Sequence-specific detection of femtomolar DNA via a chronocoulometric DNA sensor (CDS): effects of nanoparticle-mediated amplification and nanoscale control of DNA assembly at electrodes

We herein report a novel nanoparticle-based electrochemical DNA detection approach. This DNA sensor is based on a "sandwich" detection strategy, which involves capture probe DNA immobilized on gold electrodes and reporter probe DNA labeled with gold nanoparticles that flank the target DNA sequence. Electrochemical signals are generated by chronocoulometric interrogation of [Ru(NH(3))(6)](3+) that quantitatively binds to surface-confined capture probe DNA via electrostatic interactions. We demonstrated that the incorporation of a gold nanoparticle in this sensor design significantly enhanced the sensitivity and the selectivity. Nanoscale control of the self-assembly process of DNA probes at gold electrodes further increased the sensor performance. As a result of these two combined effects, this DNA sensor could detect as low as femtomolar (zeptomoles) DNA targets and exhibited excellent selectivity against even a single-base mismatch. In addition, this novel DNA sensor showed fairly good reproducibility, stability, and reusability.     

Cationic gold carbonyl complex on a phosphine support

A cationic gold carbonyl complex has been synthesized and characterized using several techniques including X-ray crystallography. [(Mes(3)P)Au(CO)][SbF(6)] (Mes = 2,4,6-Me(3)C(6)H(2)) has a linear, two-coordinate gold atom. This compound displays the CO stretching frequency at 2185 cm(-1). The (13)C NMR signal of the gold-bound (13)CO appears as a doublet centered at δ 182.6 ((2)J(C,P) = 115 Hz). A computational study shows that the Au-CO bond consists of electrostatic attraction, Au ← CO donation, and significant Au → CO π-back-bonding components. Polarization of the CO bond caused by the electrostatic effect of the cationic gold center is mainly responsible for the large blue shift in the CO stretching frequency.     

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^-.     

Probing BSA binding to citrate-coated gold nanoparticles and surfaces

The interaction of bovine serum albumin (BSA) with gold colloids and surfaces was studied using zeta-potential and quartz crystal microbalance (QCM) measurements, respectively, to determine the surface charge and coverage. The combination of these two measurements suggests that BSA binding to gold nanoparticles and gold surfaces occurs by an electrostatic mechanism when citrate is present. The binding of BSA to bare gold is nearly two times greater than the binding of BSA to a citrate-coated gold surface, suggesting that protein spreading (denaturation) on the surface may occur followed by secondary protein binding. On the other hand, binding to citrate-coated gold surfaces can be fit to a Langmuir isotherm model to obtain a maximum surface coverage of (3.7 +/- 0.2) x 10(12) molecules/cm(2) and a binding constant of 1.0 +/- 0.3 microM(-1). The zeta-potential measurements show that the stabilization of colloids by BSA has a significant contribution from a steric mechanism because the colloids are stable, even at their isoelectric point (pI approximately 4.6). To be consistent with the observed phenomena, the electrostatic interactions between BSA and citrate must consist of salt-bridges, for example, of the carboxylate-ammonium type, between the citrate and the lysine on the protein surface. The data support the role of strong electrostatic binding but do not exclude contributions from steric or hydrophobic interactions with the surface adlayer.     

Determination of DNA based on localized surface plasmon resonance light scattering using unmodified gold bipyramids

The DNA was determined based on resonance light scattering (RLS) spectrometry and the localized surface plasmon resonance. The gold bipyramids were used as the probes and synthesized by a seed-mediated method. Cetyltrimethylammonium bromide was used as stabilizing agent. DNA can be bound to the gold bipyramids due to electrostatic interaction and aggregates, which results in a strong enhancement of the RLS intensity. Under the optimal conditions, the intensity of RLS is directly proportional to the concentration of DNA in the range from 0.1 to 2.0 μg mL(-1).     

