A simple visual method for DNA detection based on the formation of gold nanoparticles

A simple visual method for DNA detection during the formation of gold nanoparticles (AuNPs) was developed based on different electrostatic properties of single strand DNA (ssDNA) and double strand DNA (dsDNA). Since the ssDNA is easy to bind to AuNPs due to its exposed bases which could prevent salt-induced aggregation of AuNPs. The dsDNA always present negative charge because its negatively charged phosphate backbone is exposed. In this case, the dsDNA could disturb the adsorption between dsDNA and AuNPs and result in non-aggregation of AuNPs. After hybridization, chloroauric acid and ascorbic acid were added to the mixture solution, and the solution changed to red immediately and turned to purple in 10 min in the present of target DNA. TEM results confirmed that the change of color stemed from aggregation of AuNPs. In order to obtain accurate results by naked eye, the DNA detection assay should be conducted under pH 7.0.     

Mechanism of mercury detection based on interaction of single-strand DNA and hybridized DNA with gold nanoparticles

Mechanisms of interaction of single-strand DNA and hybridized DNA on gold nanoparticles in the presence of Hg²⁺ was studied in this work. Recently the detection of Hg²⁺ using unmodified gold nanoparticles (AuNPs) combined with DNA is becoming a promising technique with the advantages of simplicity, cost-effectiveness and high sensitivity. However, few studies focused on the interaction of ssDNA and hybridized DNA on AuNPs to date. In the present work, we compared the interactions of different DNA probes on AuNPs using both absorption and fluorescence detection. It was found that there were only small partial dsDNA dissociated from the surface of AuNPs after hybridization in the presence of Hg²⁺. Moreover, we found that the aggregated AuNPs/DNA system tended to be dispersed again with increasing Hg²⁺ concentration up to 250 μM. Based on these results, the mechanisms of mercury detection based on interaction between DNA-conjugated gold nanoparticles were investigated. Positively charged dsDNA could bind to the surface of AuNPs and dominate the electrostatic interactions and consequently aggregation of the AuNPs/DNA system.     

A Label-Free Deoxyribozymes Resonance Rayleigh Scattering Assay for Trace Lead(II) Based on Nanogold Catalysis of Chloroauric Acid-Vitamin C Particle Reaction

In pH 7.2 Tris-HCl buffer solution, the substrate strand DNA (SDNA) was hybridized to the enzyme strand DNA (EDNA) forming a double strand DNA (dsDNA). The SDNA in dsDNA could be cleaved by lead(II) to release a cleavaged single-stranded (ssDNA) that prevented the gold nanoparticles (AuNPs) from forming a stable AuNPs-ssDNA conjugate. The unconjugated AuNPs were aggregated to form AuNP aggregation (AuNPsA) that appeared as a resonance Rayleigh scattering (RS) peak at 532 nm. When the lead(II) concentration increased, the AuNPs-ssDNA increased, the AuNPsA decreased, the color changed from blue to red, and the RS intensity at 532 nm decreased. The decreased RS intensity ΔI _532 nm was linear to the lead(II) concentration in the range of 0.67–60 nmol/L, with a detection limit of 0.3 nmol/L. The AuNPs-ssDNA exhibited a strong catalytic effect on the reaction between chloroauric acid and vitamin C (VC) that can be detected by an RS method at 620 nm. When the lead(II) concentration increased, the intensity at 620 nm increased, and the increased intensity ΔI _620 nm was linear to the lead(II) concentration in the range of 1.33–120 pmol/L, with a detection limit of 0.5 pmol/L. The proposed method was applied to detect lead(II) in water samples, with satisfactory results.     

Label-free colorimetric sensing of ascorbic acid based on Fenton reaction with unmodified gold nanoparticle probes and multiple molecular logic gates

A label-free strategy based on Fenton reaction with unmodified gold nanoparticles (AuNPs) as probe is demonstrated for ascorbic acid (AA) sensing. AuNPs is stable in the presence of single stranded DNA (ssDNA) which prevents salt-induced aggregation of AuNPs in solution. The hydroxyl free radicals generated by Fenton reaction lead to ssDNA cleavage into different sequence fragments which induce aggregation of AuNPs to produce a red-to-blue color change. As an efficient biological antioxidant, AA could effectively scavenge free radicals to avoid the cleavage of ssDNA, so that it prevents color change of the AuNPs solution. Thus, the color change of AuNPs in the presence and absence of AA provides a new approach for the detection of AA. The absorbance ratio at two wavelengths, A₆₇₀/A₅₂₀, decreases linearly with AA content within 1–15 μM, giving rise to a detection limit of 0.3 μM and a RSD of 2.8% (10 μM). The color display of AuNPs solution makes it feasible for the estimation of AA content by naked eye visualization. Moreover, based on Fenton reaction and unmodified gold nanoparticles, a multiple logic gate system includes two logic operations, i.e., INHIBIT and NOR, has been designed with small molecules (AA, l-cysteine, glutathione) as inputs and the colorimetric changes of AuNPs solution as outputs.     

