Interaction of DNA with echinomycin at the mercury electrode surface as detected by impedance and chronopotentiometric measurements

Semiautomated Electrochemical Melting Curve Analysis Device for the Detection of an Osteoporosis Associated Single Nucleotide Polymorphism in Blood

The detection of single nucleotide polymorphisms (SNPs) is of increasing importance in many areas including clinical diagnostics, patient stratification for pharmacogenomics, and advanced forensic analysis. In the work reported, we apply a semiautomated system for solid-phase electrochemical melting curve analysis (éMCA) for the identification of the allele present at a specific SNP site associated with an increased risk of bone fracture and predisposition to osteoporosis. Asymmetric isothermal recombinase polymerase amplification using ferrocene labeled forward primers was employed to generate single stranded redox labeled amplicons. In a first approach to demonstrate the proof of concept of combining asymmetric RPA with solid-phase éMCA, a simplified system housing a multielectrode array within a polymeric microsystem, sandwiched between two aluminum plates of a heater device, was used. Sample manipulation through the microfluidic channel was controlled by a syringe pump, and an external Ag/AgCl reference electrode was employed. Individual electrodes of the array were functionalized with four different oligonucleotide probes, each probe equivalent in design with the exception of the middle nucleotide. The isothermally generated amplicons were allowed to hybridize to the surface-tethered probes and subsequently subjected to a controlled temperature ramp, and the melting of the duplex was monitored electrochemically. A clear difference between the fully complementary and a single mismatch was observed. Having demonstrated the proof-of-concept, a device for automated éMCA with increased flexibility to house diverse electrode arrays with internal quasi-gold reference electrodes, higher resolution, and broader melting temperature range was developed and exploited for the detection of SNP hetero/homozygosity. Using the optimized conditions, the system was applied to the identification of the allele present at an osteoporosis associated SNP site, rs2741856, in 10 real fingerprick/venous blood samples, with results validated using Sanger sequencing.

Low-Cost Platform for Multiplexed Electrochemical Melting Curve Analysis

Detection and identification of single nucleotide polymorphisms (SNPs) have garnered increasing interest in the past decade, finding potential application in detection of antibiotic resistance, advanced forensic science, as well as clinical diagnostics and prognostics, moving toward the realization of personalized medicine. Many different techniques have been developed for genotyping SNPs, and ideally these techniques should be rapid, easy-to-use, cost-effective, flexible, scalable, easily automated, and requiring minimal end-user intervention. While high-resolution melting curve analysis has been widely used for the detection of SNPs, fluorescence detection does not meet many of the desired requirements, and electrochemical detection is an attractive alternative due to its high sensitivity, simplicity, cost-effectiveness, and compatibility with microfabrication. Herein, we describe the multiplexed electrochemical melting curve analysis of duplex surfaces tethered to electrodes of an array. In this approach, thiolated probes designed to hybridize to a DNA sequence containing the SNP to be interrogated are immobilized on gold electrodes. Asymmetric PCR using a ferrocene-labeled forward primer is used to generate this single-stranded redox-labeled PCR amplicon. Following hybridization with the probe immobilized on the electrode surface, the electrode array is exposed to a controlled ramping of temperature, with concomitant constant washing of the electrode array surface while simultaneously carrying out voltammetric measurements. The optimum position of the site complementary to the SNP site in the immobilized probe to achieve maximum differentiation in melting temperature between wild-type and single base mismatch, thus facilitating allelic discrimination, was determined and applied to the detection of a cardiomyopathy associated SNP.

Molecular conductance of double-stranded DNA evaluated by electrochemical capacitance spectroscopy

Conductance was measured in two different double stranded DNA (both with 20 bases), the more conducting poly(dG)-poly(dC) (ds-DNAc) and the less conducting poly(dA)-poly(dT) (ds-DNAi), by means of Electrochemical Capacitance Spectroscopy (ECS). The use of the ECS approach, exemplified herein with DNA nanowires, is equally a suitable and time-dependent advantageous alternative for conductance measurement of molecular systems, additionally allowing better understanding of the alignment existing between molecular scale conductance and electron transfer rate.

