Surface science of DNA adsorption onto citrate-capped gold nanoparticles

Applications of DNA functionalized gold nanozymes in biosensing

In recent years, nanozymes have emerged as highly potential substitutes, surpassing the performance of natural enzymes. Among them, gold nanoparticles (AuNPs) and their metal hybrids have become a hot topic in nanozyme research due to their facile synthesis, easy surface modification, high stability, and excellent enzymatic activity. The integration of DNA with AuNPs, by precisely controlling the assembly, arrangement, and functionalization of nanoparticles, greatly facilitates the development of highly sensitive and selective biosensors. This review comprehensively elaborates on three core strategies for the combination of DNA with AuNPs, and deeply analyzes two widely applied enzyme activities in the field of sensing technology and the catalytic principles behind them. On this basis, we systematically summarize various methods for regulating the activity of gold nanozymes by DNA. Following that, we comprehensively review the latest research trends of DNA-Au nanozymes in the field of biosensing, with a particular focus on several crucial application areas such as food safety, environmental monitoring, and disease diagnosis. In the conclusion of the article, we not only discuss the main challenges faced in current research but also look forward to potential future research directions.

Gold Nanoprobes for Robust Colorimetric Detection of Nucleic Acid Sequences Related to Disease Diagnostics

Gold nanoparticles (AuNPs) are highly attractive for applications in the field of biosensing, particularly for colorimetric nucleic acid detection. Their unique optical properties, which are highly sensitive to changes in their environment, make them ideal candidates for developing simple, rapid, and cost-effective assays. When functionalized with oligonucleotides (Au-nanoprobes), they can undergo aggregation or dispersion in the presence of complementary sequences, leading to distinct color changes that serve as a visual signal for detection. Aggregation-based assays offer significant advantages over other homogeneous assays, such as fluorescence-based methods, namely, label-free protocols, rapid interactions in homogeneous solutions, and detection by the naked eye or using low-cost instruments. Despite promising results, the application of Au-nanoprobe-based colorimetric assays in complex biological matrices faces several challenges. The most significant are related to the colloidal stability and oligonucleotide functionalization of the Au-nanoprobes but also to the mode of detection. The type of functionalization method, type of spacer, the oligo-AuNPs ratio, changes in pH, temperature, or ionic strength influence the Au-nanoprobe colloidal stability and thus the performance of the assay. This review elucidates characteristics of the Au-nanoprobes that are determined for colorimetric gold nanoparticles (AuNPs)-based nucleic acid detection, and how they influence the sensitivity and specificity of the colorimetric assay. These characteristics of the assay are fundamental to developing low-cost, robust biomedical sensors that perform effectively in biological fluids.

A comprehensive adsorption and desorption study on the interaction of DNA oligonucleotides with TiO2 nanolayers

The utilization of TiO2 nanolayers that possess excellent biocompatibility and physical properties in DNA sensing and sequencing remains largely to be explored. To examine their applicability in gene sequencing, a comprehensive study on the interaction of DNA oligonucleotides with TiO2 nanolayers was performed through adsorption and desorption experiments. TiO2 nanolayers with 10 nm thickness were fabricated via magnetron sputtering onto a 6-inch silicon wafer. A simple chip block method, validated via quartz crystal microbalance experiments with dissipation monitoring (QCM-D), was proposed to study the adsorption behaviors and interaction mechanisms under a variety of critical influencing factors, including DNA concentration, length, and type, adsorption time, pH, and metal ions. It is determined that the adsorption takes 2 h to reach saturation in the MES solution and the adsorption capacity is significantly enhanced by lowering the pH due to the isoelectric point being pH = 6 for TiO2. The adsorption percentages of nucleobases are largely similar in the MES solution while following 5T = 5G > 5C > 5A in HEPES buffer for an adsorption duration of 2.5 h. Through pre-adsorption experiments, it is deduced that DNA oligonucleotides are horizontally adsorbed on the nanolayer. This further demonstrates that mono-, di-, and tri-valent metal ions promote the adsorption, whereas Zn2+ has strong adsorption by inducing DNA condensation. Based on the desorption experiments, it is revealed that electrostatic force dominates the adsorption over van der Waals force and hydrogen bonds. The phosphate group is the main functional group for adsorption, and the adsorption strength increases with the length of the oligonucleotide. This study provides comprehensive data on the adsorption of DNA oligonucleotides onto TiO2 nanolayers and clarifies the interaction mechanisms therein, which will be valuable for applications of TiO2 in DNA-related applications.

Investigation of interactions between biological thiols and gold nanoparticles by capillary electrophoresis with laser-induced fluorescence

Biological thiols spontaneously form a stable Au-S dative bond with gold nanoparticles (AuNP) that might be used for their selective extraction and enrichment in biological samples. In this work, interactions of selected biological thiols (glutathione, cysteine, homocysteine [Hcys], cysteamine [CA], and N-acetylcysteine) with AuNP stabilized by different capping agents (citrate, Tween 20, Brij 35, CTAB, SDS) were investigated by UV-Vis spectroscopy and capillary electrophoresis with laser-induced fluorescence. Spectrophotometric measurements showed aggregation of Hcys and CA with AuNP. In contrast, it was confirmed by CE-LIF that biological thiols were adsorbed to all types of AuNP. Citrate-capped AuNP were selected for AuNP-based extraction of biological thiols from exhaled breath condensate (EBC). Dithiothreitol was utilized for desorption of biological thiols from the AuNP surface, which was followed by derivatization with eosin-5-maleimide and CE-LIF analysis. AuNP-based extraction increased the sensitivity of CE-LIF analysis; however, further optimization of methodology is necessary for accurate quantification of biological thiols in EBC.

Ultrasensitive Dual ELONA/SERS-RPA Multiplex Diagnosis of Antimicrobial Resistance

Antimicrobial resistance (AMR) is a significant global health threat concern, necessitating healthcare practitioners to accurately prescribe the most effective antimicrobial agents with correct doses to combat resistant infections. This is necessary to improve the therapeutic outcomes for patients and prevent further increase in AMR. Consequently, there is an urgent need to implement rapid and sensitive clinical diagnostic methods to identify resistant pathogenic strains and monitor the efficacy of antimicrobials. In this study, we report a novel proof-of-concept magnetic scaffold-recombinase polymerase amplification (RPA) technique, coupled with an enzyme-linked oligonucleotide assay (ELONA) and surface-enhanced Raman scattering (SERS) detection, aimed at selectively amplifying and detecting the DNA signature of three resistant carbapenemase genes, VIM, KPC, and IMP. To achieve this, streptavidin-coated magnetic beads were functionalized with biotin-modified forward primers. RPA was conducted on the surface of the beads, resulting in an immobilized duplex amplicon featuring a single overhang tail specific to each gene. These tails were subsequently hybridized with recognition HRP probes conjugated to a complementary single-stranded oligonucleotide and detected colorimetrically. Additionally, they underwent hybridization with similar selective SERS probes and were measured using a handheld Raman spectrometer. The resulting quantification limits were at subpicomolar level for both assays, allowing the potential for early diagnosis. Moreover, we demonstrated the platform capability to conduct a multiplex RPA-SERS detection of the three genes in a single tube. Compared to similar approaches like PCR, RPA offers advantages of speed, affordability, and isothermal operation at 37 °C, eliminating the need for a thermal cycler. The whole assay was completed within <2 h. Therefore, this novel magnetic scaffold ELONA/SERS-RPA platform, for DNA detection, demonstrated excellent capability for the rapid monitoring of AMR in point-of-care applications, in terms of sensitivity, portability, and speed of analysis.

