Selective recognition of the amyloid marker single thioflavin T using DNA origami-based gold nanobipyramid nanoantennas

Nucleic acid-mediated SERS Biosensors: Signal enhancement strategies and applications

Surface Enhanced Raman Spectroscopy (SERS) is a powerful spectroscopic analysis technique applied in various fields due to its high selectivity, ultra-high sensitivity, and non-destructiveness. As natural biological macromolecules, nucleic acids perform a significant role in SERS biosensing. In this review, we first summarize how nucleic acids mediate the signal enhancement of SERS biosensors from three aspects: substrate self-assembly, analyte biorecognition, and molecular amplification. Among them, SERS substrates can be self-assembled by both DNA modification and coordination or electrostatic interactions. In the field of biorecognition, analyte biorecognition based on three nucleic acid recognition elements can enhance SERS signals by regulating the distance of analytes or Raman reporter molecules to the SERS substrate. In addition, nucleic acid-based enzyme and enzyme-free amplification can enhance SERS signals by enlarging the quantity of analytes or its nucleic acid intermediates. Subsequently, multidimensional applications of nucleic acid-mediated SERS signal enhancement in biomedicine, food safety, and environmental monitoring are listed. Finally, the current challenges and future exploration of nucleic acid-mediated SERS signal enhancement are discussed.

Water-stable perovskite/metallic nanocomposites-based SERS aptasensor for detection of neuron-specific enolase

Perovskite/metallic heterojunction-based surface enhanced Raman scattering (SERS) substrates have been proven to be capable of providing Raman enhancement. However, the inherent water instability and poor dispersibility of perovskite/metallic nanocomposites-based SERS substrates pose significant challenges to their application in aqueous environments. Herein, polydopamine (PDA)-encapsulated cesium lead bromide (CsPbBr3) adsorbing gold nanoparticles (AuNPs), termed as CsPbBr3@PDA@AuNPs, is prepared as SERS substrate, which exhibits excellent water stability and SERS activity. Dopamine as organic ligand not only passivates surface defects during the growth of perovskite nanocrystals, but also forms porous PDA protective layer, effectively preventing degradation of perovskite in aqueous medium. Meanwhile, PDA with abundant functional groups and conjugated π structure will adsorb AuNPs and promote electron flow between CsPbBr3 and AuNPs, resulting in strong SERS activity. Based on the results, a SERS aptasensor has been fabricated by conjugation between CsPbBr3@PDA@AuNPs and double-stranded DNA (dsDNA), which is composed of neuron-specific enolase (NSE) aptamer and partial complementary signal-stranded DNA (ssDNA). The working strategy of as-fabricated SERS aptasensor is based on the conformational change (of ssDNA)-triggered Raman response for the detection of NSE. Upon the addition of NSE, the specific binding of NSE aptamers to NSE can convert rigid dsDNA into a flexible ssDNA, and the Cy5 signal molecule modified at the end of ssDNA will close to CsPbBr3@PDA@AuNPs SERS substrate, generating significant Raman signals with the lower limit of detection (1.02 pg/mL) of NSE. The SERS aptasensor has broad application prospect in the field of life/medicine science fields (e.g. early diagnosis and screening of disease).

Advances in Functional Nucleic Acid SERS Sensing Strategies

Functional nucleic acids constitute a distinct category of nucleic acids that diverge from conventional nucleic acid amplification methodologies. They are capable of forming intricate hybrid structures through Hoogsteen and reverse Hoogsteen hydrogen bonding interactions between double-stranded and single-stranded DNA, thereby broadening the spectrum of DNA interactions. In recent years, functional DNA/RNA-based surface-enhanced Raman spectroscopy (SERS) has emerged as a potent platform capable of ultrasensitive and multiplexed detection of a variety of analytes of interest. This review aims to elucidate the operational principles of several functional nucleic acids in SERS detection, including DNAzymes, G-quadruplexes, aptamers, CRISPR, origami etc., alongside the design methodologies and practical applications of functional DNA/RNA-based SERS sensing. Initially, an overview is summarized encompassing the structural attributes and SERS sensing mechanisms inherent to diverse functional DNA/RNA. Following this, various innovative strategies for constructing functional nucleic acid-based SERS sensors are illustrated in detail, aimed at improving the present detection capabilities. A comprehensive summing up is then conducted on the applications of these sensors in crucial fields, such as disease diagnosis, environmental monitoring, and food safety detection, with a particular focus on SERS sensitivity, specificity, and analytical versatility. Finally, conclusive remarks are offered along with an exploration of the existing challenges and prospective avenues for future research in this developed field.

