DNA Gold Nanoparticles Research Articles

Advancing understanding of molecular interactions: computational studies on DNA nucleobases and gold nanoparticles using density functional theory

Advancing understanding of molecular interactions: computational studies on DNA nucleobases and gold nanoparticles using density functional theory

A Tunable Threshold Colorimetric DNA Logic Gate for Intuitive Assessment of Chemical Contaminant Exceedance.

Current molecular logic gates are predominantly focused on the qualitative assessment of target presence, which has certain limitations in scenarios requiring quantitative assessment, such as chemical contaminant monitoring. To bridge this gap, we have developed a novel DNA logic gate featuring a tunable threshold, specifically tailored to the limits of contaminants. At the core of this logic gate is a DNA-gold nanoparticle (AuNP) hybrid film that incorporates aptamer sequences to selectively bind to acetamiprid (ACE) and atrazine (ATR). Upon interaction with these contaminants, the film degrades, releasing AuNPs that, in the presence of Hg2+, catalyze the oxidation of TMB, resulting in a visible blue coloration on test paper. This aptamer-enabled process effectively establishes an OR logic gate, with ACE and ATR as inputs and the appearance of blue color as the output. A key innovation of our system is its tunable input threshold. By adjusting the concentration of Hg2+, we can fine-tune the color mutation points to match the input threshold to predefined limits, such as Maximum Residue Limits (MRLs). This alignment allows semiquantitative assessment of contaminant levels, providing intuitive visual feedback of contaminant exceedance. Validation experiments with spiked samples confirm its accuracy and reliability by closely matching HPLC results. Therefore, our colorimetric DNA logic gate is emerging as a promising tool for easy and semiquantitative monitoring of chemical contaminants across diverse applications.

Highly sensitive tetracycline detection using a triple amplification aptasensor based on graphene-carbon nanotube, Exonuclease I, and gold nanoprobes

Enhancing the sensitivity of targeted substance detection is crucial, yet prior research seldom incorporates more than two signal amplification methods. In this study, we introduced a novel triple signal amplification strategy for tetracycline detection using an aptasensor. This strategy integrates a graphene and multi-walled carbon nanotubes composite (GO-MWCNTs), Exonuclease I (Exo I), and a hybrid DNA-gold nanoparticle (AuNPs)-horseradish peroxidase (HRP) system. The GO-MWCNTs serve as a conductive carrier, boosting electron transfer for initial signal amplification. Exo I, targeting single-stranded DNA, facilitates target recovery and secondary signal amplification. The gold nanoprobe, through specific base pairing, binds to the tetracycline aptamer’s complementary chains on the electrode surface. Horseradish peroxidase’s catalytic action then generates a robust electrochemical signal, culminating in three-stage signal amplification. This optimized approach achieved a low detection limit of 3.3 × 10−4 ng mL−1, with a range from 1 × 10−3 ng mL−1 to 1 × 103 ng mL−1. Notably, the aptasensor demonstrated high selectivity, repeatability, stability, and reliability. These findings offer a promising reference for developing effective aptasensors in antibiotic detection.

Interfacing DNA and Aptamers with Gold Nanoparticles: From Fundamental Colloid and Interface Sciences to Biosensors

Comprehensive SummaryInterfacing DNA oligonucleotides and DNA aptamers with gold nanoparticles has generated numerous functional hybrid materials for sensing, self‐assembly and drug delivery applications. Our lab has been working in this area for 15 years. In this article, the current understanding of the adsorption of DNA to gold nanoparticles is summarized, and related applications in bioconjugation of DNA to gold surface is described. In addition, problems of using gold nanoparticles to signaling aptamer binding are discussed. Finally, re‐selection of aptamers for previously reported targets using the library‐immobilization method is reviewed. What is the most favorite and original chemistry developed in your research group?My most favorite and original work is the study of biointerface chemistry between DNA oligonucleotides and gold nanoparticles enabling rapid DNA bioconjugation by lowering the pH and freezing.How do you get into this specific field? Could you please share some experiences with our readers?My PhD training was focused on catalytic DNA for the detection of metal ions, when I used gold nanoparticles to signal the reactions catalyzed by DNA. When I started my independent career in the University of Waterloo in 2009, I realized that there were many fundamental issues regarding gold nanoparticles and DNA to be studied. My first teaching assignment was a course named ‘Surfaces and Interfaces’. By teaching this course, I learned a lot of surface science concepts that were later used in my research. That was the starting point for me to set up my own research program in this area.What is the most important personality for scientific research?Curiosity, careful observation, critical thinking, and keep trying.How do you keep balance between research and family?Research and personal life don’t have to be always in conflict. New ideas may spark when I am in a relaxed family environment.What are your favorite journals?Journal of the American Chemical Society, Angewandte Chemie International Edition, Nucleic Acids Research, Analytical Chemistry, Langmuir.What are your hobbies?Running; traveling; watching movies.

