Electronic detection of single-base mismatches in DNA with ferrocene-modified probes

Chemistry of organometallic nucleic acid components: personal perspectives and prospects for the future

Organometallic modifications of biologically important compounds such as drugs, secondary natural products, peptides, and nucleic acids, to name just a few, represent a well-established strategy for the development of new anticancer and antimicrobial agents. Supported by these reasons, over 12 years ago, we initiated a research program into organometallic modifications of nucleic acid components. This account summarizes key results regarding the synthetic chemistry and biological activities of the obtained compounds. As synthetic chemists, our main goal over the last 12 years has been to develop new strategies that allow for the exploration of the chemical space of organometallic nucleic acid components. Accordingly, we have developed a Michael addition reaction-based methodology that enabled the synthesis of an entirely new class of glycol nucleic acid (GNA) constituents. Concerning GNA chemistry, we also reported the synthesis of the first-ever ferrocenyl GNA-RNA "mixed" dinucleoside phosphate analog. Recently, we developed a Cu(I)-catalyzed Huisgen azide-alkyne 1,3-dipolar cycloaddition reaction-based approach for the synthesis of novel 1,2,3-triazole-linked ("click") nucleosides. The high value of this approach is because it allows for the introduction of functional (e.g., luminescent and redox-active) groups that protrude from the main oligomer sequence. With respect to biological activity studies, we identified several promising anticancer and antimicrobial compounds. Furthermore, we found that simple ferrocenyl-nucleobase conjugates have potential as modulators of Aβ21-40 amyloid aggregation. The final section of this article serves as a guide for future studies, as it presents some challenging goals yet to be achieved within the rapidly growing field of nucleic acid chemistry.

Curcumin-capped gold nanorods as optical sensing platform for sequence specific detection of DNA based on their self-assembly

We are reporting curcumin-induced gold nanorods as an optical sensing platform for the detection of sequence-specific DNA target through their self-assembly. The combined effect of eco-friendly reducing agent (i.e., curcumin) and silver nitrate in a basic medium (i.e., pH 10) has been attributed for the formation of small gold nanorods (AuNRs) having approximate length and diameter i.e., 19.7 ± 0.8 nm and 6.0 ± 0.5 nm, respectively, and lower longitudinal surface plasmon resonance (SPR) enable to detect and analyse different biomarkers. Further, for evaluating cellular uptake of as-synthesized AuNRs, the cytotoxicity study has been carried out by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay on A549 cells and HEPG2 cell lines, respectively, and shown approximately similar cytotoxicity. Interestingly, as-synthesized optically and electronically active AuNRs based nanobiosensing platform enable to detect sequence-specific DNA targets with low level of detection limit i.e., LOD 8.6 ± 0.15 pM for complimentary target (CT) DNA with higher sensitivity and better selectivity. Finally, this study is suggesting a simplistic bio-mediated approach of tuning the shape and size of AuNRs for sensitive, selective and reliable nanobiosensing platform for sequence-specific DNA detection related to cancer cells.

Catalytic Undirected Meta-Selective C-H Borylation of Metallocenes

Metallocenes are privileged backbones in the fields of synthetic chemistry, catalysis, polymer science, etc. Direct C-H functionalization is undoubtedly the simplest approach for tuning the properties of metallocenes. However, owing to the presence of multiple identical C(sp2 )-H sites, this protocol often suffers from low reactivity and selectivity issues, especially for the regioselective synthesis of 1,3-difunctionalized metallocenes. Herein, an efficient iridium-catalyzed meta-selective C-H borylation of metallocenes is reported. With no need of preinstalled directing groups, this approach enables a rapid synthesis of various boronic esters based on benzoferrocenes, ferrocenes, ruthenocene, and related half sandwich complex. A broad range of electron-deficient and -rich functional groups are all compatible with the process. Notably, C-H borylation of benzoferrocenes takes place exclusively at the benzene ring, which is likely ascribed to the shielding effect of pentamethylcyclopentadiene. The synthetic utility is further demonstrated by easy scalability to gram quantities, the conversion of boron to heteroatoms including N3 , SePh, and OAc, as well as diverse cross-coupling reactions.

