Designed diblock oligonucleotide for the synthesis of spatially isolated and highly hybridizable functionalization of DNA-gold nanoparticle nanoconjugates

Conjugates of DNA and gold nanoparticles (AuNPs) typically exploit the strong Au-S chemistry to self-assemble thiolated oligonucleotides at AuNPs. However, it remains challenging to precisely control the orientation and conformation of surface-tethered oligonucleotides and finely tune the hybridization ability. We herein report a novel strategy for spatially controlled functionalization of AuNPs with designed diblock oligonucleotides that are free of modifications. We have demonstrated that poly adenine (polyA) can serve as an effective anchoring block for preferential binding with the AuNP surface, and the appended recognition block adopts an upright conformation that favors DNA hybridization. The lateral spacing and surface density of DNA on AuNPs can also be systematically modulated by adjusting the length of the polyA block. Significantly, this diblock oligonucleotide strategy results in DNA-AuNPs nanoconjugates with high and tunable hybridization ability, which form the basis of a rapid plasmonic DNA sensor.     

Instantaneous and quantitative functionalization of gold nanoparticles with thiolated DNA using a pH-assisted and surfactant-free route

The attachment of thiolated DNA to gold nanoparticles (AuNPs) has enabled many landmark works in nanobiotechnology. This conjugate chemistry is typically performed using a salt-aging protocol where, in the presence of an excess amount of DNA, NaCl is gradually added to increase DNA loading over 1-2 days. To functionalize large AuNPs, surfactants need to be used, which may generate difficulties for downstream biological applications. We report herein a novel method using a pH 3.0 citrate buffer to complete the attachment process in a few minutes. More importantly, it allows for quantitative DNA adsorption, eliminating the need to quantify the number of adsorbed DNA and allowing the adsorption of multiple DNAs with different sequences at predetermined ratios. The method has been tested for various DNAs over a wide range of AuNP sizes. Our work suggests a synergistic effect between pH and salt in DNA attachment and reveals the fundamental kinetics of AuNP aggregation versus DNA adsorption, providing a novel means to modulate the interactions between DNA and AuNPs.     

基于金纳米颗粒信号放大效应电化学检测DNA聚合酶

基于金纳米颗粒(AuNPs)比表面积大、 尺寸小和能够承载大量DNA片段的特点, 建立了一种免标记、 简便、 快速检测DNA聚合酶Klenow fragment exo-(KF^-)的电化学方法. 首先将巯基化的DNA引物片段修饰在金电极上, 然后加入模板DNA链以及修饰有报告DNA链的金纳米颗粒(AuNPs-DNA), 模板DNA链能同时与DNA引物片段和修饰在AuNPs上的报告DNA链进行互补杂交形成"三明治"结构, 从而将AuNPs-DNA修饰在电极表面; 当加入电活性物质钌铵(RuHex)后, RuHex可通过静电吸附作用结合在DNA上. AuNPs上修饰的报告DNA链能够吸附大量RuHex, 导致电化学信号放大. 当加入脱氧核糖核苷三磷酸(dNTPs)以及KF^-聚合酶后, 引物片段发生延伸反应, 将与模板DNA链杂交的AuNPs-DNA竞争下来, 带走大量的RuHex, 使电信号降低, 从而实现对聚合酶的检测. 实验结果表明, 利用该方法可以检测到5 U/mL的KF^-.     

Selective DNA detection at Zeptomole level based on coulometric measurement of gold nanoparticle-mediated electron transfer across a self-assembled monolayer

