Graphene Oxide-Assisted and DNA-Modulated SERS of AuCu Alloy for the Fabrication of Apurinic/Apyrimidinic Endonuclease 1 Biosensor

Dual-driven AND molecular logic gates for label-free and sensitive ratiometric fluorescence sensing and inhibitors screening

Due to the complexity of regulatory networks of disease-related biomarkers, developing simple, sensitive, and accurate methods has remained challenging for precise diagnosis. Herein, an "AND" logic gates DNA molecular machine (LGDM) was constructed, which was powered by the catalytic hairpin assembly (CHA). It was coupled with dual-emission CdTe quantum dots (QDs)-based cation exchange reaction (CER) for label-free, sensitive, and ratiometric fluorescence detection of APE1 and miRNA biomarkers. Benefiting from synergistic signal amplification strategies and a ratiometric fluorometric output mode, this LGDM enables accurate logic computing with robust and significant output signals from weak inputs. It offers improved sensitivity and selectivity even in cell extracts. Using dual-emission spectra CdTe QDs, with a ratiometric signal output mode, ensured good stability and effectively prevented false-positive signals from intrinsic biological interferences compared to the approach relying on a single signal output mode, which enabled the LGDM to achieve rapid, efficient, and accurate natural drug screening against APE1 inhibitors in vitro and cells. The developed method provides impetus to streamline research related to miRNA and APE1, offering significant promise for widespread application in drug development and clinical analysis.

Pyrenecarboxaldehyde@Graphene Oxide Acted as a Highly Efficient ECL Emitter and Target-Triggered the Recyclable Cascade System as an Amplifier for Ultrasensitive APE1 Activity Detection

Herein, pyrenecarboxaldehyde@graphene oxide (Pyc@GO) sheets with highly efficient electrochemiluminescence (ECL) as emitters were prepared by a noncovalent combination to develop a neoteric ECL biosensing platform for the ultrasensitive assessment of human apurinic/apyrimidinic endonuclease1 (APE1) activity. Impressively, the pyrenecarboxaldehyde (Pyc) molecules were able to form stable polar functional groups on the surface of GO sheets through the noncovalent π-π stacking mechanism to prevent intermolecular restacking and simultaneously generate Pyc@GO sheets. Compared with the tightly packed PAH nanocrystals, the Pyc@GO sheets significantly reduced internal filtering effects and diminished nonactivated emitters to enhance ECL intensity and achieve strong ECL emission. Furthermore, the APE1-activated initiators could trigger the recyclable cascade amplified system based on the synergistic cross-activation between catalytic hairpin assembly (CHA) and DNAzyme, which improved the signal amplification and transduction ability. Consequently, the developed ECL platform for the detection of APE1 activity displayed exceptional sensitivity with a low detection limit of 4.6 × 10-9 U·mL-1 ranging from 10-8 to 10-2 U·mL-1. Therefore, the proposed strategy holds great promise for the future development of sensitive and reliable biosensing platforms for the detection of various biomarkers.

Flexible 3D Substrate of Ag Nanoparticle-Loaded Carbon Aerogels with Outstanding Surface-Enhanced Raman Scattering Performance

Surface-enhanced Raman scattering (SERS), an ultra-sensitive and non-destructive analytic technique, has attracted wide attention from the scientific community. Despite its rapid development, limited hotspots on the SERS substrates have restricted their potential in practical applications. Herein, we developed a facile method to fabricate a flexible three-dimensional (3D) SERS substrate composed of silver nanoparticles (Ag NPs)-loaded carbon aerogels (CAs). Such a flexible Ag NPs/CAs substrate exhibited numerous hotspots, which can facilely be adjusted not only by tuning the density of Ag NPs but also by controlling the bending degree of the flexible substrate. In addition, the influence of hotspots on the local electric field enhancement was investigated by theoretical calculations. Moreover, the 3D network structure of the CAs with a large specific surface area and strong adsorption ability can improve the capture of target molecules. Consequently, the optimal Ag NPs/CAs substrate has a low detection limit of 10^-12 M for rhodamine 6G molecules as well as good repeatability. Furthermore, based on the good performance of SERS detection of the Ag NPs/CAs substrate, it can also be practically used for the detection of thiram molecules on the surface of cherry tomatoes. Such a flexible 3D Ag NPs/CAs substrate has great potential for practical environmental monitoring applications.

