Direct electrochemical detection of oligonucleotide hybridization on poly(5-hydroxy-1,4-naphthoquinone- co-5-hydroxy-3-thioacetic acid-1,4-naphthoquinone) film

Self-signal electrochemical identification of circulating tumor DNA employing poly-xanthurenic acid assembled on black phosphorus nanosheets

A self-signal electrochemical identification interface was prepared for the determination of circulating tumor DNA (ctDNA) in peripheral blood based on poly-xanthurenic acid (PXTA) assembled on black phosphorus nanosheets (BPNSs) acquired through simple ultrasonication method. The BPNSs with large surface area could be integrated with the xanthurenic acid (XTA) monomers by right of physisorption, and hence improved the electropolymerization efficiency and was beneficial to the enlargement of the signal response of PXTA. The assembled PXTA/BPNSs composite with attractive electrochemical activity was adopted as a platform for the recognition of DNA immobilization and hybridization. The probe ssDNA was covalently fixed onto the PXTA/BPNSs composite with plentiful carboxyl groups through the terminate free amines of DNA probes by use of the 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydrosulfosuccinimide cross-linking reaction, accompanied with the decline of the self-signal response. When the hybridization between the probe ssDNA and the target DNA was accomplished, the self-signal response of the composite interface reproduced by virtue of the shaping of helix construction. The determination limit of the assembled DNA identification interface was 2.1 × 10-19 mol/L, and the complementary target DNA concentrations varied from 1.0 × 10-18 mol/L to 1.0 × 10-12 mol/L. The DNA identification platform displayed magnificent sensitivity, specificity and stability, and was efficaciously implemented to the mensuration of ctDNA derived from colorectal cancer.

In Vitro and in Cellulo Sensing of Transition Metals Using Time-Resolved Fluorescence Spectroscopy and Microscopy

In this work we demonstrate that time domain techniques can be used successfully to monitor realtively weak modulations of the fluorescence in sensing applications. The metal sensing complex Newport Green DCF™ can detect selected transition metals in vivo as well as in vitro. Incremental addition of Ni and/or Zn (in vitro) lead to a substantial reduction in the yield of the fast component in a bi-exponential fluorescence decay (τ₁ = 150-250 ps) from 60% to 30-35%. This is rationalised as an inhibition of intra-molecular electron transfer in the NPG sensing complex due to metal complexation. In order to explore this effect in cellulo, NIH 3 T3 mouse skin fibroplast cells were pre-incubated with set levels of Ni and Zn, at a constant concentration of NPG. The fluorescence modulation in cellullo was subsequently studied employing both time-resolved fluorescence microscopy and confocal fluorescence microscopy. In correlation with the in vitro observations, similar effects were observed on the fluorescence decay in cellulo.

E-DNA detection of rpoB gene resistance in Mycobacterium tuberculosis in real samples using Fe3O4/polypyrrole nanocomposite

In this work, we achieved the selective detection of wild and mutated rpoB gene in M. tuberculosis using an electrochemical DNA (E-DNA) sensor based on polypyrrole/Fe₃O₄ nanocomposite bearing redox naphthoquinone tag on PAMAM (spaNQ/PAMAM/PPy/Fe₃O₄). The hybridization between a given probe and the complementary DNA target induced a large decrease in the naphthoquinone redox signal as measured by SWV and no cross-hybridization with single nucleotide mismatch DNA target occurred. Thanks to the catalytic properties of iron oxide nanoparticles combined with conducting properties of polypyrrole platform, we demonstrated that the transducing system allowed the detection of 1 fM of DNA target in a 50-µL drop corresponding to 3 × 10⁴ copies of DNA. The sensor was able to detect the rpoB gene in PCR-amplified samples of genomic DNA and could also discriminate between the wild type rpoB gene and a single nucleotide mutated rpoB gene that provides resistance to rifampicin. Furthermore, the sensor could selectively detect the wild and mutant DNA in genomic samples without PCR amplification.