A target-triggered strand displacement-assisted target recycling based on carbon dots-based fluorescent probe and MSNs@PDA nanoparticles for miRNA amplified detection and fluorescence imaging.

A target-triggered strand displacement-assisted target recycling based on carbon dots-based fluorescent probe and mesoporous silica nanoparticles@polydopamine (MSNs@PDA) was established to detect miRNA. The surface of MSNs rich in mesopores was coated with a layer of PDA, which can adsorb and quench the fluorescence of single-stranded Fuel DNA with fluorescent carbon dots (CDs) modified at the end through fluorescence resonance energy transfer (FRET). After adding double-stranded DNA-gold nanoparticles (dsDNA-AuNPs) and target let-7a, it will trigger two toehold-mediated strand displacement reactions (TSDR), leading to the recovery of fluorescence and the recycling of target let-7a (excitation wavelength: 380nm; emission wavelength: 458nm). The recovery value of fluorescence is proportional to the logarithm of the target microRNA let-7a concentration, thus realizing the sensitivity amplification detection of disease markers. The MSNs@PDA@Fuel DNA-CDs/dsDNA-AuNPs nanoplatform based on the strategy of "on-off-on" and TSDR cyclic amplification may hold great potential as an effective and safe nanoprobe for accurate fluorescence imaging of diseases related to miRNA with low abundances.

Customized Self-Assembled Gold Nanoparticle-DNA Origami Composite Templates for Shape-Directed Growth of Plasmonic Structures.

The metal plasmonic nanostructure has the optical property of plasmon resonance, which holds great potential for development in nanophotonics, bioelectronics, and molecular detection. However, developing a general and straightforward method to prepare metal plasmonic nanostructures with a controllable size and morphology still poses a challenge. Herein, we proposed a synthesis strategy that utilized a customizable self-assembly template for shape-directed growth of metal structures. We employed gold nanoparticles (AuNPs) as connectors and DNA nanotubes as branches, customizing gold nanoparticle-DNA origami composite nanostructures with different branches by adjusting the assembly ratio between the connectors and branches. Subsequently, various morphologies of plasmonic metal nanostructures were created using this template shape guided strategy, which exhibited enhancement of surface-enhanced Raman scattering (SERS) signals. This strategy provides a new approach for synthesizing metallic nanostructures with multiple morphologies and opens up another possibility for the development of customizable metallic plasmonic structures with broader applications.

Bimodal 3D DNA nanomachines coupling with bioconjugates powered electrochemical and visual-driven dual-enzyme cascade sensing of Let-7a

A dual-enzyme self-powered biosensor utilizing bimodal 3D DNA nanomachines and gold nanoparticle (AuNPs)/carbon/disulfide molybdenum hollow nanorods bioconjugates is developed for the electrochemical and visual detection of the tumor biomarker let-7a. DNA probes are immobilized on a flexible electrode substrate of AuNPs/graphdiyne/carbon cloth to improve probe loading capacity and electron transfer efficiency. The presence of let-7a initiates the work of dual-enzyme 3D DNA nanomachine, and the output DNA single strand cleaved by Nb.BbvCI is served as a bridge to connect glucose oxidase (GOD)-DNA conjugate. The GOD coordinates with the cathodic enzyme bilirubin oxidase and produces an increased open circuit voltage signal, which is attributed to the hexaammine ruthenium in the double-stranded adsorption system of the biocathode. By utilizing the H2O2 generated during the oxidation process of GOD, a linear relationship between the color of 3,3′,5,5′-tetramethylbenzidine and the concentration of let-7a is established, enhancing the reliability of the detection results through the independent signal conversion mechanisms of electrochemical/colorimetric modes. The results demonstrate a wide dynamic range of 0.0001–0.1 pM with detection limits of 31.04 aM (S/N=3) in electrochemical mode and 59.99 aM (S/N=3) in the colorimetric mode. This dual-mode biosensing strategy can be expanded to detect additional nucleic acid biomarkers, providing a promising support and reference for biological analysis and medical diagnosis.

