Electron transport by molecular motion of redox-DNA strands: unexpectedly slow rotational dynamics of 20-mer ds-DNA chains end-grafted onto surfaces via C6 linkers

The dynamics of electron transport within molecular layers of 3'-ferrocenylated 20-mer oligonucleotide, 5'-thiol end-grafted onto gold electrode surfaces via a six-carbon (C6) linker, is studied by cyclic voltammetry. Single-stranded Fc-DNA layers are observed to behave as diffusionless systems reflecting the rapid dynamics of the ssDNA strand. Following hybridization, the Fc-dsDNA-C6 layers give rise to a characteristic cyclic voltammetry behavior evidencing that the Fc head is animated by a purely diffusional motion, which is ascribed to free rotation of the rigid DNA duplex around its C6 anchoring linker. A model, describing the motion of the Fc head as resulting from hinge motion of the DNA duplex, is developed allowing the motional dynamics of the Fc-dsDNA-C6 chains to be quantified in terms of an apparent rotational diffusion coefficient, Dr. The value found for Dr is approximately 3-4 orders of magnitude slower than expected for free rotation of dsDNA in solution, pointing to a drastic motion-slowing role of the anchoring surface. Accessibility of the Fc head for the electron transfer at the electrode is also shown to modulate the apparent dsDNA dynamics. The dynamics of Fc-dsDNA-C 6 is found to be insensitive to the presence of a single mismatch in the middle of the strand, confirming that charge transport by dsDNA conduction (DNA CT) is not present for the systems studied here. However, electron transport by free hinge motion of the dsDNA chain is shown to be fast enough to, a priori, compete favorably with DNA CT.     

Exploring the motional dynamics of end-grafted DNA oligonucleotides by in situ electrochemical atomic force microscopy

We introduce herein the use of atomic-force electrochemical microscopy (AFM-SECM) to simultaneously probe locally the conformation and motional dynamics of nanometer-sized single-stranded (ss) and double-stranded (ds) DNA oligonucleotides end-tethered to electrode surfaces. The ss-DNA system studied here consists of a low-density monolayer of (dT)20 oligonucleotides, 5'-thiol end-tethered onto a flat gold surface via a C6 alkyl linker and bearing at their free 3'-end a redox ferrocene label. It is shown that, as a result of the flexibility of the relatively long C6 linker, hinge motion, rather than elastic deformation of the DNA chain, is the major component of the dynamics of both the (dT)20 strand and its post-hybridized (dT-dA)20 duplex. DNA chain elasticity is nevertheless sufficiently contributing to the overall dynamics to result in approximately 4 times slower dynamics for (dT-dA)20 than for (dT)20. Taking advantage of this dissimilar dynamical behavior of ss- and ds-DNA, it is demonstrated that hybridization can be easily locally detected at the scale of approximately 200 molecules by AFM-SECM.     

The detection of DNA deamination by electrocatalysis at DNA-modified electrodes

The method of electrocatalysis based on using a methylene blue (MB) as an electrochemical indicator and ferricyanide ions [Fe(CN)6]3- as an electron acceptor was applied in screening DNA for lesions caused by deamination of nucleobases. The damaged DNA was modeled by short 18-mer oligonucleotides containing the different number of mismatched target bases (uracil instead of cytosine residues). The hybridization capacity of these oligomers with complementary probes (immobilized on gold electrodes or free) was investigated by both electrochemical methods and UV spectroscopy. We have shown that the amplitude of the reduction signal corresponding to ferricyanide ions considerably increases in the presence of MB. This electrocatalytic effect allowed us to detect the changes in electrochemical properties of DNA caused by dU.dG mismatches. Using differential pulse voltammetry and cyclic voltammetry, we showed that the electron transport from the electrode through the double-stranded DNA to MB and then to ferricyanide ions is suppressed by the mismatches in duplex structure. According to UV-monitored melting data, single or multiple wobble dU.dG base pairs destabilize 18-mer DNA duplex by 9-27 degrees C.     

Attachment of DNA to the carbon fiber microelectrode via gold nanoparticles for simultaneous determination of dopamine and serotonin.