DNA Computing Systems Activated by Electrochemically‐triggered DNA Release from a Polymer‐brush‐modified Electrode Array

An array of four independently wired indium tin oxide (ITO) electrodes was used for electrochemically stimulated DNA release and activation of DNA‐based Identity, AND and XOR logic gates. Single‐stranded DNA molecules were loaded on the mixed poly(N ,N ‐dimethylaminoethyl methacrylate) (PDMAEMA)/poly(methacrylic acid) (PMAA) brush covalently attached to the ITO electrodes. The DNA deposition was performed at pH 5.0 when the polymer brush is positively charged due to protonation of tertiary amino groups in PDMAEMA, thus resulting in electrostatic attraction of the negatively charged DNA. By applying electrolysis at −1.0 V(vs. Ag/AgCl reference) electrochemical oxygen reduction resulted in the consumption of hydrogen ions and local pH increase near the electrode surface. The process resulted in recharging the polymer brush to the negative state due to dissociation of carboxylic groups of PMAA, thus repulsing the negatively charged DNA and releasing it from the electrode surface. The DNA release was performed in various combinations from different electrodes in the array assembly. The released DNA operated as input signals for activation of the Boolean logic gates. The developed system represents a step forward in DNA computing, combining for the first time DNA chemical processes with electronic input signals.     

DNA-templated assembly and electropolymerization of aniline on gold surface

Biomolecule template gives new opportunities for the fabrication of novel materials with special features. Here we report a route to the formation of DNA–polyaniline (PAn) complex, using immobilized DNA as a template. A gold electrode was first modified with monolayer of 2-aminoethanethiol by self-assembly. Thereafter, by simply immersing the gold electrode into DNA solution, DNA molecules can be attached onto the gold surface, followed by the DNA-templated assembly and electropolymerization of protonated aniline. The electrostatic interactions between DNA and aniline can keep the aniline monomers aligning along the DNA strands. Investigations by surface plasmon resonance (SPR), electrochemistry and reflection–absorption UV/Vis–Near IR spectroscopy substantially convince that PAn can be electrochemically grown around DNA template on gold surface. This work may be provides fundamental aspects for building PAn nanowires with DNA as template on solid surface if DNA molecules can be individually separated and stretched.     

基于计时库仑技术的可再生型三磷酸腺苷适配体电化学传感器的研究

构建了一种可再生型三磷酸腺苷(ATP)适配体计时库仑电化学传感器.将一条短链DNA通过AuS键自组装固定在电极表面, ATP的核酸适配体与该短链DNA杂交而结合在电极表面.带负电的DNA通过静电吸引结合电解液中的六氨合钌(RuHex)阳离子.当传感器和靶分子ATP孵育后,ATP与核酸适配体结合,使适配体链从电极表面解离,电极表面吸附的DNA量减少,结合RuHex的量随之降低.通过计时库仑技术检测RuHex响应信号降低的量 ,可以对ATP进行定量测定.此传感器的电化学响应信号与ATP浓度对数值呈线性关系,线性检测范围为0.001~100 μmol/L,检出限(S/N=3)为0.5 nmol/L.此传感器检测靶分子ATP后,可以通过简单的操作步骤再生,再生5次后的响应信号为初始信号的90%以上.采用此传感器检测大鼠脑透析液中ATP的含量为(19.2±3.7) nmol/L (n=3).     

Controlled Release of a Sparingly Water‐Soluble Anticancer Drug through pH‐Responsive Functionalized Gold‐Nanoparticle‐Decorated Liposomes

The binding and detachment of carboxyl‐modified gold nanoparticles from liposomes is used for controlled drug delivery. This study reveals that the binding and detachment of nanoparticles from liposomes depends on the degree of hydration of the liposomes. Liposomes with a lower hydration level undergo stronger electrostatic interactions with negatively charged gold nanoparticles, thus leading to a slower detachment of the carboxyl‐modified gold nanoparticles under gastric conditions. Therefore, under gastric conditions, gold‐nanoparticle‐decorated dipalmitoylphosphatidylcholine (DPPC) liposomes exhibit an at least ten‐times‐slower drug release compared to gold‐nanoparticle‐decorated 1,2‐dimyristoyl‐sn‐glycero‐3‐phosphocholine (DMPC) liposomes, although both liposomes in the bare state fail to pursue controlled release. Our study also reveals that one can modulate the drug‐release rate by simply varying the concentration of nanoparticles. This study highlights a novel strategy for the controlled release of drug molecules from liposomes.     

