Immobilization of single-stranded deoxyribonucleic acid on gold electrode with self-assembled aminoethanethiol monolayer for DNA electrochemical sensor applications

A synthesized 24-mer single-stranded deoxyribonucleic acid (ssDNA) was covalently immobilized onto a self-assembled aminoethanethiol monolayer modified gold electrode, using water-soluble 1-ethyl-3(3-dimethylaminopropyl)-carbodiimide (EDC). The covalently immobilized ssDNAs were hybridized with complementary ssDNA (cDNA) or yAL(3) gene in solution, forming double-stranded DNAs (dsDNA). Meanwhile, daunomycin as an electrochemical active intercalator in the hybridization buffer solution was intercalated into the dsDNA to form a dsDNA/daunomycin system on the gold electrode surface, which was used for DNA electrochemical sensor. The cathodic waves of daunomycin bound to the double-stranded DNA (dsDNA) by linear sweep voltammetry were utilized to detect the cDNA. The cathodic peak current (i(pc)) of duanomycin was linearly related to the concentrations of cDNA between 0.1 mug ml(-1) and 0.1 ng ml(-1). The detection limit was about 30 pg ml(-1).     

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

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

以乙二胺为手臂分子制备的DNA修饰电极及其伏安性能

Carboxyl was formed on the surface of glassy carbon electrode(GCE) by electrochemical oxidation. Ethylenediamine(En) was used as the arm molecule to link carboxyl with dsDNA using 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) and N- hydroxysuccinimide (NHS) as the activators to prepare dsDNA modified electrode(dsDNA/En/GCE). It was shown that dsDNA couM be covalently immobilized on the surface of GCE. ssDNA modified electrode(ssDNA/En/GCE) was obtained via the thermal denaturation of dsDNA/En/GCE. The dsDNA/En/GCE and ssDNA/En/GCE were characterized by voltammetry with methylene blue(MB) as the indicator. The results indicated that the currents of the redox peaks of MB at ssDNA/En/GCE were larger than those at dsDNA/En/GCE, and the currents of the redox peaks at En/GCE were the smallest. The peak-currents of MB at the DNA modified electrode had good reproducibility after multi-denaturation and hybridization cycles.     

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

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

Towards the optimization of an optical DNA sensor: control of selectivity coefficients and relative surface affinities

Short single-stranded DNA (ssDNA) oligonucleotides can be grown on the surface of fused silica by automated nucleic acid synthesis. The immobilized ssDNA can be deposited at a desired average density. The density of ssDNA provides a controlled parameter that in combination with temperature, ionic strength and pH, can be used to define the selectivity of hybridization. Furthermore, the density of ssDNA can be used to control the affinity of complementary DNA so that it associates with the nucleic acids on the surface rather than areas that are not coated with ssDNA. The characteristic melt temperature observed for immobilized double-stranded DNA (dsDNA) 20mer shifts by up to 10 °C when a single base pair mismatch is present in the center of a target oligonucleotide. Optimization of quantitative analysis of such single base pair mismatches requires use of select experimental conditions to maximize the formation of the fully matched target duplex while minimizing the formation of the mismatched duplex. Results based on fiber optic biosensors that are used to study binding of fluorescein-labeled complementary DNA demonstrate that it is possible to achieve a selectivity coefficient of fully matched to single base pair mismatch of approximately 85-1, while maintaining >55% of the maximum possible signal that can be obtained from the fully matched target duplex.     

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。     

Synthesis and properties of 2-azidodeoxyadenosine and its incorporation into oligodeoxynucleotides

2-Azidodeoxyadenosine (7) was conveniently synthesized from deoxyguanosine (2) by use of a combined reagent of TMSN₃–BuONO. The structure of the tautomer of the azido derivative was determined by ¹H NMR. Reaction of 7 with iPr₂NP(OEt)₂ gave an intermediate 10 of the Staudinger reaction. Incorporation of 7 into a DNA 13mer resulted in a significant decrease of the T_m value of the DNA duplex upon hybridization with the complementary strand. The thermal stability was discussed based on the hydrogen bond energy and electrostatic repulsion.     

