Fluorescence Detection of Single‐Nucleotide Polymorphisms with a Single,Self‐Complementary,Triple‐Stem DNA Probe

Singled out for its singularity : In a single‐step, single‐component, fluorescence‐based method for the detection of single‐nucleotide polymorphisms at room temperature, the sensor is comprised of a single, self‐complementary DNA strand that forms a triple‐stem structure. The large conformational change that occurs upon binding to perfectly matched (PM) targets results in a significant increase in fluorescence (see picture; F=fluorophore, Q=quencher).

     

Efficient Discrimination of Single Nucleotide Polymorphisms (SNPs) Using Oligonucleotides Modified with C5‐Pyrene‐Functionalized DNA and Flanking Locked Nucleic Acid (LNA) Monomers

Oligodeoxyribonucleotides modified with 5‐[3‐(1‐pyrenecarboxamido)propynyl]‐2′‐deoxyuridine monomer X and proximal LNA monomers display higher affinity for complementary DNA, more pronounced increases in fluorescence emission upon DNA binding, and improved discrimination of SNPs at non‐stringent conditions, relative to the corresponding LNA‐free probes across a range of sequence contexts. The results reported herein suggest that the introduction of LNA monomers influences the position of nearby fluorophores via indirect conformational restriction, a characteristic that can be utilized to develop optimized fluorophore‐labeled probes for SNP‐discrimination studies.     

Interaction of Mitomycin C with DNA Immobilized onto Single‐walled Carbon Nanotube/Polymer Modified Pencil Graphite Electrode

The electrochemical investigation of the interaction between the anticancer drug mitomycin C (MC) and DNA was described using a single‐walled carbon nanotube (SWCNT)/poly(vinylferrocenium) (PVF⁺) modified pencil graphite electrode (PGE). The electrochemical oxidation signals of guanine were monitored before and after the interaction between MC and DNA by using differential pulse voltammetry. The effects of DNA and MC concentration and MC interaction time were examined based on the electrode response. Cyclic voltammetry and electrochemical impedance spectroscopy were used for the characterization of SWCNT/PVF⁺ modified and PVF⁺ modified PGEs. The detection limit corresponded to 625 ng/mL for MC using calf thymus double‐stranded DNA immobilized SWCNT/PVF⁺ modified PGE.     

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.     

Electrochemical Detection of Duplex DNA Using Intercalation‐Triggered Decomplexation of Ferrocene with β‐Cyclodextrin

The redox peak of ferrocenylnaphthalene diimide used as a threading intercalator shifted positively due to the formation of its complex with β‐cyclodextrin. This complex collapsed upon the addition of double‐stranded DNA, and its redox potential shifted negatively. This behavior was applied for the homogenous detection of a polymerase chain reaction (PCR) product from Porphyromonas gingivalis, which is important for the diagnosis of periodontal disease, and its quantitative detection was achieved with a detection limit of 2.7 nM.     

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.     

Differential Pulse Voltammetric Detection of Hepatitis C Virus 1a Oligonucleotide Chain by a Label‐Free Electrochemical DNA Hybridization Biosensor Using Consensus Sequence of Hepatitis C Virus 1a Probe on the Pencil Graphite Electrode

The short sequence related to hepatitis C virus (HCV1) is detected by a label‐free DNA hybridization biosensor. The sensor relies on the immobilization of a 20‐mer oligonucleotide containing 2 guanine and 11 cytosine bases denoted PHCV1 as probe on the pencil graphite electrode (PGE). The hybridization event was monitored by differential pulse voltammetry (DPV) using the guanine signal. The selectivity of the biosensor was studied using some noncomplementary oligonucleotides. Diagnostic performance of the biosensor is described and the detection limit was found to be 6.5 nM.     

Investigation of the Interactions of β‐Peptides with DNA Duplexes by Circular Dichroism Spectroscopy

The interaction of β‐peptides with the DNA duplexes of dA₂₀dT₂₀ and a GCN4‐binding CRE sequence was examined. To gauge the factors that govern these interactions, two β‐pentadecapeptides, 1 and 2 , a β‐dodecapeptide, 3 , three β‐decapeptides, 4 – 6 , three β‐heptapeptides, 7 – 9 , and β‐octaarginine 10 were designed and synthesized. The β‐peptides were conceived to adopt a β‐peptide 3₁₄ helix, in which the side chains at position i and i + 3 are aligned vertically along one side of the helix. The side chains of Lys, Asn, and Arg were positioned such that potential H‐bonding sites were created for a helical conformation to interact with the base pairs of DNA. CD Analysis showed that β‐peptides 1, 2 , and 10 interacted with dA₂₀dT₂₀. In addition, β‐peptides 1 and 2 showed significant interaction with a DNA‐duplex 20mer containing the ATF/CREB recognition sequence for the regulatory protein GCN4. It is impossible, at this stage of the investigation, to make a safe proposal about the actual nature of the interaction of the structures(s) of the complexes, the formation of which is suggested by the CD spectra reported herein.     