A sensitive, label free electrochemical aptasensor for ATP detection

A sensitive, label free electrochemical aptasensor for small molecular detection has been developed in this work based on gold nanoparticles (AuNPs) amplification. This aptasensor was fabricated as a tertiary hybrid DNA-AuNPs system, which involved the anchored DNA (ADNA) immobilized on gold electrode, reporter DNA (RDNA) tethered with AuNPs and target-responsive DNA (TRDNA) linking ADNA and RDNA. Electrochemical signal is derived from chronocoulometric interrogation of [Ru(NH₃)₆]³⁺ (RuHex) that quantitatively binds to surface-confined DNA via electrostatic interaction. Using adenosine triphosphate (ATP) as a model analyte and ATP-binding aptamer as a model molecular reorganization element, the introduction of ATP triggers the structure switching of the TRDNA to form aptamer-ATP complex, which results in the dissociation of the RDNA capped AuNPs (RDNA-AuNPs) and release of abundant RuHex molecules trapped by RDNA-AuNPs. The incorporation of AuNPs in this strategy significantly enhances the sensitivity because of the amplification of electrochemical signal by the RDNA-AuNPs/RuHex system. Under optimized conditions, a wide linear dynamic range of 4 orders of magnitude (1 nM-10 μM) was reached with the minimum detectable concentration at sub-nanomolar level (0.2 nM). Those results demonstrate that our nanoparticles-based amplification strategy is feasible for ATP assay and presents a potential universal method for other small molecular aptasensors.     

High Sensitive Electrochemiluminescence Biosensor Based on Ru(phen)32+-loaded Double Strand DNA as Signal Tags use to Detect DNA Methyltransferase Activity

DNA methyltransferase (DNA MTase) can act as biomarker for many diseases and it is important to develop some new methods for sensitive detection of DNA MTase. In this work, a highly efficient electrochemiluminescence (ECL) sensor had been designed for detection of DNA MTase based on Ru(phen)₃²⁺ loaded double strand DNA (dsDNA- Ru(phen)₃²⁺) as signal tags. Ru(phen)₃²⁺ had been efficiently embed in the dsDNA produced through a simple hybridization chain reaction. First, a hairpin probe was designed, which can be specifically recognized by Dam MTase and modified with -SH at one end. It was modified on the surface of gold electrode by -SH as an immobilization probe (IP). This IP will be methylated in the present of Dam MTase and digested by DpnI following. Results in the release of capture probe (CP) which remains on the surface of gold electrode. The CP can hybridize with the single stand part of the dsDNA- Ru(phen)₃²⁺ and make the immobilization of ECL tags on the electrode surface, which results in a strong ECL signals detected. However, without the effect of Dam MTase, the hairpin structure of IP remains stable and cannot capture signal tags, and can only detecte weak ECL signals. The biosensor can detect the activity of Dam MTase in the concentration range of 0.01 U/mL to 20 U/mL with the ECL intensity and the logarithm of the concentration have a linear relationship, and the detection limit is calculated to be 7.6 mU/mL. The developed sensor has the ability to specifically detect Dam MTase, which can be differentiated from other types of DNA MTase. In addition, the designed method has good applicability to detect Dam MTase activity in serum samples and been applied to detect its inhibitor with high efficiency.     