Electrochemical detection of DNA hybridization using methylene blue and electro-deposited zirconia thin films on gold electrodes

A novel electrochemical DNA biosensor based on methylene blue (MB) and zirconia (ZrO₂) thin films modified gold electrode for DNA hybridization detection is presented. Zirconia thin films were electrodynamically deposited onto the bare gold electrode in an aqueous electrolyte of ZrOCl₂ and KCl by cycling the potential between −1.1 and +0.7 V (versus Ag/AgCl) at a scan rate of 20 mV s⁻¹. Oligonucleotide probes with phosphate group at the 5′ end were attached onto the zirconia thin films because zirconia is affinity for phosphoric group. The surface density of the immobilized DNA molecules at the zirconia interface was investigated by fluorescence spectroscopy method. Hybridization was induced by exposure of the ssDNA-containing Au electrode to complementary ssDNA in solution. The decreases in the peak currents of MB, an electroactive label, were observed upon hybridization of probe with the target. The cathodic peak current (i_p) of MB after hybridization with the target DNA was linearly related to the logarithmic value of the target DNA concentration ranging from 2.25×10⁻¹⁰ to 2.25×10⁻⁸ mol l⁻¹. A detection limit of 1.0×10⁻¹⁰ mol l⁻¹ of oligonucleotides can be estimated.     

Tethered thiazole orange intercalating dye for development of fibre-optic nucleic acid biosensors

Single-stranded DNA (ssDNA) oligonucleotide in solution, or that is immobilized onto a surface to create a biosensor, can be used as a selective probe to bind to a complementary single-stranded sequence. Fluorescence enhancement of thiazole orange (TO) occurs when the dye intercalates into double-stranded DNA (dsDNA). TO dye has been covalently attached to probe oligonucleotides (homopolymer and mixed base 10mer and 20mer) through the 5′ terminal phosphate group using polyethylene glycol linker. The tethered TO dye was able to intercalate when dsDNA formed in solution, and also at fused silica surfaces using immobilized ssDNA. The results indicated the potential for development of a self-contained biosensor where the fluorescent label was available as part of the immobilized oligonucleotide probe chemistry. The approach was shown to be able to operate in a reversible manner for multiple cycles of detection of targeted DNA sequences.     

Osmotic effects on the enclosed volume and interlamellar spacing of multilamellar DODAC vesicles

Dispersions of multilamellar dioctadecyldimethylammonium chloride (DODAC) vesicles are known to have a wide range of sizes and lamellarities. Osmotic effects on these dispersions were investigated by means of NMR diffusometry and small angle X-ray scattering (SAXS). A clear decrease in the enclosed volume and d-spacing was observed upon a hyperosmotic stress (sucrose and CaCl₂). However, the decrease was lower than theoretically predicted for ideal osmometers. The difference was explained by the electrostatic repulsion between the charged bilayers and the finite bilayer membrane flexibility. No significant differences were observed when the osmotic stress was applied either above or below the transition temperature (T_m) when sucrose was used. Using CaCl₂ as the osmotic agent, the reduction of the enclosed volume was smaller when the hyperosmotic pressure was applied above T_m compared to when it was applied below T_m. This can be explained by similar specific shape changes as observed when unilamellar vesicles were osmotically stressed in the presence of a salt above T_m.     

Label‐Free and Label Based Electrochemical Detection of Hybridization by Using Methylene Blue and Peptide Nucleic Acid Probes at Chitosan Modified Carbon Paste Electrodes

A chitosan modified carbon paste electrode (ChiCPE) based DNA biosensor for the recognition of calf thymus double stranded DNA (dsDNA), single stranded DNA (ssDNA) and hybridization detection between complementary DNA oligonucleotides is presented. DNA and oligonucleotides were electrostatically attached by using chitosan onto CPE. The amino groups of chitosan formed a strong complex with the phosphate backbone of DNA. The immobilized probe could selectively hybridize with the target DNA to form hybrid on the CPE surface. The detection of hybridization was observed by using the label‐free and label based protocols. The oxidation signals of guanine and adenine greatly decreased when a hybrid was formed on the ChiCPE surface. The changes in the peak currents of methylene blue (MB), an electroactive label, were observed upon hybridization of probe with target. The signals of MB were investigated at dsDNA modified ChiCPE and ssDNA modified ChiCPE and the increased peak currents were observed, in respect to the order of electrodes. The hybridization of peptide nucleic acid (PNA) probes with the DNA target sequences at ChiCPE was also investigated. Performance characteristics of the sensor were described, along with future prospects.     