Recent Advances in Transition-Metal-Catalyzed C-H Functionalization of Ferrocene Amides

During the past decades, in synthetic organic chemistry, directing-group-assisted C-H functionalization is found to be a key tool for the expedient and site-selective construction of C-C and hybrid bonds. Among C-H functionalization of ferrocene derivatives, the directed group strategy is undoubtedly the most commonly used method. Compared to the other directing groups, ferrocene amides can be synthesized easily and are now recognized as one of the most efficient devices for the selective functionalization of certain positions because its metal centre permits fine, tuneable and reversible coordination. The family of amide directing groups mainly comprises monodentate and bidentate directing groups, which are categorized on the basis of coordination sites. In this review, various C-H bond functionalization reactions of ferrocene using amide directing groups are broadly discussed.

Electronic Coupling in 1,2,3-Triazole Bridged Ferrocenes and Its Impact on Reactive Oxygen Species Generation and Deleterious Activity in Cancer Cells

Mixed-valence (MV) binuclear ferrocenyl compounds have long been studied as models for testing theories of electron transfer and in attempts to design molecular-scale electronic devices (e.g., molecular wires). In contrary to that, far less attention has been paid to MV binuclear ferrocenes as anticancer agents. Herein, we discuss the synthesis of six 1,2,3-triazole ferrocenyl compounds for combined (spectro)electrochemical, electron paramagnetic resonance (EPR), computational, and anticancer activity studies. Our synthetic approach was based on the copper-catalyzed 1,3-dipolar azide–alkyne cycloaddition reaction and enabled us to obtain in one step compounds bearing either one, two, or three ferrocenyl entities linked to the common 1,2,3-triazole core. Thus, two series of complexes were obtained, which pertain to derivatives of 3′-azido-3′-deoxythymidine (AZT) and 3-azidopropionylferrocene, respectively. Based on the experimental and theoretical data, the two mono-oxidized species corresponding to binuclear AZT and trinuclear 3-azidopropionylferrocene complexes have been categorized as class II mixed-valence according to the classification proposed by Robin and Day. Of importance is the observation that these two compounds are more active against human A549 and H1975 non-small-cell lung cancer cells than their congeners, which do not show MV characteristics. Moreover, the anticancer activity of MV species competes or surpasses, dependent on the cell line, the activity of reference anticancer drugs such as cisplatin, tamoxifen, and 5-fluorouracil. The most active from the entire series of compounds was the binuclear thymidine derivative with the lowest IC₅₀ value of 5 ± 2 μM against lung H1975 cancer cells. The major mechanism of antiproliferative activity for the investigated MV compounds is based on reactive oxygen species generation in cancer cells. This hypothesis was substantiated by EPR spin-trapping experiments and the observation of decreased anticancer activity in the presence of N-acetyl cysteine (NAC) free-radical scavenger.

The 1,2,3-triazole bridged bi- and triferrocenyl compounds were prepared via a “click” reaction. Their corresponding mono-oxidized forms have been categorized as class II MV species. The biferrocenyl thymidine derivative showed remarkable anticancer activity against human A549 and H1975 cancer cells and negligible activity against nonmalignant human BEAS-2B cells. The anticancer activity mechanism is mainly due to ROS generation, and it originates from the combination of electronic coupling and the thymidine moiety, combined all together in one molecular scaffold.

An Allosteric Transcription Factor DNA-Binding Electrochemical Biosensor for Progesterone

We describe an electrochemical strategy to transduce allosteric transcription factor (aTF) binding affinity to sense steroid hormones. Our approach utilizes square wave voltammetry to monitor changes in current output as a progesterone (PRG)-specific aTF (SRTF1) unbinds from the cognate DNA sequence in the presence of PRG. The sensor detects PRG in artificial urine samples with sufficient sensitivity suitable for clinical applications. Our results highlight the capability of using aTFs as the biorecognition elements to develop electrochemical point-of-care biosensors for the detection of small-molecule biomarkers and analytes.

