A Novel DNA Probe Based on Molecularly Imprinted Polymer Modified Electrode for the Electrochemical Monitoring of DNA

A DNA probe that was based on methylene blue (MB) imprinted polyvinyl pyridine polymer (MIP) modified carbon paste electrodes were developed for the first time for electrochemical monitoring of DNA. Probes were built up by adsorbing MB onto modified electrodes prior to DNA immobilization. It was shown that DNA strongly immobilizes on MIP modified electrodes when MB was adsorbed in advance of DNA immobilization. The performance of the MB imprinted polymer modified carbon paste electrodes (MIP‐CPE) to rebind the template molecule (MB) were compared to those of control polymer modified (non‐imprinted polymer NIP‐CPE) and bare (CPE) electrodes. Electrochemical signal resulting from the oxidation of guanine moiety of the immobilized probe DNA was high enough on the constructed platform, implicating that probes of this kind could be favorably used for DNA analysis. These probes exhibited high selectivity for its complementary DNA sequences (target). HBV‐DNA hybridization was studied to evaluate the selectivity of the probes for complementary, non‐complementary and mismatch sequences. The detection limit of the probe for the target DNA was 8.72 µg/mL (1.38 µM), which was better than those attained by some earlier DNA sensor studies.     

Hydroxyapatite Nanoparticles Modified Graphite Electrodes for Electrochemical DNA Detection

Hydroxyapatite nanoparticles (HaNP) modified pencil graphite electrodes (PGEs) were developed for the first time in the literature, and accordingly they were applied for electrochemical monitoring of sequence‐selective DNA hybridization. The experimental conditions for HaNP modification of PGE, and DNA hybridization related to Hepatitis B Virus (HBV) DNA sequence were optimized. The microscopic and electrochemical characterization of HaNP‐PGE in contrast to the unmodified one was utilized. Under optimized experimental conditions, the selectivity of HBV DNA probe immobilized biosensor was tested against to non‐complementary (NC), mismatch (MM) sequences and the mixture of target:NC (1 : 1) or target: MM (1 : 1).     

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.     

Label‐Free Bioelectronic Detection of Point Mutation by Using Peptide Nucleic Acid Probes

An electrochemical hybridization biosensor based on peptide nucleic acid (PNA) probes with a label‐free protocol is described. The detection of PNA‐DNA and DNA‐DNA hybridizations were accomplished based on the oxidation signal of guanine by using differential pulse voltammetry (DPV) at carbon paste electrode (CPE). It was observed that the oxidation signals of guanine obtained from the PNA and DNA probe modified CPEs were higher than those obtained from the PNA‐DNA and DNA‐DNA hybrid modified CPEs due to the accessible unbound guanine bases. The detection of hybridization between PNA probe and point mutation containing DNA target sequences was clearly observed due to the difference of the oxidation signals of guanine bases, because the point mutation was guanine nearly at the middle of the sequence. The effect of the DNA target concentration on the hybridization signal was also observed. The PNA probe was also challenged with excessive and equal amount of noncomplementary DNA and also mixtures of point mutation and target DNA.     

Biocompatible core-shell nanoparticle-based surface-enhanced Raman scattering probes for detection of DNA related to HIV gene using silica-coated magnetic nanoparticles as separation tools

A novel, highly selective DNA hybridization assay has been developed based on surface-enhanced Raman scattering (SERS) for DNA sequences related to HIV. This strategy employs the Ag/SiO₂ core-shell nanoparticle-based Raman tags and the amino group modified silica-coated magnetic nanoparticles as immobilization matrix and separation tool. The hybridization reaction was performed between Raman tags functionalized with 3′-amino-labeled oligonucleotides as detection probes and the amino group modified silica-coated magnetic nanoparticles functionalized with 5′-amino-labeled oligonucleotides as capture probes. The Raman spectra of Raman tags can be used to monitor the presence of target oligonucleotides. The utilization of silica-coated magnetic nanoparticles not only avoided time-consuming washing, but also amplified the signal of hybridization assay. Additionally, the results of control experiments show that no or very low signal would be obtained if the hybridization assay is conducted in the presence of DNA sequences other than complementary oligonucleotides related to HIV gene such as non-complementary oligonucleotides, four bases mismatch oligonucleotides, two bases mismatch oligonucleotides and even single base mismatch oligonucleotides. It was demonstrated that the method developed in this work has high selectivity and sensitivity for DNA detection related to HIV gene.     

