Homogeneous DNA Detection Based on Fluorescence Quenching by Nanoparticles in Single-step Format :Target-Induced Configuration Transform

A new strategy for homogeneous detection of DNA hybridization in single-step format was developed based on fluorescence quenching by gold nanoparticles. The gold nanoparticle is functionalized with 5’-thiolated 48-base oligonucleotide (probe sequence), whose 3’-terminus is labeled with fluorescein (FAM), a negatively charged fluorescence dye. The oligonucleotide adopts an extended configuration due to the electrostatic repulsion between negatively charged gold nanoparticle and the FAM-attached probe sequence. After addition of the complementary target sequence, specific DNA hybridization induces a conformation change of the probe from an extended structure to an arch-like configuration, which brings the fluorophore and the gold nanoparticle in close proximity. The fluorescence is efficiently quenched by gold nanoparticles. The fluorescence quenching efficiency is related to the target concentration, which allows the quantitative detection for target sequence in a sample. A linear detection range from 1.6 to 209.4 nmol/L was obtained under the optimized experimental conditions with a detection limit of 0.1 nmol/L. In the assay system, the gold nanoparticles act as both nanoscaffolds and nanoquenchers. Furthermore, the proposed strategy, in which only two DNA sequences are involved, is not only different from the traditional molecular beacons or reverse molecular beacons but also different from the commonly used sandwich hybridization methods. In addition, the DNA hybridization detection was achieved in homogenous solution in a single-step format, which allows real-time detection and quantification with other advantages such as easy operation and elimination of washing steps.     

A one-step highly sensitive method for DNA detection using dynamic light scattering

A one-step homogeneous DNA detection method with high sensitivity was developed using gold nanoparticles (AuNPs) coupled with dynamic light scattering (DLS) measurement. Citrate-protected AuNPs with a diameter of 30 nm were first functionalized with two sets of single-stranded DNA probes and then used as optical probes for DNA detection. In the presence of target DNA, the hybridization between target DNA and the two nanoparticle probes caused the formation of nanoparticle dimers, trimers, and oligomers. As a result, the nanoparticle aggregation increased the average diameter of the whole nanoparticle population, which can be monitored simply by DLS measurement. A quantitative correlation can be established between the average diameter of the nanoparticles and the target DNA concentration. This DLS-based assay is extremely easy to conduct and requires no additional separation and amplification steps. The detection limit is around 1 pM, which is 4 orders of magnitude better than that of light-absorption-based methods. Single base pair mismatched DNAs can be readily discriminated from perfectly matched target DNAs using this assay.     

Postsynthesis racemization and place exchange reactions. Another step to unravel the origin of chirality for chiral ligand-capped gold nanoparticles

We examine how postsynthesis nanoparticle ligand shell modifications as a general approach can help in the understanding of currently proposed mechanisms for gold nanoparticle chirality. We compare the CD response of chirally decorated mixed-monolayer-protected gold nanoparticles synthesized in situ with quasi-identical gold nanoparticles either prepared by place exchange reactions or subjected to an aqueous base, resulting in partial hydrolysis and simultaneous partial racemization. We find that the CD response at wavelengths where the free chiral ligand does not absorb strongly depends on the preparation conditions, i.e., in situ synthesis vs place exchange, and that postsynthesis racemization of the chiral ligand produces racemic nanoparticles with no CD response, i.e., no induction of a chiral bias during reductive nanoparticle formation. Considering all experimental results for the described gold nanoparticle system with a C12H24 spacer between the nanoparticle surface and chiral center, the so-called "vicinal effect" with the formation of a supramolecular assembly of the chiral moieties seems to be active. Finally, we argue that postsynthesis nanoparticle ligand shell modifications such as racemization and/or place exchange reactions are very powerful tools to unravel contributions of the different gold nanoparticle chirality mechanisms.     

Extinction coefficient of gold nanoparticles with different sizes and different capping ligands

Extinction coefficients of gold nanoparticles with core size ranging from approximately 4 to 40 nm were determined by high resolution transmission electron microscopy analysis and UV-vis absorption spectroscopic measurement. Three different types of gold nanoparticles were prepared and studied: citrate-stabilized nanoparticles in five different sizes; oleylamide-protected gold nanoparticles with a core diameter of 8 nm, and a decanethiol-protected nanoparticle with a diameter of around 4 nm. A linear relationship between the logarithms of extinction coefficients and core diameters of gold particles was found independent of the capping ligands on the particle surface and the solvents used to dissolve the nanoparticles. This linear relation may be used as a calibration curve to determine the concentration or average size of an unknown nanoparticle or nanoparticle-biomolecule conjugate sample.     