A novel DNA binding protein-based platform for electrochemical detection of miRNA

We present a novel amplification-free sandwich type platform assay for electrochemical detection of miRNA. The assay is based on T4 DNA polymerase mediated synthesis of the p53 binding DNA sequence at the 3' end of target miRNA. The resulting miRNA-DNA chimera is detected via an electrochemical sandwich hybridization assay where HRP-labelled p53 binds to its recognition sequence and an amperometric signal is generated by hydroquinone-mediated enzymatic reduction of H2O2. The limit of detection of our assay was estimated to be 22 fM with a linear dynamic range of 100 fM-1 nM. This new platform method of detecting miRNA shows superior performance to conventional electrochemical miRNA biosensors and has the potential for amplification-free analysis of miRNA with high specificity and sensitivity.

Multi-signal amplification electrochemical DNA biosensor based on exonuclease III and tetraferrocene

Homogeneous electrochemical DNA biosensors' unique qualities have been of great interest to researchers, mainly due to their high recognition efficiency in solutions. However, the processes of introducing additional markers and extra operations to obtain a signal are tedious and time consuming, which limits their overall potential applications. Herein, a novel tetraferrocene was synthesized and used as a homogeneous electrochemical DNA biosensor probe label. It contains four ferrocene units, which provide greater signaling potential compared to monoferrocene. Furthermore, the target DNA triggers the digestion of the double hairpin DNA probe with the aid of exonuclease III, promoting short single stranded DNA probe formation. With the combination of the incorporated tetraferrocene labeled short DNA probe strands and graphene's ability to adsorb single stranded DNA, the hybridization process can produce an electrode signal provided by tetraferrocene. A low detection limit of 8.2 fM toward target DNA with excellent selectivity was achieved. The proposed sensing system avoids tedious and time-consuming steps of DNA modification, making the experimental processes simpler and convenient. The advantages of high sensitivity, selectivity and simple operation make this strategy applicable to DNA detection.

Electrochemical primer extension based on polyoxometalate electroactive labels for multiplexed detection of single nucleotide polymorphisms

Polyoxymetalates (POMs) ([SiW₁₁O₃₉{Sn(CH₂)₂CO)}]^4- and [P₂W₁₇O₆₁{Sn(CH₂)₂CO)}]^6-) were used to modify dideoxynucleotides (ddNTPs) through amide bond formation, and applied to the multiplexed detection of single nucleotide polymorphisms (SNPs) in an electrochemical primer extension reaction. Each gold electrode of an array was functionalised with a short single stranded thiolated DNA probe, specifically designed to extend with the POM-ddNTP at the SNP site to be interrogated. The system was applied to the simultaneous detection of 4 SNPs within a single stranded 103-mer model target generated using asymmetric PCR, highlighting the potential of POM-ddNTPs for targeted, multiplexed SNP detection. The four DNA bases were successfully labelled with both ([SiW₁₁O₃₉{Sn(CH₂)₂CO)}]^4- and [P₂W₁₇O₆₁{Sn(CH₂)₂CO)}]^6-), and [SiW₁₁O₃₉{Sn(CH₂)₂CO)}]^4- demonstrated to be the more suitable due to its single oxidation peak, which provides an unequivocal signal. The POM-ddNTP enzymatically incorporated to the DNA anchored to the surface was visualised by AFM using gold coated mica. The developed assay has been demonstrated to be highly reproducible, simple to carry out and with very low non-specific background signals. Future work will focus on applying the developed platform to the detection of SNPs associated with rifampicin resistance in real samples from patients suffering from tuberculosis.

Innovations in biomedical nanoengineering: nanowell array biosensor

Nanostructured biosensors have pioneered biomedical engineering by providing highly sensitive analyses of biomolecules. The nanowell array (NWA)-based biosensing platform is particularly innovative, where the small size of NWs within the array permits extremely profound sensing of a small quantity of biomolecules. Undoubtedly, the NWA geometry of a gently-sloped vertical wall is critical for selective docking of specific proteins without capillary resistances, and nanoprocessing has contributed to the fabrication of NWA electrodes on gold substrate such as molding process, e-beam lithography, and krypton-fluoride (KrF) stepper semiconductor method. The Lee group at the Mara Nanotech has established this NW-based biosensing technology during the past two decades by engineering highly sensitive electrochemical sensors and providing a broad range of detection methods from large molecules (e.g., cells or proteins) to small molecules (e.g., DNA and RNA). Nanosized gold dots in the NWA enhance the detection of electrochemical biosensing to the range of zeptomoles in precision against the complementary target DNA molecules. In this review, we discuss recent innovations in biomedical nanoengineering with a specific focus on novel NWA-based biosensors. We also describe our continuous efforts in achieving a label-free detection without non-specific binding while maintaining the activity and stability of immobilized biomolecules. This research can lay the foundation of a new platform for biomedical nanoengineering systems.