A pendulum-type electrochemical aptamer-based sensor for continuous, real-time and stable detection of proteins

Continuous detection of proteins is crucial for health management and biomedical research. Electrochemical aptamer-based (E-AB) sensor that relies on binding affinity between a recognition oligonucleotide and its specific target is a versatile platform to fulfill this purpose. Yet, the vast majority of E-AB sensors are characterized by voltammetric methods, which suffer from signal drifts and low-frequency data acquisition during continuous operations. To overcome these limitations, we developed a novel E-AB sensor empowered by Gold nanoparticle-DNA Pendulum (GDP). Using chronoamperometric interrogation, the developed sensor enabled drift-resistant, high-frequency, and real-time monitoring of vascular endothelial growth factor (VEGF), a vital signaling protein that regulates angiogenesis, endothelial cell proliferation and vasculogenesis. We assembled VEGF aptamer-anchored GDP probes to a reduced graphene modified electrode, where a fast chronoamperometric current transient occurs as the GDP rapidly transport to the electrode surface. In the presence of target molecules, longer and concentration-dependent time decays were observed because of slower motion of the GDP in its bound state. After optimizing several decisive parameters, including composition ratios of GDP, probe density, and incubation time, the GDP empowered E-AB sensor achieves continuous, selective, and reversible monitoring of VEGF in both phosphate buffered saline (PBS) solutions and artificial urine with a wide detection range from 13 fM to 130 nM. Moreover, the developed sensor acquires signals on a millisecond timescale, and remains resistant to signal degradation during operation. This study offers a new approach to designing E-AB architectures for continuous biomolecular monitoring.

Noncovalent Adsorption of Single-Stranded and Double-Stranded DNA on the Surface of Gold Nanoparticles

Understanding the patterns of noncovalent adsorption of double-stranded nucleic acids (dsDNA) on gold nanoparticles (GNPs) was the aim of this study. It was found that the high-affinity motifs in DNA can and do act as an “anchor” for the fixation of the whole molecule on the GNP (up to 98 ± 2 single-stranded (ss)DNA molecules per particle with diameter of 13 ± 2 nm). At the same time, the involvement of an “anchor” in the intramolecular DNA interaction can negatively affect the efficiency of the formation of ss(ds)DNA–GNP structures. It has been shown that the interaction of GNP with DNA duplexes is accompanied by their dissociation and competitive adsorption of ssDNAs on GNP, wherein the crucial factor of DNA adsorption efficiency is the intrinsic affinity of ssDNA to GNP. We propose a detailed scheme for the interaction of dsDNA with GNPs, which should be taken into account in studies of this type. Researchers focused on this field should accept the complicated nature of such objects and take into account the many competing processes, including the processes of adsorption and desorption of DNA on gold as well as the formation of secondary structures by individual DNA strands.

Comparison of DNA-Gold Nanoparticle Conjugation Methods: Application in Lateral Flow Nucleic Acid Biosensors.

Lateral flow nucleic acid biosensors (LFNABs) have attracted extensive attention due to their rapid turnaround time, low cost, and results that are visible to the naked eye. One of the key steps to develop LFNABs is to prepare DNA-gold nanoparticle (DNA-AuNP) conjugates, which affect the sensitivity of LFNABs significantly. To date, various conjugation methods-including the salt-aging method, microwave-assisted dry heating method, freeze-thaw method, low-pH method, and butanol dehydration method-have been reported to prepare DNA-AuNP conjugates. In this study, we conducted a comparative analysis of the analytical performances of LFNABs prepared with the above five conjugation methods, and we found that the butanol dehydration method gave the lowest detection limit. After systematic optimization, the LFNAB prepared with the butanol dehydration method had a detection limit of 5 pM for single-strand DNA, which is 100 times lower than that of the salt-aging method. The as-prepared LFNAB was applied to detect miRNA-21 in human serum, with satisfactory results. The butanol dehydration method thus offers a rapid conjugation approach to prepare DNA-AuNP conjugates for LFNABs, and it can also be extended to other types of DNA biosensors and biomedical applications.

