DNA AuNPs Research Articles

Condensed DNA incorporating mercaptoundecahydro-closo-dodecaborate (BSH) coated gold nanoparticles as a model system for boron neutron capture therapy (BNCT)

The experimental radiation therapy involving thermal neutron capture by boron (boron neutron capture therapy, BNCT) offers the advantage of high-LET ions with ranges on the order of a cell nucleus. Efforts to implement it have encountered serious difficulties. A practical model system would be able to address the underlying mechanisms of DNA damage and also calibrate Monte Carlo simulations. We describe the characterization of a plasmid-based model in which DNA condensed with a tetra-arginine peptide is co-aggregated with mercapto-closo-dodecaborate (BSH) coated gold nanoparticles (AuNPs). Condensed DNA is an excellent model for cellular chromatin, and the AuNPs are able to function as boron carriers and neutron dosimeters. Data from light scattering, UV–visible spectroscopy, fluorescence spectroscopy, sedimentation behavior, gel electrophoresis, and atomic force microscopy all indicate that the basic peptide acts to co-aggregate the two polyanionic species DNA and BSH-coated AuNPs. This aggregation is easily reversed by an increase in ionic strength to free the plasmid for subsequent assay. We argue that this three-component system is simpler, more convenient, and more flexible than other models requiring covalent attachments between DNA, boron, and/or gold.

Carbon Quantum Dots Coupled Au Nanoparticle as Fluorescence-Based DNA Biosensors for Dengue Virus Detection

This study introduces a novel DNA biosensor probe comprising carbon quantum dots (CQDs) derived from palm kernel shell biomass and gold nanoparticles (AuNPs) synthesized via the citrate reduction method. The CQDs were doped with ethylenediamine using a hydrothermal process employing a one-pot synthesis method in an autoclave batch reactor. The resulting CQDs exhibited exceptional photoluminescent (PL) properties, with an excitation wavelength of 360 nm and an emission wavelength of 430 nm. Transmission electron microscope (TEM) images showed the average particle sizes of the CQDs and AuNPs to be 2 nm and 15 nm, respectively. Carboxylic acid-modified CQDs were coupled to amine-modified ssDNA (PA) to construct the biosensor through the amine coupling technique. The AuNPs were modified through thiol coupling with Rhodamine B, L-cysteine, and thiol-modified ssDNA (PT). Both PA and PT probes were designed to complement the DEN-3 virus oligonucleotide. CQDs acted as fluorophores and energy donors in the biosensor, while the AuNPs functioned as nanoquenchers of fluorophores and energy acceptors. The resulting probe pair, CQDs-PA, and AuNPs-PT demonstrated remarkable Förster resonance energy transfer (FRET) and exhibited fluorescence turn-on upon titration with DEN-3. The biosensor displayed excellent sensitivity with a logarithmic calibration equation of 5.22LogC + 20.79 (R2 = 0.979), covering a linear range of 0.001 nM to 100 nM. The limit of detection (LOD) was determined to be 1.57 ± 0.71 nM. This innovative DNA biosensor, incorporating CQDs and AuNPs, holds promising potential for sensitive and specific detection of the DEN-3 virus.

Branched DNA-Based Electrochemical Biosensor for Sensitive Nucleic Acids Analysis with Gold Nanoparticles as Amplifier.

A branched DNA-based electrochemical biosensor was designed to sensitively detect specific nucleic acids. On this platform, novel a branched DNA with three sticky ends could be used as a biosensor to sensitively and specifically detect nucleic acids. Meanwhile, we also employed branched DNA-modified AuNPs as a signal amplifier to further improve the sensitivity. Branched DNA sensors, target DNA, and DNA-modified AuNPs formed a sandwich structure to produce an electronic signal for target DNA detection. The reaction primarily involved DNA hybridization without bulky thermal cyclers and enzymes. We proved that the hybridization reaction easily occurred under different conditions, such as the NaCl concentration, reaction time, pH, and temperature, except for a pH lower than 4. The limit of detection could go as low as 0.09 pM (S/N = 3) with excellent specificity and selectivity. There was a correlation curve relationship between the peak current and the logarithm of the target DNA concentration (0.10 pM to 10 nM). The correlation coefficient reached 0.987. The electrochemical platform enables a branched DNA nanostructure to determine nucleic acids for disease diagnosis.

