Tail-labelling of DNA probes using modified deoxynucleotide triphosphates and terminal deoxynucleotidyl transferase. Application in electrochemical DNA hybridization and protein-DNA binding assays

A simple approach to DNA tail-labelling using terminal deoxynucleotidyl transferase and modified deoxynucleoside triphosphates is presented. Amino- and nitrophenyl-modified dNTPs were found to be good substrates for this enzyme giving 3'-end stretches of different lengths depending on the nucleotide and concentration. 3-Nitrophenyl-7-deazaG was selected as the most useful label because its dNTP was efficiently incorporated by the transferase to form long tail-labels at any oligonucleotide. Accumulation of many nitrophenyl tags per oligonucleotide resulted in a considerable enhancement of voltammetric signals due to the nitro group reduction, thus improving the sensitivity of electrochemical detection of the tail-labelled probes. We demonstrate a perfect discrimination between complementary and non-complementary target DNAs sequences by tail-labelled hybridization probes as well as the ability of tumour suppressor p53 protein to recognize a specific binding site within tail-labelled DNA substrates, making the methodology useful in electrochemical DNA hybridization and DNA-protein interaction assays.     

Synthesis of Selenium‐Triphosphates (dNTPαSe) for More Specific DNA Polymerization

2′‐Deoxynucleoside 5′‐(alpha‐P‐seleno)‐triphosphates (dNTPαSe) have been conveniently synthesized using a protection‐free, one‐pot strategy. One of two diastereomers of each dNTPαSe can be efficiently recognized by DNA polymerases, while the other is neither a substrate nor an inhibitor. Furthermore, this Se‐atom modification can significantly inhibit non‐specific DNA polymerization caused by mis‐priming. Se–DNAs amplified with dNTPαSe via polymerase chain reaction have sequences identical to the corresponding native DNA. In conclusion, a simple strategy for more specific DNA polymerization has been established by replacing native dNTPs with dNTPαSe.     

Femtomolar electrochemical detection of DNA targets using metal sulfide nanoparticles

A new electrochemical DNA sensor providing detection capabilities down to 100 attomol of target DNA has been developed. The method applies CdS, ZnS, and PbS nanoparticles conjugated with short DNA sequences which are immobilized via hybridization with complementary sequences on a gold surface. When the DNA target is added, it can be identified by ousting the existing hybridization between one of the DNA-nanoparticle conjugates and the surface DNA. The nanoparticles remaining at the surface are detected by stripping voltammetry. The setup is constructed to give a signal-off response with a build-in control signal as only one of two different metal sulfide signaling probes on the surface is removed by hybridization with the DNA target. The competition assay is, in principle, label-free since no labels are required for detection after addition of DNA target. The dissociation of PbS nanoparticles from the surface after addition of the DNA target has been imaged by fluid phase AFM.     

Hairpin Assembly Amplified Electrochemical Biosensor for Highly Sensitive and Specific Detection of DNA

In this report, a simple electrochemical biosensor has been developed for highly sensitive and specific detection of DNA based on hairpin assembly amplification. In the presence of target DNA, the biotin‐labelled hairpin H1 is opened by hybridizing with target DNA through complementary sequences. Then the opened hairpin H1 assembles with the hairpin H2 to displace the target DNA, generating H1‐H2 complex. The displaced target DNA could trigger the next cycle of hairpins assembly, resulting in the generation of numerous H1‐H2 complexes. Subsequently, the H1‐H2 complex hybridizes with the capture probe immobilized on the electrode. Finally, the streptavidin alkaline phosphatase (ST‐ALP) binds to biotin in the capture probe‐H1‐H2 complex and catalyzes the substrate α‐naphthol (α‐NP) to produce electrochemical signal. To make a more fascinating hairpin assembly amplification strategy in signal amplification, mismatched base sequences are designed in hairpin H2 to decrease non‐specific binding of the hairpin substrates. The developed biosensor achieves a sensitivity of 20 pM with a linear range from 25 pM to 25 nM, and shows high selectivity toward single‐base mismatch. Thus, the proposed electrochemical biosensor might have the potential for early clinical diagnosis and therapy.     