A new strategy for highly sensitive immunoassay based on single-particle mode detection by inductively coupled plasma mass spectrometry

A highly sensitive immunoassay is proposed based on time-resolved inductively coupled plasma mass spectrometry with nanoparticles as tags to antibody. Instead of using traditional integral mode detection, the transient signals induced by the flash of ions in the plasma torch from the ionization of nanoparticles tagged on antibody were recorded in a time-resolved mode. Since, under certain conditions, the frequency of transient signals is directly correlated to the concentration of nanoparticle tags, the concentration of nanoparticle-tagged antibodies can be quantified by the frequency of transient signals. With the present instrument setup, gold nanoparticle (Au-NP) tags, as small as about 15 nm in diameter, can be detected. This protocol is evaluated for a competitive immunoassay and the linear range for α-fetoprotein is 0. 016–6. 8 µg/L (between 20 and 80% inhibition). The limit of quantification is 0. 016 µg/L (20% inhibition, IC₂₀) with a relative standard deviation of 4.2% (20% inhibition, 4 replicates) for α-fetoprotein. The present strategy provides a sensitive readout method for nanoparticle tags, which is quite promising for numerous applications in immunoassay, DNA hybridization, and other biological analyses.     

电化学石英晶体微天平实时表征和定量检测短序列DNA

利用电化学石英晶体微天平(EQCM)这一灵敏的质量和电化学传感器测定特定序列DNA。应用自组装膜技术在压电石英晶振表面自组装一带羧基的α－硫辛酸单层膜,通过盐酸1-乙基-3-(3-二甲基氨基丙基)碳二亚胺(EDC)及N-羟基琥珀酰亚胺(NHS)共价固化寡聚核苷酸为探针,用于测定与其碱基序列互补的DNA。实验中EQCM实时监测了α-硫辛酸的自组装过程、探针固化过程及其与cDNA杂交过程。定量得出了探针固化量及cDNA杂交量。在酸性、中性和碱性条件下,分别对固化和杂交过程进行表征,实验发现探针固化及DNA杂交都受pH影响,本文对此现象进行了解释。同时,利用染料Hoechst33258的电化学活性,使其与双链DNA嵌合,通过测量Hoechst33258的电化学信息进一步验证了DNA杂交关键步骤。     

Direct monitoring kinetic studies of DNA polymerase reactions on a DNA-immobilized quartz-crystal microbalance

Catalytic reactions of DNA polymerase I from E. coli (Klenow fragment, KF) were monitored directly with a template/primer (40/25- or 75/25-mer)-immobilized 27-MHz quartz-crystal microbalance (QCM). The 27-MHz QCM is a very sensitive mass-measuring device in aqueous solution, as the frequency decreases linearly with increasing mass on the QCM electrode at the nanogram level. Three steps in polymerase reactions which include 1) binding of DNA polymerase to the primer on the QCM (mass increase); 2) elongation of complementary nucleotides along the template (mass increase); and 3) release of the enzyme from the completely polymerized DNA (mass decrease), could be monitored continuously from the time dependencies of QCM frequency changes. The binding constant (Ka) of KF to the template/primer DNA was 10(8)M(-1) (k(on) = 10(5)M(-1)s(-1) and k(off)= 10(-3)s(-1)), and decreased to 10(6)M(-1) (k'on = 10(4)M(-1)s(-1) and k'off = 10(-2)s(-1)) for completely polymerized DNA. This is due to the 10-fold decrease in binding rate constant (k(on)) and 10-fold increase in dissociation rate constant (k(off)) for completed DNA strands. Ka values depended slightly on the template and primer sequences. The kinetic parameters in the elongation process (k(cat) and Km) depended only slightly on the DNA sequences. The repair process during the elongation catalyzed by KF could also be monitored in real time as QCM frequency changes.     

