Polyadenine-Modulated DNA Conformation Monitored by Surface-Enhanced Raman Scattering (SERS) on Multibranched Gold Nanoparticles and Its Sensing Application

Surface-enhanced Raman scattering sensing for detection and mapping of key cellular biomarkers

Cellular biomarkers mainly contain proteins, nucleic acids, glycans and many small molecules including small biomolecule metabolites, reactive oxygen species and other cellular chemical entities. The detection and mapping of the key cellular biomarkers can effectively help us to understand important cellular mechanisms associated with physiological and pathological processes, which greatly promote the development of clinical diagnosis and disease treatment. Surface-enhanced Raman scattering (SERS) possesses high sensitivity and is free from the influence of strong self-fluorescence in living systems as well as the photobleaching of the dyes. It exhibits rich and narrow chemical fingerprint spectra for multiplexed detection, and has become a powerful tool to detect and map cellular biomarkers. In this review, we present an overview of recent advances in the detection and mapping of different classes of cellular biomarkers based on SERS sensing. These advances fully confirm that the SERS-based sensors and sensing methods have great potential for the exploration of biological mechanisms and clinical applications. Additionally, we also discuss the limitations of present research and the future developments of the SERS technology in this field.

Nucleotide detection mechanism and comparison based on low-dimensional materials: A review

The recent pandemic has led to the fabrication of new nucleic acid sensors that can detect infinitesimal limits immediately and effectively. Therefore, various techniques have been demonstrated using low-dimensional materials that exhibit ultrahigh detection and accuracy. Numerous detection approaches have been reported, and new methods for impulse sensing are being explored. All ongoing research converges at one unique point, that is, an impetus: the enhanced limit of detection of sensors. There are several reviews on the detection of viruses and other proteins related to disease control point of care; however, to the best of our knowledge, none summarizes the various nucleotide sensors and describes their limits of detection and mechanisms. To understand the far-reaching impact of this discipline, we briefly discussed conventional and nanomaterial-based sensors, and then proposed the feature prospects of these devices. Two types of sensing mechanisms were further divided into their sub-branches: polymerase chain reaction and photospectrometric-based sensors. The nanomaterial-based sensor was further subdivided into optical and electrical sensors. The optical sensors included fluorescence (FL), surface plasmon resonance (SPR), colorimetric, and surface-enhanced Raman scattering (SERS), while electrical sensors included electrochemical luminescence (ECL), microfluidic chip, and field-effect transistor (FET). A synopsis of sensing materials, mechanisms, detection limits, and ranges has been provided. The sensing mechanism and materials used were discussed for each category in terms of length, collectively forming a fusing platform to highlight the ultrahigh detection technique of nucleotide sensors. We discussed potential trends in improving the fabrication of nucleotide nanosensors based on low-dimensional materials. In this area, particular aspects, including sensitivity, detection mechanism, stability, and challenges, were addressed. The optimization of the sensing performance and selection of the best sensor were concluded. Recent trends in the atomic-scale simulation of the development of Deoxyribonucleic acid (DNA) sensors using 2D materials were highlighted. A critical overview of the challenges and opportunities of deoxyribonucleic acid sensors was explored, and progress made in deoxyribonucleic acid detection over the past decade with a family of deoxyribonucleic acid sensors was described. Areas in which further research is needed were included in the future scope.

Gold Nanostar@Polyaniline Theranostic Agent with High Photothermal Conversion Efficiency for Photoacoustic Imaging-Guided Anticancer Phototherapy at a Low Dosage

Due to the strong and tunable photothermal effect, metallic nanoparticles are of enormous interest in light-activated biomedical applications, such as photoacoustic imaging (PAI) and photothermal therapy (PTT). However, the photothermal conversion efficiency (PCE) of existing metallic photothermal agents is still unsatisfactory. Herein, we develop an efficient photothermal theranostic agent based on a gold nanostar@polyaniline core-shell nanocomposite with high PCE for PAI-guided PTT at a low dosage. After optimizing the relative composition of polyaniline (PANI) and gold nanostars (AuNSs), this nanocomposite eventually empowers an outstanding PCE of up to 78.6%, which is much better than AuNSs or PANI alone and most of the existing photothermal theranostic agents. Besides, the nanocomposite can act as a targeted probe for tumors by hyaluronic acid (HA) modification without compromising the photothermal performance. The obtained nanoprobes named AuNSPHs exhibit promising biocompatibility and great performance of PAI-guided PTT to treat triple-negative breast cancer both in vitro and in vivo. More importantly, a single injection of AuNSPHs significantly suppresses tumor growth with a low dosage of Au (0.095 mg/kg), which is attributed to the high PCE of AuNSPHs. Taking advantage of the exhilarating photothermal conversion ability, this theranostic agent can safely potentiate the antitumor therapeutic efficacy of laser-induced ablation and holds great potential for future medical applications.