Real-time monitoring of strand-displacement DNA amplification by a contactless electrochemical microsystem using interdigitated electrodes

This paper reports the design and implementation of a contactless conductivity detection system which combines a thermal control cell, a data processing system and an electrochemical (EC) cell for label-free isothermal nucleic acid amplification and real-time monitoring. The EC cell consists of a microchamber and interdigitated electrodes as the contactless conductivity biosensor with a cover slip as insulation. In our work, contactless EC measurements, the effects of trehalose on amplification, and chip surface treatment are investigated. With the superior performance of the biosensor, the device can detect the amount of pure DNA at concentrations less than 0.1 pg μl(-1). The EC cell, integrated with a heater and a temperature sensor, has successfully implemented nicking-based strand-displacement amplification at an initial concentration of 2.5 μM and the yields are monitored directly (dismissing the use of probes or labels) on-line. This contactless detector carries important advantages: high anti-interference capability, long detector life, high reusability and low cost. In addition, the small size, low power consumption and portability of the detection cell give the system the potential to be highly integrated for use in field service and point of care applications.

Brilliant cresyl blue as electroactive indicator in electrochemical DNA oligonucleotide sensors

A new electrochemical DNA biosensor is presented based on carbon past electrode (CPE) for immobilization and detection of short DNA sequences with brilliant cresyl blue (BCB) as electroactive label. The interaction of BCB with DNA is electrochemically detected and BCB displays different signals in the interaction to ssDNA and dsDNA and variation in the BCB signal represents the extent of hybridization at the electrode surface. The effect of solution pH on electrochemical behavior of BCB was investigated. Additionally, the effect of solution pH on BCB accumulation on the CPE was studied. Furthermore, experiments showed that the solution pH could influence the differential pulse voltammetry (DPV) signal of BCB accumulated on the electrode and the highest BCB signal was obtained in pH 7.00. The effect of electrochemical pretreatment of CPE on the ability of electrode in probe adsorption, BCB accumulation and conditions of probe immobilization including potential and time was investigated and optimum conditions were suggested. The peak currents of BCB were linearly related to the concentration of the target oligonucleotide sequence in the range of 1.0x10(-8) to 5.0x10(-6)M. The detection limit of this approach was 9.00nM. The selectivity of the biosensor was studied using noncomplementary oligonucleotide.

The use of electrochemical impedance spectroscopy for biosensing

This review introduces the basic concepts and terms associated with impedance and techniques of measuring impedance. The focus of this review is on the application of this transduction method for sensing purposes. Examples of its use in combination with enzymes, antibodies, DNA and with cells will be described. Important fields of application include immune and nucleic acid analysis. Special attention is devoted to the various electrode design and amplification schemes developed for sensitivity enhancement. Electrolyte insulator semiconductor (EIS) structures will be treated separately.

Impedance spectroscopy and biosensing

This chapter introduces the basic terms of impedance and the technique of impedance measurements. Furthermore, an overview of the application of this transduction method for analytical purposes will be given. Examples for combination with enzymes, antibodies, DNA but also for the analysis of living cells will be described. Special attention is devoted to the different electrode design and amplification schemes developed for sensitivity enhancement. Finally, the last two sections will show examples from the label-free determination of DNA and the sensorial detection of autoantibodies involved in celiac disease.

Target label-free, reagentless electrochemical DNA biosensor based on sub-optimum displacement