A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles

A highly sensitive and selective colorimetric lead biosensor based on DNAzyme-directed assembly of gold nanoparticles is reported. It consists of a DNAzyme and its substrate that can hybridize to a 5'-thio-modified DNA attached to gold nanoparticles. The hybridization brings gold nanoparticles together, resulting in a blue-colored nanoparticle assembly. In the presence of lead, the DNAzyme catalyzes specific hydrolytic cleavage, which prevents the formation of the nanoparticle assembly, resulting in red-colored individual nanoparticles. The detection level can be tuned to several orders of magnitude, from 100 nM to over 200 muM, through addition of an inactive variant of the DNAzyme. The concept developed here can be applied to the design of nucleic acid enzyme/nanoparticle sensors for analytes that are subject to in vitro selection, and thus can significantly expand the scope of nanomaterial applications and provide a novel approach to designing simple colorimetric biosensors.     

A one-step homogeneous immunoassay for cancer biomarker detection using gold nanoparticle probes coupled with dynamic light scattering

A one-step homogeneous immunoassay for the detection of a prostate cancer biomarker, free-PSA (prostate specific antigen), was developed using gold nanoparticle probes coupled with dynamic light scattering (DLS) measurements. A spherical gold nanoparticle with a core diameter around 37 nm and a gold nanorod with a dimension of 40 by 10 nm were first conjugated with two different primary anti-PSA antibodies and then used as optical probes for the immunoassay. In the presence of antigen f-PSA in solution, the nanoparticles and nanorods aggregate together into pairs and oligomers through the formation of a sandwich type antibody-antigen-antibody linkage. The relative ratio of nanoparticle-nanorod pairs and oligomers versus individual nanoparticles was quantitatively monitored by DLS measurement. A correlation can be established between this relative ratio and the amount of antigen in solution. The light scattering intensity of nanoparticles and nanoparticle oligomers is several orders of magnitude higher than proteins and other typical molecules, making it possible to detect nanoparticle probes in the low picomolar concentration range. f-PSA in the concentration range from 0.1 to 10 ng/mL was detected by this one-step and washing-free homogeneous immunoassay.     

Detection of DNA immobilized on bare gold electrodes and gold nanoparticle-modified electrodes via electrogenerated chemiluminescence using a ruthenium complex as a tag

Electrogenerated chemiluminescence (ECL) for DNA hybridization detection is demonstrated based on DNA that was self-assembled onto a bare gold electrode and onto a gold nanoparticles modified gold electrode. A ruthenium complex served as an ECL tag. Gold nanoparticles were self-assembled on a gold electrode associated with a 1,6-hexanedithiol monolayer. The surface density of single stranded DNA (ssDNA) on the gold nanoparticle modified gold electrode was 4.8?×?10¹⁴ molecules per square centimeter which was 12-fold higher than that on the bare gold electrode. Hybridization was induced by exposure of the target ssDNA gold electrode to the solution of ECL probe consisting of complementary ssDNA tagged with ruthenium complex. The detection limit of target ssDNA on a gold nanoparticle modified gold electrode (6.7?×?10^?12 mol L^?1) is much lower than that on a bare gold electrode (1.2?×?10^?10 mol L^?1). The method has been applied to the detection of the DNA sequence related to cystic fibrosis. This work demonstrates that employment of gold nanoparticles self-assembled on a gold electrode is a promising strategy for the enhancement of the sensitivity of ECL detection of DNA.     

Preparation of Nanogapped Gold Nanoparticle Array for DNA Detection

A novel DNA detection technique using a gold nanoparticle array film electrode has been reported here. The gold nanoparticles molecularly linked with binder molecule (1,10‐decanedithiol) were separated 1.3 nm from each other, and the DNA conductivity change from single to double strand was measured by monitoring a voltage drop across the particles, between which a probe of a 12‐mer oligonucleotide was immobilized. In adding a complementary oligonucleotide on the nanoparticle film chip, an immediate decrease in the film resistance (ca. 1.4 Ω) due to a hybridization event occurred in a reproducible manner with this simple setup. In the paper, we have an interest in the primary sensing properties; effect of the film resistance on the sensor response, dependence of the resistance change on the DNA concentration, and the performance of the system for DNA detection including single nucleotide polymorphisms were described.     

