Comparison of DNA Hybridization at Rotating and Heated Gold Disk Electrodes

This paper reports about the influence of temperature, hybridization time and convection upon the detection of osmium tetroxide bipyridine‐labeled target oligonucleotides at rotating gold disk (RDE) and heated low temperature co‐fired ceramics (LTCC) gold disk electrodes. We used mixed self‐assembled monolayers of hexathiol‐linked probe oligonucleotides and mercaptohexanol on the gold surface of the electrodes for the hybridization detection of the labeled targets by means of square‐wave voltammetry. Due to protective strands, the osmium tetroxide‐modified target strands were still able to hybridize with the immobilized probe strands. The hybridization of such osmium tetroxide bipyridine‐modified target strands with thiol‐linked probe strands immobilized on gold yielded large reversible square‐wave‐voltammetric signals. Rotation speed and, hence, mass transport due to convection has only marginal effects. On the other hand, temperature affects greatly the hybridization step as indicated by both heated LTCC electrode in cold and RDE in warm hybridization solution. Calculated detection limits of 3.6 and 3.1 nM targets at the RDE and the LTCC electrode, respectively, have been almost the same at both types of electrodes. Applying an appropriate temperature during hybridization is more important than mechanically enhanced mass transport.     

基于纳米金胶标记DNA探针的电化学DNA传感器研究

以纳米金胶为标记物,将其标记于人工合成的5-端巯基修饰的寡聚核苷酸片段上,制成了具有电化学活性的金胶标记DNA电化学探针;在一定条件下,使其与固定在玻碳电极表面的靶序列进行杂交反应,利用ssDNA与其互补链杂交的高度序列选择性和极强的分子识别能力,以及纳米金胶的电化学活性,实现对特定序列DNA片段的电化学检测以及对DNA碱基突变的识别.     

Sharp melting in DNA-linked nanostructure systems: thermodynamic models of DNA-linked polymers

Sharp melting that has been found for DNA-linked nanostructure systems such as DNA-linked gold nanoparticles enhances the resolution of DNA sequence detection enough to distinguish between a perfect match and single base pair mismatches. One intriguing explanation of the sharp melting involves the cooperative dehybridization of DNA strands between the nanostructures. However, in the DNA-linked gold nanoparticle system, strong optical absorption by the gold nanoparticles hinders the direct observation of cooperativity. Here, with a combination of theory and experiment, we investigate a DNA-linked polymer system in which we can show that the optical profile of the system at 260 nm is directly related to the individual DNA dehybridization profile, providing a clear distinction from other possible mechanisms. We find that cooperativity plays a crucial role in determining both the value of the melting temperature and the shape of the melting profile well away from the melting temperature. Our analysis suggests that the dehybridization properties of DNA strands in confined or dense structures differ from DNA in solution.     

Scanning Electrochemical Microscopy for Electrochemical Detection of Single‐base Mismatches by Tagging Ferrocenecarboxylic Acid as a Redox Probe to DNA

Scanning electrochemical microscopy (SECM) was employed for sensitive detection of single base mismatches (SBMs) in a sandwiched dsDNA. Ferrocenecarboxylic acid (Fc), covalently conjugated to the dsDNA, was oxidized to Fc⁺ via the DNA‐mediated charge transfer from the underlying gold substrate, and reduced back to Fc by SECM tip generated ferrocyanide. The electrocatalytic oxidation of SECM tip‐generated ferrocyanide was sensitive to presence, as well as the type of SBMs. Apparent standard rate constants (k⁰_app) values for different SBMs, both near the electrode surface and far from it, were evaluated by SECM. The method can detect SBMs independent of their position in dsDNA.     

Fabrication of a Sensitive Impedance Biosensor of DNA Hybridization Based on Gold Nanoparticles Modified Gold Electrode

In this work, we report on the preparation of a simple, sensitive DNA impedance sensor. Firstly gold nanoparticles were electrodeposited on the surface of a gold electrode, and then probe DNA was immobilized on the surface of gold nanoparticles through a 5′‐thiol‐linker. Electrochemical impedance spectroscopy (EIS) was used to investigate probe DNA immobilization and hybridization. Compared to the bare gold electrode, the gold nanoparticles modified electrode could improve the density of probe DNA attachment and the sensitivity of DNA sensor greatly. The difference of electron transfer resistance (ΔR_et) was linear with the logarithm of complementary oligonucleotides sequence concentrations in the range of 2.0×10^?12 to 9.0×10^?8 M, and the detection limit was 6.7×10^?13 M. In addition, the DNA sensor showed a fairly good reproducibility and stability during repeated regeneration and hybridization cycles.     