A selective DNA sensing with zeptomole detection level is developed based on coulometric measurement of gold nanoparticle (AuNPs)-mediated electron transfer (ET) across a self-assembled monolayer on the gold electrode. After immobilization of a thiolated hairpin-structured DNA probe, an alkanethiol monolayer was self-assembled on the resultant electrode to block [Fe(CN)6 ]-3-/4in a solution from accessing the electrode. In the presence of DNA target, hybridization between the DNA probe and the DNA target breaks the stem duplex of DNA probe. Consequently, stem moiety at the 3′-end of the DNA probes was removed from the electrode surface and made available for hybridization with the reporter DNA-AuNPs conjugates (reporter DNA-AuNPs). The thiolated reporter DNA matches the stem moiety at the 3′-end of the DNA probe. AuNPs were then enlarged by immersing the electrode in a growth solution containing HAuCl 4 and H2O2 after the reporter DNA-AuNPs bound onto the electrode surface. The enlarged AuNPs on the electrode restored the ET between the electrode and the [Fe(CN)6]3 -/4- , as a result, amplified signals were achieved for DNA target detection using the coulometric measurement of Fe(CN)6 3- electro-reduction by prolonging the electrolysis time. The quantities of ET on the DNA sensor increased with the increase in DNA target concentration through a linear range of 3.0 fM to 1.0 pM when electrolysis time was set to 300 s, and the detection limit was 1.0 fM. Correspondingly, thousands of DNA (zeptomole) copies were detected in 10L samples. Furthermore, the DNA sensor showed excellent differentiation ability for single-base mismatch.     

Aptamer‐Assisted Gold Nanoparticles/PEDOT Platform for Ultrasensitive Detection of LPS

Neatly arranged gold nanoparticles (AuNPs) were directly electrodeposited on an electrochemically polymerized self‐assembled monolayer (SAM) of thiol‐functionalized 3,4‐ethylenedioxythiophene (EDOT) derivative, EDTMSHA. A thiolated single‐stranded DNA (ssDNA) aptamer with high specificity to LPS was immobilized on the AuNPs/conducting polymer composite film, serving as sensing platform for LPS detection. Electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV), scanning electron microscope (SEM), and atomic force microscopy (AFM) were utilized to characterize the modification and detection processes. The electron transfer resistance was found to have a linear relationship with LPS concentration from 0.1 pg/mL to 1 ng/mL.     

Nanocatalyst-based assay using DNA-conjugated Au nanoparticles for electrochemical DNA detection

Compared to enzymes, Au nanocatalysts show better long-term stability and are more easily prepared. Au nanoparticles (AuNPs) are used as catalytic labels to achieve ultrasensitive DNA detection via fast catalytic reactions. In addition, magnetic beads (MBs) are employed to permit low nonspecific binding of DNA-conjugated AuNPs and to minimize the electrocatalytic current of AuNPs as well as to take advantage of easy magnetic separation. In a sandwich-type electrochemical sensor, capture-probe-conjugated MBs and an indium-tin oxide electrode modified with a partially ferrocene-modified dendrimer act as the target-binding surface and the signal-generating surface, respectively. A thiolated detection-probe-conjugated AuNP exhibits a high level of unblocked active sites and permits the easy access of p-nitrophenol and NaBH 4 to these sites. Electroactive p-aminophenol is generated at these sites and is then electrooxidized to p-quinoneimine at the electrode. The p-aminophenol redox cycling by NaBH 4 offers large signal amplification. The nonspecific binding of detection-probe-conjugated AuNPs is lowered by washing DNA-linked MB-AuNP assemblies with a formamide-containing solution, and the electrocatalytic oxidation of NaBH 4 by AuNPs is minimized because long-range electron transfer between the electrode and the AuNPs bound to MBs is not feasible. The high signal amplification and low background current enable the detection of 1 fM target DNA.     

Adsorption of DNA onto gold nanoparticles and graphene oxide: surface science and applications

The interaction between DNA and inorganic surfaces has attracted intense research interest, as a detailed understanding of adsorption and desorption is required for DNA microarray optimization, biosensor development, and nanoparticle functionalization. One of the most commonly studied surfaces is gold due to its unique optical and electric properties. Through various surface science tools, it was found that thiolated DNA can interact with gold not only via the thiol group but also through the DNA bases. Most of the previous work has been performed with planar gold surfaces. However, knowledge gained from planar gold may not be directly applicable to gold nanoparticles (AuNPs) for several reasons. First, DNA adsorption affinity is a function of AuNP size. Second, DNA may interact with AuNPs differently due to the high curvature. Finally, the colloidal stability of AuNPs confines salt concentration, whereas there is no such limit for planar gold. In addition to gold, graphene oxide (GO) has emerged as a new material for interfacing with DNA. GO and AuNPs share many similar properties for DNA adsorption; both have negatively charged surfaces but can still strongly adsorb DNA, and both are excellent fluorescence quenchers. Similar analytical and biomedical applications have been demonstrated with these two surfaces. The nature of the attractive force however, is different for each of these. DNA adsorption on AuNPs occurs via specific chemical interactions but adsorption on GO occurs via aromatic stacking and hydrophobic interactions. Herein, we summarize the recent developments in studying non-thiolated DNA adsorption and desorption as a function of salt, pH, temperature and DNA secondary structures. Potential future directions and applications are also discussed.     