基于聚苯胺掺杂乙醇胺固定DNA电化学传感器的研究

本研究以电化学聚合法制备了聚苯胺掺杂乙醇胺修饰电极,并成功固定了DNA探针。文中对修饰电极的制备和DNA的固定杂交条件进行了探讨,并利用循环伏安法测定嵌入双链DNA(dsDNA)分子碱基对中的亚甲基蓝的氧化还原峰电流,识别和测定溶液中互补的单链DNA(ssDNA)片段,从而实现对溶液中不同基因片段的检测。     

Electrochemical genosensor for the detection of interaction between methylene blue and DNA

Described here are the chronocoulometric and voltammetric parameters for methylene blue [3,7-bis(dimethylamino)phenothiazin-5-ium chloride, MB] on binding to DNA at carbon paste electrode (CPE) surface. MB, which interacts with the immobilized calf thymus DNA was detected by using single stranded DNA modified CPE (ssDNA modified CPE), bare CPE and double stranded DNA modified CPE (dsDNA modified CPE) in combination with chronocoulometry and differential pulse voltammetry (DPV) techniques. The effect of ionic strength to the behavior of MB with dsDNA and ssDNA was also studied by means of voltammetry. These results demonstrated that MB could be used as an effective electroactive hybridization indicator for DNA biosensors. Performance characteristics of the sensor are described, along with future prospects.     

ssDNA/十八酸修饰碳糊电极的制备及伏安法表征

将石墨粉与十八酸在80 ℃下混合制成表面富含—COOH的基底碳糊电极(SA/CPE), 然后在活化剂N-羟基琥珀酰亚胺(NHS)和1-乙基-3-(3-二甲基氨丙基)碳二亚胺盐酸盐(EDC)存在下将ssDNA固定到电极表面制备ssDNA修饰电极(ssDNA/SA/CPE). 以亚甲基蓝(MB)为指示剂, 用循环伏安法对SA/CPE和ssDNA/SA/CPE进行电化学表征, 发现其在ssDNA/SA/CPE上较在SA/CPE上的氧化峰电流(i_pa)和还原峰电流(i_pc)分别增大1.9倍和1.7倍, 式电势(E_f)负移8 mV. 把ssDNA/SA/CPE放在互补ssDNA溶液中杂交后, MB的i_pa 和i_pc较在SA/CPE上分别增大1.0倍和0.8倍, E_f负移18 mV. 用0.5 mol/L 的NaOH溶液冲洗使电极表面杂交而成的dsDNA变性洗脱, MB的伏安信号几乎与在ssDNA/SA/CPE上一样. i_pc与SA/CPE上固定的ssDNA质量在1.0×10^－7～5.0×10^－6 g范围内成线性关系, 检测限为2.0×10^－9 g (S/N＝3). 这种既廉价又灵敏的电化学生物传感器有望在转基因植物产品检测研究中得到应用.     

吡啶基离子液体[C_6py][DCA]热力学性质及利用新E?tv?s方程预测其表面张力

制备了吡啶类离子液体N-己基吡啶二氰胺盐[C_6py][DCA],并用核磁共振氢谱(~1H NMR)、核磁共振碳谱(~(13)C NMR)、差热扫描量热(DSC)、傅里叶变换红外(FT-IR)光谱对其进行表征。在288.15–338.15 K温度范围内,采用标准加入法,测定其密度(ρ)、表面张力(γ)和折光率(n_D)。在测得的实验数据的基础上,得到了离子液体[C_6py][DCA]的分子体积(V_m)、表面能(E_a)、摩尔极化度(R_m)和极化率(α_p)。结果显示E_a、R_m和α_p几乎不随温度的变化而发生改变。本文还提出了摩尔表面Gibbs自由能(g_s)的概念,并改进了E?tv?s方程。同时还计算了gs、临界温度(T_c)和E?tv?s方程经验参数(kE),并预测了离子液体[C_6py][DCA]的表面张力,预测值与实验值具有较好的一致性。     

Packing structures of single-stranded DNA and double-stranded DNA thiolates on Au(111): a molecular simulation study

The packing structures of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) thiolates on implicit gold surfaces were studied in explicit aqueous solutions of 1M NaCl using molecular dynamics simulations. The simulations were based on individual DNA chains placed in hexagonal simulation boxes of different sizes, representing various packing densities. The total potential energy per DNA chain was compared. The optimal packing structures were determined based on the minimal potential energy within the limits of the conditions that were evaluated in this study. The optimal packing density of ssDNA was found to be 0.19 DNA chains/nm(2), which is consistent with that determined experimentally. Furthermore, the optimal packing density of dsDNA was shown to be approximately 58% of the packing density for ssDNA, indicating that the packing of ssDNA should be approximately 58% of its optimal packing in order to achieve the best hybridization.     