Retention of nucleic acids in ion‐pair reversed‐phase high‐performance liquid chromatography depends not only on base composition but also on base sequence

The study on nucleic acid retention in ion‐pair reversed‐phase high‐performance liquid chromatography mainly focuses on size‐dependence, however, other factors influencing retention behaviors have not been comprehensively clarified up to date. In this present work, the retention behaviors of oligonucleotides and double‐stranded DNAs were investigated on silica‐based C₁₈ stationary phase by ion‐pair reversed‐phase high‐performance liquid chromatography. It is found that the retention of oligonucleotides was influenced by base composition and base sequence as well as size, and oligonucleotides prone to self‐dimerization have weaker retention than those not prone to self‐dimerization but with the same base composition. However, homo‐oligonucleotides are suitable for the size‐dependent separation as a special case of oligonucleotides. For double‐stranded DNAs, the retention is also influenced by base composition and base sequence, as well as size. This may be attributed to the interaction of exposed bases in major or minor grooves with the hydrophobic alky chains of stationary phase. In addition, no specific influence of guanine and cytosine content was confirmed on retention of double‐stranded DNAs. Notably, the space effect resulted from the stereostructure of nucleic acids also influences the retention behavior in ion‐pair reversed‐phase high‐performance liquid chromatography.     

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.     

Electrochemical Detection of Avian Influenza Virus Genotype Using Amino‐ssDNA Probe Modified Gold Electrodes

A DNA biosensor for the detection of specific oligonucleotide sequences of Avian Influenza Virus type H5N1 has been proposed. The NH₂‐ssDNA probe was deposited onto a gold electrode surface to form an amide bond between the carboxyl group of thioacid and the amino group from ssDNA probe. The signals generated as a result of hybridization were registered in square wave voltammetry and electrochemical impedance spectroscopy in the presence of [Fe(CN)₆]^3?/4? as a redox marker. The genosensor is capable to determine 20‐mer and 180‐bp (PCR products) oligonucleotides complementary sequences with detection limit in the fM range. The genosensor displays good selectivity and sensitivity. The 20‐mer as well as 180‐bp oligonucleotides without a complementary sequence generate very low signal.     

Development of a Novel Electrochemical Biosensor for Detection and Discrimination of DNA Sequence and Single Base Mutation in dsDNA Samples Based on PNA‐dsDNA Hybridization – a new Platform Technology

In spite of the extensive attention paid on the development of various DNA detection strategies, very few studies have been reported regarding direct detection of DNA sequence and mutation in dsDNA. Here, we describe the feasibility of detection and discrimination of target DNA sequences and single base mutations (SBM) directly in double‐stranded oligonucleotides and PCR products without the need for denaturation of the target dsDNA samples. This goal was achieved by employing a peptide nucleic acid (PNA) chain, self‐assembled on the gold electrode as a probe, which binds to dsDNA and forms PNA‐dsDNA hybrid.     

Defects can increase the melting temperature of DNA-nanoparticle assemblies

DNA-gold nanoparticle assemblies have shown promise as an alternative technology to DNA microarrays for DNA detection and RNA profiling. Understanding the effect of DNA sequences on the melting temperature of the system is central to developing reliable detection technology. We studied the effects of DNA base-pairing defects, such as mismatches and deletions, on the melting temperature of DNA-nanoparticle assemblies. We found that, contrary to the general assumption that defects lower the melting temperature of DNA, some defects increase the melting temperature of DNA-linked nanoparticle assemblies. The effects of mismatches and deletions were found to depend on the specific base pair, the sequence, and the location of the defects. Our results demonstrate that the surface-bound DNA exhibit hybridization behavior different from that of free DNA. Such findings indicate that a detailed understanding of DNA-nanoparticle assembly phase behavior is required for quantitative interpretation of DNA-nanoparticle aggregation.     

Immunosensors Based on Layer‐by‐Layer Self‐Assembled Au Colloidal Electrode for the Electrochemical Detection of Antigen

Colloidal Au particles have been deposited on the gold electrode through layer‐by‐layer self‐assembly using cysteamine as cross‐linkers. Self‐assembly of colloidal Au on the gold electrode resulted in an easier attachment of antibody, larger electrode surface and ideal electrode behavior. The redox reactions of [Fe(CN)₆]^4?/[Fe(CN)₆]^3? on the gold surface were blocked due to antibody immobilization, which were investigated by cyclic voltammetry and impedance spectroscopy. The interaction of antigen with grafted antibody recognition layers was carried out by soaking the modified electrode into a phosphate buffer at pH 7.0 with various concentrations of antigen at 37 °C for 30 min. Further, an amplification strategy to use biotin conjugated antibody was introduced for improving the sensitivity of impedance measurements. Thus, the sensor based on this immobilization method exhibits a large linear dynamic range, from 5–400 μg/L for detection of Human IgG. The detection limit is about 0.5 μg/L.     