Stoichiometric functionalization of gold nanoparticles in solution through a free radical polymerization approach

A new simple concept for the stoichiometrical functionalization of nanoparticles based on free radical polymerization of vinyl protected nanoparticles is presented. To demonstrate this concept 2-bis(4-vinylphenyl)disulfane was synthesized and used in the synthesis of gold nanoparticles, leading to 4-vinylthiophenol functionalized nanoparticles. Simple free radical polymerization of these particles initiated by 4,4'-azobis-(4-cyanopentanoic acid) delivered nanoparticles with a single carboxyl group. These monofunctionalized gold nanoparticles were utilized for chemical preparation of gold nanoparticle dimers as well as for construction of gold nanoparticle arrays via binding to polyallylamine.     

Determination of the concentration and the average number of gold atoms in a gold nanoparticle by osmotic pressure

For an ideal solution, an analytical expression for the macromolecule concentration, electrolyte concentration, and solution osmotic pressure is obtained on the basis of the van't Hoff equation and the Donnan equilibrium. The expression was further applied to a colloid solution of about 3 nm glutathione-stabilized gold nanoparticles. The concentration of the colloid solution and the average net ion charge number for each gold nanoparticle were determined with the measured osmotic pressure data. Meanwhile, the gold contents of the solutions were analyzed by means of atomic absorption spectrophotometry, and the results were combined with the determined concentration of gold nanoparticle colloids to determine that the average number of gold atoms per 3 nm gold nanoparticle is 479, which is 1/1.7 times the number of atoms in bulk metallic gold of the same size. The same proportion also occurred in the 2 nm 4-mercaptobenzoic acid monolayer-protected gold nanoparticles prepared by Ackerson et al., who utilized the quantitative high-angle annular dark-field scanning transmission electron microscope to determine the average number of gold atoms per nanoparticle (Ackerson, C. J.; Jadzinsky, P. D.; Sexton J. Z.; Bushnell, D. A.; Kornberg, R. D. Synthesis and Bioconjugation of 2 and 3 nm-Diameter Gold Nanoparticles. Bioconjugate Chem. 2010, 21, 214-218).     

Electrochemical Determination of the p53 Tumor Suppressor Gene Using a Gold Nanoparticle-Graphene Nanocomposite Modified Glassy Carbon Electrode

A novel sensitive and simple electrochemical DNA sensor is reported for the determination of p53 tumor suppressor gene. A gold nanoparticle/graphene nanocomposite-modified glassy carbon electrode was prepared and methylene blue was used as the hybridization redox indicator. Scanning electron microscopic and electrochemical characterization demonstrated that the gold nanoparticles and graphene were present on the electrode. The resulting sensor provided suitable electrochemical response to the p53 tumor suppressor gene with a linear dynamic range from 0.1 to 1000?nM. The limit of detection was 0.012?nM. The sensor was able to differentiate a complete complementary DNA sequence, single-base mismatched DNA sequence, and a three-base mismatched DNA sequence. The precision of the device was satisfactory, with a relative standard deviation of 4.1% for 11 measurements. The combination of gold nanoparticles and a graphene nanocomposite provided enhanced capabilities for the determination of DNA for clinical applications.     

Formation of gold nanoparticles in aqueous solutions of cellulose derivatives and a study of the properties of these nanoparticles

It was demonstrated that gold nanoparticles can be obtained by using cellulose ethers, methyl hydroxyethyl cellulose and carboxymethylcellulose as reducing agents and also as nanoparticle stabilizers. IR spectral studies revealed a difference between the mechanisms of reduction and nanoparticle stabilization by these cellulose derivatives. A scanning tunnel microscope was used to examine composite films formed from nanoparticle dispersions on the surface of polycrystalline gold films. It was demonstrated that, in the case of gold nanoparticles, densely packed globular structures are formed in a carboxymethyl cellulose solution. A fibril-like structure of layers is formed in the Au+(methyl hydroxyethyl cellulose) system.     