Aptamer and Electrochemical Aptasensor towards Selenate Ions (SeO42-)

Selenium is an essential inorganic compound in human and animal nutrition, involved in the proper functioning of the body. As a micronutrient, it actively contributes to the regulation of various metabolic activities, i.e., thyroid hormone, and protection against oxidative stress. However, Se exhibits a narrow concentration window between having a positive effect and exerting a toxic effect. In higher doses, it negatively affects living organisms and causes DNA damage through the formation of free radicals. Increased reactivity of Se anions can also disrupt the integrity and function of DNA-repairing proteins. As the permissible concentration of Se in drinking water is 10 µg/L, it is vital to develop sensitive and robust methods of Se detection in aqueous samples. In this study, for the first time, we proposed a selective aptamer for selenate ion detection, chosen following the SELEX process, and its application in the construction of an electrochemical aptasensor towards SeO42- ions. Measurement conditions such as the used redox marker and pH value of the measurement solution were chosen. The proposed aptasensor is characterized by good selectivity and an LOD of 1 nM. Conditions for biosensor regeneration and storage were also investigated in this research.

Aptamer-conjugated gold nanoparticles for portable, ultrasensitive naked-eye detection of C-reactive protein based on the Tyndall effect

BACKGROUND

C-reactive protein (CRP) represents an early clinical biomarker that indicates the presence of inflammatory or infectious conditions in the human body. Today's procedures approved by the Food and Drug Administration (FDA) imply expensive equipment and highly trained personnel to perform the test. Therefore, a new diagnostic method with high detection efficiency and less cost is urgently needed for delivering rapid and timely results in point-of-care (POC) service.

RESULTS

Herein, we propose a new, equipment-free, and portable sensing method for the future POC detection of CRP based on the Tyndall effect (TE). In our study, aptamer-conjugated citrate-stabilized gold nanoparticles (apta-AuNPs) are exploited as the sensing platform. The apta-AuNPs' interaction with CRP in a saline environment leads to their aggregation, thus enhancing the scattering of light when the solution is exposed to a 640 nm pointer laser line. Firstly, the enhancement of the scattering light as a function of increasing concentration of CRP in solution is measured spectroscopically using a typical 90-degree angle spectrofluorometer and then the measurements are compared to the classic colorimetric detection using an UV-Vis spectrophotometer. Finally, to achieve high portability and accessibility, we demonstrate that the measurement of CRP concentration can be performed with similar accuracy but in a more direct and inexpensive way by using a laser pointer pen as the excitation source and a camera of a low-budget smartphone as a quantitative reader instead of most expensive spectrofluorometer.

SIGNIFICANCE

The portable TE-based assay exhibits a wide linear dynamic range (1-60 μg/mL) for the detection of CRP with a limit of detection (LOD) of 92 ng/mL The proposed method is capable to integrate both standard and high-sensitivity CRP analysis in a single procedure with increased sensitivity and prompt delivery of analysis results. Moreover, the sensing procedure is significantly faster than the FDA approved ones with a detection time of only 10 min. Finally, as a proof-of-concept, our findings demonstrate excellent recovery for CRP detection in spiked and diluted urine samples, highlighting the strong potential of this sensing method for POC applications.

Liposomal drug delivery strategies to eradicate bacterial biofilms: Challenges, recent advances, and future perspectives

Typical antibiotic treatments are often ineffectual against biofilm-related infections since bacteria residing within biofilms have developed various mechanisms to resist antibiotics. To overcome these limitations, antimicrobial-loaded liposomal nanoparticles are a promising anti-biofilm strategy as they have demonstrated improved antibiotic delivery and eradication of bacteria residing in biofilms. Antibiotic-loaded liposomal nanoparticles revealed remarkably higher antibacterial and anti-biofilm activities than free drugs in experimental settings. Moreover, liposomal nanoparticles can be used efficaciously for the combinational delivery of antibiotics and other antimicrobial compounds/peptide which facilitate, for instance, significant breakdown of the biofilm matrix, increased bacterial elimination from biofilms and depletion of metabolic activity of various pathogens. Drug-loaded liposomes have mitigated recurrent infections and are considered a promising tool to address challenges associated to antibiotic resistance. Furthermore, it has been demonstrated that surface charge and polyethylene glycol modification of liposomes have a notable impact on their antibacterial biofilm activity. Future investigations should tackle the persistent hurdles associated with development of safe and effective liposomes for clinical application and investigate novel antibacterial treatments, including CRISPR-Cas gene editing, natural compounds, phages, and nano-mediated approaches. Herein, we emphasize the significance of liposomes in inhibition and eradication of various bacterial biofilms, their challenges, recent advances, and future perspectives.

The Development of Aptamer-Based Gold Nanoparticle Lateral Flow Test Strips for the Detection of SARS-CoV-2 S Proteins on the Surface of Cold-Chain Food Packaging

The COVID-19 pandemic over recent years has shown a great need for the rapid, low-cost, and on-site detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, an aptamer-based colloidal gold nanoparticle lateral flow test strip was well developed to realize the visual detection of wild-type SARS-CoV-2 spike proteins (SPs) and multiple variants. Under the optimal reaction conditions, a low detection limit of SARS-CoV-2 S proteins of 0.68 nM was acquired, and the actual detection recovery was 83.3% to 108.8% for real-world samples. This suggests a potential tool for the prompt detection of SARS-CoV-2 with good sensitivity and accuracy, and a new method for the development of alternative antibody test strips for the detection of other viral targets.

Cellular Alterations Due to Direct and Indirect Interaction of Nanomaterials with Nucleic Acids

Deoxyribonucleic acid (DNA) represents the main reservoir of genetic information in the cells, which is why it is protected in the nucleus. Entry into the nucleus is, in general, difficult, as the nuclear membrane is a selective barrier to molecules longer than 40 kDa. However, in some cases, the size of certain nanoparticles (NPs) allows their internalization into the nucleus, thus causing a direct effect on the DNA structure. NPs can also induce indirect effects on DNA through reactive oxygen species (ROS) generation. In this context, nanomaterials are emerging as a disruptive tool for the development of novel therapies in a broad range of biomedical fields; although their effect on cell viability is commonly studied, further interactions with DNA or indirect alterations triggered by the internalization of these materials are not always clarified, since the small size of these materials makes them perfectly suitable for interaction with subcellular structures, such as the nucleus. In this context, and using as a reference the predicted interactions presented in a computational model, we describe and discuss the observed direct and indirect effects of the implicated nanomaterials on DNA.

