Dynamic-light-scattering-based sequence-specific recognition of double-stranded DNA with oligonucleotide-functionalized gold nanoparticles

An ultrasensitive and simple dynamic-light-scattering (DLS) assay for the sequence-specific recognition of double-stranded DNA (dsDNA) was developed based on detection of the average diameter change of Au nanoparticle (AuNP) probes modified with oligonucleotides 5'-TTTCTCTTCCTT- CTCTTC-(T)(12)-SH-3' (Oligo 1) and 5'-TTCTTTCTTTTCTTTTTC-(T)(12)- SH-3' (Oligo 2). The target dsDNA was composed of two complementary oligonucleotides: 5'-AAAGAGAAGGAAGAGAAGAAGAAAGAAAAGAAAAAG-3' (Oligo 3) and 3'-TTTCTCTTCCTTCTCTTCTTCTTTCTTTTCTTTTTC-5' (Oligo 4). Hybridization of the two AuNPs-Oligo probes with the target dsDNA induced aggregation of the target dsDNA by forming triplex DNA, which accordingly increased the average diameter. This diameter change could then be detected by DLS. The average diameter was proportional to the target dsDNA concentration over the range from 593 fM to 40 pM, with a detection limit of 593 fM. Moreover, the assay had good sequence specificity for the target dsDNA.     

One-step assay for detecting influenza virus using dynamic light scattering and gold nanoparticles

Herein we detail the development of a simple, rapid, and sensitive method for quantitative detection of influenza A virus using dynamic light scattering (DLS) and gold nanoparticle (AuNP) labels. Influenza-specific antibodies are conjugated to AuNPs, and aggregation of the AuNP probes is induced upon addition of the target virus. DLS is used to measure the extent of aggregation and the mean hydrodynamic diameter is correlated to virus concentration. The effects of nanoparticle concentration and size on the analytical performance of the assay were systematically investigated. It was determined that decreasing the AuNP probe concentration improves the detection limit while the effect of changing the AuNP size is minimal. Optimization of the assay provided a detection limit of <100 TCID(50)/mL which is 1-2 orders of magnitude improved over commercial diagnostic kits without increasing the assay time or complexity. Additionally, this assay was demonstrated to perform equivalently for influenza virus prepared in different biological matrices.     

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.     

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.     

Simultaneous electrochemical determination of two analytes based on nuclease-assisted target recycling amplification

In the present study, a method for simultaneous determination of two different DNAs is developed based on nuclease-assisted target recycling and nanoparticle amplification. The target recycling process is accomplished by taking advantage of the cleavage property of nicking endonuclease (NEase) for specific nucleotide sequences in duplex. In the presence of target DNA, the linker DNA in our detection system can hybridize with the target and be cleaved to form short fragments. Thus the target DNA is released and recognized by another linker DNA, activating the next round of cleavage reaction. On the other hand, two bio-barcode probes, a PbS nanoparticles (NPs)-DNA probe and a CdS NPs-DNA probe, are used for tracing two target DNAs to further amplify the detection signals. Based on a sensitive differential pulse anodic stripping voltammetry (DPASV) method for the simultaneous detection of Pb²⁺ and Cd²⁺ obtained by dissolving two probes, two different target DNAs are determined with high sensitivity and single-base mismatch selectivity.     

Direct visual detection of DNA based on the light scattering of silica nanoparticles on a human papillomavirus DNA chip

A detection system for a human papillomavirus (HPV) DNA chip based on the light scattering of aggregated silica nanoparticle probes is presented. In the assay, a target HPV DNA is sandwiched between the capture DNA immobilized on the chip and the probe DNA immobilized on the plain silica nanoparticle. The spot where the sandwich reaction occurs appears bright white and is readily distinguishable to the naked eye. Scanning electron microscopy images clearly show the aggregation of the silica nanoparticle probes. When three different sized (55 nm, 137 nm, 286 nm) plain silica nanoparticles were compared, probes of the larger silica nanoparticles showed a higher scattering intensity. Using 286-nm silica nanoparticles, the spots obtained with 200 pM of target DNA were visually detectable. The demonstrated capability to detect a disease related target DNA with direct visualization without using a complex detection instrument provides the prerequisite for the development of portable testing kits for genotyping.     