Visual and on-site detection of mercury(II) ions on lateral flow strips using DNA-functionalized gold nanoparticles

A test strip for detection of Hg(2+) in aqueous solution based on the DNA-functionalized gold nanoparticles (DNA-AuNPs) was developed and evaluated. When Hg(2+) ions were introduced, the biotinylated DNA(2) hybridized with thiolated DNA(1) functionalized on the AuNPs (DNA(1)-AuNPs) to form mismatch complexes through thymine-Hg(2+)-thymine (T-Hg(2+)-T) coordination. The formed mismatch complexes and excess DNA(1)-AuNPs could be captured on the test line formed by streptavidin and the control line formed by DNA(3)-BSA, respectively. Two red lines appeared due to the accumulation of AuNPs, enabling visual detection of Hg(2+) with a detection limit of about 6 nM. The assay results can be obtained within 5 min. The results show that the test strip has excellent sensitivity and selectivity for detection of Hg(2+); thus it holds a great potential for rapid, on-site and real time detection of Hg(2+).     

Polymolecular adsorption and capillary condensation in narrow slit pores

Capillary condensation and polymolecular adsorption in narrow slits has been calculated, where the fields of surface forces overlap one another. The calculations were carried out on the basis of macroscopic theory of dispersion forces and the isotherms of lone adsorption layers at the free surface. It has been shown that under the effect of mutual attraction through a gap, polymolecular adsorption films lose their stability long before their thickness has approached the half-width of a flat slit. This results in hysteresis of the capillary condensation in an ensemble of plane-parallel slits.

In the case of systems having strong adsorbate-adsorbate interaction, there has been detected the existence of the lower limit of sizes of slit pores, wherein the capillary meniscus can coexist with adsorption films. With a slit width smaller than the critical one, the meniscus is likely to form a finite contact angle with “dry” surfaces of a slit. Thus an explanation has been given of the lower limit of the capillary condensation in an ensemble of flat-surface, slit pores. In the case of strong adsorbate-adsorbent interaction, the coexistence of meniscus with adsorption films within the scope of the approach used is possible in slits of any width.

The value of corrections for the surface forces effect to be entered in the calculations of slit pores dimensions has been analyzed on the basis of the capillary condensation data obtained.

In wedge-shaped slits there also exists, besides lower limit the upper limit of capillary hysteresis.     

Monte Carlo Simulations of Polymers in Nanoslits

Summary: Monte Carlo computer simulations have been performed for model polymers confined in slits of thickness comparable to the transverse diameter of the chains. The density of polymer within the slits is allowed to vary with the slit thickness in such a way that the content of the slits is always in equilibrium with a large reservoir of bulk polymer. The calculations reveal the presence of polymer‐mediated attractive or repulsive interactions between the slit plates, oscillating with the slit thickness in good agreement with experimental results.

The base cell used in the simulations.     