Selection and characterization of ssDNA aptamer targeting Macrobrachium rosenbergii nodavirus capsid protein: A potential capture agent in gold-nanoparticle-based aptasensor for viral protein detection

The giant freshwater prawn holds a significant position as a valuable crustacean species cultivated in the aquaculture industry, particularly well-known and demanded among the Southeast Asian countries. Aquaculture production of this species has been impacted by Macrobrachium rosenbergii nodavirus (MrNV) infection, which particularly affects the larvae and post-larvae stages of the prawn. The infection has been recorded to cause mortality rates of up to 100% among the affected prawns. A simple, fast, and easy to deploy on-site detection or diagnostic method is crucial for early detection of MrNV to control the disease outbreak. In the present study, novel single-stranded DNA aptamers targeting the MrNV capsid protein were identified using the systematic evolution of ligands by exponential enrichment (SELEX) approach. The aptamer was then conjugated with the citrate-capped gold nanoparticles (AuNPs), and the sensitivity of this AuNP-based aptasensor for the detection of MrNV capsid protein was evaluated. Findings revealed that the aptamer candidate, APT-MrNV-CP-1 was enriched throughout the SELEX cycle 4, 9, and 12 with the sequence percentage of 1.76%, 9.09%, and 12.42%, respectively. The conjugation of APT-MrNV-CP-1 with citrate-capped AuNPs exhibited the highest sensitivity in detecting the MrNV capsid protein, where the presence of 62.5 nM of the viral capsid protein led to a significant agglomeration of the AuNPs. This study demonstrated the practicality of an AuNP-based aptasensor for disease diagnosis, particularly for detecting MrNV infection in giant freshwater prawns.

A comprehensive review of cancer therapies mediated by conjugated gold nanoparticles with nucleic acid

Nucleic acids provide a promising therapeutic platform by targeting various cell signaling pathways involved in cancer and genetic disorders. However, maintaining optimal stability during delivery limits their utility. Nucleic acid delivery vehicles are generally categorized into biological and synthetic carriers. Regardless of the efficiency of biological vectors, such as viral vectors, issues related to their immunogenicity and carcinogenesis are very important and vital for clinical applications. On the other hand, synthetic vectors such as lipids or polymers, have been widely used for nucleic acid delivery. Despite their transfection efficiency, low storage stability, targeting inefficiency, and tracking limitations are among the limitations of the clinical application of these vectors. In the past decades, gold nanoparticles with unique properties have been shown to be highly efficient mineral vectors for overcoming these obstacles. In this review, we focus on gold nanoparticle-nucleic acid combinations and highlight their use in the treatment of various types of cancers. Furthermore, by stating the biological applications of these structures, we will discuss their clinical applications.

Construction and bioanalytical applications of poly-adenine-mediated gold nanoparticle-based spherical nucleic acids

Owing to the versatile photophysical and chemical properties, spherical nucleic acids (SNAs) have been widely used in biosensing. However, traditional SNAs are formed by self-assembly of thiolated DNA on the surface of a gold nanoparticle (AuNP), where it is challenging to precisely control the orientation and surface density of DNA. As a new SNA, a polyadenine (polyA)-mediated SNA using the high binding affinity of consecutive adenines to AuNPs shows controllable surface density and configuration of DNA, which can be used to improve the performance of a biosensor. Herein, we first introduce the properties of polyA-mediated SNAs and fundamental principles regarding the polyA-AuNP interaction. Then, we provide an overview of current representative synthesis methods of polyA-mediated SNAs and their advantages and disadvantages. After that, we summarize the application of polyA-mediated SNAs in biosensing based on fluorescence and colorimetric methods, followed by discussion and an outlook of future challenges in this field.

Effect of DNA density immobilized on gold nanoparticles on nucleic acid detection

Gold nanoparticles (AuNPs) have been utilized as colorimetric biosensors, where target molecule-induced AuNP aggregation can be recognized by a colour change from red to blue. Particularly, single-stranded DNA (ssDNA)-immobilized AuNPs (ssDNA-AuNPs) have been applied to genetic diagnosis due to their rapid and sequence-specific aggregation properties. However, the effect of the density of immobilized ssDNA have not been investigated yet. In this study, we developed a method to control the amount of immobilized ssDNA by use of ethylene glycol, which is expected to control the ice crystal spacing in a freezing-thawing ssDNA-AuNP synthesis method. We also investigated the effect of the DNA density on the sensitivity of the target ssDNA detection, and found that the detection sensitivity was improved at lower DNA densities. To discuss the reason for the improved detection sensitivity, we modified the ssDNA-AuNPs with alkane thiol for better dispersion stability against salt. The results suggest that the DNA density, rather than the dispersion stability, has a significant impact on detection sensitivity.

Recent Advances in DNA Nanomaterials

Applications of DNA-containing nanomaterials (DNA-NMs) in science and technology are currently attracting increasing attention in the fields of medicine, environment, engineering, etc. Such objects have become important for various branches of science and industries due to their outstanding characteristics such as small size, high controllability, clustering actions, and strong permeability. For these reasons, DNA-NMs deserve a review with respect to their recent advancements. On the other hand, precise cluster control, targeted drug distribution in vivo, and cellular micro-nano operation remain as problems. This review summarizes the recent progress in DNA-NMs and their crossover and integration into multiple disciplines (including in vivo/in vitro, microcircles excisions, and plasmid oligomers). We hope that this review will motivate relevant practitioners to generate new research perspectives and boost the advancement of nanomanipulation.

DNA-directed assembly of nanomaterials and their biomedical applications

In the past decades, DNA has been widely used in the field of nanostructures due to its unique programmable properties. Besides being used to form its own diverse structures such as the assembly of DNA origami, DNA can also be used for the assembly of nanostructures with other materials. In this review, different strategies for the functionalization of DNA on nanoparticle surfaces are listed, and the roles of DNA in the assembly of nanostructures as well as the influencing factors are discussed. Finally, the biomedical applications of DNA-assembled nanostructures were summarized. This review provided new insight into the application of DNA in nanostructure assembly.

