Electrochemical detection of DNA hybridization by means of osmium tetroxide complexes and protective oligonucleotides

Strategies in the optimization of DNA hybridization conditions and its role in electrochemical detection of dengue virus (DENV) using response surface methodology (RSM)

In recent years, limited research has been conducted on enhancing DNA hybridization-based biosensor approaches using statistical models. This study explores the application of response surface methodology (RSM) to improve the performance of a DNA hybridization biosensor for dengue virus (DENV) detection. The biosensor is based on silicon nanowires decorated with gold nanoparticles (SiNWs/AuNPs) and utilizes methylene blue as a redox indicator. The DNA hybridization process between the immobilized DNA probe and the target DENV gene was monitored using differential pulse voltammetry (DPV) based on the reduction of methylene blue. Fourier-transform infrared spectroscopy (FTIR) and electrochemical impedance spectroscopy (EIS) were employed to confirm successful DNA hybridization events on the modified screen-printed gold electrode (SPGE) surface. Several parameters, including pH buffer, NaCl concentration, temperature, and hybridization time, were simultaneously optimized, with NaCl concentration having the most significant impact on DNA hybridization events. This study enhances the understanding of the role of each parameter in influencing DNA hybridization detection in electrochemical biosensors. The optimized biosensor demonstrated the ability to detect complementary oligonucleotide and amplified DENV gene concentrations as low as 0.0891 ng µL^-1 (10 pM) and 2.8 ng µL^-1, respectively. The developed biosensor shows promise for rapid clinical diagnosis of dengue virus infection.

Immunoassays of chemically modified polysaccharides, glycans in glycoproteins and ribose in nucleic acids

Glycosylation of proteins plays an important role in health and diseases. At present new simple and inexpensive methods of glycoprotein analysis are sought. We developed a monoclonal antibody Manost 2.1 in mice after immunization with the adduct of mannan with Os(VI)temed complex (temed is N,N,N',N'-tetramethylethylenediamine). The specificity of this antibody to different biomolecules treated with Os(VI)temed was tested using dot blot immunoassay. Manost 2.1 showed specificity toward Os(VI)temed-modified polysaccharides, glycoproteins and ribonucleotide at the 3'-end in DNA. The antibody recognized neither the unmodified compounds nor the non-glycosylated proteins treated with Os(VI)temed. We also performed western blotting and Coomassie silver blue staining of mixtures of biomacromolecules treated with Os(VI)temed and identified specifically the modified glycoproteins. The immunochemical method using Manost 2.1 was compared with electrochemical analyses based on redox signals of the Os(VI)temed adducts, with similar results in terms of sensitivity. This new antibody-based approach opens the door for rapid and inexpensive analysis of glycans and glycoproteins in various scientific and medical fields, including cancer research and the future application of glycoprotein detection in clinical practice.

Sequence and Temperature Influence on Kinetics of DNA Strand Displacement at Gold Electrode Surfaces

Understanding complex contributions of surface environment to tethered nucleic acid sensing experiments has proven challenging, yet it is important because it is essential for interpretation and calibration of indispensable methods, such as microarrays. We investigate the effects of DNA sequence and solution temperature gradients on the kinetics of strand displacement at heated gold wire electrodes, and at gold disc electrodes in a heated solution. Addition of a terminal double mismatch (toehold) provides a reduction in strand displacement energy barriers sufficient to probe the secondary mechanisms involved in the hybridization process. In four different DNA capture probe sequences (relevant for the identification of genetically modified maize MON810), all but one revealed a high activation energy up to 200 kJ/mol during hybridization, that we attribute to displacement of protective strands by capture probes. Protective strands contain 4 to 5 mismatches to ease their displacement by the surface-confined probes at the gold electrodes. A low activation energy (30 kJ/mol) was observed for the sequence whose protective strand contained a toehold and one central mismatch, its kinetic curves displayed significantly different shapes, and we observed a reduced maximum signal intensity as compared to other sequences. These findings point to potential sequence-related contributions to oligonucleotide diffusion influencing kinetics. Additionally, for all sequences studied with heated wire electrodes, we observed a 23 K lower optimal hybridization temperature in comparison with disc electrodes in heated solution, and greatly reduced voltammetric signals after taking into account electrode surface area. We propose that thermodiffusion due to temperature gradients may influence both hybridization and strand displacement kinetics at heated microelectrodes, an explanation supported by computational fluid dynamics. DNA assays with surface-confined capture probes and temperature gradients should not neglect potential influences of thermodiffusion as well as sequence-related effects. Furthermore, studies attempting to characterize surface-tethered environments should consider thermodiffusion if temperature gradients are involved.