Silver-dendrimer nanocomposites as oligonucleotide labels for electrochemical stripping detection of DNA hybridization

Silver-dendrimer nanocomposites were synthesized and used as oligonucleotide labels for electrochemical stripping detection of DNA hybridization. The synthesized silver-dendrimer nanocomposites were characterized by UV-vis spectrophotometry, X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM). Ratios of silver/dendrimer were optimized in order to obtain stable nanocomposites with maximal silver loading in the interior of a polymeric shell. The silver-dendrimer nanocomposites were attached to sequence-known DNA probes specific to colitoxin, and used to detect probe hybridization by dissolution of the silver nanoparticles in the interior of dendrimer in a diluted nitric acid, followed by measurement of Ag⁺ ions by anodic stripping voltammetry (ASV). Use of differential pulse voltammetry for the stripping step, along with optimization of the ASV conditions, enabled a detection limit of 0.78 pM. The present strategy, in combination with dendrimer-encapsulated copper labeled oligonucleotides probe reported previously, could potentially be used to detect single or multiple DNA targets in one sample.

Identifying DNA mismatches at single-nucleotide resolution by probing individual surface potentials of DNA-capped nanoparticles

Here, we demonstrate a powerful method to discriminate DNA mismatches at single-nucleotide resolution from 0 to 5 mismatches (χ₀ to χ₅) using Kelvin probe force microscopy (KPFM). Using our previously developed method, we quantified the surface potentials (SPs) of individual DNA-capped nanoparticles (DCNPs, ∼100 nm). On each DCNP, DNA hybridization occurs between ∼2200 immobilized probe DNA (pDNA) and target DNA with mismatches (tDNA, ∼80 nM). Thus, each DCNP used in the bioassay (each pDNA-tDNA interaction) corresponds to a single ensemble in which a large number of pDNA-tDNA interactions take place. Moreover, one KPFM image can scan at least dozens of ensembles, which allows statistical analysis (i.e., an ensemble average) of many bioassay cases (ensembles) under the same conditions. We found that as the χ_n increased from χ₀ to χ₅ in the tDNA, the average SP of dozens of ensembles (DCNPs) was attenuated owing to fewer hybridization events between the pDNA and the tDNA. Remarkably, the SP attenuation vs. the χ_n showed an inverse-linear correlation, albeit the equilibrium constant for DNA hybridization exponentially decreased asymptotically as the χ_n increased. In addition, we observed a cascade reaction at a 100-fold lower concentration of tDNA (∼0.8 nM); the average SP of DCNPs exhibited no significant decrease but rather split into two separate states (no-hybridization vs. full-hybridization). Compared to complementary tDNA (i.e., χ₀), the ratio of no-hybridization/full-hybridization within a given set of DCNPs became ∼1.6 times higher in the presence of tDNA with single mismatches (i.e., χ₁). The results imply that our method opens new avenues not only in the research on the DNA hybridization mechanism in the presence of DNA mismatches but also in the development of a robust technology for DNA mismatch detection.