Optimization of the Surfactant Ratio in the Formation of Penta-Twinned Seeds for Precision Synthesis of Gold Nanobipyramids with Tunable Plasmon Resonances

The synthesis of high-purity gold nano bipyramids (Au NBPs) with a narrow size distribution and tunable plasmon resonances is of great significance for plasmon resonance-related applications. However, the synthesis Au NBP approach involves multiple steps with many parameters that can affect the purity of the final product. In this work, we were devoted to studying the effect of the molar ratio between hexadecyltrimethylammonium chloride (CTAC) and sodium citrate tribasic dihydrate (CiNa3) on the seed formation stage. The results showed that the yield of Au NBP product has dramatically increased with the seed solution made from the molar ratio of CTAC:CiNa3 at 21:1. Furthermore, using this optimal seed, we can efficiently synthesize Au NBPs with various sizes by adjusting the concentration of the seed but keeping the rest of the parameters constant. In this study, the longitudinal localized surface plasmon resonances (LSPRs) of Au NBPs exhibit tunability beyond 450 nm across the visible and near-infrared regions from 774 to 1224 nm. We were able to successfully fine-tune the LSPRs of Au NBPs in the spectral region to become resonant with the excitation wavelengths of an 808 nm near-infrared (NIR) laser. The photothermal activities of Au NBPs were studied under 808 nm laser irradiation at ambient conditions. The present work demonstrates a paradigm for the synthesis of Au NBPs with tunable LSPRs in a precise and controllable manner, achieved by examining the surfactant ratios in the formation of penta-twinned seeds.

Expanding Chemical Space in the Synthesis of Gold Bipyramids

Gold bipyramids (AuBPs), despite having superior properties compared to their spectroscopically similar counterparts, gold nanorods, have found comparatively limited applications. This discrepancy is primarily due to the lack of protocols to tailor their dimensions. Typically, the concentration of Au seeds is virtually the sole factor that determines the aspect ratio and thus, the optical properties of AuBPs. As a result, varying the volumes of AuBPs while incurring minimal changes to their optical spectra remains a synthetically non-trivial task. Here, the chemical space in the seeded growth of AuBPs, is expanded by exploiting the interplay between bromide, silver ions, and seed concentration for tuning the final dimensions and optical properties of AuBPs. Specifically, a 6 fold change in volumes of AuBPs is achieved while maintaining the fixed plasmon band position. Further overgrowth of as-prepared bipyramids broadens the realizable dimensions without compromising quality and initial morphology. Overall, the results expand the chemical toolbox in the wet-chemistry synthesis of anisotropic gold nanoparticles, which is relevant for health, colorimetric sensors, and energy applications.

Gold nanostructures in melanoma: Advances in treatment, diagnosis, and theranostic applications

Melanoma, a lethal form of skin cancer, poses a significant challenge in oncology due to its aggressive nature and high mortality rates. Gold nanostructures, including gold nanoparticles (GNPs), offer myriad opportunities in melanoma therapy and imaging due to their facile synthesis and functionalization, robust stability, tunable physicochemical and optical properties, and biocompatibility. This review explores the emerging role of gold nanostructures and their composites in revolutionizing melanoma treatment paradigms, bridging the gap between nanotechnology and clinical oncology, and offering insights for researchers, clinicians, and stakeholders. It begins by elucidating the potential of nanotechnology-driven approaches in cancer therapy, highlighting the unique physicochemical properties and versatility of GNPs in biomedical applications. Various therapeutic modalities, including photothermal therapy, photodynamic therapy, targeted drug delivery, gene delivery, and nanovaccines, are discussed in detail, along with insights from ongoing clinical trials. In addition, the utility of GNPs in melanoma imaging and theranostics is explored, showcasing their potential in diagnosis, treatment monitoring, and personalized medicine. Furthermore, safety considerations and potential toxicities associated with GNPs are addressed, underscoring the importance of comprehensive risk assessment in clinical translation. Finally, the review concludes by discussing current challenges and future directions, emphasizing the need for innovative strategies to maximize the clinical impact of GNPs in melanoma therapy.

Functionalized DNA Origami-Enabled Detection of Biomarkers

Biomarkers are crucial physiological and pathological indicators in the host. Over the years, numerous detection methods have been developed for biomarkers, given their significant potential in various biological and biomedical applications. Among these, the detection system based on functionalized DNA origami has emerged as a promising approach due to its precise control over sensing modules, enabling sensitive, specific, and programmable biomarker detection. We summarize the advancements in biomarker detection using functionalized DNA origami, focusing on strategies for DNA origami functionalization, mechanisms of biomarker recognition, and applications in disease diagnosis and monitoring. These applications are organized into sections based on the type of biomarkers - nucleic acids, proteins, small molecules, and ions - and concludes with a discussion on the advantages and challenges associated with using functionalized DNA origami systems for biomarker detection.

Immobilising an acid-cleavable dimeric phthalocyanine on gold nanobipyramids for intracellular pH detection and photodynamic elimination of cancer cells

An acetal-linked dimeric phthalocyanine has been synthesised and immobilised on the surface of gold nanobipyramids. The resulting nanocomposite serves as a highly sensitive probe for intracellular pH through its acid-responsive fluorescence and surface-enhanced Raman scattering signals. The phthalocyanine units released in the acidic intracellular environment can also effectively eliminate the cancer cells upon light irradiation, rendering this simple fabricated nanosystem a bimodal and bifunctional theranostic agent.