Electrochemical detection of DNA binding by tumor suppressor p53 protein using osmium-labeled oligonucleotide probes and catalytic hydrogen evolution at the mercury electrode

In this paper, we present an electrochemical DNA-protein interaction assay based on a combination of protein-specific immunoprecipitation at magnetic beads (MBIP) with application of oligonucleotide (ON) probes labeled with an electroactive oxoosmium complex (Os,bipy). We show that double-stranded ONs bearing a dT20 tail labeled with Os,bipy are specifically recognized by the tumor suppressor p53 protein according to the presence or absence of a specific binding site (p53CON) in the double-stranded segment. We demonstrate the applicability of the Os,bipy-labeled probes in titration as well as competition MBIP assays to evaluate p53 relative affinity to various sequence-specific or structurally distinct unlabeled DNA substrates upon modulation of the p53-DNA binding by monoclonal antibodies used for the immunoprecipitation. To detect the p53-bound osmium-labeled probes, we took advantage of a catalytic peak yielded by Os,bipy-modified DNA at the mercury-based electrodes, allowing facile determination of subnanogram quantities of the labeled oligonucleotides. Versatility of the electrochemical MBIP technique and its general applicability in studies of any DNA-binding protein is discussed.

Capillary electrophoretic separation-based approach to determine the labeling kinetics of oligodeoxynucleotides

With the recent advances in electron microscopy (EM), computation, and nanofabrication, the original idea of reading DNA sequence directly from an image can now be tested. One approach is to develop heavy atom labels that can provide the contrast required for EM imaging. While evaluating tentative labels for the respective nucleobases in synthetic oligodeoxynucleotides (oligos), we developed a streamlined CE protocol to assess the label stability, reactivity, and selectivity. We report our protocol using osmium tetroxide 2,2'-bipyridine (Osbipy) as a thymidine (T) specific label. The observed rates show that the labeling process is kinetically independent of both the oligo length, and the base composition. The conditions, i.e. temperature, optimal Osbipy concentration, and molar ratio of reagents, to promote 100% conversion of the starting oligo to labeled product were established. Hence, the optimized conditions developed with the oligos could be leveraged to allow osmylation of effectively all Ts in ssDNA, while achieving minimal mislabeling. In addition, the approach and methods employed here may be adapted to the evaluation of other prospective contrasting agents/labels to facilitate next-generation DNA sequencing by EM.

Nucleobase modification as redox DNA labelling for electrochemical detection

Basic aspects of DNA electrochemistry with a strong focus on the use of modified nucleobases as redox probes for electrochemical bioanalysis are reviewed. Intrinsic electrochemical properties of nucleobases in combination with artificial redox-active nucleobase modifications are frequently applied in this field. Synthetic approaches (both chemical and enzymatic) to base-modified nucleic acids are briefly summarized and their applications in redox labelling are discussed. Finally, analytical applications including DNA hybridization, primer extension, PCR, SNP typing, DNA damage and DNA-protein interaction analysis are presented (critical review, 91 references).

Electrochemical nucleic acid-based biosensors: Concepts, terms, and methodology (IUPAC Technical Report)

An electrochemical nucleic acid (NA)-based biosensor is a biosensor that integrates a nucleic acid as the biological recognition element and an electrode as the electrochemical signal transducer. The present report provides concepts, terms, and methodology related to biorecognition elements, detection principles, type of interactions to be addressed, and construction and performance of electrochemical NA biosensors, including their critical evaluation, which should be valuable for a wide audience, from academic, biomedical, environmental, and food-testing, drug-developing, etc. laboratories to sensor producers.

An ionic liquid supported CeO2 nanoshuttles-carbon nanotubes composite as a platform for impedance DNA hybridization sensing

A novel nanocomposite membrane, comprising of nanosized shuttle-shaped cerium oxide (CeO(2)), single-walled carbon nanotubes (SWNTs) and hydrophobic room temperature ionic liquid (RTIL) 1-butyl-3-methylimidazolium hexafluorophosphate (BMIMPF(6)), was developed on the glassy carbon electrode (GCE) for electrochemical sensing of the immobilization and hybridization of DNA. The properties of the CeO(2)-SWNTs-BMIMPF(6)/GCE, the characteristics of the immobilization and hybridization of DNA were studied by cyclic voltammetry and electrochemical impedance spectroscopy (EIS) using [Fe(CN)(6)](3-/4-) as the redox indicator. The synergistic effect of nano-CeO(2), SWNTs and RTIL could dramatically enhance the sensitivity of DNA hybridization recognition. The electron transfer resistance (R(et)) of the electrode surface increased after the immobilization of probe ssDNA on the CeO(2)-SWNTs-BMIMPF(6) membrane and rose further after the hybridization of the probe ssDNA with its complementary sequence. The remarkable difference between the R(et) value at the probe DNA-immobilized electrode and that at the hybridized electrode could be used for label-free EIS detection of the target DNA. The sequence-specific DNA of phosphoenolpyruvate carboxylase (PEPCase) gene from transgenically modified rape was detected by this DNA electrochemical biosensor. Under optimal conditions, the dynamic range for detecting the sequence-specific DNA of the PEPCase gene was from 1.0x10(-12) mol/L to 1.0x10(-7) mol/L, and the detection limit was 2.3x10(-13) mol/L, suggesting that the CeO(2)-SWNTs-BMIMPF(6) nanocomposite hold great promises for the applications in sensitive electrochemical biosensor.