Electrochemical Genoassay Design for Allele‐Specific Detection of Toll‐Like Receptor‐2 Gene Polymorphism

An allele‐specific voltammetric genoassay for the detection of allele‐specific toll‐like receptor‐2 gene arg753gln polymorphism (TLR‐2) from polymerase chain reaction (PCR) amplified real samples was described in this study. Meldola blue (MDB), an intercalator molecule, was used as hybridization label. The wild‐type and mutant type oligonucleotide probes were immobilized onto disposable graphite electrode surfaces by covalent attachment method. The extent of hybridization between probe and target sequences was determined by using differential pulse voltammetry (DPV). As a result of the interaction between MDB and DNA at electrode surface, the MDB signal observed from probe sequence before hybridization and after hybridization with MM sequence is lower than that observed after hybridization with complementary sequence. The differences between the MDB reduction peaks obtained from probe modified, hybrid modified and MM modified electrode were used to detect TLR‐2 from PCR amplified real samples. The discrimination of homozygous and heterozygous alleles was also established by comparing the peak currents of MDB reduction signals. Numerous factors affecting the target hybridization and indicator binding reactions are optimized to maximize the sensitivity.     

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.     

An Electrochemical DNA Biosensor for the Detection of the Apa I Polymorphism in the Vitamin D Receptor Gene Using Meldola's Blue as a Hybridization Indicator

Electrochemical detection of nucleic acid base mismatches related to Apa I single nucleotide polymorphism (SNP) in the vitamin D receptor gene was performed successfully using 7‐dimethyl‐amino‐1,2‐benzophenoxazinium salt (Meldola's blue, MDB) with 10.9 pmol/100 μL of detection limit. MDB reduction signals obtained from probe, mismatch(probe‐SNP containing target) and hybrid(probe‐target) modified pencil graphite electrode(PGE) increased respectively. The sensor was able to clearly distinguish perfect match from mismatch DNA in a 30 min. detection time. Several factors affecting on the hybridization and indicator response are studied to maximize sensitivity and selectivity. The advantages of the biosensor are discussed in comparison with previous electrochemical assays for DNA hybridization.     

A Sequence‐Selective Electrochemical DNA Biosensor Based on HRP‐Labeled Probe for Colorectal Cancer DNA Detection

Abstract

A highly‐sensitive sequence‐selective DNA sensor based on HRP‐labeled probe to detect specific K‐ras gene which is highly associated with colorectal cancer has been reported. Capture probe modified with–SH was first chemically adsorbed on the gold electrode through self‐assembly. Then, the hybridization of a complementary nucleic acid (target DNA:K‐ras gene) and HRP labeled oligonucleotide detection probe occurred in a sandwich way. Finally, H₂O₂ electroreduction current catalyzed by HRP was measured amperometrically in the presence of hydroquinon as mediator. The sequence selectivity is double guaranteed by the complementary hybridization of target DNA with capture and detection probes. The experimental conditions were optimized. The linear range is 1.17×10^?11～1.17×10^?7 mol l^?1 with a detection limit of 5.85×10^?12 mol l^?1. The electrode with capture probe can be reused after regeneration in boiling water.     

A novel route for immobilization of oligonucleotides onto modified silica nanoparticles

A novel approach for immobilization of probe oligonucleotides that uses zirconium phosphate modified silica nanoparticles is proposed. The surface modification of nanoparticles was carried out in two stages. Initially binding of Zr4+ to the surface of silica nanoparticles and later treated with phosphoric acid for terminal phosphate groups. Oligonucleotide probes modified with amine group at 5'-end were strongly binds to the phosphate terminated silica nanoparticles with imidazole in presence of 0.1 mol L(-1) EDC [N-ethyl-N'-(3-dimethylaminopropyl) carbodiimide], as phosphate groups are more reactive towards amine group. Various studies, i.e., synthesis of silica nanoparticles, their surface modification, probe immobilization, measurement of hybridization and effect of bovine serum albumin (BSA) were carried out during optimization of reaction conditions. The significant reduction in the background signal was observed by treating the probe modified silica nanoparticles with bovine serum albumin prior to hybridization. The probe modified silica nanoparticles were retained their properties and the hybridization was induced by exposure of single-stranded DNA (ssDNA) containing silica nanoparticles to the complementary DNA in solution. The decrease in the fluorescence signal for one mismatch and three mismatch was observed upon hybridization of probe with target DNAs, while there was no response for the random target ssDNA under the same experimental conditions. The intensity of fluorescence signal was linear to the concentration of target DNA ranging from 3.9 x 10(-9) to 3.0 x 10(-6)mol L(-1). A detection limit of 1.22 x 10(-9) mol L(-1) of oligonucleotides can be estimated. The proposed hybridization assay is simple and possesses good analytical characteristics and it can provide an effective and efficient route in the development of DNA biosensors and biochips.     