Non-Invasive, Reliable, and Fast Quantification of DNA Loading on Gold Nanoparticles by a One-Step Optical Measurement.

An exquisite, versatile, and reproducible quantification of DNA loading on gold nanoparticles (Au NPs) has long been pursued because this loading influences the analytical, therapeutic, and self-assembly behaviors of DNA-Au NPs. Nevertheless, the existing methods used thus far rely solely on the invasive detachment and subsequent spectroscopic quantification of DNA, which are error-prone and highly dependent on trained personnel. Here, we present a non-invasive optical framework that can determine the number of DNA strands on Au NPs by versatile one-step measurement of the visible absorption spectra of DNA-Au NP solutions without any invasive modifications or downstream processes. Using effective medium theory in conjunction with electromagnetic numerical calculation, the change in DNA loading density, resulting from varying the ion concentration, Au NP size, DNA strand length, and surrounding temperature, can be tracked in situ merely by the one-step measurement of visible absorption spectra, which is otherwise impossible to achieve. Moreover, the simplicity and robustness of this method promote reproducible DNA loading quantification regardless of experimental adeptness, which is in stark contrast with existing invasive and multistep methods. Overall, the optical framework outlined in this work can contribute to democratizing research on DNA-Au NPs and facilitating their rapid adoption in transformative applications.

Highly Sensitive Aptasensor for Detecting Cancerous Exosomes Based on Clover-like Gold Nanoclusters.

Exosome-based liquid biopsy technologies play an increasingly prominent role in tumor diagnosis. However, the simple and sensitive method for counting exosomes still faces considerable challenges. In this work, the CD63 aptamer-modified DNA tetrahedrons on the gold electrode were used as recognition elements for the specific capture of exosomes. Partially complementary DNA probes act as bridges linking trapped exosomes and three AuNP-DNA signal probes. This clover-like structure can tackle the recognition and sensitivity issues arising from the undesired AuNP aggregation event. When cancerous exosomes are present in the system, the high accumulation of methylene blue molecules from DNA-AuNP nanocomposites on the surface of the electrode leads to an intense current signal. According to the results, the aptasensor responds to MCF-7 cell-derived exosomes in the concentration range from 1.0 × 103 to 1.0 × 108 particles·μL-1, with the detection limit of 158 particles·μL-1. Furthermore, the aptasensor has been extended to serum samples from breast cancer patients and exhibited excellent specificity. To sum it up, the aptasensor is sensitive, straightforward, less expensive, and fully capable of receiving widespread application in clinics for tumor monitoring.

DNA Nanostructure-Guided Plasmon Coupling Architectures

DNA Nanostructure-Guided Plasmon Coupling Architectures

A Label-Free Colorimetric Aptasensor Containing DNA Triplex Molecular Switch and AuNP Nanozyme for Highly Sensitive Detection of Saxitoxin

A Label-Free Colorimetric Aptasensor Containing DNA Triplex Molecular Switch and AuNP Nanozyme for Highly Sensitive Detection of Saxitoxin

Simulation Studies on Signature Interactions between Cancer DNA and Cysteamine-Decorated AuNPs for Universal Cancer Screening

Simulation Studies on Signature Interactions between Cancer DNA and Cysteamine-Decorated AuNPs for Universal Cancer Screening

Gold-Nanoparticle-Mediated Assembly of High-Order DNA Nano-Architectures.

Constructing high-order DNA nano-architectures in large sizes is of critical significance for the application of DNA nanotechnology. Robust and flexible design strategies together with easy protocols to construct high-order large-size DNA nano-architectures remain highly desirable. In this work, the authors report a simple and versatile one-pot strategy to fabricate DNA architectures with the assistance of spherical gold nanoparticles modified with thiolated oligonucleotide strands (SH-DNA-AuNPs), which serve as "power strips" to connect various DNA nanostructures carrying complementary ssDNA strands as "plugs". By modulating the plug numbers and positions on each DNA nanostructure and the ratios between DNA nanostructures and AuNPs, the desired architectures are formed via the stochastic co-assembly of different modules. This SH-DNA-AuNP-mediated plug-in assembly (SAMPA) strategy offers new opportunities to drive macroscopic self-assembly to meet the demand of the fabrication of well-defined nanomaterials and nanodevices.

