New approaches in the development of DNA sensors: hybridization and electrochemical detection of DNA and RNA at two different surfaces

One-Electron Oxidation Potentials and Hole Delocalization in Heterogeneous Single-Stranded DNA

The study of DNA processes is essential to understand not only its intrinsic biological functions but also its role in many innovative applications. The use of DNA as a nanowire or electrochemical biosensor leads to the need for a deep investigation of the charge transfer process along the strand as well as of the redox properties. In this contribution, the one-electron oxidation potential and the charge delocalization of the hole formed after oxidation are computationally investigated for different heterogeneous single-stranded DNA strands. We have established a two-step protocol: (i) molecular dynamics simulations in the frame of quantum mechanics/molecular mechanics (QM/MM) were performed to sample the conformational space; (ii) energetic properties were then obtained within a QM1/QM2/continuum approach in combination with the Marcus theory over an ensemble of selected geometries. The results reveal that the one-electron oxidation potential in the heterogeneous strands can be seen as a linear combination of that property within the homogeneous strands. In addition, the hole delocalization between different nucleobases is, in general, small, supporting the conclusion of a hopping mechanism for charge transport along the strands. However, charge delocalization becomes more important, and so does the tunneling mechanism contribution, when the reducing power of the nucleobases forming the strand is similar. Moreover, charge delocalization is slightly enhanced when there is a correlation between pairs of some of the interbase coordinates of the strand: twist/shift, twist/slide, shift/slide, and rise/tilt. However, the internal structure of the strand is not the predominant factor for hole delocalization but the specific sequence of nucleotides that compose the strand.

Electrochemistry in sensing of molecular interactions of proteins and their behavior in an electric field

Electrochemical methods can be used not only for the sensitive analysis of proteins but also for deeper research into their structure, transport functions (transfer of electrons and protons), and sensing their interactions with soft and solid surfaces. Last but not least, electrochemical tools are useful for investigating the effect of an electric field on protein structure, the direct application of electrochemical methods for controlling protein function, or the micromanipulation of supramolecular protein structures. There are many experimental arrangements (modalities), from the classic configuration that works with an electrochemical cell to miniaturized electrochemical sensors and microchip platforms. The support of computational chemistry methods which appropriately complement the interpretation framework of experimental results is also important. This text describes recent directions in electrochemical methods for the determination of proteins and briefly summarizes available methodologies for the selective labeling of proteins using redox-active probes. Attention is also paid to the theoretical aspects of electron transport and the effect of an external electric field on the structure of selected proteins. Instead of providing a comprehensive overview, we aim to highlight areas of interest that have not been summarized recently, but, at the same time, represent current trends in the field.

Improvement of Sensitivity and Speed of Virus Sensing Technologies Using nm- and μm-Scale Components

Various viral diseases can be widespread and cause severe disruption to global society. Highly sensitive virus detection methods are needed to take effective measures to prevent the spread of viral infection. This required the development of rapid virus detection technology to detect viruses at low concentrations, even in the biological fluid of patients in the early stages of the disease or environmental samples. This review describes an overview of various virus detection technologies and then refers to typical technologies such as beads-based assay, digital assay, and pore-based sensing, which are the three modern approaches to improve the performance of viral sensing in terms of speed and sensitivity.

Intramolecular and intermolecular hole delocalization rules the reducer character of isolated nucleobases and homogeneous single-stranded DNA

The use of DNA strands as nanowires or electrochemical biosensors requires a deep understanding of charge transfer processes along the strand, as well as of the redox properties. These properties are computationally assessed in detail throughout this study. By applying molecular dynamics and hybrid QM/continuum and QM/QM/continuum schemes, the vertical ionization energies, adiabatic ionization energies, vertical attachment energies, one-electron oxidation potentials, and delocalization of the hole generated upon oxidation have been determined for nucleobases in their free form and as part of a pure single-stranded DNA. We show that the reducer ability of the isolated nucleobases is explained by the intramolecular delocalization of the positively charged hole, while the enhancement of the reducer character when going from aqueous solution to the strand correlates very well with the intermolecular hole delocalization. Our simulations suggest that the redox properties of DNA strands can be tuned by playing with the balance between intramolecular and intermolecular charge delocalization.

Application strategies of peptide nucleic acids toward electrochemical nucleic acid sensors

Peptide nucleic acids (PNAs) have attracted tremendous interest in the fabrication of highly sensitive electrochemical nucleic acid biosensors due to their higher stability and increased sensitivity than common DNA probes. The neutral pseudopeptide backbone of PNAs not only makes the PNA/DNA duplexes more stable but also provides many opportunities to construct ultrasensitive nucleic acid sensors. This review presents the details of various protocols for the construction of PNA-based electrochemical nucleic acid sensors. The crucial factors, origin, and development of PNA, immobilization methods of PNA probes and signal generation mechanisms, are discussed. This review aims to provide a reference for ultrasensitive PNA electrochemical biosensor preparation.

