A new method towards the detection of DNA mutation by Surface-Enhanced Raman Spectroscopy

Probing the Local Field Enhancement Using SERS Detection of DNA Strands with Different Lengths and Grafting Strategies on Graphene Oxide Plasmonic Nanoplatforms

Surface-enhanced Raman spectroscopy (SERS) has emerged as a powerful tool for analyzing nucleic acids due to its exceptional sensitivity and specificity. This study rigorously investigates not only the impact of polyA strands of different lengths (i.e., 5, 10, 15, and 20 adenine bases) but also their distinct grafting strategy (SH at 5' and NH2 at 5' end) on the SERS signal of DNA strand using in situ synthesized gold nanoparticles (AuNPs) on graphene oxide sheets (GO-AuNPs). By comparing the thiol vs amine bonding onto the GO-AuNP nanoplatform, we found a strong correlation between the adenine peak intensity at 732 cm-1 and the strand length for both grafting methods (SH at 5' end or NH2 at 5' end). We demonstrated that these intensity variations are highly influenced by the electromagnetic fields from the metallic surface proximity or in between SERS hot-spots formed by the AuNP dimer, as confirmed by numerical simulations. Such results have allowed us to probe the local field enhancement generated by individual AuNPs or dimers and its decay length.

Label-Free Detection of DNA Base Mutation and Hybridized DNA by an Electrostatically Modified 3D Plasmonic Array

Surface-enhanced Raman scattering (SERS) represents a promising avenue for DNA detection as it offers intrinsic chemical insights with high sensitivity compared to conventional methods. However, label-free and quantitative detection of unmodified DNA by SERS remains a major challenge in DNA analysis. To overcome this challenge, we propose a positively charged plasmonic nanosurface for DNA capture and quantitative analysis. Highly sensitive and uniform SERS enhancement was realized by a three-dimensional plasmonic array supporting well-designed hybrid plasmonic modes. Subsequently, the plasmonic array was modified with an electrostatically functionalized PDDA (poly(diene-dimethylammonium-chloride)) self-assembled monolayer in a single step. The effectiveness of the resulting PDDA-SERS substrate was demonstrated by the label-free and quantitative detection of base content and base mutation in hybridized DNA. The PDDA-SERS substrate provides a robust platform for SERS analysis not only of DNA but also of other electronegative analytes.

Rapid detection of Pseudomonas syringae pv. actinidiae by electrochemical surface-enhanced Raman spectroscopy

Bacterial cancer caused by Pseudomonas syringae pv. actinidiae (Psa) is a major threat to kiwifruit in the world, and there is still a lack of effective control measures. The field of bacterial detection needs a fast, easy-to-use and sensitive identification platform. The current bacterial identification methods are lack of time efficiency, which brings problems to many sectors of society. Surface-enhanced Raman spectroscopy (SERS) and electrochemistry (EC) have been studied as possible candidates for bacterial detection because of their high sensitivity for the detection of biomolecules. In this work, SERS, EC and electrochemical surface-enhanced Raman spectroscopy (EC-SERS) were used for the first time to study the adsorption and EC behavior of Psa on the surface of nanostructured silver electrodes. Two different Raman spectra of a single analyte were obtained, and this dual detection was realized. Silver nanoparticles with iodide and calcium ions (Ag@ICNPs) were synthesized as SERS substrates significantly enhanced the characteristic signal peaks of Psa, and the limit of detection (LOD) is as low as 1.0 × 102 cfu/mL. Chemical imaging results show that the application of negative voltage can significantly improve the spectrum quality, showing a higher signal at -0.8 V, indicating that Psa molecules may have potential-induced reorientation on the electrode surface. Therefore, EC-SERS has the ability to greatly improve the SERS performance of bacteria in terms of peak intensity and spectral richness.

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.