A highly sensitive sensor for Cu2+ with unmodified gold nanoparticles and DNAzyme by using the dynamic light scattering technique

Copper ion (Cu(2+)) plays an important role in many biological reactions, and a suitable level of Cu(2+) is necessary for the regular metabolism of life. Thus developing a sensitive and simple method for determination of Cu(2+) is essential. Here, a novel and sensitive Cu(2+) sensor was developed based on detecting the average hydrodynamic diameter of AuNPs by using dynamic light scattering (DLS). Cu(2+)-specific DNAzyme was double-strand and could not adsorb on the surface of AuNPs, accordingly AuNPs aggregation would occur with the addition of NaCl. However, Cu(2+) could cleave DNAzyme and release single-stranded DNA (ssDNA) fragments, which could adsorb on the surface of AuNPs and prevent them from aggregation. Such differences in DNA adsorption ability on AuNPs before and after the addition of Cu(2+) affected the disperse state of AuNPs directly, and then affected their average hydrodynamic diameter, which could be detected with the DLS technique. Based upon the above mentioned principle, detection of Cu(2+) could be realized over the range from 100 pM to 2.0 nM, with a linear regression equation of D = 306.73 - 89.66C (C: nM, R = 0.9953) and a detection limit of 60 pM (3δ/slope). Moreover, satisfactory results were obtained when the assay was applied in the detection of Cu(2+) in water samples.     

Amplification free detection of herpes simplex virus DNA

Amplification-free detection of nucleic acids in complex biological samples is an important technology for clinical diagnostics, especially in the case where the detection is quantitative and highly sensitive. Here we present the detection of a synthetic DNA sequence from Herpes Simplex Virus-1 within swine cerebrospinal fluid (CSF), using a sandwich-like, magnetic nanoparticle pull-down assay. Magnetic nanoparticles and fluorescent polystyrene nanoparticles were both modified with DNA probes, able to hybridise either end of the target DNA, forming the sandwich-like complex which can be captured magnetically and detected by fluorescence. The concentration of the target DNA was determined by counting individual and aggregated fluorescent nanoparticles on a planar glass surface within a fluidic chamber. DNA probe coupling for both nanoparticles was optimized. Polystyrene reporter nanoparticles that had been modified with amine terminated DNA probes were also treated with amine terminated polyethylene glycol, in order to reduce non-specific aggregation and target independent adhesion to the magnetic particles. This way, a limit of detection for the target DNA of 0.8 pM and 1 pM could be achieved for hybridisation buffer and CSF respectively, corresponding to 0.072 and 0.090 femtomoles of target DNA, in a volume of 0.090 mL.     

Growth and Origami Folding of DNA on Nanoparticles for High‐Efficiency Molecular Transport in Cellular Imaging and Drug Delivery

A novel three‐dimensional (3D) superstructure based on the growth and origami folding of DNA on gold nanoparticles (AuNPs) was developed. The 3D superstructure contains a nanoparticle core and dozens of two‐dimensional DNA belts folded from long single‐stranded DNAs grown in situ on the nanoparticle by rolling circle amplification (RCA). We designed two mechanisms to achieve the loading of molecules onto the 3D superstructures. In one mechanism, ligands bound to target molecules are merged into the growing DNA during the RCA process (merging mechanism). In the other mechanism, target molecules are intercalated into the double‐stranded DNAs produced by origami folding (intercalating mechanism). We demonstrated that the as‐fabricated 3D superstructures have a high molecule‐loading capacity and that they enable the high‐efficiency transport of signal reporters and drugs for cellular imaging and drug delivery, respectively.     

Surface-enhanced Raman scattering detection of DNAs derived from virus genomes using Au-coated paramagnetic nanoparticles