Tungsten disulfide nanosheets supported poly(xanthurenic acid) as a signal transduction interface for electrochemical genosensing applications

Tungsten disulfide (WS₂) nanosheets supported poly(xanthurenic acid) (PXa) was used as the signal transduction interface for electrochemical genosensing. The WS₂ nanosheets were obtained from bulk WS₂ using a simple ultrasonic method. Due to the unique physical adsorption of Xa monomers to WS₂, the electropolymerization efficiency was greatly improved, accompanied with an increased electrochemical response of PXa. The obtained PXa/WS₂ nanocomposite not only served as a substrate for DNA immobilization but also reflected the electrochemical transduction originating from DNA immobilization and hybridization without any other indicators or complicated labelling steps. Owing to the presence of abundant carboxyl groups, the probe ssDNA was covalently attached on the carboxyl-terminated PXa/WS₂ nanocomposite through the free amines of DNA sequences based on the 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydrosulfosuccinimide crosslinking reaction. The covalently immobilized probe ssDNA could selectively hybridize with its target DNA to form dsDNA on the surface of the PXa/WS₂ nanocomposite. This developed biosensor achieved a satisfactory detection limit down to 1.6 × 10⁻¹⁶ mol L⁻¹ and a dynamic range of 1.0 × 10⁻¹⁵ to 1.0 × 10⁻¹¹ mol L⁻¹ for detection of circulating tumor DNA related to gastric carcinoma. Selectivity of the biosensor has been investigated in presence of non-complementary, one-mismatched and two-mismatched DNA sequences.

An electrochemical signal transduction sensing interface for detecting PIK3CA gene was developed based on WS₂ nanosheets supported PXa.

Label-free electrochemical DNA sensor using "click"-functionalized PEDOT electrodes

Here we describe a label-free electrochemical DNA sensor based on poly(3,4-ethylenedioxythiophene)-modified (PEDOT-modified) electrodes. An acetylene-terminated DNA probe, complementary to a specific "Hepatitis C" virus sequence, was immobilized onto azido-derivatized conducting PEDOT electrodes using "click" chemistry. DNA hybridization was then detected by differential pulse voltammetry, evaluating the changes in the electrochemical properties of the polymer produced by the recognition event. A limit of detection of 0.13 nM was achieved using this highly selective PEDOT-based genosensor, without the need for labeling techniques or microelectrode fabrication processes. These results are promising for the development of label-free and reagentless DNA hybridization sensors based on conducting polymeric substrates. Biosensors can be easily prepared using any DNA sequence containing an alkyne moiety. The data presented here reveal the potential of this DNA sensor for diagnostic applications in the screening of diseases, such as "Hepatitis C", and genetic mutations.

Direct electrochemical DNA detection originated from the self-redox signal of sulfonated polyaniline enhanced by graphene oxide in neutral solution

In this paper, a type of direct DNA impedance detection using the self-redox signal change of sulfonated polyaniline (SPAN) enhanced by graphene oxide (GNO) was reported, here SPAN is a copolymer obtained from aniline and m-aminobenzenesulfonic acid. The resulting nanocomposite was characterized by scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, cyclic voltammetry, and electrochemical impedance spectroscopy. The π-π planar structure of GNO and the carboxyl groups on the surface of GNO ensured it could act as an excellent substrate for adsorption and polymerization of aniline monomer. Because of the existence of GNO, the electrochemical activities of SPAN were enhanced obviously. Because of abundant sulfonic acid groups, the resulting nanocomposite showed obvious self-redox signal even at physiological pH, which is beneficial for biosensing field. DNA probes with amine groups could be covalently attached to the modified electrode surface through the acyl chloride cross-linking reaction of sulfonic groups and amines. When the flexible probe DNA was successfully grafted, the electrode was coated and electron transfer between electrode and buffer was restrained. Thus, the inner impedance value of SPAN (rather than using outer classic EIS probe, [Fe(CN)6](3-/4-)) increased significantly. After hybridization, the rigid helix opened the electron channel, which induced impedance value decreased dramatically. As an initial application of this system, the PML/RARA fusion gene sequence formed from promyelocytic leukemia (PML) and retinoic acid receptor alpha (RARA) was successfully detected.