A novel aptasensor based on DNA hydrogel for sensitive visual detection of ochratoxin A.

Anovel visual detection mode isproposed to improve the detection sensitivityfor the determination of ochratoxin A (OTA). The mode is based on aptamer recognition and the signal amplification of rolling circle amplification (RCA) products self-assembled DNA hydrogel. Moreover, gold nanoparticles (AuNPs) were directly assembled inside the DNA hydrogel by adjusting the padlock probe sequences to achieve a stronger binding force between the DNA hydrogel and AuNPs; this avoids the need for modification of AuNPs with DNA sequences. In the presence of OTA, DNA hydrogel is formed. With higher concentrations of OTA, a larger amount of DNA hydrogel is formed. When AuNPs are added to the DNA hydrogel, AuNPs can be enclosed inside the DNA hydrogel. With more DNA hydrogel, there is less AuNPs in the supernatant. Thus, the absorbance of the supernatant is anti-correlated with the concentration of OTA. After optimization of the experimental conditions, the change in the absorbance of the supernatant was linearly correlated with the concentration of OTA, in the range 0.05 to 10ng/mL; the limit of detection was 0.005ng/mL. The good specificity of the developed biosensor was confirmed in the presence of other mycotoxins that are coexistent withor analogues of OTA. By comparing the developed method with the ELISA method, the accuracy and stability of this new method were also verified, with good performance obtained in real samples. Diagram of the principle of the colorimetric aptasensor for OTA detection based on rolling circle amplification product self-assembled DNA hydrogel.

Cathode-Anode Spatial Division Photoelectrochemical Platform Based on a One-Step DNA Walker for Monitoring of miRNA-21.

Photoelectrochemical (PEC) biosensors carried out the whole reaction process in the same solution, which would limit the sensitivity and selectivity of detection in the sensing system. Herein, we reported a promising new cathode-anode spatial division PEC platform based on the two-electrode synergistic enhancement strategy. With the photoanode and photocathode integrated in the same current circuit, the platform exhibited an increased photocurrent response, as well as an improved anti-interference ability led by separating the two electrodes spatially. In this proposal, red light-driven AgInS2 nanoparticles (NPs) served as the photoanode to build biometric steps and amplify the signal, whereas p-type PbS quantum dots were selected as the photocathode to increase the signal. With the participation of alkaline phosphatase (ALP) labeled on Au NPs-DNA, ascorbic acid 2-phosphate was catalyzed to produce ascorbic acid as an electron donor, resulting in the enhancement of the PEC signal. Interestingly, in the presence of miRNA-21 and T7 Exo, the one-step DNA walker amplification can be triggered to reduce the PEC signal by releasing ALP-Au NP-DNA. The constructed PEC biosensor exhibited a detection limit of as low as 3.4 fM for miRNA-21, which was expected to be applied to early clinical diagnosis. Also, we believe that the proposed cathode-anode spatial division PEC platform can open up a new view for the establishment of other types of PEC biosensors.

Logic gates in nanoscale based on interaction of thiolated DNA with AuNPs and strand displacement

Both DNA molecules and AuNPs are promising materials in Nanotechnology due to their special properties and also their interaction between each other. In this article, we present a series of methods via combining the DNA strand displacement reaction with the interaction of thiolated DNA and AuNPs to construct several logic gates, such as NOT, YES, NAND, XOR gates. The results demonstrate the computing power in nanoscale molecules and reactions.

Gold Nanoparticle-Enhanced Detection of DNA Hybridization by a Block Copolymer-Templating Fiber-Optic Localized Surface Plasmon Resonance Biosensor.

To overcome low surface coverage and aggregation of particles, which usually restricts the sensitivity and resolution of conventional localized surface plasmon resonance (LSPR) fiber-optic sensors, we propose a simple self-assembled templating technique that uses a nanometer thickness block copolymer (BCP) layer of poly(styrene-b-4-vinylpyridine) to form a 33 nm gold nanoparticle (AuNP) monolayer with high uniformity and density for LSPR sensing. The LSPR resonance wavelength for this PS-b-P4VP templated methodology is 592 nm and its refractive index sensitivity is up to 386.36 nm/RIU, both of which are significantly improved compared to those of conventional LSPR techniques. Calibrated by a layer-by-layer polyelectrolyte deposition procedure, the decay length of this LSPR sensor is calculated to be 78 nm, which is lower than other traditional self-assembled LSPR sensors. Furthermore, hybridization between target ssDNA, which is linked with capture ssDNA on the LSPR biosensor and DNA–AuNP conjugates, leads to a low detection limit of 67 pM. These enhanced performances are significant and valuable for high-sensitivity and cost-effective LSPR biosensing applications.