Role of Gemini Surfactants with Variable Spacers and SiO2 Nanoparticles in ct-DNA Compaction and Applications toward In Vitro/In Vivo Gene Delivery

Compaction of calf thymus DNA (ct-DNA) by two cationic gemini surfactants, 12-4-12 and 12-8-12, in the absence and presence of negatively charged SiO₂ nanoparticles (NPs) (∼100 nm) has been explored using various techniques. 12-8-12 having a longer hydrophobic spacer induces a greater extent of ct-DNA compaction than 12-4-12, which becomes more efficient with SiO₂ NPs. While 50% ct-DNA compaction in the presence of SiO₂ NPs occurs at ∼77 nM of 12-8-12 and ∼130 nM of 12-4-12, but a conventional counterpart surfactant, DTAB, does it at its concentration as high as ∼7 μM. Time-resolved fluorescence anisotropy measurements show changes in the rotational dynamics of a fluorescent probe, DAPI, and helix segments in the condensed DNA. Fluorescence lifetime data and ethidium bromide exclusion assays reveal the binding sites of surfactants to ct-DNA. 12-8-12 with SiO₂ NPs has shown the highest cell viability (≥90%) and least cell death in the human embryonic kidney (HEK) 293 cell lines in contrast to the cell viability of ≤80% for DTAB. These results show that 12-8-12 with SiO₂ NPs has the highest time and dose-dependent cytotoxicity compared to 12-8-12 and 12-4-12 in the murine breast cancer 4T1 cell line. Fluorescence microscopy and flow cytometry are performed for in vitro cellular uptake of YOYO-1-labeled ct-DNA with surfactants and SiO₂ NPs using 4T1 cells after 3 and 6 h incubations. The in vivo tumor accumulation studies are carried out using a real-time in vivo imaging system after intravenous injection of the samples into 4T1 tumor-bearing mice. 12-8-12 with SiO₂ has delivered the highest amount of ct-DNA in cells and tumors in a time-dependent manner. Thus, the application of a gemini surfactant with a hydrophobic spacer and SiO₂ NPs in compacting and delivering ct-DNA to the tumor is proven, warranting its further exploration in nucleic acid therapy for cancer treatment.

Rapid visual detection of Mycobacterium tuberculosis DNA using gold nanoparticles

Tuberculosis (TB) is one of the world's deadliest infections caused by Mycobacterium tuberculosis (MTB). Though curable, the disease goes undetected in early stages owing to the lack of rapid, simple, cost-effective, and sensitive detection methods. In this investigation, we describe a procedure which is superior, more sensitive, and easier to handle, as compared to the previously reported, nanoparticle-based visual colorimetric assays for rapid detection of TB DNA, after its PCR amplification. This assay employs plasmonic gold nanoparticles (GNP) as a colorimetric agent and ethanol to promote aggregation of GNPs, thereby specifically detecting the amplified MTB DNA. An unambiguous response was achieved within 3 min after adding the DNA amplicon to the reaction tube. This conclusion was supported by spectroscopic data. The assay is sensitive up to ∼340 femtomole levels of MTB DNA, which was amplified using 0.125 ng μL^-1 of the MTB DNA template. Thus, the technique developed here may be employed as a sensitive screening tool for early diagnosis of TB infection and is valuable for low-resource settings in remote areas, because of its simplicity. This ethanol-based visual TB DNA detection method is more sensitive, and fool-proof as compared to the commonly used salt-based colorimetric TB DNA assays, to the best of our knowledge.

DNA-Guided Metallization of Nanomaterials and Their Biomedical Applications

Precise control of the structure of metallic nanomaterials is critical for the advancement of nanobiotechnology. As DNA (deoxyribonucleic acid) can readily modify various moieties, such as sulfhydryl, carboxyl, and amino groups, using DNA as a directing ligand to modulate the morphology of nanomaterials is a promising strategy. In this review, we focus on the use of DNA as a template to control the morphology of metallic nanoparticles and their biomedical applications, discuss the use of DNA for the metallization of gold and silver, explore the factors that influence the process, and outline its biomedical applications. This review aims to provide valuable insights into the DNA-guided growth of nanomaterials. The challenges and future directions are also discussed.

DNA-Programmed Tuning of the Growth and Enzyme-Like Activity of a Bimetallic Nanozyme and Its Biosensing Applications

Nanozymes, which combine the merits of both nanomaterials and natural enzymes, have aroused tremendous attention as new representatives of artificial enzyme mimics. However, it still remains to be a great challenge to rationally engineer the morphologies and surface properties of nanostructures that lead to the desired enzyme-like activities. Here, we report a DNA-programming seed-growth strategy to mediate the growth of platinum nanoparticles (PtNPs) on gold bipyramids (AuBPs) for the synthesis of a bimetallic nanozyme. We find that the preparation of a bimetallic nanozyme is in a sequence-dependent manner, and the encoding of a polyT sequence allows the successful formation of bimetallic nanohybrids with greatly enhanced peroxidase-like activity. We further observe that the morphologies and optical properties of T15-mediated Au/Pt nanostructures (Au/T15/Pt) change over the reaction time, and the nanozymatic activity can be tuned by controlling the experimental conditions. As a concept application, Au/T15/Pt nanozymes are used to establish a simple, sensitive, and selective colorimetric assay for the determination of ascorbic acid (AA), alkaline phosphatase (ALP), and the inhibitor sodium vanadate (Na₃VO₄), demonstrating excellent analytical performance. This work provides a new avenue for the rational design of bimetallic nanozymes for biosensing applications.

Spatiotemporal Monitoring of Subcellular mRNAs In Situ via Polyadenine-Mediated Dual-Color Sticky Flares

Spatiotemporal monitoring of multiple low-abundance messenger RNAs (mRNAs) is vitally important for the diagnosis and pathologic analysis of cancer. However, it remains a clinical challenge to monitor and track multiple mRNAs location simultaneously in situ at subcellular level with high efficiency. Herein, we proposed polyA-mediated dual-color sticky flares for simultaneous imaging of two kinds of intracellular mRNA biomarkers. Two kinds of fluorescent DNA specific for GalNac-T mRNA and c-Myc mRNA were functionalized onto gold nanoparticles (AuNPs) through efficient polyadenine (polyA) attachment. By tuning polyA length, the lateral spacing and densities of DNA on AuNPs could be precisely engineered. Compared to the traditional thio-DNA-modified nanoprobes, the uniformity, detection sensitivity, and response kinetics of sticky flares were greatly improved, which enables live-cell imaging of mRNAs with enhanced efficiency. With a sticky-end design, the fluorescent DNA could dynamically trace mRNAs after binding with target mRNAs, which realized spatiotemporal monitoring of subcellular mRNAs in situ. Compared to one target mRNA imaging mode, the multiple target imaging mode allows more accurate diagnosis of cancer. Furthermore, the proposed polyA-mediated dual-color sticky flares exhibit excellent cell entry efficiency and low cytotoxicity with a low-cost and simple assembling process, which provide a pivotal tool for multiple targets imaging in living cells.