Synthesis,Molecular Recognition,and Enzymology of Oligonucleotides Containing the Non-standard Base Pair between 5-Aza-7-deazaisoguanine and 6-Amino-3-methylpyrazin-2(1H)-one,a Donor-Acceptor-Acceptor Purine Analog and an Acceptor-Donor-Donor Pyrimidine Analog

A 6-aminopyrazin-2(1H)-one (pyADD), when incorporated as a pyrimidine-base analog into an oligonucleotide chain, presents a H-bond acceptor-donor-donor pattern to 5-aza-7-deazaisoguanine (puDAA), the complementrary donor-acceptor-acceptor purine analog. Reported here are the syntheses of the phosphoramidite of the 2′-deoxyribonucleoside bearing the puDAA base, oligonucleotides containing this nucleoside unit, the enzyme-assisted synthesis of oligoribonucleotides containing the pyADD ribonucleoside, and the molecular-recognition properties of this non-standard base pair in an oligonucleotide context. A series of melting experiments suggests that the pyADD · puDAA base pair contributes to the relative stability of a duplex structure approximately the same as an A · T base pair, and significantly more than mismatches between these non-standard bases and certain standard nucleobases. The pyADD nucleoside bisphosphate is accepted by T4 RNA ligase, but the triphosphate of the pyADD nucleoside was not incorported by T7 RNA polymerase opposite the puDAA nucleobase in a template. Oligonucleotides containing the pyADD base slowly undergo a reversible first-order reaction, presumably an epimerization process to give the α-D -anomer. These experiments provide the tools for laboratory-based use of the pyADD · puDAA base pair as a component of an oligonucleotide-like molecular-recognition system based on an expanded genetic alphabet.     

Water‐soluble cationic polypyrrole based probe for fluorometric and voltammetric detection of base pair mismatched oligonucleotides

Water‐soluble cationic polypyrrole, poly(N‐(4‐butyl‐(1‐methylimidazole)) pyrrole bromide) (PNBMIP‐Br), was synthesized and applied for base pair mismatched oligonucleotides detection. Interactions between PNBMIP‐Br and a series of oligonucleotides, including ss‐DNA and base pair mismatched ds‐DNA were studied by fluorometric spectra, circular dichroism spectra and voltammetric detection. The results showed that the electrostatic attraction and fluorescence resonance energy transfer of PNBMIP‐Br/DNA complexes resulted in an amplification and effective recognition of the fluorescence signals. The results of cyclic voltammograms indicate that voltammetric detection is an effective method to distinguish ss‐DNA and ds‐DNA. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 1600–1605     

Effects of shape and charge of colloidal gold nanoparticles in colorimetric determination of DNA sequences

The principles of colorimetric detecting oligonucleotides with the help of gold nanospheres and nanorods are discussed. Marker sequences of fragments of HIV-1 genome and Bacillus anthracis are used as models. Experimental data are reported that demonstrate the influence of gold nanorod morphology on the reproducibility of colorimetric tests. A new method is proposed for detecting oligonucleotides based on the application of positively charged gold nanospheres in combination with absorption spectroscopy and dynamic light scattering. Charge reversal of negatively charged gold nanospheres is implemented through the bilayer adsorption of cetyltrimethylammonium bromide molecules. The sensitivity of the proposed method is comparable with the detection of DNA sequences via the colorimetric protocol using nanorods, but it is more simple and stable from the viewpoint of realization. It is shown that the colorimetric tests using gold nanorods and nanospheres do not provide reliable information on the presence of single- and three-base mismatches in target oligonucleotides.     

Base‐Pairing Properties of 8‐Aza‐7‐deazaadenine Linked via the 8‐Position to the DNA Backbone

The base‐pairing properties of oligonucleotides containing the unusual N⁸‐linked 8‐aza‐7‐deazaadenine 2′‐deoxyribonucleoside ( 2a ) as well as its 7‐bromo derivative 2b are described. The oligonucleotides were prepared by solid‐phase synthesis employing phosphoramidite chemistry. Compound 2a forms a strong base pair with T_d for which a reverse Watson‐Crick pair is suggested (Fig. 9). Compound 2a displays a lower N‐glycosylic‐bond stability than its N⁹‐nucleoside and shows strong stacking interactions when incorporated into oligonucleotides. The replacement of 2′‐deoxyadenosine by 2a does not significantly influence the duplex stability. However, this behavior depends on the position of the incorporation.     

Hybridization Detection of Osmium Tetroxide Bipyridine‐Labeled DNA and RNA on Heated Gold Wire Electrodes

We report about hybridization detection of different nucleic acids on capture probe‐modified heated gold wire electrodes. We have compared three kinds of nucleic acid targets: DNA, uracil‐conjugated DNA, and RNA. All three sorts of nucleic acids targets could be labeled with osmium tetroxide bipyridine, hybridized with immobilized DNA capture probes and then detected by square‐wave voltammetry. Heating the gold electrode instead of the entire bulk hybridization solution leads to improved hybridization efficiency in most cases. The reason could be found in a thermal micro‐stirring effect around the heated wire electrode. Also selectivity was improved. Mismatches could be discriminated for DNA and uracil‐conjugated DNA targets. Mismatches in RNA strands, however, are more difficult to detect due to relatively stable secondary structures.     