A novel biochemical sensor was fabricated on a carbon fiber microelectrode, which consisted of an inner layer of electrodeposited gold nanoparticles, as a nano-array electrode, and an outer layer of electrodeposited calf thymus ds-DNA at +1.5 V vs. SCE. This modified electrode was characterized by X-ray photoelectron spectroscopy, scanning electron microscope, atomic force microscopy, cyclic voltammetry and differential pulse voltammetry (DPV). It was found that this electrochemical sensor exhibits a strong catalytic activity toward the oxidation of dopamine (DA), serotonin (5-HT) and ascorbic acid (AA), as a result of resolving the anodic voltammetric peaks of DA, 5-HT and AA into three well-defined peaks. Simutaneous DPV determination of DA and 5-HT can be achieved in the presence of 2000-fold AA. The modified electrode shows good sensitivity, selectivity and stability.     

Conformational flexibility of DNA

Pulsed Electron-Electron Double Resonance (PELDOR) on double-stranded DNA (ds-DNA) was used to investigate the conformational flexibility of helical DNA. Stretching, twisting, and bending flexibility of ds-DNA was determined by incorporation of two rigid nitroxide spin labels into a series of 20 base pair (bp) DNA duplexes. Orientation-selective PELDOR experiments performed at both X-band (9 GHz/0.3 T) and G-band (180 GHz/6.4 T) with spin label distances in the range of 2-4 nm allowed us to differentiate between different simple models of DNA dynamics existing in the literature. All of our experimental results are in full agreement with a dynamic model for ds-DNA molecules, where stretching of the molecule leads to a slightly reduced radius of the helix induced by a cooperative twist-stretch coupling.     

Electrochemical studies on the permeable characteristics of thiol-modified double-stranded DNA self-assembled monolayers on gold

In this article we studied the permeable characteristics of thiol-modified double-stranded DNA (ds-DNA) self-assembled monolayers (SAMs) on a gold substrate assembled under different NaCl concentrations by electrochemical methods. It was based on the inspection of five important parameters including interfacial capacitance (C), phase angle (Φ(1?Hz)), ions transfer resistance (R(it)*), current density difference (Δj) and electron transfer rate (k(et)) through cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). Three sections were included: (1) Investigation of the relationships of C, Φ(1?Hz), R(it)*, Δj and k(et) with NaCl concentrations and comparison with the reports from literature. Experimental results showed that ds-DNA-SAMs were permeable films. (2) Construction of a simple model for exploring the permeable characteristics of ds-DNA-SAMs on gold. (3) Confirmation of the simple model by chronocoulometry (CC) and application of the model to explain the permeable mechanism. This study was significant for exploring the mechanism of electron transfer through the interior of ds-DNA duplex helix.     

2，3—二氨基吩嗪的薄层光谱电化学研究

研究了2，3—二氨基吩嗪(DAP)在金圆盘电极、金超微电极上的循环伏安行为 和在金网栅电极上的薄层循环伏安行为．在pH2．0的B—R缓冲溶液中的2，3—二氨 基吩嗪在金圆盘电极上为准可逆氧还过程；以超微电极法求得了2，3—二氨基吩嗪 在pH2．0的B—R缓冲溶液中的扩散系数，由耗竭性库仑电解和循环伏安法求得其电 极反应电子转移数和H+反应级数均为2，实验说明参与电极反应的H+也为2，并用循 环伏安法求得其标准电极反应速率常数．采用紫外—可见薄层光谱电化学方法测得 2，3—二氨基吩嗪的克式量电位和电子转移数，与电化学实验结果一致；双电位阶 跃—计时吸收紫外—可见薄层光谱电化学实验说明，2，3—二氨基吩嗪电还原无随 后化学反应，其在电极上经历了H+eH+e的两步一电子过程，生成产物2，3—二氨基 -5，10-二氢吩嗪．     

Fluorescence quenching studies of potential-dependent DNA reorientation dynamics at glassy carbon electrode surfaces