A Novel Electrochemical Biosensor Based on a Double-Signal Technique for d(CAG)n Trinucleotide Repeats

Electrochemical sensors now play an important role in analysis and detection of nucleic acids. In this work, we present a novel double-signal technique for electrochemically measuring the sequence and length of the d(CAG)_n repeat. The double-signal technique used an electrochemical molecular beacon (a hairpin DNA labeled with ferrocene), which was directly modified on the surface of a gold electrode, while a reporter probe (a DNA sequence labeled with horseradish peroxidase) was hybridized to the target DNA. First a simple single-signal sensor was characterized in which d(CAG)_n repeats were detected using a short reporter DNA strand labeled with horseradish peroxidase. To obtain a reliable signal that was dependent on repeat number, a double-signal biosensor was created in which the single strand capture DNA in single-signal sensor was replaced by an electrochemical molecular beacon labeled with ferrocene. When the hairpin DNA hybridized to the target-reporter DNA complex, it opened, resulting in a decreased ferrocene current. Both electrochemical biosensors exhibited high selectivity and sensitivity with low detection limits of 0.21 and 0.15 pM, respectively, for the detection of d(CAG)_n repeats. The double-signal sensor was more accurate for the determination of repeat length, which was measured from the ratio of signals for HRP and ferrocene (H/F). A linear relationship was found between H/F and the number of repeats (n), H/F = 0.1398n + 9.89788, with a correlation coefficient of 0.974. Only 10 nM of target DNA was required for measurements based on the value of H/F in the double-signal technique. These results indicated that this new double-signal electrochemical sensor provided a reliable method for the analysis of CAG trinucleotide repeats.

Ferrocene conjugated oligonucleotide for electrochemical detection of DNA base mismatch

We describe the synthesis, binding, and electrochemical properties of ferrocene-conjugated oligonucleotides (Fc-oligos). The key step for the preparation of Fc-oligos contains the coupling of vinylferrocene to 5-iododeoxyuridine via Heck reaction. The Fc-conjugated deoxyuridine phosphoramidite was used in the Fc-oligonucleotide synthesis. We show that thiol-modified Fc-oligos deposited onto gold electrodes possess potential ability in electrochemical detection of DNA base mismatch.

DNA sensors to assess the effect of VKORC1 and CYP2C9 gene polymorphisms on warfarin dose requirement in Chinese patients with atrial fibrillation

The optimal dose of warfarin depends on polymorphisms in the VKORC1 (the vitamin K epoxide reductase complex subunit (1) and CYP2C9 (cytochrome P450 2C9) genes. To minimize the risk of adverse reactions, warfarin dosages should be adjusted according to results from rapid and simple monitoring methods. However, there are few pharmacogenetic-guided warfarin dosing algorithms that are based on large cohorts from the Chinese population, especially patients with atrial fibrillation. This study aimed to validate a pharmacogenetic-guided warfarin dosing algorithm based on results from a new rapid electrochemical detection method used in a multicenter study. Three SNPs (CYP2C9 *2, *3 and VKORC1 c.-1639G > A) were genotyped by electrochemical detection using a sandwich-type format that included a 3' short thiol capture probe and a 5' ferrocene-labeled signal probe. A total of 1285 samples from four clinical hospitals were evaluated. Concordance rates between the results from the electrochemical DNA biosensor and the sequencing test were 99.8%. The results for gene distribution showed that most Chinese patients had higher warfarin susceptibility because mutant-type and heterozygotes were present in the majority of subjects (99.4%) at locus c.-1639G > A. When the International Warfarin Pharmacogenetics Consortium algorithm was used to estimate therapeutic dosages for 362 patients with AF and the values were compared with their actual dosages, the results revealed that 56.9% were similar to actual dosages (within the 20% range). A novel electrochemical detection method of CYP2C9 *2, *3and VKORC1 c.-1639G > A alleles was evaluated. The warfarin dosing algorithm based on data gathered from a large patient cohort can facilitate the reasonable and effective use of warfarin in Chinese patients with AF.

Printable Electrochemical Biosensors: A Focus on Screen-Printed Electrodes and Their Application

In this review we present electrochemical biosensor developments, focusing on screen-printed electrodes (SPEs) and their applications. In particular, we discuss how SPEs enable simple integration, and the portability needed for on-field applications. First, we briefly discuss the general concept of biosensors and quickly move on to electrochemical biosensors. Drawing from research undertaken in this area, we cover the development of electrochemical DNA biosensors in great detail. Through specific examples, we describe the fabrication and surface modification of printed electrodes for sensitive and selective detection of targeted DNA sequences, as well as integration with reverse transcription-polymerase chain reaction (RT-PCR). For a more rounded approach, we also touch on electrochemical immunosensors and enzyme-based biosensors. Last, we present some electrochemical devices specifically developed for use with SPEs, including USB-powered compact mini potentiostat. The coupling demonstrates the practical use of printable electrode technologies for application at point-of-use. Although tremendous advances have indeed been made in this area, a few challenges remain. One of the main challenges is application of these technologies for on-field analysis, which involves complicated sample matrices.