Enhanced electrochemical biosensing on gold electrodes with a ferri/ferrocyanide redox couple

Detection of specific DNA is important in many fields. Label-free DNA sensing performed by electrochemical impedance spectroscopy (EIS) or using a quartz crystal microbalance (QCM) is widely employed for this purpose. Gold electrodes are mainly used for these techniques due to their chemical stability. However, ferro/ferricyanide used as a redox couple was found to etch the gold electrode and this significantly limited the repeatability of the EIS measurement. Inductively coupled plasma mass spectrometry (ICP-MS) and QCM experiments provided important clues about the gold dissolution mechanism and revealed that phosphate buffer promotes the dissolution of gold in the presence of the ferri/ferrocyanide redox couple. Tris buffered conditions, which provide the most stable environment, enabled the investigation of experimental parameters with a Q-sense electrochemistry module (QEM), which can perform QCM and EIS measurements simultaneously and revealed the principal factors that influence changes in the impedance. With the reproducible measurements, the estimation of an optimum probe-DNA concentration for detecting complementary DNA is demonstrated. In order to amplify the detection signal of target DNA, we sought to maximize the difference in response between the probe-only and target DNA by controlling the concentration of probe DNA. We showed that an intermediate probe-DNA concentration yields optimum signal amplification.

Hybridizing clinical translatability with enzyme-free DNA signal amplifiers: recent advances in nucleic acid detection and imaging

Nucleic acids have become viable prognostic and diagnostic biomarkers for a diverse class of diseases, particularly cancer. However, the low femtomolar to attomolar concentration of nucleic acids in human samples require sensors with excellent detection capabilities; many past and current platforms fall short or are economically difficult. Strand-mediated signal amplifiers such as hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) are superior methods for detecting trace amounts of biomolecules because one target molecule triggers the continuous production of synthetic double-helical DNA. This cascade event is highly discriminatory to the target via sequence specificity, and it can be coupled with fluorescence, electrochemistry, magnetic moment, and electrochemiluminescence for signal reporting. Here, we review recent advances in enhancing the sensing abilities in HCR and CHA for improved live-cell imaging efficiency, lowered limit of detection, and optimized multiplexity. We further outline the potential for clinical translatability of HCR and CHA by summarizing progress in employing these two tools for in vivo imaging, human sample testing, and sensing-treating dualities. We finally discuss their future prospects and suggest clinically-relevant experiments to supplement further related research.

A miniaturized electrochemical platform with an integrated PDMS reservoir for label-free DNA hybridization detection using nanostructured Au electrodes

We report the fabrication and characterization of a miniaturized electrochemical platform for the label-free detection of DNA hybridization. The proposed platform is fabricated using microfabrication and electrodeposition techniques. Comprising a Ti working electrode with electrodeposited Au nanostructures, and Pt/Au pseudo-reference and counter electrodes, the device accounts for a limit of detection of 0.97 fM and a sensitivity of 20.78 (μA μM-1) cm-2 with respect to Dengue virus specific consensus primer detection in the range of 10 fM-1 μM. Here, the incorporation of nanostructured Au in the active sensing area not only enhances the current response by increasing the overall surface area, but it also facilitates facile probe DNA immobilization by gold-thiol self-assembly. We have used differential pulse voltammetry analysis in this study to monitor the changes in reaction kinetics with respect to target hybridization. Furthermore, the evaluation of reproducibility of the biosensor and its selectivity against interference has yielded acceptable outcomes. Additionally, in order to evaluate the system's selectivity, we have successfully distinguished PCR amplified wild type and mutant target DNAs corresponding to the BRCA1 specific gene. Here, the mutant and the wild type target DNAs differ by a two base deletion, and the fact that the system is able to differentiate even such minute dissimilarities under hybridization conditions is indicative of its superior performance.

Smart Bandages: The Future of Wound Care

Chronic non-healing wounds are major healthcare challenges that affect a noticeable number of people; they exert a severe financial burden and are the leading cause of limb amputation. Although chronic wounds are locked in a persisting inflamed state, they are dynamic and proper therapy requires identifying abnormalities, administering proper drugs and growth factors, and modulating the conditions of the environment. In this review article, we discuss technologies that have been developed to actively monitor the wound environment. We also highlight drug delivery tools that have been integrated with bandages to facilitate precise temporal and spatial control over drug release and review automated or semi-automated systems that can respond to the wound environment.