Application of SERS in In-Vitro Biomedical Detection

Surface-enhanced Raman scattering (SERS), as a rapid and nondestructive biological detection method, holds great promise for clinical on spot and early diagnosis. In order to address the challenging demands of on spot detection of biomedical samples, a variety of strategies has been developed. These strategies include substrate structural and component engineering, data processing techniques, as well as combination with other analytical methods. This report summarizes the recent SERS developments for biomedical detection, and their promising applications in cancer detection, virus or bacterial infection detection, miscarriage spotting, neurological disease screening et al. The first part discusses the frequently used SERS substrate component and structures, the second part reports on the detection strategies for nucleic acids, proteins, bacteria, and virus, the third part summarizes their promising applications in clinical detection in a variety of illnesses, and the forth part reports on recent development of SERS in combination with other analytical techniques. The special merits, challenges, and perspectives are discussed in both introduction and conclusion sections.

Nanowire-in-bowl-shaped piezoelectric cavity structure for SERS directional detection of nanoplastics less than 50 nm

The accurate detection of nanoplastics is crucial due to their harmful effects on the environment and human beings. However, there is a lack of detection methods for nanoplastics smaller than 50 nm. In this research, we successfully constructed an Ag/CuO nanowire (NW)/BaTiO₃@Polyvinylidene fluoride (PVDF) Bowl-shaped substrate with a nanowire-in-Bowl-shaped piezoelectric cavity structure that can modulate surface-enhanced Raman scattering (SERS) by the piezoelectric effect by the virtue of the tip effect of the CuO NW and light focusing effect of the Bowl-shaped cavity. Due to its unique nanowire-in-Bowl-shaped structure and piezoelectrically modifiable ability, nanoplastics less than 50 nm were successfully detected and quantitatively analyzed. We believe that the Ag/CuO NW/BaTiO₃@PVDF Bowl-shaped substrate can provide an efficient, accurate, and feasible way to achieve qualitative and quantitative detection of nanoplastics.

Revealing the alloying and dealloying behaviours in AuAg nanorods by thermal stimulus

Binary metallic nanocrystals are attractive as they offer an extra degree of freedom for structure and phase modulation to generate synergistic effects and extraordinary properties. However, whether the binary structures and phases at the nanoscale still follow the rules established on the bulk counterparts remains unclear. In this work, AuAg nanorods were used as a sample to probe into this issue. An in situ heating method by combining aberration-corrected transmission electron microscopes with a chip-based heating holder was employed to perform the heating experiments. It was found that the AuAg nanorods, which initially possessed heterostructures, can be designed and engineered to be gradient phase alloys with thermal pulses over 350 °C. Atomic diffusion inside the rod structures did not alter the shape of the rods but provided a route to fine-tune their properties. At higher temperatures, the discrepant sublimation behaviours between Au and Ag lead to dealloying of the nanorods. Durative sublimation of the Ag element can continuously tailor the lengths of the nanorods while concentrating the Au composition simultaneously. Especially, nearly pure Au nanocrystals can be obtained with the depletion of Ag by sublimation. These findings give insights into the nanoscale structure and phase behaviours in binary alloys and provide an alternative way to fine-tune their structure, phase, and properties.

Flexible surface-enhanced Raman scatting substrates: recent advances in their principles, design strategies, diversified material selections and applications

Surface-enhanced Raman scattering (SERS) is widely used as a powerful analytical technology in cutting-edge areas such as food safety, biology, chemistry, and medical diagnosis, providing ultra-fast, ultra-sensitive, nondestructive characterization and achieving ultra-high detection sensitivity even down to the single-molecule level. Development of Raman spectroscopy is strongly dependent on high-performance SERS substrates, which have long evolved from the early days of rough metal electrodes to periodic nanopatterned arrays building on solid supporting substrates. For rigid SERS substrates, however, their applications are restricted by sophisticated pretreatments for detecting solid samples with non-planar surfaces. It is therefore essential to reassert the principles in constructing flexible SERS substrates. Herein, we comprehensively review the state-of-the-art in understanding, preparing and using flexible SERS. The basic mechanisms behind the flexible SERS are briefly outlined, typical design strategies are highlighted and diversified selection of materials in preparing flexible SERS substrates are reviewed. Then the recent achievements of various interdisciplinary applications based on flexible SERS substrates are summarized. Finally, the challenges and perspectives for future evolution of flexible SERS and their applications are demonstrated. We propose new research directions focused on stimulating the real potential of SERS as an advanced analytical technique for commercialization.