The potential-dependent reorientation dynamics of double-stranded DNA (ds-DNA) attached to planar glassy carbon electrode (GCE) surfaces were investigated. The orientation state of surface-bound ds-DNA was followed by monitoring the fluorescence from a 6-carboxyfluorescein (FAM6) fluorophore covalently linked to the distal end of the DNA. Positive potentials (i.e., +0.2 V vs open circuit potential, OCP) caused the ds-DNA to align parallel to the electrode surface, resulting in strong dipole-electrode quenching of FAM6 fluorescence. Switching of the GCE potential to negative values (i.e., -0.2 V vs OCP) caused the ds-DNA to reorient perpendicular to the electrode surface, with a concomitant increase in FAM6 fluorescence. In addition to the very fast (submilliseconds) dynamics of the initial reorientation process, slow (0.1-0.9 s) relaxation of FAM6 fluorescence to intermediate levels was also observed after potential switching. These dynamics have not been previously described in the literature. They are too slow to be explained by double layer charging, and chronoamperometry data showed no evidence of such effects. Both the amplitude and rate of the dynamics were found to depend upon buffer concentration, and ds-DNA length, demonstrating a dependence on the double layer field. The dynamics are concluded to arise from previously undetected complexities in the mechanism of potential-dependent ds-DNA reorientation. The possible origins of these dynamics are discussed. A better understanding of these dynamics will lead to improved models for potential-dependent ds-DNA reorientation at electrode surfaces and will facilitate the development of advanced electrochemical devices for detection of target DNAs.     

An electrochemical DNA sensor for determination of 6-thioguanine using adsorptive stripping voltammetry at HMDE: An anticancer drug DNA interaction study

In the present study, the electrochemical behavior of 6-Thioguanine (6-TG) and its interaction with double-strand DNA (ds-DNA) were investigated at the surface of hanging mercury drop electrode (HMDE) in neutral media. The interaction of 6-TG with ds-DNA in neutral buffer was clearly demonstrated by the elimination of 6-TG signal and the advent of a new reduction peak. To investigate the interaction, various parameters including accumulation time and potential as well as ds-DNA concentration were optimized using a combination of adsorptive stripping voltammetry (AdSV) and square wave voltammetry (SWV) techniques. As a consequence a low detection limit of 1.1 μM was obtained in a dynamic range of 16.0 to 360.0 μM. To better understand the interaction mechanism between 6-TG anti-cancer drug and ds-DNA, cyclic voltammetry and UV-Vis spectroscopy measurements were carried out and the intercalation of 6-TG into ds-DNA was proposed as the plausible mechanism. The application of this screening assay in real sample analysis was investigated by using the procedure for determination of 6-TG in 6-Thioguanine tablets and also in spiked 6-TG blood serum. Overall, the results were indicative of a DNA sensor which could be applied effectively in the analysis of 6-TG in vitro.     

Electron transfer dynamics of iridium oxide nanoparticles attached to electrodes by self-assembled monolayers

Self-assembled monolayers (SAMs) of carboxylated alkanethiolates (-S(CH(2))(n-1)CO(2)(-)) on flat gold electrode surfaces are used to tether small (ca. 2 nm d.) iridium(IV) oxide nanoparticles (Ir(IV)O(X) NPs) to the electrode. Peak potential separations in cyclic voltammetry (CV) of the nanoparticle Ir(IV/III) wave, in pH 13 aqueous base, increase with n, showing that the Ir(IV/III) apparent electron transfer kinetics of metal oxide sites in the nanoparticles respond to the imposed SAM electron transfer tunneling barrier. Estimated apparent electron transfer rate constants (k(app)(0)) for n = 12 and 16 are 9.8 and 0.12 s(-1). Owing to uncompensated solution resistance, k(app)(0) for n = 8 was too large to measure in the potential sweep experiment. For the cathodic scans, coulometric charges under the Ir(IV/III) voltammetric waves were independent of potential scan rate, suggesting participation of all of the iridium oxide redox sites (ca. 130 per NP) in the NPs. These experiments show that it is possible to control and study electron transfer dynamics of electroactive nanoparticles including, as shown by preliminary experiments, that of the electrocatalysis of water oxidation by iridium oxide nanoparticles.     

Photoelectrochemical evaluation of pH effect on hole transport through triplex-forming DNA immobilized on a gold electrode

We characterized pH effect on hole transport through DNA duplexes possessing a partial triplex-forming region. Direct electrochemical measurement of the current response of photosensitizer-tethered DNA immobilized on a gold electrode revealed that the partial triplex formation under acidic conditions suppressed photocurrent due to hole transport, while dissociation of the triplex into the duplex as occurred upon increasing pH values recovered the photocurrent efficiency. Reversible conversion between duplex and triplex induced upon cyclic alternation of pH values resulted in a rise and fall of photocurrent responses, indicating that pH change may feature in the switching function of hole transport in DNA. These electrochemical behaviors could be correlated to the results obtained in long-range photo-oxidative DNA cleavage experiments, in which DNA cleavage at the hole trapping site beyond the triplex region was significantly suppressed under triplex-forming acidic conditions.     