A Simple, Rapid, and Highly Sensitive Electrochemical DNA Sensor for the Detection of α- and β-Thalassemia in China

BACKGROUND

Because of the life-consuming treatment and severe consequences associated with thalassemia, it is more effective to prevent than cure thalassemia. Rapid and sensitive detection is critical for controlling thalassemia. In this study, we developed a rapid and accurate test to genotype nondeletional α- and β-thalassemia mutations by an electrochemical DNA sensor.

METHODS

Screen-printed electrodes were used as electrochemical transducers for the sensor, in which the capture probe DNA was attached to the golden surface of the working electrode via an S-Au covalent bond, which is highly suitable for immobilizing the biological element. In addition, two types of ferrocene with varying redox potentials for modified signal probe DNA were adopted. The hybridization signal is detected by alternating current voltammetry when the capture probe and signal probe hybridize with the target DNA.

RESULTS

With this technique, 12 types of nondeletional α- and β-thalassemia mutations were detected, which constitute more than 90% of all the nondeletional types of thalassemia mutation determinants found in China, including the CD142 (TAA>CAA) Constand spring, CD125 (CTG>CCG) Quonsze, CD122 (CAC>CAG) Weastmead, -28 (A>G), Cap+1 (A>C), initiation codon (ATG>AGG), CD17 (AAG>TAG), CD26 (GAG>AAG), CD31(-C), CD41-42 (-CTTT), CD71-72 (+A), and IVS-II-654 (C>T) mutations. Concordance levels were 100% within the 20 blood samples of homozygous wild-type individuals and 238 blood samples of heterozygous mutant individuals.

CONCLUSIONS

The electrochemical DNA sensor developed here can be applied for rapid genotyping of thalassemia or other clinical genotyping applications and is useful for early screening of thalassemia in high-risk groups by minimizing the time and investment cost.

A novel electrochemical DNA biosensor based on a modified magnetic bar carbon paste electrode with Fe3O4NPs-reduced graphene oxide/PANHS nanocomposite

In this study, we have designed a label free DNA biosensor based on a magnetic bar carbon paste electrode (MBCPE) modified with nanomaterial of Fe3O4/reduced graphene oxide (Fe3O4NP-RGO) as a composite and 1- pyrenebutyric acid-N- hydroxysuccinimide ester (PANHS) as a linker for detection of DNA sequences. Probe (BRCA1 5382 insC mutation detection) strands were immobilized on the MBCPE/Fe3O4-RGO/PANHS electrode for the exact incubation time. The characterization of the modified electrode was studied using different techniques such as scanning electron microscopy (SEM), infrared spectroscopy (IR), vibrating sample magnetometer (VSM), electrochemical impedance spectroscopy (EIS) and cyclic voltammetry methods. Some experimental parameters such as immobilization time of probe DNA, time and temperature of hybridization process were investigated. Under the optimum conditions, the immobilization of the probe and its hybridization with the target DNA (Complementary DNA) were tested. This DNA biosensor revealed a good linear relationship between ∆Rct and logarithm of the complementary target DNA concentration ranging from 1.0×10(-18)molL(-1) to 1.0×10(-8)molL(-1) with a correlation coefficient of 0.9935 and a detection limit of 2.8×10(-19)molL(-1). In addition, the mentioned biosensor was satisfactorily applied for discriminating of complementary sequences from non-complementary sequences. The constructed biosensor (MBCPE/Fe3O4-RGO/PANHS/ssDNA) with high sensitivity, selectivity, stability, reproducibility and low cost can be used for detection of BRCA1 5382 insC mutation.