Easy Entry into Reduced Ar‐BIANH2 Compounds: A New Class of Quinone/Hydroquinone‐Type Redox‐Active Couples with an Easily Tunable Potential

Ar‐BIANH₂ bearing different substituents on the aryl rings have been synthesized in high yield by reduction of the corresponding bis(aryl)acenaphthenequinonediimine (Ar‐BIAN) compounds. The structure of p‐CH₃C₆H₄‐BIANH₂ in the solid state was determined by X‐ray diffraction. An exhaustive voltammetric investigation of the two parallel BIAN and BIANH₂ series afforded a first rationalization of the redox properties of these molecules, highlighting their analogies with quinone/hydroquinone systems. Such analogies, in combination with the much more negative reduction potential range of Ar‐BIAN compounds with respect to quinones, can afford to extend the range of reduction potentials so far obtainable by the use of quinones.     

Separation of single‐base sequential isomers of single‐stranded DNA by capillary electrophoresis and its application in the discrimination of single‐base DNA mutations

Separation of single‐base substitution sequential DNA isomers remains one of the most challenging tasks in DNA separation by capillary electrophoresis. We developed a simple, versatile capillary electrophoresis technique for the separation of single‐base sequential isomers of DNA having the same chain length. This technique is based on charge differences resulting from the different protonation (acid dissociation) properties of the four DNA bases. A mixture of 13 single‐base sequential isomers of 12‐mer single‐stranded DNA was separated by using an electrophoretic buffer solution containing 20 mM phosphoric acid (pH 2.0) and 8 M urea. We demonstrated that our method could separate all possible mutation patterns under identical experimental conditions. In addition, application of our method to the separation of the polymerase chain reaction product of a 68‐mer gene fragment and its single‐base isomers indicates that in combination with the appropriate genomic DNA extraction techniques, the method can detect single‐base gene mutations.     

A Voltammetric Electronic Tongue Based on Commercial Screen‐printed Electrodes for the Analysis of Aminothiols by Differential Pulse Voltammetry

A voltammetric electronic tongue has been designed as a proof of concept for the analysis of aminothiols by differential pulse voltammetry and has been tested in ternary mixtures of cysteine (Cys), homocysteine (hCys) and glutathione (GSH). It consists of three screen‐printed electrodes of carbon, carbon nanofibers and gold cured at low temperature. A preliminary calibration study carried out separately for each aminothiol confirmed that, working at an optimal pH value of 7.4, every electrode produces differentiated responses for every analyte (cross‐response). As for the tongue, it was applied to calibration and validation mixtures of Cys, hCys and GSH and provided voltammograms that, baseline‐corrected, normalized and combined in different ways were submitted to partial least squares (PLS) calibration. The calibration models produced good predictions of the concentrations of all three analytes, which suggest that the proposed voltammetric tongue improves the performance of a previous design based on linear sweep voltammetric measurements under acidic conditions.     

Electrodeposition of Silver Amalgam on Thin Gold Film Electrodes for Voltammetric Detection of 4‐Nitrophenol and DNA Labeled with Osmium Tetroxide‐Bipyridine Complex

Alternative electrode materials suitable to prepare novel working electrode applicable in detecting biopolymers such as nucleic acids, proteins or glycoproteins, represent a significant contribution to bio‐electroanalysis. Herein, electrodes made of vapor‐deposited thin gold films (vAuE) were used as an alternative substrate for the electrodeposition of silver amalgam particles (AgAPs), next to indium tin oxide and pyrolytic graphite, which are already used. The conditions and parameters of double pulse chronoamperometry were optimized for the most‐sensitive voltammetric detection of 4‐nitrophenol (4‐NP). The resulting electrodes were characterized by scanning electron microscope with energy dispersive X‐ray spectroscopy. While 4‐NP could not be detected by bare nonactivated vAuEs at all, their electrochemical activation offered a limit of detection (LoD) of 25 and 5 μmol.l^?1 by means of CV and DPV, respectively. AgAP electrodeposited on vAuE, offered 2.5‐times lower LoDs 10 μmol.l^?1 by CV and comparable LoD 5 μmol.l^?1 by DPV. Advantageously, AgAPs could be repeatedly deposited on and anodically dissolved from the vAuE with a relative standard deviation 13 % of the ten‐times repeated DPV signal of 4‐NP (100 μmol.l^?1). In comparison to vAuE, the vAuE‐AgAP offered about 400 mV broader potential window, which allowed detection of single strand DNA fragment labeled by osmium tetroxide?bipyridine complex down to 2 ng.μl^?1 by means of DPV.     

Thread Insertion of a Bis(dipyridophenazine) Diruthenium Complex into the DNA Double Helix by the Extrusion of AT Base Pairs and Cross‐Linking of DNA Duplexes

The crystal structure of the Δ,Δ enantiomer of the binuclear “light‐switch” ruthenium complex [μ‐(11,11′‐bidppz)(1,10‐phenanthroline)₄ Ru₂]⁴⁺ bound to the oligonucleotide d(CGTACG) shows that one dppz moiety of the dumbbell‐like compound inserts into the DNA stack through the extrusion of an AT base pair. The second dppz moiety recruits a neighboring DNA molecule, and the complex thus cross‐links two adjacent duplexes by bridging their major grooves.