Conformational change detection of DNA with the fluorogenic reagent of o-phthalaldehyde-beta-mercaptoethanol

o-Phthalaldehyde-beta-mercaptoethanol (OPAME) as a fluorogenic reagent has been found wide applications in the detection of amino acids based on its reaction with primary amino groups. In this contribution, we report our new findings concerning the reactions of OPAME with single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), respectively. It has been found that ssDNA can react with OPAME easily as a result of giving rise to strong fluorescence emissions, while dsDNA, prepared by hybridizing ssDNA with its complementary target prior to the reaction, displays inert chemical activity and gives out weak fluorescence emission. Mechanism investigations have shown that the reaction activity between OPAME and DNA depends on the amino groups that are related to the conformation of uncoiled and exposed extent of DNA structure, and thus the inert chemical activity of dsDNA results from screening of the dsDNA bases in the interior of the double strands. Therefore, we could design a way to detect conformation change of DNA with OPAME and further develop a novel, simple label-free sequence detection method for complementary and single-base mismatched ssDNA in the hybridization of DNA.     

Glucose detection at attomole levels using dynamic light scattering and gold nanoparticles

Glucose is directly related to brain activity and to diabetes.Therefore,developing a rapid and sensitive method for glucose detection is essential.Here,label-free glucose detection at attomole levels was realized by detecting the average diameter change of gold nanoparticles(AuNPs)utilizing dynamic light scattering(DLS).Single-strand DNA(ssDNA)adsorbed into the AuNPs’surfaces and prevented them from aggregating in solution that contained NaCl.However,ssDNA cleaved onto ssDNA fragments upon addition of glucose,and these fragments could not adsorb onto the AuNPs’surfaces.Therefore,in high-salt solution,AuNPs would aggregate and their average diameter would increase.Based on monitoring the average diameter of AuNPs with DLS,glucose could be detected in the range from 15 pmol/L to 2.0 nmol/L,with a detection limit of 8.3 pmol/L.Satisfactory results were also obtained when the proposed method was applied in human serum glucose detection.     

Characterization of single- and double-stranded DNA on gold surfaces

Single- and double-stranded deoxy ribonucleic acid (DNA) molecules attached to self-assembled monolayers (SAMs) on gold surfaces were characterized by a number of optical and electronic spectroscopic techniques. The DNA-modified gold surfaces were prepared through the self-assembly of 6-mercapto-1-hexanol and 5'-C(6)H(12)SH -modified single-stranded DNA (ssDNA). Upon hybridization of the surface-bound probe ssDNA with its complimentary target, formation of double-stranded DNA (dsDNA) on the gold surface is observed and in a competing process, probe ssDNA is desorbed from the gold surface. The competition between hybridization of ssDNA with its complimentary target and ssDNA probe desorption from the gold surface has been investigated in this paper using X-ray photoelectron spectroscopy, chronocoulometry, fluorescence, and polarization modulation-infrared reflection absorption spectroscopy (PM-IRRAS). The formation of dsDNA on the surface was identified by PM-IRRAS by a dsDNA IR signature at approximately 1678 cm(-)(1) that was confirmed by density functional theory calculations of the nucleotides and the nucleotides' base pairs. The presence of dsDNA through the specific DNA hybridization was additionally confirmed by atomic force microscopy through colloidal gold nanoparticle labeling of the target ssDNA. Using these methods, strand loss was observed even for DNA hybridization performed at 25 degrees C for the DNA monolayers studied here consisting of attachment to the gold surfaces by single Au-S bonds. This finding has significant consequence for the application of SAM technology in the detection of oligonucleotide hybridization on gold surfaces.     

Colorimetric detection of peroxynitrite-induced DNA damage using gold nanoparticles, and on the scavenging effects of antioxidants

We describe a rapid and convenient colorimetric method for the detection of oxidative DNA damage caused by peroxynitrite (ONOO^?) using unmodified gold nanoparticles (AuNPs). AuNPs are stable in the presence of single-stranded DNA (ssDNA) against the aggregation induced by a high ionic strength. If adsorbed ssDNA are cleaved by ONOO^? to form smaller fragments, the AuNPs rapidly aggregate due to electrostatic attraction. As a result, the color of the solution changes from red to blue, and this can be seen with bare eyes. We also have evaluated the activity of the antioxidants gallic acid, ascorbic acid and caffeic acid to scavenge ONOO^?. This method therefore also can be applied to screen for anti-oxidation drugs and agents.