Macrocyclic Metal Complex-DNA Conjugates for Electrochemical Sensing of Single Nucleobase Changes in DNA

The direct incorporation of macrocyclic cyclidene complexes into DNA via automated synthesis results in a new family of metal-functionalized DNA derivatives that readily demonstrate their utility through the ability of one redox-active copper(II)-containing strand to distinguish electrochemically between all four canonical DNA nucleobases at a single site within a target sequence of DNA.

A signal-on electrochemical DNA biosensor based on potential-assisted Cu(I)-catalyzed azide-alkyne cycloaddition mediated labeling of hairpin-like oligonucleotide with electroactive probe

A novel electrochemical biosensor was developed for the signal-on detection of sequence-specific DNA by exploiting potential-assisted Cu(I)-catalyzed azide-alkyne cycloaddition (φCuAAC) as an efficient approach for the labeling of hairpin-like oligonucleotide (hairpin) with electroactive probe. The hairpins, dually labeled with thiol and azide at either terminal, were firstly self-assembled on gold electrode and served as the capture probes for the specific recognition of target DNA. Upon hybridization with target DNA, the surface-confined hairpins were unfolded, liberating the azide-containing terminals away from electrode surface. Subsequently, the unfolded hairpins were conveniently and efficiently labeled with ethynylferrocene (EFC) via the φCuAAC. The quantitatively labeled EFC was finally measured via differential pulse voltammetry (DPV) for the signal-on electrochemical detection of sequence-specific DNA. The biosensor presented a good linear response over the range from 1pM to 1nM with a detection limit of 0.62pM. Results also revealed that it was highly specific and held a good detection capability in serum samples. Furthermore, the ability to chemoselectively label hairpin-like oligonucleotide with signal reporter by electrical addressing, together with the simplicity and efficiency of the φCuAAC, makes it compatible with microfluidic devices and microelectrode arrays to achieve the miniaturized and multiplexed detections.

Electrochemical Label-Free Nucleotide Sensors

Numerous researchers have devoted a great deal of effort over the last few decades to the development of electrochemical oligonucleotide detection techniques, owing to their advantages of simple design, inherently small dimensions, and low power requirements. Their simplicity and rapidity of detection makes label-free oligonucleotide sensors of great potential use as first-aid screening tools in the analytical field of environmental measurements and healthcare management. This review article covers label-free oligonucleotide sensors, focusing specifically on topical electrochemical techniques, including intrinsic redox reaction of bases, conductive polymers, the use of electrochemical indicators, and highly ordered probe structures.

Simple and fast electrochemical detection of sequence-specific DNA via click chemistry-mediated labeling of hairpin DNA probes with ethynylferrocene

In this work, the azido-containing hairpins were exploited as the capture probes; after hybridization, labeling of electroactive probes, ethynylferrocene, was conveniently and efficiently achieved via the Cu(i)-catalyzed azide–alkyne cycloaddition.

Direct quantification of microRNA at low picomolar level in sera of glioma patients using a competitive hybridization followed by amplified voltammetric detection

MicroRNAs (miRNAs), acting as oncogenes or tumor suppressors in humans, play a key role in regulating gene expression and are believed to be important for developing novel therapeutic treatments and clinical prognoses. Due to their short lengths (17-25 nucleotides) and extremely low concentrations (typically < picomolar) in biological samples, quantification of miRNAs has been challenging to conventional biochemical methods, such as Northern blotting, microarray, and quantitative polymerase chain reaction (qPCR). In this work, a biotinylated miRNA (biotin-miRNA) whose sequence is the same as that of a miRNA target is introduced into samples of interest and allowed to compete with the miRNA target for the oligonucleotide (ODN) probe preimmobilized onto an electrode. Voltammetric quantification of the miRNA target was accomplished after complexation of the biotin-miRNA with ferrocene (Fc)-capped gold nanoparticle/streptavidin conjugates. The Fc oxidation current was found to be inversely proportional to the concentration of target miRNA between 10 fM and 2.0 pM. The method is highly reproducible (relative standard deviation (RSD) < 5%), regenerable (at least 8 regeneration/assay cycles without discernible signal decrease), and selective (with sequence specificity down to a single nucleotide mismatch). The low detection levels (10 fM or 0.1 attomoles of miRNA in a 10 μL solution) allow the direct quantification of miRNA-182, a marker correlated to the progression of glioma in patients, to be performed in serum samples without sample pretreatment and RNA extraction and enrichment. The concentration of miRNA-182 in glioma patients was found to be 3.1 times as high as that in healthy persons, a conclusion in excellent agreement with a separate qPCR measurement of the expression level. The obviations of the requirement of an internal reference in qPCR, simplicity, and cost-effectiveness are other additional advantages of this method for detection of nucleic acids in clinical samples.