A portable colorimetric point-of-care testing platform for MicroRNA detection based on programmable entropy-driven dynamic DNA network modulated DNA-gold nanoparticle hybrid hydrogel film

Point-of-care testing (POCT) platforms for microRNA (miRNA) detection have attracted considerable attention in recent years, due to the increasingly important role of miRNA as biomarkers for the diagnosis of many diseases, such as cancers. However, several limitations such as the requirement of enzyme-related amplification system, expensive preservation cost, sophisticated analysis instruments and tedious operations of conventional miRNA biosensing devices severely hinder their widespread applications. In this work, a portable and smart colorimetric analysis platform was developed by employing the ultrathin DNA-gold nanoparticle (AuNP) hybrid hydrogel film as the signaling unit and the enzyme-free entropy-driven dynamic DNA network (EDN) as the signal converter and amplification unit. By programming the DNA sequences of the EDN, the EDN could respond to a specific miRNA, with miRNA-155 or miRNA-21 as the model target, and release a converter DNA with amplified concentration to further trigger the release of AuNPs from the hydrogel film as a colorimetric signal output. To avoid the use of sophisticated spectral instruments, digital analysis based on primary three-color channel (R/G/B) was further introduced by using user-friendly camera and image processing software, and a detection limit at pM level was achieved. Moreover, by introducing H2O2-mediated AuNPs enlargement procedure in the colorimetric analysis platform, the detection limit for miRNA target could further be enhanced to fM level. The POCT platform is also portable and storable with a good storage stability for at least 45 days, suggesting its great potential in practical diagnosis applications.

DNA Nanostructure-Guided Plasmon Coupling Architectures

DNA Nanostructure-Guided Plasmon Coupling Architectures

SARS-CoV-2 detection by targeting four loci of viral genome using graphene oxide and gold nanoparticle DNA biosensor

The current COVID-19 pandemic outbreak poses a serious threat to public health, demonstrating the critical need for the development of effective and reproducible detection tests. Since the RT-qPCR primers are highly specific and can only be designed based on the known sequence, mutation sensitivity is its limitation. Moreover, the mutations in the severe acute respiratory syndrome β-coronavirus (SARS-CoV-2) genome led to new highly transmissible variants such as Delta and Omicron variants. In the case of mutation, RT-qPCR primers cannot recognize and attach to the target sequence. This research presents an accurate dual-platform DNA biosensor based on the colorimetric assay of gold nanoparticles and the surface-enhanced Raman scattering (SERS) technique. It simultaneously targets four different regions of the viral genome for detection of SARS-CoV-2 and its new variants prior to any sequencing. Hence, in the case of mutation in one of the target sequences, the other three probes could detect the SARS-CoV-2 genome. The method is based on visible biosensor color shift and a locally enhanced electromagnetic field and significantly amplified SERS signal due to the proximity of Sulfo-Cyanine 3 (Cy3) and AuNPs intensity peak at 1468 cm-1. The dual-platform DNA/GO/AuNP biosensor exhibits high sensitivity toward the viral genome with a LOD of 0.16 ng/µL. This is a safe point-of-care, naked-eye, equipment-free, and rapid (10 min) detection biosensor for diagnosing COVID-19 cases at home using a nasopharyngeal sample.

Signal-enhanced strategy for ratiometric aptasensing of aflatoxin B1: Plasmon-modulated competition between photoelectrochemistry-driven and electrochemistry-driven redox of methylene blue