Selective enzymatic labeling to detect packing-induced denaturation of double-stranded DNA at interfaces

The adsorption of DNA on surfaces is a widespread procedure and is a common way for fabrication of biosensors, DNA chips, and nanoelectronic devices. Although the biologically relevant and prevailing in vivo structure of DNA is its double-stranded (dsDNA) conformation, the characterization of DNA on surfaces has mainly focused on single-stranded DNA (ssDNA). Studying the structure of dsDNA on surfaces is of invaluable importance to microarray performance since their effectiveness relies on the ability of two DNA molecules to hybridize and remain stable. In addition, many of the enzymatic transactions performed on DNA require dsDNA, rather than ssDNA, as a substrate. However, it is not established that adsorbed dsDNA remains in its structure and does not denature. Here, two methodologies have been developed for distinguishing between surface-adsorbed single- and double-stranded DNA. We demonstrate that, upon formation of a dense monolayer, the nonthiolated strand comprising the dsDNA is released and the monolayer consists of mostly ssDNA. The fraction of dsDNA within the ssDNA monolayer depends on the length of the oligomers. A likely mechanism leading to this rearrangement is discussed.     

Sequence-specific recognition of HIV-1 DNA based upon nicking-assisted strand displacement amplification and triplex DNA

Nucleic acid amplification test is a reliable method for primary human immunodeficiency virus(HIV) infection diagnosis.Herein, a novel fluorescent method for sequence-specific recognition of DNA fragment of HIV-1 was established based upon nicking-assisted strand displacement amplification(SDA) and triplex DNA. In the presence of target dsDNA, nicking-assisted SDA process generated a lot of ssDNA, which hybridized with molecular beacon to produce signal. The fluorescence intensity was proportional to the concentration of target dsDNA within the range from 5 to 1000 pmol/L, with a detection limit of 1.4 pmol/L. Moreover, it successfully distinguished target dsDNA from the nucleic acid extractive of human blood. Thus this method has the merit of high sensitivity, and it is suitable for sequence-specific recognition of target dsDNA in complex matrices, which made it a potential application in diagnosis of acquired immunodeficiency syndrome(AIDS) in the future.     

Gold nanoparticles immobilized on metal–organic frameworks with enhanced catalytic performance for DNA detection

In this work, gold nanoparticles (AuNPs) assembled on the surface of iron based metal–organic frameworks (MOFs), Fe-MIL-88, are facilely prepared through electrostatic interactions using polyethyleneimine (PEI) molecules as linker. The resulting hybrid materials possess synergetic peroxidase-like activity. Because iron based metal–organic frameworks, Fe-MIL-88, exhibits highly peroxidase-like activity, and AuNPs has the distinct adsorption property to single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). The peroxidase-like activity of Au@Fe-MIL-88 exhibit excellent switchable in response to specific DNA, ssDNA is easily adsorbed on the surface of the Au@Fe-MIL-88 hybrids, resulting in the reduce of the peroxidase-like activity of the hybrids. While it is recovered by the addition of target DNA, and the recovery degree is proportional to the target DNA concentration over the range of 30–150 nM with a detection limit of 11.4 nM. Based on these unique properties, we develop a label-free colorimetric method for DNA hybridization detection. In control experiment, base-mismatched DNA cannot induce recovery of the peroxidase-like activity. This detection method is simple, cheap, rapid and colorimetric.     

Lable‐Free Electrochemical DNA Sensor Based on Gold Nanoparticles/Poly(neutral red) Modified Electrode

We present a new strategy for the label‐free electrochemical detection of DNA hybridization based on gold nanoparticles (AuNPs)/poly(neutral red) (PNR) modified electrode. Probe oligonucledotides with thiol groups at the 5‐end were covalently linked onto the surface of AuNPs/PNR modified electrode via S‐Au binding. The hybridization event was monitored by using differential pulse voltammetry (DPV) upon hybridization generates electrochemical changes at the PNR‐solution interface. A significant decrease in the peak current was observed upon hybridization of probe with complementary target ssDNA, whereas no obvious change was observed with noncomplementary target ssDNA. And the DNA sensor also showed a high selectivity for detecting one‐mismatched and three‐mismatched target ssDNA and a high sensitivity for detecting complementary target ssDNA, the detection limit is 4.2×10^?12 M for complementary target ssDNA. In addition, the DNA biosensor showed an excellent reproducibility and stability under the DNA‐hybridization conditions.     