Electrophoresis of a bead-rod chain through a narrow slit: a Brownian dynamics study

We use two-dimensional Brownian dynamics simulations to study the electrophoresis of a bead-rod chain through a narrow slit. A constant electric field is assumed to act inside and outside of the slit, and each bead on the chain is assigned a constant uniform charge. We calculate the dependence of the polymer transit velocity on chain length, slit dimensions (width-to-length ratio), and electric-field strength. For sufficiently narrow slits, the transit velocity increases nonlinearly with the applied field for low-field strengths, whereas it increases linearly for high-field strengths. In the low-field strength region and for sufficiently narrow slits, the transit velocity decreases rapidly for small chain lengths and then decreases slowly beyond a critical chain length. As the slit width increases, the transit velocity decreases with chain length in more continuous manner, and for sufficiently large slits the transit velocity becomes independent of chain length as expected. Distributions of the chain end-to-end distances and the translocation times depend strongly on the relative size of the chain to the slit. These results show the sensitivity of the transit velocity vs chain length relationship to the slit dimensions and applied electric-field strength, and suggest that there may be an optimal slit width for a given field strength and vice versa. The results may be useful for microfluidic separations and for understanding the motion of biological polymers through narrow constrictions.     

Experimental characterization of straight spectrometer slits

A technique for calibrating slit width for straight spectrometer slits based on the diffraction of laser radiation is described. Related slit properties and calibration apparatus are discussed.     

Hybridization induced ion-barrier effect for the label-free and sensitive electrochemical sensing of Hepatocellular Carcinoma biomarker of miRNA-122

A label-free and sensitive electrochemical biosensing strategy for a hepatocellular carcinoma biomarker of miRNA-122 has been proposed based on hybridization induced ion-barrier effect on the electroactive sensing interface.First,a bifunctional electroactive electrode with the nanocomposite of Prussian blue(PB) and gold nanoparticles(AuNPs) was prepared through a two-step electrodeposition process.The PB endows the electrode excellent K~+-dependent voltammetric signal and the AuNPs act as the matrix for the self-assembly immobilization of the thiolated probe DNA.Upon specific hybridization of probe DNA with the target miRNA-122,the formed double duplex induced the ion-barrier effect,which blocked the diffusion of the K~+ from the bulk solution to the electrode surface.As a result,the voltammetric signal of the PB on the electrode was surpressed,and thus the target miRNA-122 was monitored.The sensing assay showed that the miRNA-122 could be analyzed in the concentration range from 0.1 fmol/L to 1.0 nmol/L,with a detection limit of 0.021 fmol/L.The practical applicability of the biosensor was also verified by the spiking serum assay.     

Symmetry breaking of the fluid density profiles in closed nanoslits

The density profiles in a fluid interacting with the two identical solid walls of a closed long slit were calculated for wide ranges of the number of fluid molecules in the slit and temperature by employing a nonlocal density functional theory. Using argon as the sample fluid and considering the walls composed of solid carbon dioxide, it is shown that the density profile corresponding to the stable state of the fluid considerably changes its shape with increasing average density rho(av) of the fluid inside the slit. Temperature dependent critical values rho(sb1) and rho(sb2) of rho(av) were identified, such that for rho(sb1)相似文献   

Highly Sensitive Voltammetric Thrombin Aptamer Sensor Based on the Synergistic Effect of Doping/Depositing Gold Nanoparticles in Polydopamine Film

A highly sensitive square‐wave voltammetric thrombin (TB) aptamer sensor was developed using functional polydopamine (PD) film by doping and depositing gold nanoparticles into the bulk and the surface of PD. The aptamer sensor was fabricated by immobilizing a thiolated TB‐binding aptamer (TBA) on the AuNPs‐doped/deposited PD film. AuNPs‐supported methylene blue labels were used for the detection of human α‐TB. Under the optimized conditions, the aptamer sensor’s dynamic range and the detection limit were determined to be 2.0 pM–50 nM and 0.97±0.06 pM, respectively. Finally, the proposed aptamer sensor was successfully examined in human serum samples and satisfactory results were obtained.     

Molecular arrangements and conformations of liquid unbranched alkanes in narrow slits

Realistic, atomistic models of liquid tridecane in broad slits (>3 nm) and in narrow slits of thickness 1,2 nm and 1,0 nm have been obtained using the Monte Carlo technique. The setup of the models is such that the molecules in the slits are in equilibrium with the bulk liquid. The surfaces of the plates are modelled as two-dimensional arrays of hexagonally packed units having the same size and interaction parameters of a methylene group. The regions adjacent to the plates in slits with thickness > 3 nm are characterized by a well defined tendency to form partially ordered layer structures, while molecules at a distance from the plates larger than 1,5 nm are unperturbed. The simultaneous presence of two plates increases the tendency to form layer structures when their distance is 1,2 nm, while this tendency is almost totally destroyed when the slit is squeezed down to a thickness of 1,0 nm. This is also associated with a 10% decrease of the density in the latter slit.     