Ethanol and NaCl-Induced Gold Nanoparticle Aggregation Toxicity toward DNA Investigated with a DNA/GCE Biosensor

Engineered nanomaterials are becoming increasingly common in commercial and consumer products and pose a serious toxicological threat. Exposure of human organisms to nanomaterials can occur by inhalation, oral intake, or dermal transport. Together with the consumption of alcohol in the physiological environment of the body containing NaCl, this has raised concerns about the potentially harmful effects of ingested nanomaterials on human health. Although gold nanoparticles (AuNPs) exhibit great potential for various biomedical applications, there is some inconsistency in the case of the unambiguous genotoxicity of AuNPs due to differences in their shape, size, solubility, and exposure time. A DNA/GCE (DNA/glassy carbon electrode) biosensor was used to study ethanol (EtOH) and NaCl-induced gold nanoparticle aggregation genotoxicity under UV light in this study. The genotoxic effect of dispersed and aggregated negatively charged gold nanoparticles AuNP1 (8 nm) and AuNP2 (30 nm) toward salmon sperm double-stranded dsDNA was monitored by cyclic and square-wave voltammetry (CV, SWV). Electrochemical impedance spectroscopy (EIS) was used for a surface study of the biosensor. The aggregation of AuNPs was monitored by UV-vis spectroscopy. AuNP1 aggregates formed by 30% v/v EtOH and 0.15 mol·L^-1 NaCl caused the greatest damage to the biosensor DNA layer.

Suppressed DNA base pair stacking assembly of gold nanoparticles in an alcoholic solvent for enhanced ochratoxin A detection in Baijiu

The currently established DNA nanoprobes for the detection of mycotoxin from beverages have been limited by complicated sample pretreatment and uncontrollable nanoparticle flocculation in complex systems. We develop a rapid colorimetric approach for ochratoxin A (OTA) detection in Baijiu in a sample-in/"yes" or "no" answer-out fashion through target-modulated base pair stacking assembly of DNA-functionalized gold nanoparticles (DNA-AuNPs). The colorimetric signification of OTA relies on the competition of OTA with the AuNP surface-grafted DNA in binding with an OTA-targeted aptamer. The specific recognition of OTA by the aptamer prevents DNA duplex formation on the AuNP surface, thereby inhibiting the base pair stacking assembly of the DNA-AuNPs and giving rise to a "turn-on" color. By further suppressing DNA hybridization using a bulged loop design and an alcohol solution, the DNA-AuNPs exhibit an improved reproducibility for OTA sensing while maintaining excellent susceptivity to OTA. A detection limit of 88 nM was achieved along with high specificity towards OTA, which is lower than the maximum tolerated level of OTA in foodstuffs defined by countries worldwide. The entire reaction time, avoiding sample pretreatment, is less than 17 min. The DNA-AuNPs with anti-interference features and sensitive "turn-on" performance promise convenient on-site detection of mycotoxin from daily beverages.

ssDNA-Modified Gold Nanoparticles as a Tool to Detect miRNA Biomarkers in Osteoarthritis

Recently, miRNAs have been established as promising, specific biomarkers for the diagnosis of many diseases, including osteoarthritis. Herein, we report a ssDNA-based detection method for miRNAs implicated in osteoarthritis, specifically, miR-93 and miR-223. In this study, gold nanoparticles (AuNPs) were modified with oligonucleotide ssDNA to detect miRNAs circulating in the blood in healthy subjects and patients suffering from osteoarthritis. The detection method was based on the colorimetric and spectrophotometric assessment of biofunctionalized AuNPs upon interaction with the target and their subsequent aggregation. Results showed that these methods could be used to detect easily and rapidly miR-93 but not miR-223 in osteoarthritic patients, and they could potentially be used as a diagnostic tool for blood biomarkers. Visual-based detection as well as spectroscopic methods are simple, rapid, and label-free, due to which they can be used as a diagnostic tool.

Gold Nanoparticles Synthesized Using Various Reducing Agents and the Effect of Aging for DNA Sensing

Gold nanoparticles (AuNPs) are one of the most commonly used reagents in colloidal science and biosensor technology. In this work, we first compared AuNPs prepared using four different reducing agents including citrate, glucose, ascorbate, and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES). At the same absorbance at the surface plasmon peak of 520-530 nm, citrate-AuNPs and glucose-AuNPs adsorbed more DNA and achieved higher affinity to the adsorbed DNA. In addition, citrate-AuNPs had better sensitivity than glucose-AuNPs for label-free DNA detection. Then, using citrate-AuNPs, the effect of aging was studied by incubation of the AuNPs at 22 °C (room temperature) and at 4 °C for up to 6 months. During aging, the colloidal stability and DNA adsorption efficiency gradually decreased. In addition, the DNA sensing sensitivity using a label-free method also dropped around 4-fold after 6 months. Heating at boiling temperature of the aged citrate-AuNPs could not rejuvenate the sensing performance. This study shows that while citrate-AuNPs are initially better than the other three AuNPs in their colloid properties and sensing properties, this edge in performance might gradually decrease due to constantly changing surface properties caused from the aging effect.

Hybridization-Driven Adsorption of Polyadenine DNA onto Gold Nanoparticles

The attachment of functional DNA to gold nanoparticles via polyadenine adsorption is a well-established technology. This approach was mainly viewed through the lens of changing the DNA charge in order to reduce the electrostatic barrier created by a similarly charged gold surface. However, altering the DNA charge results in the loss of its functionality. This work considers the adsorption process of polyadenines by force that artificially brings them closer to the surface. As a force source, we used the hybridization of a DNA strand carrying polyadenines with a complementary strand already attached to the surface. It was shown that the hybridization forces facilitated the adsorption of polyadenines. We believe that this approach is applicable in various areas where it is essential to preserve the functionality of DNA during conjugation with nanoparticles.

Recent advances in gold nanoparticle-based colorimetric aptasensors for chemical and biological analyses

Aptasensors are amazing among many currently formed procedures due to their excellent particularity, selectivity and responsiveness. These biosensors get more popular in combination with gold nanoparticles (AuNPs) to detect chemical and biological molecules. The response of AuNPs by changing color provides a simple explanation of outcomes. The authors review the recent developments in AuNP-based colorimetric aptasensors designed to sense different chemical and biological molecules. They summarize the procedure of AuNP-based detection and the ordinary instances of currently formed AuNP-based colorimetric procedures. Furthermore, their uses for detecting different analytes based on analyte types are given and the present challenges, overview, and positive views for forming new aptasensors are also regarded.