DNA–Gold Nanozyme-Modified Paper Device for Enhanced Colorimetric Detection of Mercury Ions

In this work, a paper device consisted of a patterned paper chip, wicking pads, and a base was fabricated. On the paper chip, DNA–gold nanoparticles (DNA–AuNPs) were deposited and Hg2+ ions could be adsorbed by the DNA–AuNPs. The formed DNA–AuNP/Hg2+ nanozyme could catalyze the tetramethylbenzidine (TMB)–H2O2 chromogenic reaction. Due to the wicking pads, a larger volume of Hg2+ sample could be applied to the paper device for Hg2+ detection and therefore the color response could be enhanced. The paper device achieved a cut-off value of 50 nM by the naked eye for Hg2+ under optimized conditions. Moreover, quantitative measurements could be implemented by using a desktop scanner and extracting grayscale values. A linear range of 50–2000 nM Hg2+ was obtained with a detection limit of 10 nM. In addition, the paper device could be applied in the detection of environmental water samples with high recoveries ranging from 85.7% to 105.6%. The paper-device-based colorimetric detection was low-cost, simple, and demonstrated high potential in real-sample applications.

Colorimetric method for PARP-1 detection based on preventing AuNRs from etching by molybdate

As a tumor-related enzyme, PARP-1 activity is closely related to the occurrence of cancer. Sensitive detection of PARP-1 activity is of significance in the early diagnosis and treatment of cancer. Therefore, the gold nanorods (AuNRs) based biological nanoprobe was constructed for the visual and label-free detection of PARP-1 activity. dsDNA which activate PARP-1 was modified on AuNPs (AuNPs@DNA). MoO42− is added to catalyze H2O2 and KI to accelerate the etching of AuNRs. In the presence of PARP-1, hyperbranched poly (ADP-ribose) polymers (PAR) formed on the surface of AuNPs@DNA (AuNPs@DNA@PAR). A large number of PO43- of the PAR reacted with MoO42− to generate PMo12O403-. Thus, PO43- diminished MoO42− concentration in solution, preventing the etching of AuNRs. Therefore, PARP-1 prevented the etching of AuNRs. With the increasing concentration of PARP-1, the color of the solution changed from light blue to brown obviously. The method was applied to assay actual samples with satisfactory results. The strategy has the advantages of rapid quantitative analysis of PARP-1 activity with naked eyes, simple operation and good application prospect.

Solvo-Driven Dimeric Nanoplasmon Coupling Under DNA Direction

Strong coupling is a prerequisite for nanoassemblies to deliver functions and applications unrealizable by noninteracting building units. DNA-Directed metamaterials, albeit highly programmable, oft...

Sandwich-Type DNA Micro-Optode Based on Gold-Latex Spheres Label for Reflectance Dengue Virus Detection.

A DNA micro-optode for dengue virus detection was developed based on the sandwich hybridization strategy of DNAs on succinimide-functionalized poly(n-butyl acrylate) (poly(nBA-NAS)) microspheres. Gold nanoparticles (AuNPs) with an average diameter of ~20 nm were synthesized using a centrifugation-based method and adsorbed on the submicrometer-sized polyelectrolyte-coated poly(styrene-co-acrylic acid) (PSA) latex particles via an electrostatic method. The AuNP–latex spheres were attached to the thiolated reporter probe (rDNA) by Au–thiol binding to functionalize as an optical gold–latex–rDNA label. The one-step sandwich hybridization recognition involved a pair of a DNA probe, i.e., capture probe (pDNA), and AuNP–PSA reporter label that flanked the target DNA (complementary DNA (cDNA)). The concentration of dengue virus cDNA was optically transduced by immobilized AuNP–PSA–rDNA conjugates as the DNA micro-optode exhibited a violet hue upon the DNA sandwich hybridization reaction, which could be monitored by a fiber-optic reflectance spectrophotometer at 637 nm. The optical genosensor showed a linear reflectance response over a wide cDNA concentration range from 1.0 × 10−21 M to 1.0 × 10−12 M cDNA (R2 = 0.9807) with a limit of detection (LOD) of 1 × 10−29 M. The DNA biosensor was reusable for three consecutive applications after regeneration with mild sodium hydroxide. The sandwich-type optical biosensor was well validated with a molecular reverse transcription polymerase chain reaction (RT-PCR) technique for screening of dengue virus in clinical samples, e.g., serum, urine, and saliva from dengue virus-infected patients under informed consent.