Synthesis,Chemical Characterization,DNA Interaction and Antioxidant,Studies of New Nitrosubstituted Thioureas and Their Copper Complexes

In the present work new nitro substituted thioureas, and their copper complexes have been synthesized and characterized by FTIR and multinuclear NMR techniques. Some of the compounds namely 1‐benzoyl‐3‐(4‐chloro‐3‐nitrophenyl) thiourea (A‐1), 1‐benzoyl‐3‐(4‐chloro‐3‐nitrophenyl) thiourea (A‐2) and 1‐benzoyl‐3‐(2‐methoxy‐4‐nitrophenyl) thiourea (A‐2) have also been characterized by single crystal XRD. All the synthesized compounds have been screened for DNA binding potencies (using cyclic voltametry, UV‐vis spectroscopy) and free radical scavanging activities.     

Electrochemical Kinetic Characterization of Redox Mediated Glucose Oxidase Reactions: A Simplified Approach

One of the main drawbacks affecting first‐generation electrochemical biosensors in the analysis of real matrices is the interference of electroactive species present in the sample under investigation. Several approaches have been attempted to overcome this problem in the past ten years but the best results were achieved by using mediated based electrochemical biosensors. Despite this, the kinetic of the redox mediators‐enzymatic proteins interaction has not been studied deeply enough. In this work we have developed a theoretical‐methodological approach for the characterization of the kinetic of interaction between redox enzymes and substrates and/or redox mediators. Particularly, the interaction of glucose oxidase (GOx) with several commercially available redox mediators has been studied by means of amperometry and cyclic voltammetry. The main kinetic parameters for different mediators were exploited and discussed with the aim of finding the best mediator for a glucose biosensor to be used on real samples.     

An Electropolymerized Membrane Biosensor for Speciffic DNA Recognition

A sensitive electrochemical biosensor for detecting the sequence of short DNA oligomers is represented. The biosensor is based on a platinum electrode covered a polymerized membrane of conductive monomer N‐[6‐(thien‐3‐yl)acetoxy]‐pyrrolidine‐2, 5‐dione (TAPD). The membrane of TAPD immobilizes a probe DNA on the electrode. The hybridization of the probe with a sequence‐specific DNA in sample solutions is monitored by a self‐synthesized electroactive indicator, which specifically intercalates in the hybrids on the electrode surface. The current signal of the biosensor is proportional to the concentration of the target DNA in samples, and a very low detection limit of 5 × 10^?10 mol/L is found. The biosensor has been used to detect the short oligomers containing of HTV‐1 and mycobacterrium nucleotide sequences.     

Amplified Electrochemical Immunosensor for Calmodulin Detection Based on Gold‐Silver‐Graphene Hybrid Nanomaterials and Enhanced Gold Nanorods Labels

Calmodulin (CaM) is an important intracellular calcium‐binding protein. It plays a critical role in a variety of biological and biochemical processes. In this paper, a new electrochemical immunosensing protocol for sensitive detection of CaM was developed by using gold‐silver‐graphene (AuAgGP) hybrid nanomaterials as protein immobilization matrices and gold nanorods (GNRs) as enhanced electrochemical labels. Electrode was first modified with thionine‐chitosan film to provide an immobilization support for gold‐silver‐graphene hybrid nanomaterials. The hybrid materials formed an effective matrix for binding of CaM with high density and improved the electrochemical responses as well. Gold nanorods were prepared for the fabrication of enhanced labels (HRP‐Ab₂‐GNRs), which provided a large capacity for HRP‐Ab₂ immobilization and a facile pathway for electron transfer. With two‐step immunoassay format, the HRP‐Ab₂‐GNRs labels were introduced onto the electrode surface, and produced electrochemical responses by catalytic reaction of HRP toward enzyme substrate of hydrogen peroxide (H₂O₂) in the presence of thionine. The proposed immunosensor showed an excellent analytical performance for the detection of CaM ranging from 50 pg mL^?1 to 200 ng mL^?1 with a detection limit of 18 pg mL^?1. The immunosensor has also been successfully applied to the CaM analysis in two cancer cells (HepG2 and MCF‐7) with high sensitivity, which has shown great potency for improving clinic diagnosis and treatment for cancer study.     