A Label-Free Gold Nanoparticles-Based Optical Aptasensor for the Detection of Retinol Binding Protein 4

Retinol-binding protein 4 (RBP4) has been implicated in insulin resistance in rodents and humans with obesity and T2DM, making it a potential biomarker for the early diagnosis of T2DM. However, diagnostic tools for low-level detection of RBP4 are still lagging behind. Therefore, there is an urgent need for the development of T2DM diagnostics that are rapid, cost-effective and that can be used at the point-of-care (POC). Recently, nano-enabled biosensors integrating highly selective optical detection techniques and specificity of aptamers have been widely developed for the rapid detection of various targets. This study reports on the development of a rapid gold nanoparticles (AuNPs)-based aptasensor for the detection of RBP4. The retinol-binding protein aptamer (RBP-A) is adsorbed on the surface of the AuNPs through van der Waals and hydrophobic interactions, stabilizing the AuNPs against sodium chloride (NaCl)-induced aggregation. Upon the addition of RBP4, the RBP-A binds to RBP4 and detaches from the surface of the AuNPs, leaving the AuNPs unprotected. Addition of NaCl causes aggregation of AuNPs, leading to a visible colour change of the AuNPs solution from ruby red to purple/blue. The test result was available within 5 min and the assay had a limit of detection of 90.76 ± 2.81 nM. This study demonstrates the successful development of a simple yet effective, specific, and colorimetric rapid assay for RBP4 detection.

On-site colorimetric detection of Salmonella typhimurium

Rapid qualitative and quantitative detection of Salmonella typhimurium (S. typhimurium) takes an important role in ensuring food safety. Herein, a colorimetric assay aptasensor for S. typhimurium utilizing intrinsic peroxidase-like activity of gold nanoparticles embedded spherical covalent organic framework and the affinity and specificity of S. typhimurium-aptamer has been explored. This aptasensor can capture the S. typhimurium via the selective binding effect of aptamer, and the catalytically active sites were shielded. As a result, the colorimetric signals of the 3,3′,5,5′-tetramethylbenzidine-H₂O₂ system were turned off. Under optimum conditions, the aptasensor gave a linear response over the range of 10 to 10⁷ CFU/mL for S. typhimurium. The detection limit of 7 CFU/mL was obtained within 45 min and was effectively applied to detect S. typhimurium in milk and lake water samples with recoveries in the range from 96.4 to 101.0%. More importantly, combined with a self-developed smartphone-based image analysis system, the proposed aptasensor can be used for point-of-care testing applications.

Application of α-Fe2O3 nanoparticles in controlling antibiotic resistance gene transport and interception in porous media

Metal oxide nanoparticles (MONPs) with a large specific surface area are expected to bind with antibiotic resistance genes (ARGs), thereby controlling ARGs' contamination by reducing their concentration and mobilization. Here, adsorption experiments were carried out and it was found that α-Fe₂O₃ NPs could chemically bind with ARGs (tetM-carrying plasmids) in water with an adsorption rate of 0.04 min^-1 and an adsorption capacity of 7.88 g/kg. Mixing α-Fe₂O₃ NPs into quartz sand column markedly increased the interceptive removal of ARGs from inflow water. The interception rate of 1.0 μg/mL ARGs in ultrapure water (25 mL, 5 pore volumes) through the sand column (plexiglass, length 8 cm, internal diameter 1.4 cm) with 1 g/kg α-Fe₂O₃ NPs was 1.73 times of that through the pure sand column; the interception rate overall increased with increasing addition of α-Fe₂O₃ NPs, reaching 68.8% with 20 g/kg α-Fe₂O₃ NPs. Coexisting Na⁺ (20 mM), Ca²⁺ (20 mM), and acidic condition (pH 4.0) could further increase the interception rate of ARGs by 1 g/kg α-Fe₂O₃ NPs from 21.1% to 86.2%, 90.7%, and 96.2%, respectively. The presence of PO₄^3- and humic acid at environmentally relevant concentrations would not significantly affect the interception of ARGs. In the treatment groups with PO₄^3- and humic acid, the removal rate decreased by only 1.8% and 0.1%, respectively. In addition, the interceptive removal of ARGs by α-Fe₂O₃ NPs-incorporated sand column was even better in actual surface water samples (87.2%) than that in the ultrapure water (21.1%). The findings provide a promising approach to treat ARGs-polluted water.

Accounting for Interaction Kinetics between Gold Nanoparticles and Aptamers Enables High-Performance Colorimetric Sensors

DNA aptamers have emerged as promising probes for challenging analytes that cannot be easily detected by conventional probes, including small-molecule targets. Among the different signal transduction approaches, gold nanoparticle (AuNP) aggregation assays have been widely used to generate a colorimetric response from aptamer-target interactions. This sensor design relies on the competition between the aptamer adsorbing to the AuNP surface versus interacting with the target, whereby target binding reduces the number of adsorbed aptamers that destabilizes AuNPs toward salt-induced aggregation, thereby inducing a color change. However, this thermodynamic framework overlooks the potential influence of interaction kinetics of different aptamer conformations with AuNP surfaces and with targets in solution or near surfaces. Here, we show that aptamers become more strongly adsorbed on AuNPs over time, and these trapped aptamers are less responsive toward the target analyte. By varying the sequence of addition in sensing assays, we demonstrate that these interaction kinetics have a significant effect on the sensor response and thereby produce an effective sensor for methamphetamine (meth) at biologically relevant levels in oral fluids. Along with underpinning new tools for assay development, this new knowledge also highlights the need for aptamer selection strategies that evolve aptamer sequences based on the functionality that they need to exhibit in an actual sensor.

Simultaneous colorimetric and electrochemical detection of trace mercury (Hg2+) using a portable and miniaturized aptasensor

We report a novel aptasensor for the simultaneous colorimetric and electrochemical detection of mercury (Hg²⁺). This device consists of a paper-based microfluidic component (μ-PAD) incorporated into a miniaturized three-electrode system fabricated through printed circuit board (PCB) technology. This biosensor is portable, rapid, versatile, and can detect Hg²⁺ down to 0.01 ppm based on 3σ of the blank/slope criteria. Moreover, it is highly selective against As²⁺, Cu²⁺, Zn²⁺, Pb²⁺, Cd²⁺, Mg²⁺, and Fe²⁺, reaching up to 13 times more of the input signal than the other heavy metals. The colorimetric detection mechanism uses aptamer functionalized polystyrene (PS)-AgNPs and Ps-AuNPs microparticles' specific aggregation. The Ps-AuNPs-based system allows qualitative detection (LOD 5 ppm) and stability over seven days (up to 97.59% signal retention). For the Ps-AgNPs-based system, the detection limit is 0.5 ppm with a linear range from 0.5 to 20 ppm (adjusted R²= 0.986) and stability over 30 days (up to 94.95% signal retention). The electrochemical component measures changes in charge transfer resistance upon target-aptamer hybridization using a [Ru (NH₃)₆]³⁺Cl₃] redox probe. The latest component presents a linear range from 0.01 to 1 ppm (adjusted R²= 0.935) with a LOD of 0.01 ppm and performance stability over seven days (up to 102.52 ± 11.7 signal retention). This device offers a universal dual detection platform with multiplexing, multi-replication, quantitative color analysis, and minimization of false results. Furthermore, detection results in river samples showed recoveries up to 91.12% (RSD 0.85) and 105.61% (RSD 1.62) for the electrochemical and colorimetric components, respectively. The proposed system is highly selective with no false-positive or false-negative results in an overall wide linear range and can safeguard the accuracy of detection results in aptasensing platforms in general.