未修饰的纳米金结合等位特异性扩增来检测K-ras基因点突变

将等位基因特异性扩增的特异性与纳米金特殊的光学性质相结合, 发展了一种新的基因点突变检测方法. 以肿瘤中常见的K-ras癌基因第12位密码子作为点突变检测对象, 采用突变型引物对待测序列进行等位特异性扩增. 突变型样品扩增产物中大部分是双链DNA; 而野生型样品由于不能被顺利扩增, 产物中大部分是单链DNA. 以纳米金颗粒作为报告基团, 向两种不同基因型扩增产物中依次加入纳米金胶和盐溶液, 野生型基因扩增产物中的单链引物被吸附到纳米金颗粒表面, 使得纳米金在适宜浓度的盐溶液中不发生聚集; 突变型样品扩增产物中的双链DNA由于与纳米金颗粒间存在静电斥力而不能被吸附到纳米金颗粒表面, 纳米金在该浓度的盐溶液中发生聚集, 导致两种基因型的混合液在吸收光谱和颜色方面均存在显著差异, 从而实现了检测基因点突变的目的. 该检测方法直观、快速、简便, 实验成本低, 能够检测到pmol量级的样品, 为点突变检测提供了一种实用的新方法.     

Adsorption behavior of plasmid DNA on binary self-assembled monolayers modified gold substrates

Gold is known to have good biocompatibility because of its inert activity and the surface property can be easily tailored with self-assembled monolayers (SAMs). In previous works, gold surfaces were tailored with homogeneously mixed amine and carboxylic acid functional groups to generate surfaces with a series of isoelectronic points (IEPs). In other words, by tailoring the chemical composition in binary SAMs, different surface potentials can be obtained under controlled pH environments. To understand how the surface potentials affect the interaction at the interface, a binary-SAMs-modified Au electrode on a quartz crystal microbalance with dissipation detection (QCM-D) was used owing to the high weight sensitivity of QCM-D. In QCM-D, the frequency shift and the energy dissipation are monitored simultaneously to determine the adsorption behaviors of the plasmid DNA to surfaces of various potentials in Tris-buffered NaCl solutions of different pH. The results revealed that the plasmid DNA can be adsorbed on the SAM-modified surfaces electrostatically; thus, in general, the amount of adsorbed plasmid DNA decreased with increasing environmental pH and the decreasing ratio of the amine functional groups on the surfaces owing to weaker positive potentials on the surface. For the high amine-containing surfaces, due to the strong electrostatic attraction, denser films were observed, and thus, the apparent thickness decreased slightly. The negatively charged carboxylic acid surfaces can still adsorb the negatively charged plasmid DNA at some conditions. In other words, the electrostatic model cannot explain the adsorption behavior completely, and the induced dipole (Debye) interaction between the charged and polarizable molecules needs to be considered as well.     

Gold nanoparticles decorated with oligo(ethylene glycol) thiols: protein resistance and colloidal stability

The interactions between proteins and gold colloids functionalized with protein-resistant oligo(ethylene glycol) (OEG) thiol, HS(CH2)11(OCH2CH2)6OMe (EG6OMe), in aqueous solution have been studied by small-angle X-ray scattering (SAXS) and UV-vis spectroscopy. The mean size, 2R, and the size distribution of the decorated gold colloids have been characterized by SAXS. The monolayer-protected gold colloids have no correlations due to the low volume fraction in solution and are stable in a wide range of temperatures (5-70 degrees C), pH (1.3-12.4), and ionic strength (0-1.0 M). In contrast, protein (bovine serum albumin) solutions with concentrations in the range of 60-200 mg/mL (4.6-14.5 vol %) show a pronounced correlation peak in SAXS, which results from the repulsive electrostatic interaction between charged proteins. These protein interactions show significant dependence on ionic strength, as would be expected for an electrostatic interaction (Zhang et al. J. Phys. Chem. B 2007, 111, 251). For a mixture of proteins and gold colloids, the protein-protein interaction changes little upon mixing with OEG-decorated gold colloids. In contrast, the colloid-colloid interaction is found to be strongly dependent on the protein concentration and the size of the colloid itself. Adding protein to a colloidal solution results in an attractive depletion interaction between functionalized gold colloids, and above a critical protein concentration, c*, the colloids form aggregates and flocculate. Adding salt to such mixtures enhances the depletion effect and decreases the critical protein concentration. The aggregation is a reversible process (i.e., diluting the solution leads to dissolution of aggregates). The results also indicate that the charge of the OEG self-assembled monolayer at a curved interface has a rather limited effect on the colloidal stabilization and the repulsive interaction with proteins.     