Modeling of ultrasensitive DNA hybridization detection based on gold nanoparticles/carbon-nanotubes/chitosan-modified electrodes

In this work, we developed an ultrasensitive and ultraselective electrochemical biosensor for detection of a specific sequence DNA. It was fabricated based on a glassy carbon electrode (GCE) modified with Multi-walled carbon nanotubes (MWCNTs)-Chitosan (CHIT) nanocomposite and a thin film of gold nanoparticles (AuNPs). Immobilization is based on the covalent reaction between thiol group in DNA probe and AuNPs on electrode surface. Cyclic Voltametry (CV) and Differential Pulse Voltammetry (DPV) techniques were used for hybridization detection by methylene blue (MB) as indicator. The surface modification increased significantly DNA immobilization quantity and complementary DNA detection sensitivity. The response signal increased linearly with the increase of the target DNA concentration in the range of (1 × 10-14 M to 9 × 10-14 M) with the detection limit of 7.2 fM (LOD =3SXm). The presented method exhibited excellent specificity and selectivity for complementary and single-mismatch, three-base-mismatch and non-complementary sequences of DNA.

Construction of Bio/Nanointerfaces: Stable Gold Nanoparticle Bioconjugates in Complex Systems.

The real application of DNA-functionalized gold nanoparticles (DNA-Au NPs) was limited by decreased stability and irreversible aggregation in high-ionic strength solutions and complex systems. Therefore, exploring a kind of DNA-Au NPs with excellent stability in high-ionic strength solutions and complex systems is challenging and significant. Herein, a novel universal bioconjugate strategy for constructing ultrastable DNA-Au NPs was designed based on the combination of polydopamine (PDA) shell and DNA linker. The obtained DNA-linked Au@polydopamine nanoparticles (DNA-Au@PDA NPs) showed colloidal stability in high-ionic strength solution and complex systems (such as human serum and cell culture supernatant). Moreover, the nanoparticles still maintained good dispersion after multiple freeze-thaw cycles. The high stability of DNA-Au@PDA NPs may be attributed to increasing the electrostatic and steric repulsions among nanoparticles through the effect of both PDA shell and DNA linker on Au@PDA NPs. For investigating the application of such nanoparticles, a highly sensitive assay for miRNA 141 detection was developed using DNA-Au@PDA NPs coupled with dynamic light scattering (DLS). Comparing with the regular DNA-Au NPs, DNA-Au@PDA NPs could detect as low as 50 pM miRNA 141 even in human whole serum. Taken together, the features of Bio/Nanointerface make the nanoparticle suitable for various applications in harsh biological and environmental conditions due to the stability. This work may provide a universal modification method for obtaining stable nanoparticles.

Precise, direct, and rapid detection of Shigella Spa gene by a novel unmodified AuNPs-based optical genosensing system

Early detection of infectious bacteria is a necessity for combating infectious diseases. Due to low infectious dose of Shigella, rapid and sensitive detection is needed. Compared to the presented genes, Spa gene can be introduced as a novel sequence for all species of Shigella detection. Herein, the possibility of Spa genes for detection of four species of Shigella was investigated for the first time by AuNPs-based optical genosensing system. In this method, AuNP–DNA probes were hybridized with Spa gene sequence. When the complementary target is present, it prevents the aggregation of the complex under acid environment and the solution remains red whereas in the absence of the specific sequence, it turns to purple. Therefore, visual detection is possible with bare eye. The comparison of this Optical DNA biosensor and PCR-based method showed that the proposed method is simple, cost-effective, rapid operation, with high or comparable detection limit of (LOD and LOQ: 8.14 and 26.6 ng mLl−1, respectively), without need of any expensive techniques, and equipments compared to the conventional methods. In conclusion, the described method may develop into a platform that could be utilized for detection of various bacterial species with high accuracy and prompt screening of samples.