Diastereoselectivity of 5-Methyluridine Osmylation Is Inverted inside an RNA Chain

In this study, we investigated the reaction of the osmium tetroxide-bipyridine complex with pyrimidines in RNA. This reagent, which reacts with the diastereotopic 5-6 double bond, thus leading to the formation of two diastereomers, was used in the past to label thymidine and 5-methylcytosine in DNA. In light of the growing interest in post-transcriptional RNA modifications, we addressed the question of whether this reagent could be used for labeling of the naturally occurring RNA modifications 5-methylcytosine and 5-methyluridine. On nucleoside level, 5-methylcytosine and 5-methyluridine revealed a 5- and 12-fold preference, respectively, over their nonmethylated equivalents. Performing the reaction on an RNA level, we could show that the steric environment of a pentanucleotide has a major detrimental impact on the reaction rate of osmylation. Interestingly, this drop in reactivity was due to a dramatic change in diastereoselectivity, which in turn resulted from impediment of the preferred attack via the si side. Thus, while on the nucleoside level, the absolute configuration of the major product of osmylation of 5-methyluridine was (5R,6S)-5-methyluridine glycol-dioxoosmium-bipyridine, reaction with an RNA pentanucleotide afforded the corresponding (5S,6R)-diastereomer as the major product. The change in diastereoselectivity lead to an almost complete loss of selectivity toward 5-methylcytosine in a pentanucleotide context, while 5-methyluridine remained about 8 times more reactive than the canonical pyrimidines. On the basis of these findings, we evaluate the usefulness of osmium tetroxide-bipyridine as a potential label for the 5-methyluridine modification in transcriptome-wide studies.

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.

Multiplex electrochemical DNA platform for femtomolar-level quantification of genetically modified soybean

Current EU regulations on the mandatory labeling of genetically modified organisms (GMOs) with a minimum content of 0.9% would benefit from the availability of reliable and rapid methods to detect and quantify DNA sequences specific for GMOs. Different genosensors have been developed to this aim, mainly intended for GMO screening. A remaining challenge, however, is the development of genosensing platforms for GMO quantification, which should be expressed as the number of event-specific DNA sequences per taxon-specific sequences. Here we report a simple and sensitive multiplexed electrochemical approach for the quantification of Roundup-Ready Soybean (RRS). Two DNA sequences, taxon (lectin) and event-specific (RR), are targeted via hybridization onto magnetic beads. Both sequences are simultaneously detected by performing the immobilization, hybridization and labeling steps in a single tube and parallel electrochemical readout. Hybridization is performed in a sandwich format using signaling probes labeled with fluorescein isothiocyanate (FITC) or digoxigenin (Dig), followed by dual enzymatic labeling using Fab fragments of anti-Dig and anti-FITC conjugated to peroxidase or alkaline phosphatase, respectively. Electrochemical measurement of the enzyme activity is finally performed on screen-printed carbon electrodes. The assay gave a linear range of 2-250 pM for both targets, with LOD values of 650 fM (160 amol) and 190 fM (50 amol) for the event-specific and the taxon-specific targets, respectively. Results indicate that the method could be applied for GMO quantification below the European labeling threshold level (0.9%), offering a general approach for the rapid quantification of specific GMO events in foods.

Biorecognition on graphene: physical, covalent, and affinity immobilization methods exhibiting dramatic differences

The preparation of biorecognition layers on the surface of a sensing platform is a very crucial step for the development of sensitive and selective biosensors. Different protocols have been used thus far for the immobilization of biomolecules onto various electrode surfaces. In this work, we investigate how the protocol followed for the immobilization of a DNA aptamer affects the performance of the fabricated thrombin aptasensor. Specifically, the differences in selectivity and optimum amount of immobilized aptamer of the fabricated aptasensors adopting either physical, covalent, or affinity immobilization were compared. It was discovered that while all three methods of immobilization uniformly show a similar optimum amount of immobilized aptamer, physical, and covalent immobilization methods exhibit higher selectivity than affinity immobilization. Hence, it is believed that our findings are very important in order to optimize and improve the performance of graphene-based aptasensors.

Early stage of nucleic acid electrochemistry. Detection of DNA damage in X-ray-irradiated rats

First papers on electroactivity of DNA and RNA were published more then 50 years ago. For about 8 years oscillographic polarography at controlled a.c. (OP, proposed by J. Heyrovský already in 1941) was the method of choice for DNA analysis. Since approximately 1954 Robert Kalvoda developed OP for wide application in various fields. It is shown that already before 1960 it was possible to detect damage to DNA in X-ray-irradiated rats by means of OP. DNA samples from irradiated animals produced significantly larger OP anodic guanine signal indicating changes in the DNA structure. At present, radiation-induced strand breaks and damage to bases in DNA can be electrochemically detected at high sensitivity.

