights the new thoughts on design and nanofabrication of SERS-active substrates for solving these challenges and introduces the recent advances of SERS applications in this area. We hope that our discussion will encourage more researches to address these challenges and eventually help to bring SERS technology out of the laboratory.

Thrombin Assessment on Nanostructured Label-Free Aptamer-Based Sensors: A Mapping Investigation via Surface-Enhanced Raman Spectroscopy

Aptamers, synthetic single-stranded DNA or RNA molecules, can be regarded as a valuable improvement to develop novel ad hoc sensors to diagnose several clinical pathologies. Their intrinsic potential is related to the high specificity and sensitivity to the selected target biomarkers, being capable of detecting very low concentrations and thus allowing an early diagnosis of a possible disease. This kind of probe can be usefully integrated into a number of different devices in order to provide a reliable acquisition of the analyte and properly elaborate the related signal. The study presents the fabrication and characterization of a label-free aptamer sensor designed using a gold-coated silicon nanostructured substrate to map the target molecule by means of surface-enhanced Raman spectroscopy (SERS). As a proof, thrombin was used as a model at four different concentrations (i.e., 0.0873, 0.873, 8.73, and 87.3 nM). SERS mapping analysis was carried out considering each representative band of the aptamer-thrombin complex (centered at 822, 1140, and 1558 cm⁻¹) and then combining them in order to acquire a comprehensive and unambiguous measure of the target. In both cases, a valuable correlation was evaluated, even if the first approach can suffer from some limitations in the third band related to lower definition of the characteristic peak compared to those in the other two bands.

Equipment-Free Quantitative Aptamer-Based Colorimetric Assay Based on Target-Mediated Viscosity Change

In this paper, we describe an aptamer-based colorimetric assay (ABCA), which integrates enzyme-loaded microparticles for signal amplification with distance measurement for equipment-free quantitative readout. The distance measurement readout is on the basis of target-induced selective reduction in viscosity of reaction solution. Its utility is well demonstrated with inexpensive, sensitive, and selective detection of adenosine (model analyte) in buffer samples and real samples of human serum and urine with the naked eye. This ABCA method just requires operators to simply count the number of colored distance-relevant marked bars on the calibrated glass microsyringes (testing containers) to provide quantitative results. It thus holds great promise for wide applications particularly in limited-resource settings.

An ultrasensitive chemiluminescence aptasensor for thrombin detection based on iron porphyrin catalyzing luminescence desorbed from chitosan modified magnetic oxide graphene composite

In this work, an ultrasensitive chemiluminescence (CL) aptasensor was prepared for thrombin detection based on iron porphyrin catalyzing luminol - hydrogen peroxide luminescence under alkaline conditions, and iron porphyrin was desorbed from chitosan modified magnetic oxide graphene composite (CS@Fe₃O₄@GO). Firstly, CS@Fe₃O₄@GO was prepared. CS@Fe₃O₄@GO has advantages of the good biocompatibility and positively charged on its surface of CS, the large specific surface area of GO and the easy separation characteristics of Fe₃O₄. GO, Fe₃O₄ and CS@Fe₃O₄@GO were confirmed by transmission electron microscopy (TEM), scanning electron microscope (SEM), fourier transform infrared (FTIR) and X-ray powder diffraction (XRD). Then, thrombin aptamer (T-Apt) and hemin (HM, an iron porphyrin) were sequentially modified on the surface of CS@Fe₃O₄@GO to form CS@Fe₃O₄@GO@T-Apt@HM. The immobilization properties of CS@Fe₃O₄@GO to T-Apt and adsorption properties of CS@Fe₃O₄@GO@T-Apt to HM were sequentially researched through the curves of kinetics and the curves of thermodynamics. When thrombin existed in solutions, HM was desorbed from the surface of CS@Fe₃O₄@GO@T-Apt@HM owing to the strong specific recognition ability between thrombin and T-Apt, causing the changes of CL signal. Under optimized CL conditions, thrombin could be measured with the linear concentration range of 5.0×10^-15-2.5×10^-10mol/L. The detection limit was 1.5×10^-15mol/L (3δ) while the relative standard deviation (RSD) was 3.2%. Finally, the CS@Fe₃O₄@GO@T-Apt@HM-CL aptasensor was used for the determination of thrombin in practical serum samples and recoveries ranged from 95% to 103%. Those satisfactory results revealed potential application of the CS@Fe₃O₄@GO@T-Apt@HM-CL aptasensor for thrombin detection in monitoring and diagnosis of human blood diseases.