A magnetic capture-based, surface-enhanced Raman scattering (SERS) assay for DNA detection has been developed which utilizes Au-coated paramagnetic nanoparticles (Au@PMPs) as both a SERS substrate and effective bioseparation reagent for the selective removal of target DNAs from solution. Hybridization reactions contained two target DNAs, sequence complementary reporter probes conjugated with spectrally distinct Raman dyes distinct for each target, and Au@PMPs conjugated with sequence complementary capture probes. In this case, target DNAs were derived from the RNA genomes of the Rift Valley Fever virus (RVFV) or West Nile virus (WNV). The hybridization reactions were incubated for a short period and then concentrated within the focus beam of an interrogating laser by magnetic pull-down. The attendant SERS response of each individually captured DNA provided a limit of detection sensitivity in the range 20-100 nM. X-ray diffraction and UV-vis analysis validated both the desired surface plasmon resonance properties and bimetallic composition of synthesized Au@PMPs, and UV-vis spectroscopy confirmed conjugation of the Raman dye compounds malachite green (MG) and erythrosin B (EB) with the RVFV and WNV reporter probes, respectively. Finally, hybridization reactions assembled for multiplexed detection of both targets yielded mixed MG/EB spectra and clearly differentiated peaks which facilitate the quantitative detection of each DNA target. On the basis of the simple design of a single-particle DNA detection assay, the opportunity is provided to develop magnetic capture-based SERS assays that are easily assembled and adapted for high-level multiplex detection using low-cost Raman instrumentation.     

A novel electrochemiluminescence aptasensor for protein based on a sensitive N-(aminobutyl)-N-ethylisoluminol-functionalized gold nanoprobe

A novel electrochemiluminescence (ECL) aptasensor for platelet-derived growth factor B chain (PDGF-BB) assay was developed by assembling N-(aminobutyl)-N-ethylisoluminol functionalized gold nanoparticles (ABEI-AuNPs) with aptamers as nanoprobes. In the protocol, the biotinylated aptamer capture probes were first immobilized on a streptavidin coated gold nanoparticle (AuNPs) modified electrode, afterwards, the target PDGF-BB and the ABEI-AuNPs tagged aptamer signal probe were successively attached to the modified electrode by virtue of the dimer structure of PDGF-BB to fabricate a "sandwich" conjugate modified electrode, i.e. an aptasensor. ECL measurement was carried out with a double-step potential in carbonate buffer solution containing H(2)O(2). The aptasensor showed high sensitivity and selectivity toward PDGF-BB and specificity toward PDGF-BB aptamer. The detection limit was as low as 2.7 × 10(-14) M. In this work, the ABEI-AuNPs synthesized by a simple seed growth method have been successfully used as aptamer labels, which greatly amplified the ECL signal by binding numbers of ABEI molecules on the surface of AuNPs. The ABEI-AuNPs signal amplification is superior to other reported signal amplification strategies based on aptamer-related polymerase chain reaction or functionalized nanoparticles in simplicity, stability, labeling property and practical applicability. And the ABEI-AuNPs based nanoprobe is more sensitive than the luminol functionalized AuNPs based nanoprobe. Moreover, such an ultra-sensitive and low-cost assay can be accomplished with a simple and fast procedure by using a simple ECL instrumentation. The aptasensor was also applied for the detection of PDGF-BB in human serum samples, showing great application potential. Given these advantages, the ECL aptasensor is well suited for the direct, sensitive and rapid detection of protein in complex clinical samples.     

Gold‐Aryl nanoparticles coated with polyelectrolytes for adsorption and protection of DNA against nuclease degradation

Binding DNA on nanoparticles was pursued to form nanoplatform for formation of non‐viral gene system. Carboxyl derivatized gold‐aryl nanoparticles can bind with biodegradable cationic polyelectrolytes such as polydiallyldimethylammonium chloride (PDADMAC). In our study, we used gold‐aryl nanoparticles (AuNPs) treated with PDADMAC to form conjugates with non‐thiol or non‐disulfide modified oligonucleotide DNA. Both AuNPs‐DNA and PDADMAC‐AuNPs‐DNA biomaterials were characterized using UV–Vis, dynamic light scattering (DLS), atomic force microscopy (AFM), transmission electron microscopy (TEM) and agarose gel electrophoresis. UV–Vis showed a red shift in the plasmon peak as compared with unconjugated AuNPs. DLS measurements also showed difference in the size of AuNPs‐DNA and PDADMAC‐AuNPs‐DNA. AFM and TEM results showed proper conjugation of DNA with AuNPs. Gel electrophoresis proved the presence of interaction between PDADMAC‐AuNPs and negatively charged DNA. The binding of DNA in the described bioconjugate enhanced its protection against nuclease degradation and prolonged its presence in the digestive environment of DNase‐I. From the results we expect that these biomaterials can be used in nanomedicine with emphasis on non‐viral gene system.     