Covalently linked DNA/protein multilayered film for controlled DNA release

A stable, biocompatible single strand DNA (ssDNA)/bovine serum albumin (BSA) multilayered film for control release of DNA was fabricated on PEI-coated quartz slides, gold-evaporated plates and silicon wafers, respectively through a formaldehyde-induced, covalently linked layer-by-layer (LBL) assembly technique. The constructed film structure was well characterized by using UV-vis spectrometry, surface plasmon resonance (SPR) and atomic force microscopy (AFM). The results showed that the DNA incorporated LBL film was fabricated successfully and the amount of ssDNA and BSA in the film could be tailored simply by controlling the number of the bilayers. The control release of DNA from the film was also monitored in this study. UV-vis spectrometry, SPR and AFM measurements indicated that the release of ssDNA and amino acid was adjustable by changing the proteinase K incubation time. This biocompatible covalently assembled film demonstrates an innovative approach to engineer a DNA/protein based nanostructure for controlled DNA release, which could provide stability, controllability and flexibility superior to that of LBL film assembled by electrostatic attraction. Since the film in this work can be assembled on different substrates, it is very feasible to fabricate nanoparticle-based gene therapy systems with this new approach and to have great potential in biomedical applications.     

The promise of electrochemical impedance spectroscopy as novel technology for the management of patients with diabetes mellitus

Self-monitoring of blood glucose is the standard of care in management of hyperglycemia among patients with diabetes mellitus. To increase the sensitivity and specificity of current devices, a novel method of detecting glucose using electrochemical impedance spectroscopy (EIS) technology is explored. The enzyme glucose oxidase (GOx) was fixed to gold electrodes and a sine wave of sweeping frequencies was induced using a wide range of concentrations of glucose. Each frequency in the impedance sweep was analyzed for the highest response and R-squared value. The frequency with both factors optimized is specific for the glucose-GOx binding interaction and was determined to be 1.17 kHz in purified solutions in both higher and lower ranges of glucose. The correlation between the impedance response and concentration at the low range of detection (0-100 mg dL(-1) of glucose) was determined to be 3.53 ohm/ln (mg dL(-1)) with an R-squared value of 0.90 with a 39 mg dL(-1) lower limit of detection. The same frequency of 1.17 kHz was verified in whole blood under the same glucose range. The above data confirm that EIS offers a new method of glucose detection as an alternative to current technology in use by patients. Additionally, the unique frequency response of individual markers allows for modulation of signals so that several other markers important in the management of diabetes could be measured with a single sensor.     

Oligonucleotide-functionalized gold nanoparticles-enhanced QCM-D sensor for mercury(II) ions with high sensitivity and tunable dynamic range

A quartz crystal microbalance with dissipation monitoring (QCM-D) sensor was developed for highly sensitive and specific detection of mercury(II) ions (Hg(2+)) with a tunable dynamic range, using oligonucleotide-functionalized gold nanoparticles (GNPs) for both frequency and dissipation amplification. The fabrication of the sensor employed a 'sandwich-type' strategy, and formation of T-Hg(2+)-T structures in linker DNA reduced the hybridization of the GNPs-tagged DNA on the gold electrode, which could be used as the molecular switch for Hg(2+) sensing. This QCM-D mercury sensor showed a linear response of 10-200 nM, with detection limits of 4 nM and 7 nM for frequency and dissipation measurements, respectively. Moreover, the dynamic range of the sensor could be tuned by simply altering the concentration of linker DNA without designing new sensors in the cases where detection of Hg(2+) at different levels is required. This sensor afforded excellent selectivity toward Hg(2+) compared with other potential coexisting metal ions. The feasibility of the sensor was demonstrated by analyzing Hg(2+)-spiked tap- and lake-water samples with satisfactory recoveries. The proposed approach extended the application of the QCM-D system in metal ions sensing, and could be adopted for the detection of other analytes when complemented with the use of functional DNA structures.