Recent advances in DNA sensors

The concept of DNA biosensors is sustained by the need for rapid and highly sensitive analytical tools for genetic detection. Their implementation is based on three key steps: (i) immobilization of single-stranded oligonucleotide probes onto a substrate; (ii) hybridization and (iii) reading. These steps involve complementary knowledge in various disciplinary fields such as surface physics and chemistry, molecular electrochemistry, micro-technologies, optics, electronics and biochemistry. We present here, in a non-exhaustive way, the recent advances in the two steps of immobilization and detection that rely upon increasing integration of the number of reading points or/and of the reading strategy.

A PDDA/poly(2,6-pyridinedicarboxylic acid)-CNTs composite film DNA electrochemical sensor and its application for the detection of specific sequences related to PAT gene and NOS gene

2,6-Pyridinedicarboxylic acid (PDC) was electropolymerized on the glassy carbon electrode (GCE) surface combined with carboxylic group-functionalized single-walled carbon nanotubes (SWNTs) by cyclic voltammetry (CV) to form PDC-SWNTs composite film, which was rich in negatively charged carboxylic group. Then, poly(diallyldimethyl ammonium chloride) (PDDA), a linear cationic polyelectrolyte, was electrostatically adsorbed on the PDC-SWNTs/GCE surface. DNA probes with negatively charged phosphate group at the 5' end were immobilized on the PDDA/PDC-SWNTs/GCE due to the strong electrostatic attraction between PDDA and phosphate group of DNA. It has been found that modification of the electrode with PDC-SWNTs film has enhanced the effective electrode surface area and electron-transfer ability, in addition to providing negatively charged groups for the electrostatic assembly of cationic polyelectrolyte. PDDA plays a key role in the attachment of DNA probes to the PDC-SWNTs composite film and acts as a bridge to connect DNA with PDC-SWNTs film. The cathodic peak current of methylene blue (MB), an electroactive label, decreased obviously after the hybridization of DNA probe (ssDNA) with the complementary DNA (cDNA). This peak current change was used to monitor the recognition of the specific sequences related to PAT gene in the transgenic corn and the polymerase chain reaction (PCR) amplification of NOS gene from the sample of transgenic soybean with satisfactory results. Under optimal conditions, the dynamic detection range of the sensor to PAT gene target sequence was from 1.0x10(-11) to 1.0x10(-6) mol/L with the detection limit of 2.6x10(-12) mol/L.

Label-free sequence-specific DNA sensing using copper-enhanced anodic stripping of purine bases at boron-doped diamond electrodes

Stripping voltammetric determination of purine bases in the presence of copper ions at mercury, amalgam, or carbon-based electrodes has recently been utilized in analysis of DNA or synthetic oligodeoxynucleotides (ODNs). Here we report on copper-enhanced label-free anodic stripping detection of guanine and adenine bases in acid-hydrolyzed DNA at anodically oxidized boron-doped diamond electrode (AO-BDDE). The AO-BDDE was successfully applied in a three-electrode microcell in which an approximately 50 microL drop of the analyte solution can be efficiently stirred during the accumulation step by streaming of an inert gas. Accelerated mass transport due to the solution motion in the presence of copper resulted in enhancement of the guanine oxidation signal by about 2 orders of magnitude (compared to accumulation of the analyte from still solution not containing copper), allowing an easy detection of approximately 25 fmol of the ODNs. The proposed technique is shown to be suitable for a determination of purine (particularly guanine) content in DNA samples. Applications of the technique in magnetic bead-based DNA assays (such as hybridization with DNA sequences exhibiting asymmetrical distribution of purine/pyrimidine nucleotides between the complementary strands or monitoring of amplification of specific DNA fragments in a duplex polymerase chain reaction) are demonstrated.

Sensitive voltammetric detection of DNA damage at carbon electrodes using DNA repair enzymes and an electroactive osmium marker

This paper presents a new approach to electrochemical sensing of DNA damage, using osmium DNA markers and voltammetric detection at the pyrolytic graphite electrode. The technique is based on enzymatic digestion of DNA with a DNA repair enzyme exonuclease III (exoIII), followed by single-strand (ss) selective DNA modification by a complex of osmium tetroxide with 2,2'-bipyridine. In double-stranded DNA possessing free 3'-ends, the exoIII creates ss regions that can accommodate the electroactive osmium marker. Intensity of the marker signal measured at the pyrolytic graphite electrode responded well to the extent of DNA damage. The technique was successfully applied for the detection of (1) single-strand breaks (ssb) introduced in plasmid DNA by deoxyribonuclease I, and (2) apurinic sites generated in chromosomal calf thymus DNA upon treatment with the alkylating agent dimethyl sulfate. The apurinic sites were converted into the ssb by DNA repair endonuclease activity of the exoIII enzyme. We show that the presented technique is capable of detection of one lesion per approximately 10(5) nucleotides in supercoiled plasmid DNA.