A Host‐Guest‐Recognition‐Based Electrochemical Sensor for Sequence‐Specific DNA Detection

We herein constructed a sensor that converts target DNA hybridization‐induced conformational transformation of the probe DNA to electrochemical response based on host‐guest recognition and nanoparticle label. In the sensor, the hairpin DNA terminal‐labeled with 4‐((4‐(dimethylamino)phenyl)azo)benzoic acid (dabcyl) and thiol group was immobilized on Au electrode surface as the probe DNA by Au‐S bond, and the CdS nanoparticles surface‐modified with β‐cyclodextrins (CdS‐CDs) were employed as electrochemical signal provider and host‐guest recognition element. Initially, the probe DNA immobilized on electrode kept the stem‐loop configuration, which shielded dabcyl from docking with the CdS‐CDs in solution due to the steric effect. After target hybridization, the probe DNA underwent a significant conformational change, which forced dabcyl away from the electrode. As a result, formerly‐shielded dabcyl became accessible to host‐guest recognition between β‐cyclodextrin (β‐CD) and dabcyl, thus the target hybridization event could be sensitively transduced to electrochemical signal provided by CdS‐CDs. This host‐guest recognition‐based electrochemical sensor has been able to detect as low as picomolar DNA target with excellent differentiation ability for even single mismatch.     

基于纳米金探针和基因芯片的DNA检测新方法

运用荧光纳米金探针和基因芯片杂交建立一种新的DNA检测方法. 荧光纳米金探针表面标记有两种DNA探针: 一种为带有Cy5荧光分子的信号探针BP1, 起信号放大作用; 另一种为与靶DNA一部分互补的检测探针P532, 两种探针比例为5∶1. 当靶DNA存在时, 芯片上捕捉探针(与靶DNA的另一部分互补)通过碱基互补配对结合靶DNA, 将靶DNA固定于芯片上; 荧光纳米金探针通过检测探针与靶DNA及芯片结合, 在芯片上形成“三明治”复合结构, 最后通过检测信号探针上荧光分子的信号强度来确定靶DNA的量. 新方法检测灵敏度高, 可以检测浓度为1 pmol/L的靶DNA, 操作简单, 检测时间短. 通过改进纳米金探针的标记和优化杂交条件, 可进一步提高核酸检测的灵敏度, 这将在核酸检测方面具有重要的应用价值.     

A Sandwich‐Type Electrochemical Biosensor for Detection of BCR/ABL Fusion Gene Using Locked Nucleic Acids on Gold Electrode

In this study, a sandwich‐type electrochemical enzyme‐based LNA‐modified DNA biosensor was developed to detect relative gene in chronic Myelogenous Leukemia first. This biosensor is based on a ‘sandwich’ detection strategy, which involves a pair of probes (a capture probe immobilized at the electrode surface and a reporter probe labeled biotin as an affinity tag for avidin‐HRP) modified LNA. Since biotin can be connected with avidin‐HRP, this biosensor offers an enzymatically amplified electrochemical current signal for the detection of target DNA. This new pattern exhibits high sensitivity and selectivity, and this biosensor has been used for an assay of PCR real sample with satisfactory result.     

Developing a Nano‐Biosensor for DNA Hybridization Using a New Electroactive Label

Development of electrochemical DNA hybridization biosensors based on carbon paste electrode (CPE) and gold nanoparticle modified carbon paste electrode (NGMCPE) as transducers and ethyl green (EG) as a new electroactive label is described. Electrochemical impedance spectroscopy and cyclic voltammetry techniques were applied for the investigation and comparison of bare CPE and NGMCPE surfaces. Our voltammetric and spectroscopic studies showed gold nanoparticles are enable to facilitate electron transfer between the accumulated label on DNA probe modified electrode and electrode surface and enhance the electrical signals and lead to an improved detection limit. The immobilization of a 15‐mer single strand oligonucleotide probe on the working electrodes and hybridization event between the probe and its complementary sequence as a target were investigated by differential pulse voltammetry (DPV) responses of the EG accumulated on the electrodes. The effects of some experimental variables on the performance of the biosensors were investigated and optimum conditions were suggested. The selectivity of the biosensors was studied using some non‐complementary oligonucleotides. Finally the detection limits were calculated as 1.35×10^?10 mol/L and 5.16×10^?11 mol/L on the CPE and NEGCPE, respectively. In addition, the biosensors exhibited a good selectivity, reproducibility and stability for the determination of DNA sequences.     

聚四氟乙烯片基上寡核苷酸原位的合成及金标银染检测

Poly（tetrafluoroethylene） （PTFE） was treated with plasma in a mixture of nitrogen and hydrogen （1 ： 2 in volume）. X-ray photoelectron spectroscopy （XPS） demonstrated the success of amino group grafting. The as-treated PTFE slices were successively applied to the in situ synthesis of oligonucleotides. With the detection of gold-label-silver-stain, the hybridization signals were recorded with a gel document and analysis system. A target DNA concentration as low as 10 pmol/L could be detected. The complementary and mismatched sequences were distinguished clearly, and the ratio of background-subtracted gray scale values for perfect match ： 1 base mismatch ： 2 base mismatch ： 3 base mismatch was 72 ： 44.4 ： 22.5 ： 11.4. The sensitivity of in situ synthesis system was 1 order of magnitude higher than that of spotting system, and the signal of the former was about 1.5 times stronger than that of the latter under the same target DNA concentration. These plasma modified PTFE slices might open novel prospects for the in situ synthesis of DNA micro-arrays.     