电化学DNA生物传感器*

对特异DNA序列的检测在基因相关疾病的诊断、军事反恐和环境监测等方面均具有非常重要的意义,DNA传感器的研究就是为了满足对特异DNA序列的快速、便捷、高灵敏度和高选择性检测的需要。近年来涌现出了多种传感策略,根据检测方法的不同可以大致分为光学传感器、电化学传感器、声学传感器等。由于电化学检测方法本身所具有的灵敏、快速、低成本和低能耗等特点,电化学DNA传感器已成为一个非常活跃的研究领域并在近几年中得到了快速发展。本文概括了近年来在DNA传感器的重要分支——电化学DNA传感器领域内的一些重要进展,主要包括DNA探针在传感界面上的固定方法和各种电化学DNA杂交信号的检测方法。     

Redox Couple of DNA on Multiwalled Carbon Nanotube Modified Electrode

It has been envisioned that carbon nanotubes could promote electron‐transfer reactions when used as electrode materials in electrochemical cells. In the present study, calf thymus DNA was electrochemically oxidized at an electrode modified with multiwalled carbon nanotubes. The potentials for DNA oxidation at pH 7.0 were found to be 0.71 and 0.81 V versus SCE, corresponding to the oxidation of guanine and adenine residues, respectively. An initial oxidation of adenine was observed in the first scan, which was followed by a quasi‐reversible redox process of the oxidation product in the subsequent scans.     

Novel Protocol for Covalent Immobilization of Horseradish Peroxidase on Gold Electrode Surface

A novel protocol for immobilization of horseradish peroxidase (HRP) onto diazonium functionalized screen‐printed gold electrode (SPGE) has been successfully developed. This protocol involved 1) electrochemical reduction of p‐nitrophenyl diazonium salts synthesized in situ in acidic aqueous solution to graft a layer of p‐nitrophenyl on SPGE, 2) electrochemical reduction of the nitro groups to convert to amines, 3) chemical reaction with nitrous acid to transform the amine to diazonium derivative and 4) chemical coupling of the enzyme with the diazonium group to form a covalent diazo bond. The fabricated biosensor showed the direct electrochemistry of HRP and displayed electrocatalytic activity towards the reduction of hydrogen peroxide (H₂O₂) without any mediator. The biosensor exhibited fast amperometric response to H₂O₂. The catalytic current increased with increasing H₂O₂ concentration from 5 μM to 30 μM and the detection limit of the biosensor was 2 μM. The biosensor exhibited acceptable sensitivity, good reproducibility and long‐term stability.     

Base-Modified DNA Labeled by [Ru(bpy)3]2+ and [Os(bpy)3]2+ Complexes: Construction by Polymerase Incorporation of Modified Nucleoside Triphosphates,Electrochemical and Luminescent Properties,and Applications

Modified 2′-deoxynucleoside triphosphates (dNTPs) bearing [Ru(bpy)₃]²⁺ and [Os(bpy)₃]²⁺ complexes attached via an acetylene linker to the 5-position of pyrimidines (C and U) or to the 7-position of 7-deazapurines (7-deaza-A and 7-deaza-G) have been prepared in one step by aqueous cross-couplings of halogenated dNTPs with the corresponding terminal acetylenes. Polymerase incorporation by primer extension using Vent (exo-) or Pwo polymerases gave DNA labeled in specific positions with Ru²⁺ or Os²⁺ complexes. Square-wave voltammetry could be efficiently used to detect these labeled nucleic acids by reversible oxidations of Ru^2+/3+ or Os^2+/3+. The redox potentials of the Ru²⁺ complexes (1.1–1.25 V) are very close to that of G oxidation (1.1 V), while the potentials of Os²⁺ complexes (0.75 V) are sufficiently different to enable their independent detection. On the other hand, Ru²⁺-labeled DNA can be independently analyzed by luminescence. In combination with previously reported dNTPs bearing ferrocene, aminophenyl, and nitrophenyl tags, the Os-labeled dATP has been successfully used for “multicolor” redox labeling of DNA and for DNA minisequencing.     