Gold Nanoparticles as Antimicrobial Agents: A Mini-Review

Metal nanoparticles, such as gold nanoparticles, have abundant unusual chemical and physical properties owing to the effects of their quantum size and their large surface area, in comparison with other metal atoms. Gold nanoparticles (AuNPs), in particular, are becoming increasingly popular due to their biocompatibility, multifunctional and aqueous solubility. Many scientific reports described the important antimicrobial properties possessed by the gold nanoparticles. Therefore, the present mini-review summarizes an overview of gold nanoparticles as broad spectrum antimicrobial agents for biomedical applications.

Surface-enhanced Raman scattering-based immunoassay for severe acute respiratory syndrome coronavirus 2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected humans worldwide for over a year now. Although various tests have been developed for the detection of SARS-CoV-2, advanced sensing methods are required for the diagnosis, screening, and surveillance of coronavirus disease 2019 (COVID-19). Here, we report a surface-enhanced Raman scattering (SERS)-based immunoassay involving an antibody pair, SERS-active hollow Au nanoparticles (NPs), and magnetic beads for the detection of SARS-CoV-2. The selected antibody pair against the SARS-CoV-2 antigen, along with the magnetic beads, facilitates the accurate direct detection of the virus. The hollow Au NPs exhibit strong, reproducible SERS signals, allowing sensitive quantitative detection of SARS-CoV-2. This assay had detection limits of 2.56 fg/mL for the SARS-CoV-2 antigen and 3.4 plaque-forming units/mL for the SARS-CoV-2 lysates. Furthermore, it facilitated the identification of SARS-CoV-2 in human nasopharyngeal aspirates and diagnosis of COVID-19 within 30 min using a portable Raman device. Thus, this assay can be potentially used for the diagnosis and prevention of COVID-19.

Application of Gold Nanoparticle-Based Materials in Cancer Therapy and Diagnostics

Several metal nanoparticles have been developed for medical application. While all have their benefits, gold nanoparticles (AuNPs) are ideal in cancer therapy and diagnosis as they are chemically inert and minimally toxic. Several studies have shown the potential of AuNPs in the therapeutic field, as photosensitizing agents in sonochemical and photothermal therapy and as drug delivery, as well as in diagnostics and theranostics. Although there is a significant number of reviews on the application of AuNPs in cancer medicine, there is no comprehensive review on their application both in therapy and diagnostics. Therefore, considering the high number of studies on AuNPs’ applications, this review summarizes data on the application of AuNPs in cancer therapy and diagnostics. In addition, we looked at the influence of AuNPs’ shape and size on their biological properties. We also present the potential use of hybrid materials based on AuNPs in sonochemical and photothermal therapy and the possibility of their use in diagnostics. Despite their potential, the use of AuNPs and derivatives in cancer medicine still has some limitations. In this review, we provide an overview of the biological, physicochemical, and legal constraints on using AuNPs in cancer medicine.

Direct Quantification of Damaged Nucleotides in Oligonucleotides Using an Aerolysin Single Molecule Interface

DNA lesions such as metholcytosine(mC), 8-OXO-guanine (OG), inosine (I), etc. could cause genetic diseases. Identification of the varieties of lesion bases are usually beyond the capability of conventional DNA sequencing which is mainly designed to discriminate four bases only. Therefore, lesion detection remains a challenge due to massive varieties and less distinguishable readouts for structural variations at the molecular level. Moreover, standard amplification and labeling hardly work in DNA lesion detection. Herein, we designed a single molecule interface from the mutant aerolysin (K238Q), whose sensing region shows high compatibility to capture and then directly convert a minor lesion into distinguishable electrochemical readouts. Compared with previous single molecule sensing interfaces, the temporal resolution of the K238Q aerolysin nanopore is enhanced by two orders, which has the best sensing performance in all reported aerolysin nanopores. In this work, the novel K238Q could discriminate directly at least three types of lesions (mC, OG, I) without labeling and quantify modification sites under the mixed heterocomposition conditions of the oligonucleotide. Such a nanopore electrochemistry approach could be further applied to diagnose genetic diseases at high sensitivity.

Surface Enhanced Raman Spectroscopy for DNA Biosensors-How Far Are We?

A sensitive and accurate identification of specific DNA fragments (usually containing a mutation) can influence clinical decisions. Standard methods routinely used for this type of detection are PCR (Polymerase Chain Reaction, and its modifications), and, less commonly, NGS (Next Generation Sequencing). However, these methods are quite complicated, requiring time-consuming, multi-stage sample preparation, and specially trained staff. Usually, it takes weeks for patients to obtain their results. Therefore, different DNA sensors are being intensively developed by many groups. One technique often used to obtain an analytical signal from DNA sensors is Raman spectroscopy. Its modification, surface-enhanced Raman spectroscopy (SERS), is especially useful for practical analytical applications due to its extra low limit of detection. SERS takes advantage of the strong increase in the efficiency of Raman signal generation caused by a local electric field enhancement near plasmonic (typically gold and silver) nanostructures. In this condensed review, we describe the most important types of SERS-based nanosensors for genetic studies and comment on their potential for becoming diagnostic tools.