Efficient signal amplification using light irradiation in electrochemistry-based sensing attracts growing interest; however, the modulation of electrochemical and photoelectrochemical behaviors of bifunctional probes remains challenging for the better analytical performance. Here, we found that the bifunctional probe methylene blue (MB) under irradiation followed two routes, i.e., photoelectrochemistry (PEC)-driven and electrochemistry (EC)-driven route, while plasmon-modulated competition between PEC-driven and EC-driven routes efficiently enhanced the analytical performance of aptasensor. Ferrocene-labeled aptamer (Fc-apt) was applied to tune the interaction between MB labeled complementary DNA (MB-cDNA) and plasmonic gold nanoparticles (AuNPs). Under visible light illumination, the aptasensor output a weak current of MB (IMB) for the depressed EC-driven redox. The binding of Fc-apt with target led to its stripping from electrode and released MB-cDNA to approach AuNPs, and an increase in IMB was observed due to the synergy of the depressed PEC-driven redox while the restored EC-driven redox. In this way, the amplified response for target could be obtained by depressing background signal while enlarging response signal of IMB under visible light. Consequently, the developed model ratiometric aptasensor offered a higher sensitivity for the determination of aflatoxin B1. Our observation should be favorable to shed light on photo-induced electrochemical mechanism, and the proposed amplification strategy is valuable for the construction of efficient sensors.

Development of sensitive colorimetric aptasensor based on short DNA aptamer and its application to screening for paraquat residues in agricultural soil.

Paraquat is a widely used herbicide for controlling weeds and grasses in agriculture, and its contaminated residues in agricultural areas are of increasing concern. This work reports the development of the sensitive and easy-to-use colorimetric aptasensor for screening paraquat residues in agricultural soil. The short DNA fragments derived from the original aptamer were analyzed for their capability to interact with paraquat by molecular dynamic simulation. The paraquat-aptasensor was developed using the selected DNA fragment and gold nanoparticles. Its limit of detection (LOD) for paraquat is 2.76nM, which is more sensitive than the aptasensor with long-length aptamer (LOD = 12.98nM). The developed aptasensor shows the selectivity to paraquat, but not to other tested herbicides; ametryn, atrazine, difenzoquat, 2,4-D-dimethyl ammonium, and glufosinate. The recovery rates of paraquat detection in the spiked soil samples were in a range of 99.5%-105.1%, with relative standard deviation values of <4%. The developed aptasensor was used to screen for paraquat residues in agricultural soils, and three out of 23 soil samples were tested positive for paraquat, which was confirmed by a high-performance liquid chromatography analysis. These results suggested the potential application of the developed aptasensor to detect paraquat residues in agricultural sites.

Separate determination of arsenite and arsenate in groundwater samples by simple analytical methods

Abstract We investigated the interaction of As(III) with As(III)-binding DNA aptamers (Ars-3). The binding of Ars-3 to As(III) was investigated using an Ars-3 sequence and a few control DNA sequences. As a result, we conclude that Ars-3 cannot bind As(III) and As(III) can adsorb onto gold nanoparticles with selectivity. However, the As(III) concentration could be determined by a simple As(III) analysis method using Ars-3, and we measured the As(III) and As(V) concentrations separately in As(III)/As(V) mixed samples in ultrapure water and groundwater using a simple analytical method for As(III) and As(V), respectively. As(III) in the sample was measured by a simple As(III) analytical method using DNA aptamers and gold nanoparticles, and As(V) in the sample was measured by a simple As(V) analysis method using cerium oxide nanoparticles and fluorescence-labeled DNA. We can measure As(III) and As(V) concentrations in ultrapure water and groundwater in the simple analytical method for As(III) and As(V), separately.

Optical Mie Scattering by DNA-Assembled Three-Dimensional Gold Nanoparticle Superlattice Crystals

Programmable assemblies of gold nanoparticles engineered with DNA have intriguing optical properties such as Coulomb-interaction-driven strong coupling, polaritonic response in the visible range, and ultralow dispersion dielectric response in the infrared spectral range. In this work, we demonstrate the optical Mie resonances of individual microcrystals of DNA–gold nanoparticle superlattices. Broadband hyperspectral mapping of both transmission and dark-field scattering reveal a polarization-insensitive optical response with distinct spectral features in the visible and near-infrared ranges. Experimental observations are supported by numerical simulations of the microcrystals under a resonant effective medium approximation in the regime of capacitively coupled nanoparticles. The study identifies a universal characteristic optical response which is defined by a band of multipolar Mie resonances, which only weakly depend on the crystal size and light polarization. The use of gold superlattice microcrystals as scattering materials is of interest for fields such as complex nanophotonics, thermoplasmonics, photocatalysis, sensing, and nonlinear optics.