Three-layer composite magnetic nanoparticle probes for DNA

A method for synthesizing composite nanoparticles with a gold shell, an Fe3O4 inner shell, and a silica core has been developed. The approach utilizes positively charged amino-modified SiO2 particles as templates for the assembly of negatively charged 15 nm superparamagnetic water-soluble Fe3O4 nanoparticles. The SiO2-Fe3O4 particles electrostatically attract 1-3 nm Au nanoparticle seeds that act in a subsequent step as nucleation sites for the formation of a continuous gold shell around the SiO2-Fe3O4 particles upon HAuCl4 reduction. The three-layer magnetic nanoparticles, when functionalized with oligonucleotides, exhibit the surface chemistry, optical properties, and cooperative DNA binding properties of gold nanoparticle probes, but the magnetic properties of the Fe3O4 inner shell.     

Controlled interparticle spacing for surface-modified gold nanoparticle aggregates

Aggregation of gold nanoparticles of increasing size has been studied as a consequence of adsorption of 2-aminothiophenol (ATP) on gold nanoparticle surfaces. The capping property of ATP in the acidic pH range has been accounted from UV-vis absorption spectroscopy and surface-enhanced Raman scattering (SERS) studies. The effect of nanoparticle size (8-55 nm) on the nature of aggregation as well as the variation in the optical response due to variable degree of interparticle coupling effects among the gold particles have been critically examined. Various techniques such as transmission electron microscopy, X-ray diffraction, zeta-potential, and average particle size measurement were undertaken to characterize the nanoparticle aggregates. The aggregate size, interparticle distances, and absorption band wavelengths were found to be highly dependent on the pH of the medium and the concentration of the capping agent, ATP. The acquired SERS spectra of ATP relate the interparticle spacing. It has been observed that the SERS signal intensities are different for different sized gold nanoparticles.     

纳米金对荧光素的荧光增效作用

纳米金对荧光素的荧光效率具有增强作用,其增强效果取决于纳米金的尺寸大小和浓度。粒径分别为5、15、25 nm的纳米金与不同浓度的荧光素溶液作用后可以增强荧光强度3~10倍,同时讨论了溶液环境和pH值对荧光增强的影响。采用本实验提出的方法可以在生化检测方面提高荧光检测方法的灵敏度。     

Aerosol assisted chemical vapor deposition using nanoparticle precursors: a route to nanocomposite thin films

Gold nanoparticle and gold/semiconductor nanocomposite thin films have been deposited using aerosol assisted chemical vapor deposition (CVD). A preformed gold colloid in toluene was used as a precursor to deposit gold films onto silica glass. These nanoparticle films showed the characteristic plasmon absorption of Au nanoparticles at 537 nm, and scanning electron microscopic (SEM) imaging confirmed the presence of individual gold particles. Nanocomposite films were deposited from the colloid concurrently with conventional CVD precursors. A film of gold particles in a host tungsten oxide matrix resulted from co-deposition with [W(OPh)(6)], while gold particles in a host titania matrix resulted from co-deposition with [Ti(O(i)Pr)(4)]. The density of Au nanoparticles within the film could be varied by changing the Au colloid concentration in the original precursor solution. Titania/gold composite films were intensely colored and showed dichromism: blue in transmitted light and red in reflected light. They showed metal-like reflection spectra and plasmon absorption. X-ray photoelectron spectroscopy and energy-dispersive X-ray analysis confirmed the presence of metallic gold, and SEM imaging showed individual Au nanoparticles embedded in the films. X-ray diffraction detected crystalline gold in the composite films. This CVD technique can be readily extended to produce other nanocomposite films by varying the colloids and precursors used, and it offers a rapid, convenient route to nanoparticle and nanocomposite thin films.     

Analytical performance of molecular beacons on surface immobilized gold nanoparticles of varying size and density

The high quenching efficiency of metal nanoparticles has facilitated its use as quenchers in molecular beacons. To optimize this system, a good understanding of the many factors that influence molecular beacon performance is required. In this study, molecular beacon performance was evaluated as a function of gold nanoparticle size and its immobilization characteristics. Gold nanoparticles of 4 nm, 15 nm and 87 nm diameter, were immobilized onto glass slides. Each size regime offered distinctive optical properties for fluorescence quenching of molecular dyes that were conjugated to oligonucleotides that were immobilized to the gold nanoparticles. Rigid double stranded DNA was used as a model to place fluorophores at different distances from the gold nanoparticles. The effect of particle size and also the immobilization density of nanoparticles was evaluated. The 4 nm and 87 nm gold nanoparticles offered the highest sensitivity in terms of the change in fluorescence intensity as a function of distance (3-fold improvement for Cy5). The optical properties of the molecular fluorophore was of significance, with Cy5 offering higher contrast ratios than Cy3 due to the red-shifted emission spectrum relative to the plasmon peak. A high density of gold nanoparticles reduced contrast ratios, indicating preference for a monolayer of immobilized nanoparticles when considering analytical performance. Molecular beacon probes were then used in place of the double stranded oligonucleotides. There was a strong dependence of molecular beacon performance on the length of a linker used for attachment to the nanoparticle surface. The optimal optical performance was obtained with 4 nm gold nanoparticles that were immobilized as monolayers of low density (5.7 × 10¹¹ particles cm⁻²) on glass surfaces. These nanoparticle surfaces offered a 2-fold improvement in analytical performance of the molecular beacons when compared to other nanoparticle sizes investigated. The principles developed in this study would assist in the design of solid phase molecular beacons using gold nanoparticles.     