Nanoporous gold electrode as a platform for the construction of an electrochemical DNA hybridization biosensor

The application of a nanoporous gold electrode (NPGE) in the fabrication of an electrochemical sensing system for the detection of single base mismatches (SBMs) using ferrocene-modified DNA probe has been investigated in the present manuscript. Ferrocene carboxylic acid is covalently attached to the amino-modified probe using EDC/NHS chemistry. By covalent attachment of the redox reporter molecules on the top of DNA, the direct oxidation of the ferrocene on the electrode surface is avoided. On the other hand, the electrochemical signals are amplified by anodizing the electrode surface and converting it to nanoporous form. By improving the sensitivity of the biosensor, the different SBMs including the thermodynamically stable G-A and G-T mismatches, can be easily distinguished. In this research, NPGE was prepared by anodization and chemical reduction of Au surface and used for signal amplification. Nanoporous electrode enhances the sensitivity of DNA biosensor and makes it capable to detect complementary target DNA in sub-nanomole scales.

Pyrrolyl-, 2-(2-thienyl)pyrrolyl- and 2,5-bis(2-thienyl)pyrrolyl-nucleosides: synthesis, molecular and electronic structure, and redox behaviour of C5-thymidine derivatives

A series of modified nucleosides based on thymidine have been prepared by Pd-catalysed cross-coupling between N-alkyl-alkynyl functionalised pyrrolyl- (py), 2-(2-thienyl)pyrrolyl- (tp) or 2,5-bis(2-thienyl)pyrrolyl (tpt) groups with 5-iodo-2'-deoxyuridine. The length of the alkyl chain linking the nucleoside and pyrrolyl-containing unit, N(CH(2))(n)C[triple bond, length as m-dash]C-nucleoside (where n = 1-3) was also varied. The compounds have been characterised by (1)H NMR, ES-MS, UV-vis, cyclic voltammetry (CV) and, in some cases, single-crystal X-ray diffraction. Cyclic voltammetry studies demonstrated that all the py-, tp- and tpt-alkynyl derivatives 1-7 can be electrochemically polymerised to form conductive materials. It was found that increasing the N-alkyl chain length in these cases resulted in only minor changes in the oxidation potential. The same behaviour was observed for the tp- and tpt-modified nucleosides 9-12; however, the py-derivative, 8, produced a poorly conducting material. DFT calculations on the one-electron oxidised cation of the modified nucleosides bearing tp or tpt showed that spin density is located on the pyrrolyl and thienyl units in all cases and that the coplanarity of adjacent rings increases upon oxidation. In contrast, in the corresponding pyrrolyl cases the spin density is distributed over the whole molecule, suggesting that polymerisation does not occur solely at the pyrrolyl-Cα position and the conjugation is interrupted.

Sequence-specific detection of short-length DNA via template-dependent surface-hybridization events

Short-length DNA and RNA, such as mature small RNA, which contains only 17-25 nucleotides, are always a problem in hybridization-based detection assays. In this paper, we report a proof-of-concept for a new short-length DNA detection technology which encompasses a design strategy whereby capture and reporter probes that do not hybridize to each other at 20 degrees C can be made to anneal to each other in the presence of a template via the formation of a stable three-component complex. The thermodynamics of this magnetic bead-based DNA biosensor was then investigated in detail by monitoring chemiluminescence (CL) changes in the absence and presence of targets over a temperature profile. The data show that this new biosensor offers the possibility of highly selective and sensitive detection of the short-length target DNA. In view of these advantages, this template-dependent surface-hybridization assay, as a new CL strategy, might create a universal technology for developing simple biosensors in sensitive and selective detection of short-length DNA and RNA.