Label-free and highly sensitive APE1 detection based on rolling circle amplification combined with G-quadruplex

The highly sensitive detection of low-abundant apurinic/apyrimidinic endonuclease 1 (APE1) activity is of great significance for early diagnosis of disease and pathological research. Many methods for detecting APE1 based on isothermal nucleic acids amplification have been developed for improving its sensitivity. However, some of these methods have certain limitations, such as multiple reaction steps, narrow linear range, and complicated processes for fluorescent labeling. Herein, we develop a highly sensitive and label-free APE1 fluorescence detection method based on rolling circle amplification combined with G-quadruplex (RCA-G4). A hairpin probe (HP) labeled with the AP site can be recognized and cleaved by APE1, leading to the release of the primer sequence, which triggered RCA to produce long chain amplification products with a great amount of repeated sequences. The formed amplicon contains a series G-quadruplex structure, which can be combined with Thioflavin T (ThT) to produce fluorescence and achieve high sensitivity label-free detection of APE1. Benefit from the high amplification efficiency of RCA and the high fluorescence quantum yield of G-quadruplex/ThT, a detection limit as low as 1.52 × 10^-6 U/mL and the linear range from 2 × 10^-6 to 10 U/mL were obtained. The developed RCA-G4 method can be successfully used to detect APE1 in serum samples with a recovery from 96.3% to 105.7%. We believe that this approach is expected to play an important role in APE1-related disease research and drug development.

Multifunctional carbon nanomaterials for diagnostic applications in infectious diseases and tumors

Infectious diseases (such as Corona Virus Disease 2019) and tumors pose a tremendous challenge to global public health. Early diagnosis of infectious diseases and tumors can lead to effective control and early intervention of the patient's condition. Over the past few decades, carbon nanomaterials (CNs) have attracted widespread attention in different scientific disciplines. In the field of biomedicine, carbon nanotubes, graphene, carbon quantum dots and fullerenes have the ability of improving the accuracy of the diagnosis by the improvement of the diagnostic approaches. Therefore, this review highlights their applications in the diagnosis of infectious diseases and tumors over the past five years. Recent advances in the field of biosensing, bioimaging, and nucleic acid amplification by such CNs are introduced and discussed, emphasizing the importance of their unique properties in infectious disease and tumor diagnosis and the challenges and opportunities that exist for future clinical applications. Although the application of CNs in the diagnosis of several diseases is still at a beginning stage, biosensors, bioimaging technologies and nucleic acid amplification technologies built on CNs represent a new generation of promising diagnostic tools that further support their potential application in infectious disease and tumor diagnosis.

Fabrication of bifunctional G-quadruplex-hemin DNAzymes for colorimetric detection of apurinic/apyrimidinic endonuclease 1 and microRNA-21

G-quadruplex-based complexes have been widely used in various analytical methods due to their outstanding capabilities of generating colorimetric, fluorescent or electrochemical signals. However, since loop sequences in traditional G-quadruplex structures are quite short, it is difficult to establish biosensors solely using G-quadruplex-based complexes. Herein, we attempted to lengthen the loop sequences of G-quadruplex structures and found that G-quadruplex-hemin DNAzymes (G-DNAzymes) with long loops (even 30 nucleotides) maintain high peroxidase activity. In addition, the peroxidase activity is not affected by the hybridization of the long loop with its complementary counterpart. Consequently, G-DNAzyme can be endowed with an additional function by taking the long loop as a recognition element, which may facilitate the construction of diverse colorimetric biosensors. Furthermore, by designing an apurinic/apyrimidinic site or a complementary sequence of microRNA-21 (miRNA-21) in long loops, bifunctional G-DNAzymes can be split in the presence of apurinic/apyrimidinic endonuclease 1 (APE1) or miRNA-21, decreasing their peroxidase activities. Accordingly, APE1 and miRNA-21 are quantified using 3,3',5,5'-tetramethylbenzidine as a chromophore. Using the G-DNAzyme, APE1 can be detected in a linear range from 2.5 to 22.5 U mL^-1 with a LOD of 1.8 U mL^-1. It is to be noted that benefitting from duplex-specific nuclease-induced signal amplification, the linear range of the miRNA-21 biosensor is broadened to 5 orders of magnitude, while the limit of detection is as low as 73 fM. This work demonstrates that G-DNAzymes with long loops can both generate signals and recognize targets, providing an alternative strategy to design G-quadruplex-based analytical methods.