Biomagnetic glasses: preparation, characterization, and biosensor applications

In this work, a novel avenue to create a generic approach for the fabrication of biofunctional materials with magnetic capabilities to be used in the design of highly stable, magnetically separable enzyme-based systems was explored. As a model system, immobilization of acetylcholinesterase (AChE) was investigated using biomagnetic glasses composed of a magnetic core with a size tunable porous silica shell. The efficiency of the immobilization was determined by analyzing the biosensing capability of these biomagnetic glasses for the detection of the organophosphorous pesticide paraoxon. Screen printed electrodes with the AChE-biomagnetic glasses showed higher current response and stability than for the free enzyme. The detection limit of the paraoxon biosensor was in the nanomolar range.

Multi-wall carbon nanotubes (MWCNTs)-doped polypyrrole DNA biosensor for label-free detection of genetically modified organisms by QCM and EIS

In this paper, we describe DNA electrochemical detection for genetically modified organism (GMO) based on multi-wall carbon nanotubes (MWCNTs)-doped polypyrrole (PPy). DNA hybridization is studied by quartz crystal microbalance (QCM) and electrochemical impedance spectroscopy (EIS). An increase in DNA complementary target concentration results in a decrease in the faradic charge transfer resistance (R(ct)) and signifying "signal-on" behavior of MWCNTs-PPy-DNA system. QCM and EIS data indicated that the electroanalytical MWCNTs-PPy films were highly sensitive (as low as 4pM of target can be detected with QCM technique). In principle, this system can be suitable not only for DNA but also for protein biosensor construction.

Dual-stage DNA sensing: recognition and detection

Selective polynucleotide recognition and detection based on a dual-stage method are described. The method involves the development of a recognition surface based on gold nanoparticles modified with a thiolated capture probe able to hybridize with its complementary sequence (target). After hybridization, this sensing surface is removed from the solution and electrodeposited on an electrode surface. The detection of the hybridization event is achieved using the complex [Ru(NH(3))(5)L](2+), were L is [3-(2-phenanthren-9-yl-vinyl)-pyridine], as electrochemical indicator. This complex binds to double strand DNA more efficiently than to single stranded DNA. The advantage of this dual-stage DNA sensing method is the high selectivity derived from the separation of the hybridization event (occurring on one surface) from the detection step (on a different surface), enabling the analysis of long target DNAs, which is usually the case in real DNA sequence analysis. In addition, this approach not only quantifies pmol of a complementary target sequence but also is sensitive to the presence of a single mismatch and its position in the sequence.

Brilliant cresyl blue as electroactive indicator in electrochemical DNA oligonucleotide sensors

A new electrochemical DNA biosensor is presented based on carbon past electrode (CPE) for immobilization and detection of short DNA sequences with brilliant cresyl blue (BCB) as electroactive label. The interaction of BCB with DNA is electrochemically detected and BCB displays different signals in the interaction to ssDNA and dsDNA and variation in the BCB signal represents the extent of hybridization at the electrode surface. The effect of solution pH on electrochemical behavior of BCB was investigated. Additionally, the effect of solution pH on BCB accumulation on the CPE was studied. Furthermore, experiments showed that the solution pH could influence the differential pulse voltammetry (DPV) signal of BCB accumulated on the electrode and the highest BCB signal was obtained in pH 7.00. The effect of electrochemical pretreatment of CPE on the ability of electrode in probe adsorption, BCB accumulation and conditions of probe immobilization including potential and time was investigated and optimum conditions were suggested. The peak currents of BCB were linearly related to the concentration of the target oligonucleotide sequence in the range of 1.0x10(-8) to 5.0x10(-6)M. The detection limit of this approach was 9.00nM. The selectivity of the biosensor was studied using noncomplementary oligonucleotide.

Magnetic particle-based hybrid platforms for bioanalytical sensors

Biomagnetic nano and microparticles platforms have attracted considerable interest in the field of biological sensors due to their interesting physico-chemical properties, high specific surface area, good mechanical stability and opportunities for generating magneto-switchable devices. This review discusses recent advances in the development and characterization of active biomagnetic nanoassemblies, their interaction with biological molecules and their use in bioanalytical sensors.

Electrochemical detection of DNA hybridization using micro and nanoparticles

A novel, rapid, and sensitive protocol for the electrochemical detection of DNA hybridization that take the advantage of a magnetic separation/mixing process and the use of monomaleimido-gold nanoparticles of 1.4 nm diameter as label is presented. A sandwich-type assay is formed in this protocol by the capture probe DNA immobilized on the surface of magnetic beads and the double hybridization of the target (cystic fibrosis related DNA), first with the immobilized probe, and then with signaling probe DNA labeled with monomaleimido-gold nanoparticles. When the assay is completed, the final conjugate is transferred onto genomagnetic sensor surface (graphite epoxy composite electrode with a magnet inside) used as working electrode, and then the direct determination of gold nanoparticles by differential pulse voltammetry striping technique is carried out. This protocol is quite promising for numerous applications in different fields as clinical analysis, environmental control as well as other applications.