Aptamer-wrapped gold nanoparticles for the colorimetric detection of omethoate

Organophosphorous pesticide(OP) contamination has serious adverse effects on human health and the environment. Due to the toxicity of OPs and the threat presented by their accidental or intentional release in populated areas, the determination and monitoring of these OPs in food products and environment is of great importance. OPs are present in very small quantities and therefore, methods for their detection need to be highly sensitive and selective. Here, we aimed to develop a simple and selective aptamer-based colorimetric assay for the detection of omethoate, which is one of the commonly used OPs. The principle of the assay is that single-stranded DNA(ss DNA)-wrapped gold nanoparticles(Au NPs) are resistant to salt-induced aggregation. By employing an "artificial antibody" organophosphorous pesticide-binding aptamer(OBA) as the recognition element, aptamer-wrapped Au NPs(Au-apta) show high selectivity towards omethoate, resulting in the disconnection of aptamers from Au NPs and the aggregation of Au NPs. As there is a significant color change from the interparticle plasmon coupling during the aggregation of Au NPs, the established assay showed good linearity between 0.1 and 10 μmol/L, with a low detection limit of 0.1 μmol/L. Other OPs such as profenofos, phorate, and isocarbophos would not interfere with the detection of omethoate despite having similar structures. Thus, the colorimetric method shows potential for use in the detection of omethoate in real soil samples.     

Positive ion electrospray ionization mass spectrometry of double-stranded DNA/drug complexes.

Positive ion electrospray ionization mass spectra of 16 base-pair double-stranded (ds)DNA have been obtained with essentially no ions from single-stranded DNA present. Single-stranded DNA was minimized by: (1) careful choice of DNA sequences; (2) the use of a relatively high salt concentration (0.1 M ammonium acetate, pH 8.5), and, (3) a low desolvation temperature (40 degrees C). Similarly, ESI-MS complexes of dsDNA with cisplatin, daunomycin and distamycin were obtained that contained only negligible amounts of single-stranded DNA. The complexes with daunomycin and distamycin were more stable to strand separation in the gas phase than dsDNA alone. This is in agreement with solution studies and with other recent gas phase results. These data contrast with many earlier ESI-MS studies of dsDNA and DNA/drug complexes in which ions from ssDNA are also normally observed.     

DNA Dangling‐End‐Induced Colloidal Stabilization of Gold Nanoparticles for Colorimetric Single‐Nucleotide Polymorphism Genotyping

A single‐nucleotide polymorphism (SNP) detection method was developed by combining single‐base primer extension and salt‐induced aggregation of gold nanoparticles densely functionalized with double‐stranded DNA (dsDNA‐AuNP). The dsDNA‐AuNPs undergo rapid aggregation in a medium of high ionic strength, whereas particles having a single‐base protrusion at the outermost surface disperse stably, allowing detection of a single‐base difference in length by color changes. When SNP typing primers are used as analytes to hybridize to the single‐stranded DNA on the AuNP surface, the resulting dsDNA‐AuNP works as a visual indicator of single‐base extension. A set of four extension reaction mixtures is prepared using each of ddNTPs and subsequently subjected to the aggregation assay. Three mixtures involving ddNTP that is not complementary to the SNP site in the target produce the aggregates that exhibit a purple color. In contrast, one mixture with the complementary ddNTP generates the single‐base protrusion and appears red. This method could potentially be used in clinical diagnostics for personalized medicine.     

Comparison of RNA, single-stranded DNA and double-stranded DNA behavior during capillary electrophoresis in semidilute polymer solutions

We present a study of the separation of RNA, single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) in semidilute linear hydroxyethylcellulose (HEC) solution. Our results strive to provide a better understanding of the mechanisms of nucleic acid migration during electrophoresis in polymer solutions under native and denaturing conditions. From a study of the dependence of mobility on chain length and applied electric field, we found that RNA and ssDNA show better separation and higher resolution over a larger range of sizes compared to dsDNA. In addition, RNA reptation without orientation extends to longer chain lengths in comparison to ssDNA, possibly as a result of different type of short-lived secondary structure formations. Such a comparative study between nucleic acid capillary electrophoresis helps to optimize RNA separation and provides better understanding of RNA migration mechanisms in semidilute polymer solutions under denaturing conditions.     