空壳纳米金修饰的新型DNA传感器

利用新型材料金纳米空球, 通过层层修饰的技术, 分别将壳聚糖、空壳纳米金、L-半胱氨酸、细胞色素c以及ssDNA探针修饰到玻碳电极表面, 制备了一种新型的DNA生物传感器. 以紫外及透射电子显微镜(TEM)表征了空壳纳米金, 以循环伏安法、阻抗谱图等电化学方法研究了传感器的特性, 通过原子力显微镜方法观察了该DNA生物传感器不同层之间的形态差异. 结果表明, 该修饰电极所吸附的ssDNA探针为1.672×10^―10 mol•cm^－2. 在指示剂柔红霉素的帮助下, DNA探针可与互补的DNA进行杂交, 借此以微分脉冲伏安法测定DNA.     

Scanning electrochemical microscopy. 51. Studies of self-assembled monolayers of DNA in the absence and presence of metal ions

Scanning electrochemical microscopy was used to examine electron transfer across a self-assembled monolayer of thiol-modified DNA duplexes on a gold electrode. The apparent rate constant for heterogeneous ET from a solution redox probe, Fe(CN)6(3-/4-), to the gold surface through ds-DNA was 4.6 (+/-0.2) x 10(-7) cm/s. With the addition of Zn2+, which resulted in the formation of a metalated DNA (M-DNA) monolayer, the rate constant increased to 5.0 (+/-0.3) x 10(-6) cm/s. Upon treating M-DNA with EDTA, the zinc ions were released from the monolayer and the original rate constant for the DNA duplexes was restored. The enhanced ET rate was also observed at a DNA monolayer treated with Ca2+ or Mg2+, which does not complex by the DNA bases to form M-DNA. The binding of these cations facilitated the monolayer penetration by the probe mediator Fe(CN)6(3-/4-) and accordingly caused an increased redox signal of the mediator at the ds-DNA-modified electrode. Cationic or neutral mediators were not blocked by the ds-DNA monolayer. These results suggest that although the increased electron transport through M-DNA could partially be ascribed to the intrinsic enhancement of electric conductivity of M-DNA, which has been confirmed by photochemical studies, the change in the surface charge of DNA monolayers on the electrode caused by the binding of metal ions to DNA molecules may play a more important role in the enhancement of current with M-DNA.     

邻菲咯啉-铜(Ⅱ)-L-亮氨酸配合物与DNA的结合

应用循环伏安法、微分脉冲伏安法、电子吸收光谱和溴化乙锭(EB)荧光分析法研究了[Cu(phen)(H2O)(L-Leu)^ ](phen=1，10-邻菲咯啉，L-Leu=L-亮氨酸)与小牛胸腺DNA的相互作用。结果发现中心铜离子在循环伏安图上呈现一对明显的准可逆氧化还原波。当加入一定量的DNA时，配合物的氧化还原峰电流明显降低，配位阳离子的扩散系数减小，电子光谱的最大吸收峰明显红移，产生明显的减色效应。同时，配合物也能较大程度地猝灭EB-DNA体系的荧光，证明配合物与DNA存在插入结合。     

Electrochemical DNA Hybridization Detection Using DNA Cleavage

We report the new method for detection of DNA hybridization using enzymatic cleavage. The strategy is based on that S1 nuclease is able to specifically cleave only single strand DNA, but not double strand DNA. The capture probe DNA, thiolated single strand DNA labeled with electroactive ferrocene group, was immobilized on a gold electrode. After hybridization of target DNA of complementary and noncomplementary sequences, nonhybridized single strand DNA was cleaved using S1 nuclease. The difference of enzymatic cleavage on the modified gold electrode was characterized by cyclic voltammetry and differential pulse voltammetry. We successfully applied this method to the sequence‐selective discrimination between perfectly matched and mismatched target DNA including a single‐base mismatched target DNA. Our method does not require either hybridization indicators or other exogenous signaling molecules which most of the electrochemical hybridization detection systems require.     