Determination of Electrochemical Interaction between 2‐(1H‐benzimidazol‐2‐yl) Phenol and DNA Sequences

A benzimidazole derivate, 2‐(1H‐benzimidazol‐2‐yl) phenol (2‐Bip) and its interaction mechanism with sequence specific DNA was examined with Differential Pulse Voltammetry (DPV). We, for the first time, investigated the effect of 2‐Bip on sequence specific DNA with electrochemical methods by evaluating both guanine and 2‐Bip oxidation signal changes. In the study, probe sequences were immobilized to the surface of the electrodes and then hybridization was achieved by sending the complementary target onto the probe modified electrodes. Following the hybridization, 2‐Bip solution was interacted with probe and hybrid sequences to see the effect of 2‐Bip on different DNA sequences. The binding constant (K), toxicity (S%) and thermodynamic parameters, i. e., Gibbs free energy (ΔG°) of 2‐Bip‐DNA complexes were evaluated. K was calculated as 5×10⁵ and the change in the ΔG° was found as ?32.50 kJ mol^?1, which are consistent well with the literature. Furthermore, S% showed that 2‐Bip is moderately toxic to single stranded DNA (ssDNA) and toxic to double stranded DNA (dsDNA). From our experimental data, we made four conclusions (i) 2‐Bip affects both ssDNA and dsDNA, (ii) 2‐Bip interaction mode with DNA could be non‐covalent interactions, (iii) 2‐Bip could be used as new DNA hybridization indicator due to its distinct effects on ssDNA and dsDNA, (iv) 2‐Bip could be used as a drug molecule for its DNA effect.     

Conductivity, calorimetry and phase diagram of the NaHSO4–KHSO4 system

Physico-chemical properties of the binary system NaHSO₄–KHSO₄ were studied by calorimetry and conductivity. The enthalpy of mixing has been measured at 505 K in the full composition range and the phase diagram calculated. The phase diagram has also been constructed from phase transition temperatures obtained by conductivity for 10 different compositions and by differential thermal analysis. The phase diagram is of the simple eutectic type, where the eutectic is found to have the composition X(KHSO₄) = 0.44 (melting point ≈ 406 K). The conductivities in the liquid region have been fitted to polynomials of the form κ(X) = A(X) + B(X)(T − T_m) + C(X)(T − T_m)², where T_m is the intermediate temperature of the measured temperature range and X, the mole fraction of KHSO₄. The possible role of this binary system as a catalyst solvent is also discussed.     

用于DNA杂交检测的丝网印刷型生物传感器的研究

将单链DNA(ssDNA)固定到丝网印刷碳电极上构成电化学DNA传感器,采用电化学指示剂,建立DNA杂交的检测方法.Co(phen)33+电化学指示剂通过钴盐与配体邻菲罗啉络合制备,采用等离子发射光谱法(ICP-AES)和核磁共振法(NMR)表征功能基团,采用循环伏安法(CV)分析指示剂的电化学特性,并以此为基础研究ssDNA在电极表面的固定及DNA杂交过程.本研究探讨了直接吸附、静电吸附与键合等3种ssD-NA在电极表面的固定方法,结果表明,静电吸附法和键合法具有较高的ssDNA固定量,采用静电吸附法固定探针的电极杂交目标DNA后,Co(phen)33+易于嵌入双链DNA (dsDNA)中,CV峰电流(ip)信号随目标DNA浓度增加.本研究采用静电吸附ssDNA的电极检测DNA杂交,实验表明,当探针固定液中ssDNA浓度为5 mg/L时,目标DNA浓度在6.65×10- 8～4.26× 10-6mol/L范围内,Co(phen)33+在dsDNA修饰电极上ip值与DNA浓度呈良好的线性关系,R2为0.9819.本研究为建立新的微生物分子分型手段提供了初步依据.     

Programmable and Reversible Regulation of Catalytic Hemin@MOFs Activities with DNA Structures

Metal-organic frameworks(MOFs)-based nanozyme plays an important role in biosensing,therapy and catalysis.In this study,the effects of single-stranded DNA(ssDNA)with programmable sequences and its complementary DNA(Tdna)on the intrinsic peroxidase-like activity of hemin loaded MOFs(UiO-66-NH2),denoted as he-min@UiO-66-NH2,were investigated.The hemin@UiO-66-NH2 exhibited improved catalytic activity compared with free hemin.However,the catalytic activity is inhibited in the presence of ssDNA,as ssDNA can be adsorbed by MOFs and therefore protected the active sites from contact with substrates.Upon the addition of the TDNA,double-stranded DNA(dsDNA)was formed and detached from the MOFs,resulting in the recovery of catalytic activity.Sequentially adding ssDNA or its complementary DNA strands can achieve the reversible regulation of the catalytic activity of MOFs nanozymes.Moreover,the DNA hybridization-based regulation was further applied to a cascaded catalytic system composed of the nanozyme,hemin@UiO-66-NH2,and glucose oxidase.These nanozyme based programmable and reversibly regulated catalytic systems may have potential applications in future smart biosensing and catalysis systems.