Direct Capture and Amplification of Small Fragmented DNAs Using Nitrogen-Mustard-Coated Microbeads

Circulating cell-free DNA (cfDNA) has been implicated as an important biomarker and has been intensively studied for "liquid biopsy" applications in cancer diagnostics. Owing to its small fragment size and its low concentration in circulation, cfDNA extraction and purification from serum samples are complicated, and the extraction yield affects the precision of subsequent molecular diagnostic tests. Here, we report a novel approach using nitrogen-mustard-coated DNA capture beads (NMD beads) that covalently capture DNA and allow direct subsequent polymerase chain reaction (PCR) amplification from the NMD bead without elusion. The complex DNA extraction and purification processes are not required. To illustrate the diagnostic use of the NMD beads, we detected short DNA fragments (142 bp) that were spiked into fetal bovine serum (as a model serum sample). The spiked DNAs were captured directly from serum samples and detected using real-time PCR at concentrations as low as 10 fg/mL. We anticipate that this DNA capture bead technique has the potential to simplify the preanalytical processes required for cfDNA detection, which could significantly expand the diagnostic applications of liquid biopsy.

Paper-based genetic assays with bioconjugated gold nanorods and an automated readout pipeline

Paper-based biosensors featuring immunoconjugated gold nanoparticles have gained extraordinary momentum in recent times as the platform of choice in key cases of field applications, including the so-called rapid antigen tests for SARS-CoV-2. Here, we propose a revision of this format, one that may leverage on the most recent advances in materials science and data processing. In particular, we target an amplifiable DNA rather than a protein analyte, and we replace gold nanospheres with anisotropic nanorods, which are intrinsically brighter by a factor of ~ 10, and multiplexable. By comparison with a gold-standard method for dot-blot readout with digoxigenin, we show that gold nanorods entail much faster and easier processing, at the cost of a higher limit of detection (from below 1 to 10 ppm in the case of plasmid DNA containing a target transgene, in our current setup). In addition, we test a complete workflow to acquire and process photographs of dot-blot membranes with custom-made hardware and regression tools, as a strategy to gain more analytical sensitivity and potential for quantification. A leave-one-out approach for training and validation with as few as 36 sample instances already improves the limit of detection reached by the naked eye by a factor around 2. Taken together, we conjecture that the synergistic combination of new materials and innovative tools for data processing may bring the analytical sensitivity of paper-based biosensors to approach the level of lab-grade molecular tests.

Homogeneous assays for aptamer-based ethanolamine sensing: no indication of target binding

Ethanolamine is an important analyte for environmental chemistry and biological sciences. A few DNA aptamers were previously reported for binding ethanolamine with a dissociation constant (K_d) as low as 9.6 nM. However, most of the previous binding assays and sensing work used either immobilized ethanolamine or immobilized aptamers. In this work, we studied three previously reported DNA sequences, two of which were supposed to bind ethanolamine while the other could not bind. Isothermal titration calorimetry revealed no binding for any of these sequences. In addition, due to their guanine-rich sequences, thioflavin T was used as a probe. Little fluorescence change was observed with up to 1 μM ethanolamine. Responses within the millimolar range of ethanolamine were attributed to the general fluorescence quenching effect of ethanolamine instead of aptamer binding. Finally, after studying the adsorption of ethanolamine to gold nanoparticles (AuNPs), we confirmed the feasibility of using AuNPs as a probe when the concentration of ethanolamine was below 0.1 mM. However, no indication of specific aptamer binding was observed by comparing the three DNA sequences for their color changing trends. This work articulates the importance of careful homogeneous binding assays using free target molecules.

Duplex-Specific Nuclease-Triggered Fluorescence Immunoassay Based on Dual-Functionalized AuNP for Acetochlor, Metolachlor, and Propisochlor

Given the great harm of pesticide residues to the environment and public health, exploring ultrasensitive and low-cost methods for their quantitative analysis becomes intensely necessary. Herein, we proposed a double-functionalized gold nanoparticle (AuNP) probe as a signal amplification immunoassay for the detection of acetochlor (ATC), metolachlor, and propisochlor. The AuNP was modified with IgG and fluorophore-labeled duplex DNA by a polyadenine-based freezing method. The quenched fluorescence can be effectively recovered via duplex-specific nuclease (DSN) with excellent cleaving activity. This approach provided limits of detection (LODs) down to 0.03 ng/mL for ATC, 0.10 ng/mL for metolachlor, 0.14 ng/mL for propisochlor, and 0.08 ng/mL for their mixture. The average recoveries of ATC, metolachlor, and propisochlor were 93.0-106.6% from a corn sample, which are in good agreement with the commercial kit (R² = 0.9995). This "turn-off" fluorescence immunoassay presents considerable potential in the analysis of chloroacetamide herbicide due to its simple process of probe preparing and ultrahigh sensitivity.

Nanoparticle-assisted detection of nucleic acids in a polymeric nanopore with a large pore size

Rapid and accurate detection of nucleic acids is of paramount importance in many fields, including medical diagnosis, gene therapy and virus identification. In this work, by taking advantage of two DNA hybridization probes, one of which was immobilized on the surface of gold nanoparticles, while the other was free in solution, detection of short length nucleic acids was successfully achieved using a large size (20 nm tip diameter) polyethylene terephythalate (PET) nanopore. The sensor was sensitive and selective: DNA samples with concentrations at as low as 0.5 nM could be detected within minutes and the number of mismatches can be discerned from the translocation frequency. Furthermore, the nanopore can be repeatedly used many times. Our developed large-size nanopore sensing platform offers the potential for fieldable/point-of-care diagnostic applications.

Rapid point-of-need detection of bacteria and their toxins in food using gold nanoparticles

Biosensors need to meet the rising food industry demand for sensitive, selective, safe, and fast food safety quality control. Disposable colorimetric sensors based on gold nanoparticles (AuNPs) and localized surface plasmon resonance are low-cost and easy-to-perform devices intended for rapid point-of-need measurements. Recent studies demonstrate various facile and versatile AuNPs-based analytical platforms for the detection of bacteria and their toxins in milk, meat, and other foods. In this review, we introduce the general characteristics and mechanisms of AuNPs calorimetric biosensors, and highlight optimizations needed to strengthen and improve the quality of devices for their application in food matrices.