A DNAzyme-mediated target-initiated rolling circle amplification strategy based on a microchip platform for the detection of apurinic/apyrimidinic endonuclease 1 at the single-cell level

A DNAzyme-mediated target-initiated rolling circle signal amplification strategy based on a microchip platform was developed for detecting apurinic/apyrimidine endonuclease 1 (APE1) at the single-cell level. This strategy was applied to assays of lysate samples from HL-7702, HeLa and MCF-7 cells, with a detection limit of lower than 1 HeLa cell.

Surface-Enhanced Raman Scattering-Active Plasmonic Metal Nanoparticle-Persistent Luminescence Material Composite Films for Multiple Illegal Dye Detection

Uniform two-dimensional plasmonic nanoparticle (NP)-semiconductor composite films could retard the attenuation of electromagnetic evanescent wave and show intensive Raman activity for the multiplex monitoring of hazards in a practical food matrix. Here, an efficient Raman platform is developed by employing a plasmonic nanoparticle (NP)-persistent luminescence material (PLM) composite film. PLM show upconversion photoluminescence (UCPL) properties. The emitted photons are absorbed by plasmonic NPs, which further boost the surface plasmon resonance for the generation of high polarizability and induce strong electromagnetic strength for surface-enhanced Raman scattering (SERS) enhancement. A UCPL-assisted SERS-enhanced mechanism is proposed and verified. A plasmonic NP-PLM film with superior SERS activity and detection capability becomes an alternative candidate for the sensitive and multiple detection of illegal addition of dyes in a food matrix. The proposed UCPL-assisted SERS-enhanced mechanism provides promising future directions to this end to design a next-generation SERS-active plasmonic NP-PLM composite film for the specific detection in complex samples.

A facile wet-chemistry approach to engineer an Au-based SERS substrate and enhance sensitivity down to ppb-level detection

A two-dimensional flexible surface-enhanced Raman scattering (SERS) filter substrate provides an alternative strategy for the highly sensitive portable detection of various toxic molecules and biomaterials. Herein, we developed a solid-liquid interfacial reduction reaction to post-engineer a solid Au nanostructure surface on filter paper to improve the SERS effect. Among four reductants (ascorbic acid, l-dopamine, hydroquinone (HQ), and formaldehyde), HQ possessed a larger oxidation overpotential and facilitated homogeneous growth, forming small Au branch-structure nanoparticles from HAuCl4 solution. Due to the surface effect by exposing abundant -OH groups and intrinsic aromatic rings from TNA/HQ on nano-gold, the SERS effect on positively charged analytes near the plasmonic Au surface was enhanced, while forming a protective layer against severe water interruption. The resulting SERS substrate with branched nano-gold provided several SERS-enhanced sites, increased the enhancement by more than 6 times compared to original SERS sensing, and displayed a 1.4-7.4 × 105 analytical enhancement factor, which leads to a limit of detection down to several ppb. Less than 6% of deviation in the SERS intensity at different sensing sites was observed. We successfully improved the primary SERS substrate using a high overpotential reductant. Owing to its soft and flexible properties, the paper-based SERS substrate can be used conveniently in different sizes, pasting on curved materials, detecting additives in fish, and preventing the coffee-ring effect, showing high practicality and potential commercial value in the future.