Nanoparticle based enhancement of electrochemical DNA hybridization signal using nanoporous electrodes

A novel nanoparticle-based enhanced methodology for the detection of ssDNA using nanoporous alumina filter membranes, containing pores of 200 nm in diameter, is reported. The blockage of the pores due to the hybridization is detected by measuring the decrease in the differential pulse voltammetric response of the [Fe(CN)(6)](4-/3-) redox indicator and using screen-printed carbon electrodes as transducing platform. Furthermore, 20 nm gold nanoparticle (AuNPs) tags are used in order to increase the sensitivity of the assay. The enhancement mechanism of DNA detection is due to an additional blocking effect induced by hybridization reaction by bringing AuNPs inside the pores. The developed methodology can be extended to other biosensing systems with interest not only for DNA but also for proteins and cells. The developed nanochannel/nanoparticle biosensing system would have enormous potential in future miniaturized designs adapted to mass production technologies such as screen-printing technology.     

The gold-nanoparticle-based surface plasmon resonance light scattering and visual DNA aptasensor for lysozyme

We developed a new simple and sensitive assay for lysozyme based on gold nanoparticle plasmon resonance light scattering (PRLS) measurement and naked-eye detection using for the first time the lysozyme DNA aptamer as the recognition element. Lysozyme DNA aptamer could stabilize gold nanoparticles (AuNPs) at high ionic strength. Introducing lysozyme to the system easily triggered the aggregation of AuNPs, producing a red-to-blue color change of the solution, red-shifted plasmon absorption, and enhanced plasmon resonance light scattering. The linear range was found to be 0.2∼4 nM for 0.7 nM AuNPs, 0.3∼6 nM for 1.4 nM AuNPs and 0.6∼8 nM for 2.1 nM AuNPs. About 0.1 nM lysozyme can produce an observable enhancement of PRLS signal. For visual detection, 1 nM lysozyme can produce a very distinctive color change. Satisfactory recoveries were obtained for simulated saliva and diluted urine samples, indicating that the method has potential for analyses of clinical samples. The simplicity and high sensitivity that are consistent with the resources and needs of many laboratories makes this method a good choice for routine analysis.     

Gold nanoparticles for microfluidics-based biosensing of PCR products by hybridization-induced fluorescence quenching

Colloidal gold nanoparticles were used to develop a simple microfluidics-based bioassay that is able to recognize and detect specific DNA sequences via conformational change-induced fluorescence quenching. In this method, a self-assembled monolayer of gold nanoparticles was fabricated on the channel wall of a microfluidic chip, and DNA probes were bonded to the monolayer via thiol groups at one end and a fluorophore dye was attached to the other end of the probe. The created construct is spontaneously assembled into a constrained arch-like conformation on the particle surface and, under which, the fluorescence of fluorophores is quenched by gold nanoparticles. Hybridization of target DNAs results in a conformational change of the construct and then restores the fluorescence, which serves as a sensing method for the target genes. The nanocomposite constructed on the glass surface was characterized by UV absorbance measurement and the quenching efficiency for different fluorophores was evaluated by Stern-Volmer studies. The applicability of proposed assay was first demonstrated by the use of a pair of synthesized complementary and noncomplementary DNA sequences. The method was further applied for the detection of the PCR product of dengue virus with the use of enterovirus as the negative control, and results indicate that the assay is specific for the target gene. Moreover, using this approach, dehybridization, hybridization, and detection of the target genes can be performed in situ on the same microfluidic channel. Thus, this method could be regarded as one-pot reaction and it holds great promises for clinical diagnostics.     