Advances in the application of Raman spectroscopy in haematological tumours

Hematologic malignancies are a diverse collection of cancers that affect the blood, bone marrow, and organs. They have a very unpredictable prognosis and recur after treatment. Leukemia, lymphoma, and myeloma are the most prevalent symptoms. Despite advancements in chemotherapy and supportive care, the incidence rate and mortality of patients with hematological malignancies remain high. Additionally, there are issues with the clinical diagnosis because several hematological malignancies lack defined, systematic diagnostic criteria. This work provided an overview of the fundamentals, benefits, and limitations of Raman spectroscopy and its use in hematological cancers. The alterations of trace substances can be recognized using Raman spectroscopy. High sensitivity, non-destructive, quick, real-time, and other attributes define it. Clinicians must promptly identify disorders and keep track of analytes in biological fluids. For instance, surface-enhanced Raman spectroscopy is employed in diagnosing gene mutations in myelodysplastic syndromes due to its high sensitivity and multiple detection benefits. Serum indicators for multiple myeloma have been routinely used for detection. The simultaneous observation of DNA strand modifications and the production of new molecular bonds by tip-enhanced Raman spectroscopy is of tremendous significance for diagnosing lymphoma and multiple myeloma with unidentified diagnostic criteria.

Using biochar to strengthen the removal of antibiotic resistance genes: Performance and mechanism

In this study, the excess activated sludge was used for pyrolysis to produce biochar with Ce modification. The removal process and mechanism of ampicillin resistance gene (ARG_Amp) by biochar was investigated. The results showed that when pyrolyzing the excess sludge at 400 °C, the organic components in the sludge could be partially pyrolyzed and complexed with Ce. By accepting electrons from phenol or quinone, persistent free radicals (PFRs) were formed on the surface of biochar. On the optimized conditions with the initial ARG_Amp concentration of 41.43 mg/L, the removal ratios of ARG_Amp by adsorption, PFRs, hydroxyl free radicals (·OH) by adding H₂O₂ were 28.37%, 8.26%, and 27.56%. No melted DNA was detected in the treated samples. The oxidation process by PFRs and ·OH can directly destroy the ARG_Amp structure. The phosphodiester bond in the base stacking structure and the phosphate bond in the nucleotide are the possible action sites of PFRs. Treated ARG_Amp products were in the form of base pair residues or short-chain double helix structures. ·OH can be added to the bases of nucleotide molecules to form highly active free radical adducts. They can initiate molecular dehydrogenation and intermolecular proton transfer, resulting in oxidation of the base to the scission of the phosphate sugar backbone.

Optimization of hyphenated asymmetric flow field-flow fractionation for the analysis of silver nanoparticles in aqueous solutions

The extensive use of silver nanoparticles (AgNPs) in consumer products, medicine, and industry leads to their release into the environment. Thus, a characterization of the concentration, size, fate, and toxicity of AgNPs under environmental conditions is required. In this study, we present the characterization and optimization of an asymmetric flow field-flow fractionation (AF4) system coupled with UV/Vis spectrophotometer and dynamic light scattering (DLS) detector as a powerful tool for the size separation and multi-parameter characterization of AgNPs in complex matrices. The hyphenated AF4-UV/Vis-DLS system was first characterized using individual injections of the different size fractions. We used electrostatically stabilized AgNPs of 20-, 50-, and 80-nm nominal diameters coated with lipoic acid. We investigated the effect of applied cross-flows, carrier solutions, focus times, and quantity of injected particles on the nature of the AF4 fractograms and on the integrity of the AgNPs. Best size separation of a 1:1 mixture of 20- and 80-nm AgNPs was achieved using cross-flows of 0.5 and 0.7 mL/min with 1 mM NaCl and 0.05% v/v Mucasol as carrier solutions. We also researched the behavior of AgNPs in natural waters using the hyphenated AF4-UV/Vis-DLS system, under determined optimal conditions. Schematic and photograph of the AF4 setup with numbered hardware devices. Dashed lines represent electrical connections; continuous lines represent fluidic connections. For a better overview, not all fluidic connections between pump/6-way valve (2) and the Eclipse AF4 device (3) are shown in the schematic. The fluorescence detector (FL (7)) was not used in the study presented herein.