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

Fabrication of high-performance surface-enhanced Raman scattering (SERS) biosensors relies on the coordination of SERS substrates and sensing strategies. Herein, a SERS active AuCu alloy with a starfish-like structure is prepared using a surfactant-free method. By covering the anisotropic AuCu alloy with graphene oxide (GO), enhanced SERS activity is obtained owing to graphene-enhanced Raman scattering and assembly of Raman reporters. Besides, stability of SERS is promoted based on the protection of GO to the AuCu alloy. Meanwhile, it is found that SERS activity of AuCu/GO can be regulated by DNA. The regulation is sequence and length dual-dependent, and short polyT reveals the strongest ability of enhancing the SERS activity. Relying on this phenomenon, a SERS biosensor is designed to quantify apurinic/apyrimidinic endonuclease 1 (APE1). Because of the APE1-induced cycling amplification, the biosensor is able to detect APE1 sensitively and selectively. In addition, APE1 in human serum is analyzed by the SERS biosensor and enzyme-linked immunosorbent assay (ELISA). The data from the SERS method are superior to that from ELISA, indicating great potential of this biosensor in clinical applications.

Fluorescent Silicon Nanorods-Based Nanotheranostic Agents for Multimodal Imaging-Guided Photothermal Therapy

The utilization of diagnosis to guide/aid therapy procedures has shown great prospects in the era of personalized medicine along with the recognition of tumor heterogeneity and complexity. Herein, a kind of multifunctional silicon-based nanostructure, i.e., gold nanoparticles-decorated fluorescent silicon nanorods (Au@SiNRs), is fabricated and exploited for tumor-targeted multimodal imaging-guided photothermal therapy. In particular, the prepared Au@SiNRs feature high photothermal conversion efficiency (~ 43.9%) and strong photothermal stability (photothermal performance stays constant after five-cycle NIR laser irradiation), making them high-performance agents for simultaneously photoacoustic and infrared thermal imaging. The Au@SiNRs are readily modified with targeting peptide ligands, enabling an enhanced tumor accumulation with a high value of ~ 8.74% ID g-1. Taking advantages of these unique merits, the Au@SiNRs are superbly suitable for specifically ablating tumors in vivo without appreciable toxicity under the guidance of multimodal imaging. Typically, all the mice treated with the Au@SiNRs remain alive, and no distinct tumor recurrence is observed during 60-day investigation.

Robust and Universal SERS Sensing Platform for Multiplexed Detection of Alzheimer's Disease Core Biomarkers Using PAapt-AuNPs Conjugates

Multiplexed detection of Alzheimer's disease (AD) core biomarkers is of great significance to early diagnosis and personalized treatment of AD patients. Herein, we construct a robust and convenient surface-enhanced Raman scattering (SERS) biosensing platform for simultaneous detection of Aβ(1-42) oligomers and Tau protein using different Raman dye-coded polyA aptamer-AuNPs (PAapt-AuNPs) conjugates. This strategy relies on the specific protein-aptamer binding-mediated aggregation of AuNPs and the concomitant plasmonic coupling effect that allow us to "turn on" SERS detection of protein biomarkers. To the best of our knowledge, this is the first work in which PAapt-AuNPs conjugates are used for probing protein biomarkers, which may be enlightening for the exploitation of more extensive biological applications of aptamer-AuNPs conjugates. The results reveal that the present strategy displays excellent analytical performance. Moreover, the applicability of this strategy is demonstrated in the artificial cerebrospinal fluid (CSF) samples with satisfactory results. Except for the prominent sensitivity and practicality, our strategy offers additional advantages. The preparation of nanoconjugates is handy and easily repeated, and the synthesis cost is greatly reduced because it dispenses with the complicated labeling process. Moreover, the assay can be accomplished in 15 min, allowing rapid detection of protein biomarkers. Furthermore, simultaneous detection of Tau protein and Aβ(1-42) oligomers is realized by employing different Raman dye-coded nanoconjugates, which is valuable for accurately predicting and diagnosing AD disease. Thus, our PAapt-AuNPs conjugate-based multiplexed SERS strategy indeed creates a useful and universal platform for detecting multiple protein biomarkers and related clinical diagnosis.