Coupling of a Reagentless Electrochemical DNA Biosensor with Conducting Polymer Film and Nanocomposite as Matrices for the Detection of the HIV DNA Sequences

Abstract

This paper describes a reagentless electrochemical DNA biosensor applied to the detection of human immunodeficiency virus (HIV) sequences based on electrochemical impedance spectroscopy (EIS). The novel DNA biosensor has been elaborated by means of an opposite‐charged adsorption Au‐Ag nanocomposite to a conductive polymer polypyrrole (PPy) modified platinum electrode (Pt) and self‐assembly the mercapto oligonucleotide probes onto the surface of modified electrode via the nanocomposite. The duplex formation was detected by measuring the electrochemical impedance signal of nucleic acids in phosphate buffer solution (PBS). Such response is based on the concomitant conductivity changes of the PPy film and nanocomposite. The reagentless scheme has been characterised using 21‐mer synthetic oligonucleotides as models: parameters affecting the hybridization assay were explored and optimized. The detection limit is 5.0×10^?10 M of target oligonucleotides at 3σ. The potential for development of reagentless DNA hybridization analysis in the clinical diagnosis is being pursued.     

Voltammetric Characterization of 2‐Methoxy‐4‐Nitrophenyl Derivatized Carbon Powder

Carbon powder has been functionalized with 2‐methoxy‐4‐nitrophenyl groups by the reduction of 2‐methoxy‐4‐nitrobenzenediazonium‐1,5‐naphthalenedisulfonate salt in presence of hypophosporous acid as a reducing agent. This provides an easy and inexpensive methodology to modify the carbon particle surface. This derivatization is carried out in the presence of 2‐methoxy‐4‐nitrobenzenediazonium 1,5‐naphthalenedisulfonate salt along with the carbon powder and hypophosporous acid. The electrochemical behavior of the resulting 2‐methoxy‐4‐nitrophenyl functionalized carbon powder was characterized by immobilizing it onto basal plane pyrolytic graphite (bppg) electrode and studying its voltammetric behavior. The surface morphology of derivatized carbon powder has been examined by SEM studies which revealed that the size of the functionalized carbon particles are larger than bare carbon particles The effect of pH on peak potentials, scan rate and stability of the functionalized carbon particles has revealed that they are surface bound species.     

Parallel Detection of Different DNA Sequences on One Gold Electrode

Motivated by the potential of electrochemical techniques to analyze hybridization events fast and in a simple and cost‐effective way we present here a detection system allowing a parallel electrochemical DNA analysis. For this purpose different probe DNA strands have been immobilized on one electrode. By the use of two different target DNA sequences, both marked with the redox active methylene blue, we can show that hybridization with the complementary probe sh“NA strands can occur without steric hindrance. Each target has been recognized down to 3nM with a very high specificity of the sensor. In addition, we can detect two different ssDNA targets labeled with different redox active molecules, methylene blue and ferrocene, on one sensor surface simultaneously.     

Label‐free Voltammetric Detection of Products of Terminal Deoxynucleotidyl Transferase Tailing Reaction

A label‐free approach that takes advantage of intrinsic electrochemical activity of nucleobases has been applied to study the products of terminal deoxynucleotidyl transferase (TdT) tailing reaction. DNA homooligonucleotides A₃₀, C₃₀ and T₃₀ were used as primers for the tailing reaction to which a dNTP – or a mixture of dNTPs – and TdT were added to form the tails. Electrochemical detection enabled study of the tailing reaction products created by various combinations of primers and dNTPs, with pyrolytic graphite electrode (PGE) being suitable for remarkably precise analysis of the length of tailing reaction products. Furthermore, the hanging mercury drop electrode (HMDE) was able to reveal formation of various DNA structures, such as DNA hairpins and G‐quadruplexes, which influence the behavior of DNA molecules at the negatively charged surface of HMDE. Thus, the described approach proves to be an excellent tool for studying the TdT tailing reactions and for exploring how various DNA structures affect both the tailing reactions and electrochemical behavior of DNA oligonucleotides at electrode surfaces.     