Nanostructured Screen Printed Graphite Electrode for the Development of a Novel Electrochemical Genosensor

The aim of this work is the preparation of DNA‐sensing architectures based on gold nanoparticles (AuNPs) in conjunction with an enzyme‐amplified detection to improve the analytical properties of genosensor. In order to assess the utility of study as DNA‐sensing devices, a thiolated DNA capture probe sequence was immobilized on the gold nanoparticle modified surface. After labeling of the biotinylated hybrid with a streptavidin‐alkaline phosphatase conjugate, the electrochemical detection of the enzymatic product was performed on the surface of a disposable electrode. Two different enzymatic substrates to detect the hybridization event were studied. In the first case, the enzyme catalyzed the hydrolysis of α‐naphthyl phosphate; the product is electroactive and has been detected by means of differential pulse voltammetry (DPV). In the second one, the enzyme catalyzed the precipitation of an insoluble and insulating product on the sensing interface. In this case, the electrochemical transduction of the hybridization process was performed by electrochemical impedance spectroscopy (EIS).     

Tangential and nondiagonal components of pressure in a circular slit

Two local tangential and one nondiagonal components of the pressure tensor have been calculated inside circular plane-parallel empty slits with dispersion forces. Symmetric and asymmetric slits have been considered. The spatial dependences have the same character for both tangential components, although their absolute values are somewhat different. It has been shown that, in the symmetric slit, the corrections for its finite size to the tangential pressure appear to be larger than those to the normal pressure. The nondiagonal pressure component becomes noticeable only near the edges of narrow slits.     

The asymptotics of distribution functions in fluid-filled finite slits

Asymptotic formulas have been derived for distribution functions in cylindrical slits with finite cross-section radii. The problem has been solved based on the asymptotic principle of interbody interactions within the framework of dispersion forces. Symmetric and asymmetric slits between two identical cylinders and between a cylinder and a planar infinite solid surface have been considered. Calculations have been performed for a symmetric slit with a width equal to two cylinder radii.     

Ensembles of nanoelectrodes modified with gold nanoparticles: characterization and application to DNA-hybridization detection

A new method to increase the active area (A _act) of nanoelectrode ensembles (NEEs) is described. To this aim, gold nanoparticles (AuNPs) are immobilized onto the surface of NEEs using cysteamine as a cross-linker able to bind the AuNPs to the heads of the nanoelectrodes to obtain the so-called AuNPs-NEEs. The analysis of the cyclic voltammograms recorded in pure supporting electrolyte showed that the presence of the nanoparticles reflects in an, approximately, ten-times increase in the electrochemically active area of the ensemble. The measurement of the amount of electroactive polyoxometalates, which can be adsorbed on the gold surface of NEEs vs. AuNPs-NEEs, confirmed a significant increase of active area for the latter. These evidences indicate that there is a good electronic connection between the AuNPs and the underlying nanoelectrodes. The possibility to exploit AuNPs-NEEs for biosensing application was tested for the case of DNA-hybridization detection. After immobilization on the gold surface of AuNPs-NEEs of a thiolated single-stranded DNA, the hybridization with complementary sequences labeled with glucose oxidase (GOx) was performed. The detection of the hybridization was achieved by adding to the electrolyte solution the GOx substrate (i.e., glucose) and a suitable redox mediator, namely the (ferrocenylmethyl) trimethylammonium (FA⁺) cation; when the hybridization occurs, an electrocatalytic increase of the oxidation current of FA⁺ is recorded. Comparison of electrocatalytic current recorded at DNA modified NEEs and AuNPs-NEEs indicate, for the latter, a significant increase in sensitivity in the detection of the DNA-hybridization event.