Alkylthiol gold nanoparticles in sol-gel-based open tubular capillary electrochromatography

A novel open-tubular capillary electrochromatography (OTCEC) column was prepared by immobilizing dodecanethiol gold nanoparticles on prederivatised fused-silica capillary columns with sol-gel technology. 3-Mercaptopropyl-trimethoxysilane (MPTMS) was selected as sol-gel precursor to develop a sol-gel layer on the inner wall of the capillary, prior to assembly of dodecanethiol gold nanoparticles onto the generated sol-gel layer through specific interaction between the gold nanoparticles and surface terminating thiol groups. The electrochromatographic behaviour of the sol-gel gold nanoparticle capillary was compared with a gold nanoparticle capillary prepared via MPTMS surface functionalisation, through variation of the percentage of the organic modifier, pH, and separation voltage. Efficient separation for a "reversed-phase" test mixture of thiourea, naphthalene, and biphenyl and for selected polycyclic aromatic hydrocarbons (PAHs) was obtained on the sol-gel based gold nanoparticle capillaries. OTCEC separations of three selected drug substances (propiophenone, benzoin, and warfarin) were also demonstrated. Scanning electron microscopy was used for the characterization of the sol-gel gold nanoparticle capillary surface. The results confirm that dodecanethiol gold nanoparticles, bound on the sol-gel-based inner layer of fused-silica capillary, can provide sufficient solute-bonded phase interactions for OTCEC with reproducible retention as well as characteristic reversed-phase behaviour.     

金纳米粒子表面自组装巯基十一烷醇单分子层体系的制备及其光散射特性研究

采用柠檬酸钠还原法制备了水相金纳米粒子, 通过巯基的自组装, 成功获得了巯基十一烷醇(MUN)单分子层保护的金纳米粒子. 用紫外可见光谱、透射电子显微镜、激光散射粒度分析、同步散射光谱和发射光谱等手段对组装前后的金纳米粒子的性质进行了研究. 结果表明: 制备的金纳米粒子最大吸收波长518 nm, 形状规则, 粒度均匀, 平均粒径为14.6 nm, 每个粒子含有约9.64×10⁴原子; 组装之后的金纳米粒子表面等离子体共振吸收峰红移17.0 nm, 平均粒径增大为20.2 nm, 组装层的平均厚度2.8 nm, 与MUN分子长度相当, 结合量实验证明每一个金纳米粒子可以结合约7.52×10³个MUN, 表面覆盖率为83.6%, 粒子分散均匀, 稳定性增强可长期保存; 同步散射光谱变化和发射光谱中分频、差频和倍频峰的存在证明, 金纳米粒子组装前后均具有非线性光学特性.     

A two-color-change, nanoparticle-based method for DNA detection

Herein, we describe the detailed synthesis of Ag/Au core-shell nanoparticles, the surface-functionalization of these particles with thiolated oligonucleotides, and their subsequent use as probes for DNA detection. The Ag/Au core-shell nanoparticles retain the optical properties of the silver core and are easily functionalized with thiolated oligonucleotides due to the presence of the gold shell. As such, the Ag/Au core-shell nanoparticles have optical properties different from their pure gold counterparts and provide another “color” option for target DNA-directed colorimetric detection. Size-matched Ag/Au core-shell and pure gold nanoparticles perform nearly identically in DNA detection and melting experiments, but with distinct optical signatures. Based on this observation, we report the development of a two-color-change method for the detection and simultaneous validation of single-nucleotide polymorphisms in a DNA target using Ag/Au core-shell and pure gold nanoparticle probes.