One of the most time consuming and complex steps in the detection of DNA target with a biosensor is the previous labeling of the target. In this paper, a novel target label-free, reagentless and easy to use DNA biosensor is reported. Electrochemical transduction (cyclic voltammetry, differential pulse voltammetry and impedance spectroscopy) and optical red out by surface plasmon resonance were chosen for the platform optimization. This target label-free DNA detection method is based on displacement of sub-optimum labeled oligonucleotide. This strategy requires the pre-hybridization of the capture probe immobilized on the electrode surface with a sub-optimum mutated oligonucleotide pre-labeled with an electrochemically active ferrocene moiety. Due to the higher affinity of the target that is fully complementary to the capture probe, the sub-optimum ferrocene-labeled sequence is displaced when the fully complementary target is introduced into the system. The decrease of the electrochemical signal from the ferrocene verifies the presence of the target, which is proportional to the target concentration. A variation of this strategy was employed to enhance the ferrocene signal. A diffusional mediator, ferrocyanide, was introduced in the system to help in this purpose. This platform attains a stable, specific and reproducible response (5-15%), with a detection limit in the range of microM. This electrochemical sensor is the first example of this kind of sensor to detect cystic fibrosis, however, this configuration could be generically applied to any application where the detection of a DNA target is involved.

Interaction of echinomycin with guanine: electrochemistry and spectroscopy studies

The interaction of antitumor antibiotic, echinomycin (Echi) with guanine (Gua) was thoroughly investigated by adsorptive transfer stripping cyclic voltammetry, ultraviolet and visible adsorption spectra (UV/Vis) and Fourier-transform infrared spectroscopy (FTIR). Electrochemistry provided a simple tool for verifying the occurrence of interaction between Echi and Gua. Echi could be accumulated from the solution and give well-defined electrochemical signals in 0.1 M phosphate buffer solution (pH 7.0) only when Gua was present on the surface of the electrochemically pretreated glass carbon electrode (GCE), suggesting a strong binding of Echi to Gua. All the acquired spectral data showed that a new adduct between Echi and Gua was formed, and two pairs of adjacent intermolecular hydrogen bonds between the Ala backbone atoms in Echi and Gua (Ala-NH to Gua-N3 and Gua-NH2 to Ala-CO) played a dominating role in the interaction. Electrochemistry coupled with spectroscopy techniques could provide a relatively easy way to obtain useful insights into the molecular mechanism of drug-DNA interactions, which should be important in the development of new anticancer drugs with specific base recognition.

Voltammetric analysis of drugs

A review on the voltammetric analysis of drugs is presented. The review includes a summary of the rules that must be considered for drug analysis and a survey of the use of voltammetry for drug analysis in the period from 1998 till 2002.

Mercury Electrodes in Nucleic Acid Electrochemistry: Sensitive Analytical Tools and Probes of DNA Structure. A Review

This review is devoted to applications of mercury electrodes in the electrochemical analysis of nucleic acids and in studies of DNA structure and interactions. At the mercury electrodes, nucleic acids yield faradaic signals due to redox processes involving adenine, cytosine and guanine residues, and tensammetric signals due to adsorption/desorption of polynucleotide chains at the electrode surface. Some of these signals are highly sensitive to DNA structure, providing information about conformation changes of the DNA double helix, formation of DNA strand breaks as well as covalent or non-covalent DNA interactions with small molecules (including genotoxic agents, drugs, etc.). Measurements at mercury electrodes allow for determination of small quantities of unmodified or electrochemically labeled nucleic acids. DNA-modified mercury electrodes have been used as biodetectors for DNA damaging agents or as detection electrodes in DNA hybridization assays. Mercury film and solid amalgam electrodes possess similar features in the nucleic acid analysis to mercury drop electrodes. On the contrary, intrinsic (label-free) DNA electrochemical responses at other (non-mercury) solid electrodes cannot provide information about small changes of the DNA structure. A review with 188 references.

Impedimetric biosensors

Electrochemical impedance spectroscopy (EIS) is a sensitive indicator of a wide variety of chemical and physical properties. An increasing trend towards the development of impedimetric biosensors is being currently observed. Impedimetric techniques have been performed to characterize the fabrication of the biosensors and to monitor the catalyzed reactions of enzymes or the biomolecular recognition events of specific binding proteins, lectins, receptors, nucleic acids, whole cells, antibodies or antibody-related substances. However, little attention has been paid to reviewing this interesting research area. Herein, impedimetric biosensors are reviewed and many novel designs are discussed.