Simultaneous Stabilization and Functionalization of Gold Nanoparticles via Biomolecule Conjugation: Progress and Perspectives

Gold nanoparticles (AuNPs) are used in various biological applications because of their small surface area-to-volume ratios, ease of synthesis and modification, low toxicity, and unique optical properties. These properties can vary significantly with changes in AuNP size, shape, composition, and arrangement. Thus, the stabilization of AuNPs is crucial to preserve the properties required for biological applications. In recent years, various polymer-based physical and chemical methods have been extensively used for AuNP stabilization. However, a new stabilization approach using biomolecules has recently attracted considerable attention. Biomolecules such as DNA, RNA, peptides, and proteins are representative of the biomoieties that can functionalize AuNPs. According to several studies, biomolecules can stabilize AuNPs in biological media; in addition, AuNP-conjugated biomolecules can retain certain biological functions. Furthermore, the presence of biomolecules on AuNPs significantly enhances their biocompatibility. This review provides a representative overview of AuNP functionalization using various biomolecules. The strategies and mechanisms of AuNP functionalization using biomolecules are comprehensively discussed in the context of various biological fields.

High Stability Au NPs: From Design to Application in Nanomedicine

In recent years, Au-based nanomaterials are widely used in nanomedicine and biosensors due to their excellent physical and chemical properties. However, these applications require Au NPs to have excellent stability in different environments, such as extreme pH, high temperature, high concentration ions, and various biomatrix. To meet the requirement of multiple applications, many synthetic substances and natural products are used to prepare highly stable Au NPs. Because of this, we aim at offering an update comprehensive summary of preparation high stability Au NPs. In addition, we discuss its application in nanomedicine. The contents of this review are based on a balanced combination of our studies and selected research studies done by worldwide academic groups. First, we address some critical methods for preparing highly stable Au NPs using polymers, including heterocyclic substances, polyethylene glycols, amines, and thiol, then pay attention to natural product progress Au NPs. Then, we sum up the stability of various Au NPs in different stored times, ions solution, pH, temperature, and biomatrix. Finally, the application of Au NPs in nanomedicine, such as drug delivery, bioimaging, photothermal therapy (PTT), clinical diagnosis, nanozyme, and radiotherapy (RT), was addressed concentratedly.

Synthetic Tunability and Biophysical Basis for Fabricating Highly Fluorescent and Stable DNA Copper Nanoclusters

The real motivation in the present work is to tune the synthesis variables that can result in a highly fluorescent and stable DNA copper nanocluster (CuNC) and also to understand the intricate mechanism behind this process. Here, carefully optimized concentrations of various reactants enabled the creation of a DNA-encapsulated CuNC for AT-DNA, displaying a size of <1.0 nm as confirmed by transmission electron microscopy and dynamic light scattering. The extremely small size of the AT-DNACuNC supports the discrete electronic transitions, also characterized by an exceptionally strong negative circular dichroism (CD) band around 350 nm, whose intensity is well correlated with the observed strong fluorescence emission intensity. This remarkably strong CD can open new applications in the detection and quantification of a specific DNACuNC. Further, time-dependent fluorescence analysis suggested stronger photostabilization of these DNACuNCs. The simulation study, based on Cu ion distribution, explained how AT-DNA is a better candidate for NC formation than GC-DNA. In conclusion, the better-tuned synthesis procedure has resulted in a highly compact, well-defined three-dimensional conformation that promotes a more favorable microenvironment to sequester a DNA-based CuNC with high brightness and outstanding photostability.

Detection of Begomovirus in chilli and tomato plants using functionalized gold nanoparticles

Begomoviruses are a major class of Geminiviruses that affects most dicotyledonous plants and causes heavy economic losses to farmers. Early detection of begomovirus is essential to control the spread of the disease and prevent loss. Many available detection methods like ELISA, immunosorbent electron microscopy, PCR or qPCR require expertise in handling sophisticated instruments, complex data interpretation and costlier chemicals, enzymes or antibodies. Hence there is a need for a simpler detection method, here we report the development of a visual detection method based on functionalized gold nanoparticles (AuNP assay). The assay was able to detect up to 500 ag/µl of begomoviral DNA (pTZCCPp3, a clone carrying partial coat protein gene) suspended in MilliQ water. Screening of chilli plants for begomoviral infection by PCR (Deng primers) and AuNP assay showed that AuNP assay (77.7%) was better than PCR (49.4%). The AuNP assay with clccpi1 probe was able to detect begomoviral infection in chilli, tomato, common bean, green gram and black gram plants which proved the utility and versatility of the AuNP assay. The specificity of the assay was demonstrated by testing with total DNA from different plants that are not affected by begomoviruses.

Improving the detection limit of Salmonella colorimetry using long ssDNA of asymmetric-PCR and non-functionalized AuNPs

A colorimetric sensor based on gold nanoparticles (AuNPs) and single-stranded DNA (ssDNA) is a simple and rapid method for detecting foodborne pathogens. However, the colorimetric method employed in previous studies involved short ssDNA (<100 nucleotides), including the aptamer and PCR products, resulting in the high detection limit of this technique. In this study, a colorimetric sensor was developed based on long ssDNA of asymmetric PCR (aPCR) and non-functionalized AuNPs for detecting Salmonella Typhimurium (S. Typhimurium). In the presence of S. Typhimurium, the long ssDNA (547 nt) amplified by aPCR-protected AuNPs from NaCl-induced aggregation, while the solution retained a red color. After optimizing parameters, the limit of detection (LOD) of the colorimetric sensor was 2.56 CFU/mL with high specificity. Recovery studies showed its feasibility for detecting S. Typhimurium (10² CFU/mL, 10⁴ CFU/mL, and 10⁶ CFU/mL) in spiked lettuce samples. This colorimetric sensor provides new opportunities for the highly sensitive detection of bacteria in real food samples.

Effect of Fluorescent Labels on DNA Affinity for Gold Nanoparticles

Fluorophore (FD) labeling is widely used for detection and quantification of various compounds bound to nanocarriers. The systems, composed of gold nanoparticles (GNPs) and oligonucleotides (ONs) labeled with FDs, have wide applications. Our work was aimed at a systemic study of how FD structure (in composition of ON-FDs) influenced the efficiency of their non-covalent associates' formation with GNPs (ON-FD/GNPs). We examined ONs of different length and nucleotide composition, and corresponding ON-FDs (FDs from a series of xanthene, polymethine dyes; dyes based on polycyclic aromatic hydrocarbons). Methods: fluorometry, dynamic light scattering, high performance liquid chromatography, gel electrophoresis, molecular modeling and methods of thermodynamic and statistical analysis. We observed significant, differing several times, changes in surface density and Langmuir constant values of ON-FDs vs. ONs, evidence for the critical significance of FD nature for binding of ON-FDs with GNPs. Surface density of ON-FD/GNPs; hydrophobicity and total charge of ON or ON-FD; and charge and surface area of FDs were revealed as key factors determining affinity (Langmuir constant) of ON or ON-FDs for GNPs. These factors compose a specific set, which makes possible the highly reliable prediction of efficiency of ONs and ON-FDs binding with GNPs. The principal possibility of creating an algorithm for predictive calculation of efficiency of ONs and GNPs interaction was demonstrated. We proposed a hypothetical model that described the mechanism of contact interaction between negatively charged nano-objects, such as citrate-stabilized GNPs, and ONs or ON-FDs.