Hybridization detection of enzyme-labeled DNA at electrically heated electrodes

In this report we describe an electrochemical DNA hybridization sensor approach, in which signal amplification is achieved using heated electrodes together with an enzyme as DNA-label. On the surface of the heatable low temperature co-fired ceramic (LTCC) gold electrode, an immobilized thiolated capture probe was hybridized with a biotinylated target using alkaline phosphatase (SA-ALP) as reporter molecule. The enzyme label converted the redox-inactive substrate 1-naphthyl phosphate (NAP) into the redox-active 1-naphthol voltammetrically determined at the modified gold LTCC electrode. During the measurement only the electrode was heated leaving the bulk solution at ambient temperature. Elevated temperature during detection led to increased enzyme activity and enhanced analytical signals for DNA hybridization detection. The limit of detection at 53 °C electrode temperature was 1.2 nmol/L.     

EQCM and Fluoroelectrochemical Studies on the Catalytic Oxidation of NADH at a Pencil 8B‐Scrawled Gold Electrode with High Detection Sensitivity

We report for the first time the effective catalytic electrooxidation of nicotinamide adenine dinucleotide (NADH) on the pencil 8B‐scrawled gold electrode of an electrochemical quartz crystal microbalance (EQCM). The EQCM allowed us to quantitatively evaluate the catalytic activity of the pencil‐scrawled Au electrode. With increasing the mass of modified pencil powders, the peak potential for NADH oxidation shifted negatively, with maximum shift of ?0.35 V at saturated pencil modification; the NADH‐oxidation peak current density (j_p) was also notably increased, and the j_p at saturated pencil modification was found to be larger than those at conventional pencil 8B and bare Au electrodes. Sensitive amperometric detection of NADH was achieved at the gold electrode with saturated pencil modification, with low detection potential (0.4 V versus SCE), low detection limit (0.08 μmol L^?1) and wide linear range (0.2–710 μmol L^?1). The fluoroelectrochemical measurements of NADH at bare and pencil‐modified gold electrodes were also conducted with satisfactory results. The convenient and low‐cost modification of pencil powders on the Au electrode may have presented a new functional surface of the EQCM, which is recommended for wider applications to bioelectrochemical studies, especially in view of the EQCM's capability of providing abundant in situ information in relevant processes.     

Scanning electrochemical microscopy imaging of DNA microarrays using methylene blue as a redox-active intercalator

Scanning electrochemical microscopy (SECM) has been employed in the imaging of DNA microarrays fabricated on gold substrates using methylene blue (MB) as a redox-active intercalator and ferrocyanide as the SECM mediator in solution. MB intercalated between base pairs of immobilized ds-DNA is electrochemically reduced via electron transfer from the underlying gold substrate, and the product is reoxidized in solution by SECM tip-generated ferricyanide. The resulting feedback current allows a heterogeneous electron-transfer rate constant for the MB-intercalated DNA to be deduced. Moreover, DNA microarray spots can be imaged at a detection level of 14 fmol/spot for ds-DNA consisting of 15 base pairs. Microarrays prepared using 20 microM DNA solutions are easily visualized, and the feasibility of detecting base pair mismatches is also demonstrated.     

Polythymine Oligonucleotide‐Modified Gold Electrode for Voltammetric Determination of Mercury(II) in Aqueous Solution

Polythymine oligonucleotide (PTO)‐modified gold electrode (PTO/Au) was developed for selective and sensitive Hg²⁺ detection in aqueous solutions. This modified electrode was prepared by self‐assembly of thiolated polythymine oligonucleotide (5′‐SH‐T₁₅‐3′) on the gold electrode via Au? S bonds, and then the surface was passivated with 1‐mercaptohexanol solution. The proposed electrode utilizes the specific binding interactions between Hg²⁺ and thymine to selectively capture Hg²⁺, thereby reducing the interference from coexistent ions. After exchanging the medium, electrochemical reduction at ?0.2 V for 60 s, voltammetric determination was performed by differential pulse voltammetry using 10 mM HEPES; pH 7.2, 1 M NaClO₄ as supporting electrolyte. This electrode showed increasing voltammetric response in the range of 0.21 nM Hg²⁺, with a relative standard deviation of 5.32% and a practical detection limit of 60 pM. Compared with the conventional stripping approach, the modified electrode exhibits good sensitivity and selectivity, and is expected to be a new type of green electrode.