Quantifying Shape Transition in Anisotropic Plasmonic Nanoparticles through Geometric Inversion. Application to Gold Bipyramids

Unraveling the nuanced interplay between the morphology and the optical properties of plasmonic nanoparticles is crucial for targeted applications. Managing the relationship becomes significantly complex when dealing with anisotropic nanoparticles that defy a simple description using parameters like length, width, or aspect ratio. This complexity requires computationally intensive numerical modeling and advanced imaging techniques. To address these challenges, we propose a detailed structural parameter determination of gold nanoparticles using their two-dimensional projections (e.g., micrographs). Employing gold bipyramids (AuBPs) as a model morphology, we can determine their three-dimensional geometry and extract optical features computationally for comparison with the experimental data. To validate our inversion model's effectiveness, we apply it to derive the structural parameters of AuBPs undergoing shape modification through oxidative etching. In summary, our findings allow for the precise characterization of structural parameters for plasmonic nanoparticles during shape transitions, potentially enhancing the comprehension of nanocrystal growth and optimizing plasmonic material design for various applications.

DNA origami: a tool to evaluate and harness transcription factors

Alongside other players, such as CpG methylation and the "histone code," transcription factors (TFs) represent a key feature of gene regulation. TFs are implicated in critical cellular processes, ranging from cell death, growth, and differentiation, up to intranuclear signaling of steroid and other hormones, physical entities, and hypoxia regulation. Notwithstanding an extensive body of research in this field, several questions and therapeutic options remain unanswered and unexplored, respectively. Of note, many of these TFs represent therapeutic targets, which are either difficult to be pharmacologically tackled or are still not drugged via traditional approaches, such as small-molecule inhibition. Upon providing a brief overview of TFs, we focus herein on how synthetic biology/medicine could assist in their study as well as their therapeutic targeting. Specifically, we contend that DNA origami, i.e., a novel synthetic DNA nanotechnological approach, represents an excellent synthetic biology/medicine tool to accomplish the above goals, since it can harness several vital characteristics of DNA: DNA polymerization, DNA complementarity, DNA "programmability," and DNA "editability." In doing so, DNA origami can be applied to study TF dynamics during DNA transcription, to elucidate xeno-nucleic acids with distinct scaffolds and unconventional base pairs, and to use TFs as competitors of oncogene-engaged promoters. Overall, because of their potential for high-throughput design and their favorable pharmacodynamic and pharmacokinetic properties, DNA origami can be a novel armory for TF-related drug design. Last, we discuss future trends in the field, such as RNA origami and innovative DNA origami-based therapeutic delivery approaches.

DNA-Based Gold Nanoparticle Assemblies: From Structure Constructions to Sensing Applications

Gold nanoparticles (Au NPs) have become one of the building blocks for superior assembly and device fabrication due to the intrinsic, tunable physical properties of nanoparticles. With the development of DNA nanotechnology, gold nanoparticles are organized in a highly precise and controllable way under the mediation of DNA, achieving programmability and specificity unmatched by other ligands. The successful construction of abundant gold nanoparticle assembly structures has also given rise to the fabrication of a wide range of sensors, which has greatly contributed to the development of the sensing field. In this review, we focus on the progress in the DNA-mediated assembly of Au NPs and their application in sensing in the past five years. Firstly, we highlight the strategies used for the orderly organization of Au NPs with DNA. Then, we describe the DNA-based assembly of Au NPs for sensing applications and representative research therein. Finally, we summarize the advantages of DNA nanotechnology in assembling complex Au NPs and outline the challenges and limitations in constructing complex gold nanoparticle assembly structures with tailored functionalities.

Accessible hotspots for single-protein SERS in DNA-origami assembled gold nanorod dimers with tip-to-tip alignment

The label-free identification of individual proteins from liquid samples by surface-enhanced Raman scattering (SERS) spectroscopy is a highly desirable goal in biomedical diagnostics. However, the small Raman scattering cross-section of most (bio-)molecules requires a means to strongly amplify their Raman signal for successful measurement, especially for single molecules. This amplification can be achieved in a plasmonic hotspot that forms between two adjacent gold nanospheres. However, the small (≈1-2 nm) gaps typically required for single-molecule measurements are not accessible for most proteins. A useful strategy would thus involve dimer structures with gaps large enough to accommodate single proteins, whilst providing sufficient field enhancement for single-molecule SERS. Here, we report on using a DNA origami scaffold for tip-to-tip alignment of gold nanorods with an average gap size of 8 nm. The gaps are accessible to streptavidin and thrombin, which are captured at the plasmonic hotspot by specific anchoring sites on the origami template. The field enhancement achieved for the nanorod dimers is sufficient for single-protein SERS spectroscopy with sub-second integration times. This design for SERS probes composed of DNA origami with accessible hotspots promotes future use for single-molecule biodiagnostics in the near-infrared range.