Streptavidin Modified Carbon Nanotube Based Graphite Electrode for Label‐Free Sequence Specific DNA Detection

Disposable graphite pencil electrodes (PGE) modified with multiwalled carbon nanotubes (MWCNTs)‐streptavidin (STR) conjugates were used for electrochemical monitoring of label‐free DNA hybridization. The surface morphology of PGE electrode before and after hybridization was characterized by scanning electron microscopy. Electrochemical impedance spectroscopy was used to monitor each step of the construction of the DNA biosensor. The biosensor was demonstrated to have excellent selectivity, being able to differentiate complementary sequences from a noncomplementary ones and in addition select the target sequence of DNA from a mixture of other DNA without loss in current sensitivity.     

Nano‐Gold Modified Genosensor for Direct Detection of DNA Hybridization

In this paper, nano‐gold modified carbon paste electrode (NGMCPE) was employed to develop an electrochemical DNA hybridization biosensor. The proposed sensor was made up by immobilization of 15‐mer single stranded oligonucleotide probe for detection of target DNA. Hybridization detection relies on the alternation in guanine oxidation signal following hybridization of the probe with complementary genomic DNA. The guanine oxidation was monitored using differential pulse voltammetry (DPV). Different factors such as activation potential, activation time and probe immobilization conditions were optimized. The selectivity of the sensor was investigated by non‐complementary oligonucleotides. Diagnostic performance of the biosensor was described and the detection limit was found 1.9 × 10^?13 M at the NGMCPE surface. All of the investigations were performed in both CPE and NGMCPE and finally their results were compared.     

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.     

Quartz crystal microbalance genosensor for sequence specific detection of attomolar DNA targets

A mass sensitive quartz crystal microbalance (QCM) based genosensor has been developed using breast cancer 1 (BRCA1) gene as a model gene. We modified the traditional sandwich assay by conjugating reporter probe DNA (DNA-r) with an assembly of gold nanoparticles leading to an increased mass on the surface, which enhanced the sensitivity to few orders of magnitude. The unique cleavage function of endonuclease is used for achieving the selectivity to complementary DNA over mismatched DNA. With this combination, the sensor exhibited excellent sensitivity with a detection limit of 10 aM BRCA1 gene and it showed good selectivity for even single base mismatch DNA targets. This ultrasensitive and cost-effective DNA detection protocol can be extended to the direct analysis of any non-amplified genomic DNA.     

Highly Sensitive Indicator‐Free Impedance Sensing of DNA Hybridization Based on Poly(m‐aminobenzenesulfonic acid)/TiO2 Nanosheet Membranes with Pulse Potentiostatic Method Preparation

A direct electrochemical detection procedure for DNA hybridization by using the electrochemical signal changes of conductive poly(m‐aminobenzenesulfonic) acid (PABSA)/TiO₂ nanosheet membranes, which were electropolymerized by using the pulse potentiostatic method, is reported. Due to the unique properties of TiO₂ nanoparticles, m‐aminobenzenesulfonic acid monomers tend to be adsorbed around the particles, and the electropolymerization efficiency is greatly improved. The combination of TiO₂ nanoparticles and PABSA resulted in a nanocomposite membrane with unique and novel nanosheet morphology that provides more activation sites and enhances the surface electron‐transfer rate. These characteristics were propitious for the magnification of PABSA electrochemical signals and the direct detection of DNA hybridization. Owing to the presence of abundant sulfonic acid groups, PABSA could overcome the drawbacks of polyaniline and be used to detect bioanalytes at physiological pH. DNA probes could be covalently attached to the sulfonic groups through the amines of DNA sequences by using an acyl chloride cross‐linking reaction. After immobilization of probe DNA, the electrochemical impedance value increased significantly compared to that of PABSA/TiO₂ nanosheet membranes, and then decreased dramatically after the hybridization reaction of the probe DNA with the complementary DNA sequence compared to that of the probe‐immobilized electrode. Electrochemical impedance spectroscopy was adopted for indicator‐free DNA biosensing, which had an eminent ability for the recognition between double‐base mismatched sequences or non‐complementary DNA sequences and complementary DNA sequences. A gene fragment, which is related to one of the screening genes for the transgenically modified plants, the cauliflower mosaic virus 35S gene was satisfactorily detected. This is the first report for the indicator‐free impedance DNA hybridization detection by using PABSA/TiO₂ membranes under neutral conditions.