Structures of KlenTaq DNA polymerase caught while incorporating C5-modified pyrimidine and C7-modified 7-deazapurine nucleoside triphosphates

The capability of DNA polymerases to accept chemically modified nucleotides is of paramount importance for many biotechnological applications. Although these analogues are widely used, the structural basis for the acceptance of the unnatural nucleotide surrogates has been only sparsely explored. Here we present in total six crystal structures of modified 2'-deoxynucleoside-5'-O-triphosphates (dNTPs) carrying modifications at the C5 positions of pyrimidines or C7 positions of 7-deazapurines in complex with a DNA polymerase and a primer/template complex. The modified dNTPs are in positions poised for catalysis leading to incorporation. These structural data provide insight into the mechanism of incorporation and acceptance of modified dNTPs. Our results open the door for rational design of modified nucleotides, which should offer great opportunities for future applications.     

Recent Advances of Carbon Nanotubes‐based Electrochemical Immunosensors for the Detection of Protein Cancer Biomarkers

An efficient electrochemical immunosensor can offer the potential for the detection of protein cancer biomarkers due to its high sensitivity, low cost and possible integration in compact analytical devices. In the last several years, researchers have developed various electrochemical immunoassay methods for the detection of protein cancer biomarkers. Significant progresses have been made in the study of electrochemical immunosensor that based on CNTs, especially in the fields of clinical screening and diagnosis of cancer field. This is because CNTs possess unique structural, mechanical and electronic properties that can decrease over‐potential and improve the sensitivity of electrochemical immunosensor. This paper reviews recent advances in the different modified strategies of constructing electrochemical immunosensor based on CNTs for detecting protein cancer biomarkers. CNTs or CNTs hybrid nanomaterials modified electrodes have been firstly introduced as the sensing platforms for the detection of protein cancer biomarkers. On the other hand, CNTs or functional CNTs used as labels in sandwich‐type electrochemical immunosensors have been systematically summarized. These novel strategies and the general principles could increase the sensitivity of the immunosensor, thereby overcoming the limitations of its application in the biosensing field.     

A Comparative Study of Electrochemical Reduction of 4‐Nitrophenyl Covalently Grafted on Gold and Carbon

4‐Nitrophenyl layers were grafted on gold and glassy carbon surfaces by electrochemical reductive adsorption of the corresponding diazonium salt. Electrochemical conversion efficiencies of 4‐nitrophenyl moieties to 4‐aminophenyl moieties on gold versus on glassy carbon in a protic medium were investigated using X‐ray photoelectron spectroscopy (XPS). In total contrast to all previous comparative studies showing greater electrochemical reactivity of aryl diazonium salt‐derived layers on gold than on glassy carbon, a much lower rate of conversion to 4‐aminophenyl was observed on gold than on glassy carbon by both cyclic voltammetry (CV) and chronoamperometry (CA) methods. The lower electron transfer rate during conversion observed on gold versus glassy carbon was proposed to be due to a mechanism related to the molecular structure rearrangement of 4‐nitrophenyl during the process on glassy carbon. However, whilst complete conversion of 4‐nitrophenyl to 4‐aminophenyl on gold by chronoamperometry was achieved, on glassy carbon complete reduction could not be achieved under the same conditions.     

Anthraquinone as a redox label for DNA: synthesis, enzymatic incorporation, and electrochemistry of anthraquinone-modified nucleosides, nucleotides, and DNA

Modified 2'-deoxynucleosides and deoxynucleoside triphosphates (dNTPs) bearing anthraquinone (AQ) attached through an acetylene or propargylcarbamoyl linker at the 5-position of pyrimidine (C) or at the 7-position of 7-deazaadenine were prepared by Sonogashira cross-coupling of halogenated dNTPs with 2-ethynylanthraquinone or 2-(2-propynylcarbamoyl)anthraquinone. Polymerase incorporations of the AQ-labeled dNTPs into DNA by primer extension with KOD XL polymerase have been successfully developed. The electrochemical properties of the AQ-labeled nucleosides, nucleotides, and DNA were studied by cyclic and square-wave voltammetry, which show a distinct reversible couple of peaks around -0.4 V that make the AQ a suitable redox label for DNA.