Photoelectrochemical and visual dual-mode sensor for efficient detection of Cry1Ab protein based on the proximity hybridization driven specific desorption of multifunctional probe

Currently, the development of sensitive and visual strategy for Cry1Ab detection, particularly using a switchable dual-mode detection system based on a single component, remains a great challenge. Here, a photoelectrochemical (PEC) and visual dual-mode sensor was designed for Cry1Ab detection based on a proximity hybridization driven multifunctional probe. In the presence of Cry1Ab, specific desorption of the antibody-DNA conjugate was achieved via sufficient proximity hybridization, leading to the selective release of the multifunctional signal probe, i.e., antibody-labeled single-stranded DNA-gold nanoparticles (Ab1-S1-AuNPs). The released Ab1-S1-AuNPs reduced the photocurrent signal and produced a colored response, thereby achieving PEC and visual dual-mode detection based on a single component. Owing to the different signal generation mechanisms, two independent signals were obtained simultaneously, which provided self-verification to improve reliability and accuracy. Taking advantage of the PEC sensitive detection and visual prediction, the dual-mode sensor achieved efficient detection of the Cry1Ab protein. The developed sensor was successfully used to determine Cry1Ab in corn, wheat, and soil samples with satisfactory results. This method offers a promising biosensing platform for the on-site detection of Cry1Ab protein.

Development of Gold Nanoparticle (AuNP)-based Colorimetric Aptasensor for Penicillin G Detection

Antibiotics are chemical or biological substances that have the ability to kill pathogens selectively. Currently, high-performance liquid chromatography (HPLC) is used routinely in the detection of antibiotics. However, the cost of analysis and running time are bottlenecks for HPLC to be used for routine tests to detect antibiotics. Alternative methods need to be developed to overcome this issue. In this study, the development of a penicillin G specific biosensor by using a DNA aptamer and gold nanoparticles (AuNPs) was done. Optimal aptasensor conditions were achieved with the concentrations of NaCl and aptamer at 0.25 M and 2 μM, respectively. An aptasensor of this type showed LOD for penicillin G at 3 mg/L and was able to detect penicillin G in the range of 3 to 27 mg/L. The established aptasensor showed specific sensitivity toward penicillin G after testing with several antibiotics, i.e., ampicillin, kanamycin, chloramphenicol, and erythromycin. The aptasensor could detect the presence of penicillin G from culture medium of wild-type, ultraviolet irradiation mutant, gamma irradiation mutant, and ultraviolet irradiation and gamma irradiation mutant strains of P. chrysogenum, at detection concentrations of 9.75 ± 0.004; 25.25 ± 0.005; 37.5 ± 0.005; and 45 ± 0.004 mg/L, respectively.

Smart DNA-gold nanoparticle hybrid hydrogel film based portable, cost-effective and storable biosensing system for the colorimetric detection of lead (II) and uranyl ions

A portable, cost-effective and storable DNA-gold nanoparticle (AuNP) hybrid hydrogel film based biosensing system was developed, with AuNPs serving as both the crosslinking units of the film and the signaling units. Using a layer-by-layer assembly method, hydrogel film composed of three-dimensional hydrophilic network of densely packed AuNPs interconnected by responsive DNA structures was constructed onto a glass slide. By programming the sequence of DNA structures, target-responsive hybrid films were constructed. As a proof of concept, the sequence of a substrate DNA which can be identified and cleaved by Pb2+-dependent DNAzyme was encoded to construct Pb2+-responsive DNA-AuNP hybrid hydrogel film. The high-density packing of AuNPs as signal substances significantly improved the sensitivity of the ultrathin film biosensing system while reduced the cost of expensive DNA materials. A hydrogel film composed of 10 layers of assembled DNA-AuNP structures generated sufficient visual colorimetric signals for Pb2+ detection, with a detection limit of 2.6 nM. By introducing UO22+-dependent DNAzyme, the system could be further applied in the sensitive and selective detection of UO22+, with a detection limit of 10.3 nM. Compared with bulk-sized DNA hydrogel biosensing systems, the DNA-AuNP hydrogel film biosensing system exhibited faster response thanks to the sub-micrometer ultrathin film structures. Moreover, the protection of fragile non-covalently crosslinked DNA films with solid slides also facilitated the portable application and long-term storage of the resulting biosensing system, with 95% of the response signal retained after three months of storage. The DNA-AuNPs hydrogel film biosensing system is highly promising for future rapid on-site detection applications.