Label-free and reagentless electrochemical detection of PCR fragments using self-assembled quinone derivative monolayer: application to Mycobacterium tuberculosis

We report a signal-on, label-free and reagentless electrochemical DNA biosensor, based on a mixed self-assembled monolayer of thiolated hydroxynaphthoquinone and thiolated oligonucleotide. Electrochemical changes resulting from hybridization were evidenced with oligonucleotide targets (as models), as well as with polymerase chain reaction (PCR) products related to different lineages of Mycobacterium tuberculosis strains. With pure oligonucleotides, this system achieves high sensitivity (∼300 pM of DNA target, i.e. 30 fmol in a 100 μL sample) and excellent selectivity, allowing to detect a single mismatch on a sequence of 20 bases. With PCR products, current changes are specific to the bacterial strain from which the PCR fragment is produced. In addition, the sensor response is of the signal-on type, giving a positive signal change upon hybridization, and therefore does not suffer from false positive responses due to non-specific adsorption of DNA.

Electrochemical Investigation of oligonucleotide-DNA hybridization on poly(4-methoxyphenethylamine)

This work describes the immobilization of purine and pyrimidine bases and immobilization/hybridization of synthetic oligonucleotides on graphite electrodes modified with poly(4-methoxyphenethylamine) produced in acid medium. The immobilization of adenine, guanine, cytosine and thymine on these modified electrodes was efficient, producing characteristic peaks. Another relevant observation is that, according to the literature, pyrimidine bases, cytosine and thymine are more difficult to detect. However, when immobilized onto the poly(4-methoxyphenethylamine), a significant increase in the magnitude of the current was obtained. The observation of the hybridization between the poly(GA) probe and its complementary, poly(CT) target, was possible by monitoring the guanosine and adenosine peaks or through methylene blue indicator, using differential pulse voltammetry. Hybridization results in a decrease of the peak current of guanosine and adenosine or the signal of methylene blue accumulated on the modified electrode surface. The hybridization with the complementary target was also investigated by electrochemical impedance spectroscopy. The results showed a significant modification in the Nyquist plot, after addition of the complementary target, with increase of the charge transference resistance.

Direct electrochemical sensor for fast reagent-free DNA detection

A novel reagentless direct electrochemical DNA sensor has been developed using ultrathin films of the conducting polymer polypyrrole doped with an oligonucleotide probe. Our goal was to develop a prototype electrochemical DNA sensor for detection of a biowarfare pathogen, variola major virus. The sensor has been optimized for higher specificity and sensitivity. It was possible to detect 1.6 fmol of complementary oligonucleotide target in 0.1 ml in seconds by using chronoamperometry. The sensitivity of the developed sensor is comparable to indirect electrochemical DNA sensors, which use electrochemical labels and reagent-intensive amplification. The developed sensing electrode is reusable, highly stable and suitable for storage in solution or in dry state.

Investigations of the steric effect on electrochemical transduction in a quinone-based DNA sensor

Electrochemical biosensors for DNA hybridization are receiving increasing interest. A key point for their efficiency is to obtain a high signal level for low DNA concentration. This implies the design of an efficient transducing surface. Conducting polymers are interesting for this purpose but the great majority of conducting polymer-based electrodes present a signal decrease upon hybridization (a "signal-off" behavior), which impedes their response and makes them sensitive to false positive ones. The sensor described here presents a "signal-on" behavior, due to the use of a quinone group as the transducing agent. The specific aim of this work is to study the steric effect on transduction. To this end, the electrochemical response was monitored versus the DNA target length, for a constant DNA probe length. The results indicate that the current depends on the length of the double strand. A model which can explain the electrochemical behavior takes into account the steric hindrance of the ODN strands.

Selectivity and sensitivity of a reagentless electrochemical DNA sensor studied by square wave voltammetry and fluorescence

Poly(5-hydroxy-1,4-naphthoquinone-co-5-hydroxy-3-thioacetic acid-1,4-naphthoquinone)-modified electrode is used for the direct electrochemical detection of oligonucleotide hybridization. The polymer film presents well-defined electroactivity in the cathodic potential domain (between 0 and -0.8 V/SCE), due to the quinone group embedded into the polymer structure. The detection can be performed simply by square wave voltammetry. This sensor is a "signal-on" device and works with different oligonucleotide lengths, from 10 to 30 bases. Quantitative results from fluorescence are consistent with electrochemical data. It is confirmed that the signal increase in square wave voltammetry is unambiguously due to hybridization. The biosensor presents a detection limit of target of ca. 25 nM and is highly selective as it can discriminate single mismatch base.