Graphene/MoS2 Nanohybrid for Biosensors

Graphene has been studied a lot in different scientific fields because of its unique properties, including its superior conductivity, plasmonic property, and biocompatibility. More recently, transition metal dicharcogenide (TMD) nanomaterials, beyond graphene, have been widely researched due to their exceptional properties. Among the various TMD nanomaterials, molybdenum disulfide (MoS2) has attracted attention in biological fields due to its excellent biocompatibility and simple steps for synthesis. Accordingly, graphene and MoS2 have been widely studied to be applied in the development of biosensors. Moreover, nanohybrid materials developed by hybridization of graphene and MoS2 have a huge potential for developing various types of outstanding biosensors, like electrochemical-, optical-, or surface-enhanced Raman spectroscopy (SERS)-based biosensors. In this review, we will focus on materials such as graphene and MoS2. Next, their application will be discussed with regard to the development of highly sensitive biosensors based on graphene, MoS2, and nanohybrid materials composed of graphene and MoS2. In conclusion, this review will provide interdisciplinary knowledge about graphene/MoS2 nanohybrids to be applied to the biomedical field, particularly biosensors.

Ultrathin ZIF-8 wrapping on Au-dotted Ag-nanowires for highly selective SERS-based CO2 gas detection

Ultrathin ZIF-8 wrapping was constructed on Au-dotted Ag-nanowires to obtain Ag@Au@ZIF-8. A thin film (Ag@Au@ZIF-8 NWs/TF) was constructed to selectively adsorb and enrich CO2 molecules, which solved the problem that SERS signals could not be detected due to the poor affinity of the metal surface and the low concentration of gas molecules.

AuNanostar@4-MBA@Au Core-Shell Nanostructure Coupled with Exonuclease III-Assisted Cycling Amplification for Ultrasensitive SERS Detection of Ochratoxin A

The "turn-on" mode surface-enhanced Raman scattering (SERS) aptasensor for ultrasensitive ochratoxin A (OTA) detection was developed based on the SERS "hot spots" of AuNanostar@4-MBA@Au core-shell nanostructures (AuNS@4-MBA@Au) and exonuclease III (Exo III)-assisted target cycle amplification strategy. Compared with conventional gold nanoparticles, AuNS@4-MBA@Au provides a much higher SERS enhancement factor because AuNS exhibits a larger surface roughness and the lightning rod effect, as well as an excellent electromagnetic field between the AuNS core and the Au shell, which contribute to the superstrong SERS signal. Meanwhile, Exo III-assisted target cycle amplification can be used as an effective method for the further amplified detection of OTA. Additionally, the utilization of streptavidin magnesphere paramagnetic particles offers a green, economical, and facile technology for the accumulation and separation of the signal probe AuNS@4-MBA@Au from solution. All these factors lead to a significant enhancement of detectable signals and superhigh sensitivity. As a result, the limit of detection as low as 0.25 fg mL^-1 could be achieved, which was lower than that in the other reported literatures on SERS methods for OTA detection as we know. The developed SERS aptasensor also provides a promising tool for foodstuff detection.

DNA Nanofirecrackers Assembled through Hybridization Chain Reaction for Ultrasensitive SERS Immunoassay of Prostate Specific Antigen

Isothermal nucleic acid amplification technology has been widely adopted for analytical chemistry with the purpose of sensitivity improvement. Herein we present an ultrasensitive concatenated hybridization chain reaction (C-HCR) based surface-enhanced Raman scattering (SERS) immunoassay by forming antibody-antigen-aptamer heterosandwich structures with the model analyte of total prostate specific antigens (tPSA). In the C-HCR, two HCRs, one proceeds with two hairpins and the other with four biotin-modified hairpins, are coupled, making the formation of DNA nanofirecrackers with the lengths longer than 200 nm and more than four hundred million binding sites of streptavidin modified enzymes. These types of DNA nanofirecrackers through the aptamer encoded linker strand to form heterosandwich structures could provide a general signal application platform such as enzyme catalysis with high amplification efficiency. As a proof of concept, the Au@Ag core-shell nanostructure based SERS immunoassay with excellent signal amplification has been developed by employing the streptavidin modified alkaline phosphatase (SA-ALP) through its catalysis of 2-phospho-l-ascorbic acid trisodium salt (AAP) to form Au@Ag core-shell nanostructures via the formation of ascorbic acid (AA) to reduce AgNO₃ and deposition of silver element on gold nanorods (AuNRs). The newly developed method has a detection limit as low as 0.94 fg/mL and has successfully achieved the detection of serum samples from clinical patients, which was consistent with the clinical test results, showing that this C-HCR strategy to form DNA nanofirecrackers has great potential in clinical applications.