A method for DNA detection in a microchannel: fluid dynamics phenomena and optimization of microchannel structure

A simple DNA diagnosis method using microfluidics has been developed which requires simple and straightforward procedures such as injection of sample and probe DNA solutions. This method takes advantage of the highly accurate control of fluids in microchannels, and is superior to DNA microarray diagnosis methods due to its simplicity, highly quantitative determination, and high-sensitivity. The method is capable of detecting DNA hybridization for molecules as small as a 20 mer. This suggests the difference in microfluidic behavior between single strand DNA (ssDNA) and double stranded DNA (dsDNA). In this work, influence of both the inertial force exerted on DNA molecules and the diffusion of DNA molecules was investigated. Based on the determination of these parameters for both ssDNA and dsDNA by experiments, a numerical model describing the phenomena in the microchannel was designed. Computational simulation results using this model were in good agreement with previously reported experimental results. The simulation results showed that appropriate selection of the analysis point and the design of microchannel structure are important to bring out the diffusion and inertial force effects suitably and increase the sensitivity of the detection of DNA hybridization, that is, the analytical performance of the microfluidic DNA chip.     

Nanocomposite Incorporating V2O5 Nanowires and Gold Nanoparticles for Mimicking an Enzyme Cascade Reaction and Its Application in the Detection of Biomolecules

Artificial enzyme mimics are a current research interest, and many nanomaterials have been found to display enzyme‐mimicking activity. However, to the best of our knowledge, there have not hitherto been any reports on the use of pure nanomaterials to construct a system capable of mimicking an enzyme cascade reaction. Herein, we describe the construction of a novel nanocomposite consisting of V₂O₅ nanowires and gold nanoparticles (AuNPs) through a simple and facile chemical method, in which V₂O₅ and AuNPs possess intrinsic peroxidase and glucose oxidase (GOx)‐like activity, respectively. Results suggest that this material can mimic the enzyme cascade reaction of horseradish peroxidase (HRP) and GOx. Based on this mechanism, a direct and selective colorimetric method for the detection of glucose has been successfully designed. Because single‐strand and double‐strand DNA (ssDNA and dsDNA) have different deactivating effects on the GOx‐like activity of AuNPs, the sensing of target complementary DNA can also be realized and disease‐associated single‐nucleotide polymorphism of DNA can be easily distinguished. Our study opens a new avenue for the use of nanomaterials in enzyme mimetics, and holds promise for the further exploration of nanomaterials in creating alternative catalytic systems to natural enzymes.     

Impedance‐Based DNA Biosensor Employing Molecular Beacon DNA as Probe and Thionine as Charge Neutralizer

In this paper, we present an impedance‐based DNA biosensor using thionine intercalation to amplify DNA hybridization signal. Beacon single‐stranded DNA (ssDNA) probe and mercaptoacetic acid were self‐assembled onto a Au electrode by forming Au? S bonds. These beacon ssDNAs were hybridized with the complementary sequences around the loop structure. Then thionine was intercalated into the double‐stranded DNA (dsDNA) immobilized on the Au electrode surface. Due to the neutralization of the negative charges of dsDNA by the intercalated thionine, the electronic transfer resistance (R_et) of the DNA modified Au electrode was significantly diminished. Herein, the decreased value of R_et resulted from the thionine intercalating into dsDNA was employed as the hybridization signal. SDS was used to reduce the unspecific adsorption between ssDNA and thionine. Several experimental conditions, including the surface coverage of ssDNA probe on Au electrode, the hybridization temperature and time were all optimized. Moreover, the hybridization reactions of the unstructured linear ssDNA probe and the structured beacon ssDNA probe with their complementary sequences were compared in this work. The sensitivity of the presented DNA biosensor highlighted that the intercalation of thionine into dsDNA was an efficient approach to amplify the hybridization signal using impedance detection technique. Additionally, in this DNA biosensing protocol, beacon ssDNA has a good ability to distinguish target DNA sequences. This results in a higher specificity than using traditional unstructured DNA probe.     

Amplified electrochemical detection of nucleic acid hybridization via selective preconcentration of unmodified gold nanoparticles

The common drawback of optical methods for rapid detection of nucleic acid by exploiting the differential affinity of single-/double-stranded nucleic acids for unmodified gold nanoparticles (AuNPs) is its relatively low sensitivity. In this article, on the basis of selective preconcentration of AuNPs unprotected by single-stranded DNA (ssDNA) binding, a novel electrochemical strategy for nucleic acid sequence identification assay has been developed. Through detecting the redox signal mediated by AuNPs on 1, 6-hexanedithiol blocked gold electrode, the proposed method is able to ensure substantial signal amplification and a low background current. This strategy is demonstrated for quantitative analysis of the target microRNA (let-7a) in human breast adenocarcinoma cells, and a detection limit of 16 fM is readily achieved with desirable specificity and sensitivity. These results indicate that the selective preconcentration of AuNPs for electrochemical signal readout can offer a promising platform for the detection of specific nucleic acid sequence.