An Electrochemical Study of the Surface Hybridization Process of Morpholino‐DNA: Thermodynamics and Kinetics

Morpholino (MO) is a neutral analogue of DNA, which shows promise in the development of DNA biosensors and diagnostic devices. The present study explores the hybridization process of a surface‐attached MO 22‐mer with 10‐mer and 20‐mer DNA targets on a gold electrode. The melting process of the MO‐DNA duplex at the electrode/buffer interface is recorded using cyclic voltammetry. These results show that the length of target DNA, the binding location of the target DNA on the surface‐immobilized MO chain, and electrostatic forces from neighbouring duplexes all modulate the stability and hybridization kinetics of the DNA targets with the MO probes. Melting temperatures for immobilized MO‐DNA duplexes are found to be insensitive to ionic strength, provided the duplexes do not have a linker. Although the melting temperature does not shift appreciably with ionic strength, the maximum hybridization yield does. This somewhat surprising observation is considered to originate from an electrostatic limit on the extent of attainable hybridization. It is also reported that hybridization tends to initiate at the upper half of MO probes.     

Electrochemical study of thymine dimer based on DNA charge transfer

Differential pulse voltammetry was used to study the formation and level of thymine dimer in DNA duplex modified on a gold electrode. The electrochemical signal of methylene blue coupled with ferricyanide can be obtained via DNA mediated electron transfer, which would be blocked during the formation of thymine dimer. DNA duplexes with different sequences differ in the level of thymine dimer under the same UV irradiation. Futhermore, the presence of guanine base directly preceding -TT- can effectively decrease the level of thymine dimer, possibly due to the self-repair process in which guanine participates. The proposed method can be further applied to DNA self-repair analysis.     

Disposable electrochemical biosensor with multiwalled carbon nanotubes-chitosan composite layer for the detection of deep DNA damage.

A novel electrochemical DNA-based biosensor for the detection of deep DNA damage was designed employing the bionanocomposite layer of multiwalled carbon nanotubes (MWNT) in chitosan (CHIT) deposited on a screen printed carbon electrode (SPCE). The biocomponent represented by double-stranded (ds) herring sperm DNA was immobilized on this composite using layer-by-layer coverage to form a robust film. Individual and complex electrode modifiers are characterized by a differential pulse voltammetry (DPV) with the DNA redox marker [Co(phen)(3)](3+), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) with [Fe(CN)(6)](3-) as a redox probe in a phosphate buffer solution (PBS). A good correlation between the CV and EIS parameters has been found, thus confirming a strong effect of MWNT on the enhancement of the electroconductivity of the electrode surface and that of CHIT on the MWNT distribution at the electrode surface. Differences between the CV and EIS signals of the electrodes without and with DNA are used to detect deep damage to DNA, advantageously using simple working procedures in the same experiment.     

铜(Ⅱ)邻菲咯啉蛋氨酸配合物与DNA相互作用的研究

在pH=6．86磷酸盐缓冲溶液中，采用电化学(循环伏安法、微分脉冲伏安法和 交流阻抗及数据拟合技术)、粘度测定、电子吸收光谱和溴化乙锭(EB)荧光分析法 研究了[Cu(phen)(H2O)(L—Met)]^+(phen＝1，10-邻菲咯琳，L—Met=L-蛋氨酸)与 小牛胸腺DNA的相互作用。结果发现中心铜离子在循环伏安图上呈现1对明显的准可 逆氧化还原波。当加入一定量的DNA时，配合物的氧化还原峰电流明显降低，扩散 系数减小，电化学反应电阻增大，电子光谱的最大吸收峰明显红移，产生明显的减 色效应，同时，配合物也能较大程度地猝灭EB-DNA体系的荧光，说明[Cu(phen) (H2O)(L—Met)]^+与DNA的作用较强，作用模式为部分插入作用。     

Graphene-Gold Nanoparticle-modified Electrochemical Sensor for Detection of Kanamycin Based on Target-induced Aptamer Displacement

A highly sensitive and selective label-free electrochemical sensor was developed for the determination of kanamycin. To improve the sensitivity of the electrochemical sensor, graphene-gold nanoparticles were prepared by a one-step electrochemical coreduction process and were modified on the surface of a glassy carbon electrode. The double-stranded DNA(ds-DNA) duplex probe was immobilized onto the graphene-gold nanoparticle-modified electrode. The introduction of target kanamycin induced the displacement of aptamer from the ds-DNA duplex into the solution. Methylene blue(MB) as a redox indicator monitored the current change using differential pulse voltammetry. Under optimal conditions, the designed electrochemical aptasensor exhibited a wide linear range from 0.1 pmol/L to 10 pmol/L with a detection limit of 0.03 pmol/L for kanamycin. The experimental strategy enabled the direct analysis of milk samples, and the results showed high sensitivity and good selectivity.