Aptamer enzymatic cleavage protection assay for the gold nanoparticle-based colorimetric sensing of small molecules

A label-free, homogeneous aptamer-based sensor strategy was designed for the facile colorimetric detection of small target molecules. The format relied on the target-induced protection of DNA aptamer from the enzymatic digestion and its transduction into a detectable signal through the length-dependent adsorption of single-stranded DNA onto unmodified gold nanoparticles (AuNPs). The proof-of-principle of the approach was established by employing the anti-tyrosinamide aptamer as a model functional nucleic acid. In the absence of target, the aptamer was cleaved by the phosphodiesterase I enzymatic probe, leading to the release of mononucleotides and short DNA fragments. These governed effective electrostatic stabilization of AuNPs so that the nanoparticles remained dispersed and red-colored upon salt addition. Upon tyrosinamide binding, the enzymatic cleavage was impeded, resulting in the protection of the aptamer structure. As this long DNA molecule was unable to electrostatically stabilize AuNPs, the resulting colloidal solution turned blue after salt addition due to the formation of nanoparticle aggregates. The quantitative determination of the target can be achieved by monitoring the ratio of absorbance at 650 and 520 nm of the gold colloidal solution. A limit of detection of ∼5 μM and a linear range up to 100 μM were obtained. The sensing platform was further applied, through the same experimental protocol, to the adenosine detection by using its DNA aptamer as recognition tool. This strategy could extend the potentialities, in terms of both simplicity and general applicability, of the aptamer-based sensing approaches.     

采用纳米金和双链探针比色检测单碱基突变

将链置换的高度特异性与纳米金凝聚变色的光学特性相结合,设计了一种新型的单碱基突变比色检测方法。本方法直接采用纳米金作为比色报告基团,以两个末端均带有巯基的双链DNA为特异捕获探针,利用互补序列和单碱基突变序列对双链探针置换能力的差异,实现了对单碱基突变的检测。本检测方法直观、快速、简便、成本低,pmol级的样品无需仪器就可以观察到颜色的变化。     

基于纳米金探针和基因芯片的DNA检测新方法

运用荧光纳米金探针和基因芯片杂交建立一种新的DNA检测方法. 荧光纳米金探针表面标记有两种DNA探针: 一种为带有Cy5荧光分子的信号探针BP1, 起信号放大作用; 另一种为与靶DNA一部分互补的检测探针P532, 两种探针比例为5∶1. 当靶DNA存在时, 芯片上捕捉探针(与靶DNA的另一部分互补)通过碱基互补配对结合靶DNA, 将靶DNA固定于芯片上; 荧光纳米金探针通过检测探针与靶DNA及芯片结合, 在芯片上形成“三明治”复合结构, 最后通过检测信号探针上荧光分子的信号强度来确定靶DNA的量. 新方法检测灵敏度高, 可以检测浓度为1 pmol/L的靶DNA, 操作简单, 检测时间短. 通过改进纳米金探针的标记和优化杂交条件, 可进一步提高核酸检测的灵敏度, 这将在核酸检测方面具有重要的应用价值.     

A novel route for immobilization of oligonucleotides onto modified silica nanoparticles

A novel approach for immobilization of probe oligonucleotides that uses zirconium phosphate modified silica nanoparticles is proposed. The surface modification of nanoparticles was carried out in two stages. Initially binding of Zr4+ to the surface of silica nanoparticles and later treated with phosphoric acid for terminal phosphate groups. Oligonucleotide probes modified with amine group at 5'-end were strongly binds to the phosphate terminated silica nanoparticles with imidazole in presence of 0.1 mol L(-1) EDC [N-ethyl-N'-(3-dimethylaminopropyl) carbodiimide], as phosphate groups are more reactive towards amine group. Various studies, i.e., synthesis of silica nanoparticles, their surface modification, probe immobilization, measurement of hybridization and effect of bovine serum albumin (BSA) were carried out during optimization of reaction conditions. The significant reduction in the background signal was observed by treating the probe modified silica nanoparticles with bovine serum albumin prior to hybridization. The probe modified silica nanoparticles were retained their properties and the hybridization was induced by exposure of single-stranded DNA (ssDNA) containing silica nanoparticles to the complementary DNA in solution. The decrease in the fluorescence signal for one mismatch and three mismatch was observed upon hybridization of probe with target DNAs, while there was no response for the random target ssDNA under the same experimental conditions. The intensity of fluorescence signal was linear to the concentration of target DNA ranging from 3.9 x 10(-9) to 3.0 x 10(-6)mol L(-1). A detection limit of 1.22 x 10(-9) mol L(-1) of oligonucleotides can be estimated. The proposed hybridization assay is simple and possesses good analytical characteristics and it can provide an effective and efficient route in the development of DNA biosensors and biochips.     

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.