Polyadenine-mediated Immobilization of Aptamers on a Gold Substrate for the Direct Detection of Bacterial Pathogens

Nucleic acid aptamers have been widely used as synthetic probes for bioanalytical applications. Herein, we carried out a detailed study on the immobilization of a series of aptamers ranging from 37 to 88 bases, which are specific to either Escherichia coli (E. coli) or Staphylococcus aureus (S. aureus), on a planar gold substrate via a polyadenine-mediated immobilization method. The resultant surfaces were characterized by both surface plasmon resonance spectroscopy (SPR) and X-ray photoelectron spectroscopy. The results clearly show that the aptamer solution at a lower ionic strength gives rise to a higher lateral density of the aptamer when compared to that at a higher ionic strength. The SPR aptasensors are then employed for detecting their corresponding bacteria (i.e., E. coli and S. aureus, respectively). The data indicate that the SPR aptasensor with a higher density of aptamer exhibits a better capture of target bacteria.

Advances in DNA/RNA detection using nanotechnology

Specific nucleic acid detection in vitro or in vivo has become increasingly important in the discovery of genetic diseases, diagnosing pathogen infection and monitoring disease treatment. One challenge, however, is that the amount of target nucleic acid in specimens is limited. Furthermore, direct sensing methods are also unable to provide sufficient sensitivity and specificity. Fortunately, due to advances in nanotechnology and nanomaterials, nanotechnology-based bioassays have emerged as powerful and promising approaches providing ultra-high sensitivity and specificity in nucleic acid detection. This chapter presents an overview of strategies used in the development and integration of nanotechnology for nucleic acid detection, including optical and electrical detection methods, and nucleic acid assistant recycling amplification strategies. Recent 5 years representative examples are reviewed to demonstrate the proof-of-concept with promising applications for DNA/RNA detection and the underlying mechanism for detection of DNA/RNA with the higher sensitivity and selectivity. Furthermore, a brief discussion of common unresolved issues and future trends in this field is provided both from fundamental and practical point of view.

Stimuli-Responsive DNA-Switchable Biointerfaces

Switchable interfaces, also known as smart interfaces, can alter their macroscopic properties in response to external stimuli. Compared to an artificial switchable interface, DNA-based switchable biointerfaces have high diversity, uniformity, reproducibility, and functionality and are easily designed and developed with atomic precision because the sequence of the DNA strand strictly governs the structural and active properties of its assembly. Moreover, various structures such as double strands based on the Watson-Crick base-pairing rule, G-quadruplexes, i-Motifs, triplexes, and parallel-stranded duplexes exist between or among DNA strands to enrich the structures of DNA biointerfaces. In this article, the design, stimulus responses, and applications of switchable DNA biointerfaces were discussed in terms of single-switch, dual-response, and sequential operation. The applications related to sensing, imaging, delivery, logic gates, and nanomechines were introduced in terms of the design and construction of DNA biointerfaces. Future directions and challenges were also outlined for this rapidly emerging field.

DNA Nanotechnology-Enabled Interfacial Engineering for Biosensor Development

Biosensors represent biomimetic analytical tools for addressing increasing needs in medical diagnosis, environmental monitoring, security, and biodefense. Nevertheless, widespread real-world applications of biosensors remain challenging due to limitations of performance, including sensitivity, specificity, speed, and reproducibility. In this review, we present a DNA nanotechnology-enabled interfacial engineering approach for improving the performance of biosensors. We first introduce the main challenges of the biosensing interfaces, especially under the context of controlling the DNA interfacial assembly. We then summarize recent progress in DNA nanotechnology and efforts to harness DNA nanostructures to engineer various biological interfaces, with a particular focus on the use of framework nucleic acids. We also discuss the implementation of biosensors to detect physiologically relevant nucleic acids, proteins, small molecules, ions, and other biomarkers. This review highlights promising applications of DNA nanotechnology in interfacial engineering for biosensors and related areas.

Signal Amplified Gold Nanoparticles for Cancer Diagnosis on Paper-Based Analytical Devices

In this work, we report a highly sensitive colorimetric sensing strategy for cancer biomarker diagnosis using gold nanoparticles (AuNPs) labeled with biotinylated poly(adenine) ssDNA sequences and streptavidin-horseradish peroxidase for enzymatic signal enhancement. By adopting this DNA-AuNP nanoconjugate sensing strategy, we were able to eliminate the complicated and costly thiol-binding process typically used to modify AuNP surfaces with ssDNA. In addition, different antibodies can be introduced to the AuNP surfaced via electrostatic interactions to provide highly specific recognition sites for biomolecular sensing. Moreover, multiple, simultaneous tests can be rapidly performed with low sample consumption by incorporating these surface-modified AuNPs into a paper-based analytical device that can be read using just a smartphone. As a result of these innovations, we were able to achieve a detection limit of 10 pg/mL for a prostate specific antigen in a test that could be completed in as little as 15 min. These results suggest that the proposed paper platform possesses the capability for sensitive, high-throughput, and on-site prognosis in resource-limited settings.