Distinguishing cytosine methylation using electrochemical, label-free detection of DNA hybridization and ds-targets

Electrochemical Biosensor for Protein Concentration Monitoring Using Natural Wood Evaporation for Power Generation

A high-sensitivity, low-cost, self-powered biomass electrochemical biosensor based on the "evaporating potential" theory is developed for protein detection. The feasibility of experimental evaluation methods was verified with a probe protein of bovine serum albumin. The sensor was then used to detect lung cancer marker CYFRA21-1, and the potential of our sensor for clinical diagnosis was demonstrated by serum analysis. This work innovatively exploits the osmotic power generation capability of natural wood to construct a promising electrochemical biosensor that was driven by kinetics during testing. The detection methods used for this sensor, chronoamperometry and AC impedance, showed potential for quantitative analysis and specific detection, respectively. Furthermore, the sensor could facilitate new insights into the development of high-sensitivity, low-cost, and easy-to-use electrochemical biosensors.

Rapid ultra-sensitive nucleic acid detection using plasmonic fiber-optic spectral combs and gold nanoparticle-tagged targets

Nucleic acid (NA) is a widely-used biomarker for viruses. Accurate quantification of NA can provide a reliable basis for point-of-care diagnosis and treatment. Here, we propose a tilted fiber Bragg grating (TFBG)-based plasmonic fiber-optic spectral comb for fast response and ultralow limit NA detection. The TFBG is coated with a gold film which enables excitation of surface plasmon resonance (SPR), and single-stranded probe NAs with known base sequences are assembled on the gold film. To enhance sensitivity of refractive index (RI) for sensing a chosen combination of probe and target NAs around the TFBG surface, gold nanoparticles (AuNPs) are bonded to the target NA molecules as "RI-labels". The NA combination-induced aggregation of AuNPs induces significant spectral responses in the TFBG that would be below the detection threshold for the NAs in the absence of the AuNPs. The proposed TFBG-SPR NA sensor shows a fast response time of 30 s and an ultra-wide NA detection range from 1 × 10-18 mol/L to 1 × 10-7 mol/L. In the NA concentration range of 1 × 10-12 mol/L (1 pM) to 105 pM, an ultra-high sensitivity of 1.534 dB/lg(pM) is obtained. The sensor achieves an ultra-low limit of detection down to 1.0 × 10-18 mol/L (1 aM), which is more than an order of magnitude lower than the previous reports. The proposed sensor not only shows potentials in practical applications of NA detection, but also provides a new way for TFBG-SPR biochemical sensors to achieve higher RI sensitivity.

Development strategies of conducting polymer-based electrochemical biosensors for virus biomarkers: Potential for rapid COVID-19 detection

Rapid, accurate, portable, and large-scale diagnostic technologies for the detection of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) are crucial for controlling the coronavirus disease (COVID-19). The current standard technologies, i.e., reverse-transcription polymerase chain reaction, serological assays, and computed tomography (CT) exhibit practical limitations and challenges in case of massive and rapid testing. Biosensors, particularly electrochemical conducting polymer (CP)-based biosensors, are considered as potential alternatives owing to their large advantages such as high selectivity and sensitivity, rapid detection, low cost, simplicity, flexibility, long self-life, and ease of use. Therefore, CP-based biosensors can serve as multisensors, mobile biosensors, and wearable biosensors, facilitating the development of point-of-care (POC) systems and home-use biosensors for COVID-19 detection. However, the application of these biosensors for COVID-19 entails several challenges related to their degradation, low crystallinity, charge transport properties, and weak interaction with biomarkers. To overcome these problems, this study provides scientific evidence for the potential applications of CP-based electrochemical biosensors in COVID-19 detection based on their applications for the detection of various biomarkers such as DNA/RNA, proteins, whole viruses, and antigens. We then propose promising strategies for the development of CP-based electrochemical biosensors for COVID-19 detection.

A “turn-on” fluorescent sensor for cytosine in aqueous media based on diamino-bridged biphenyl acrylonitrile

A “turn-on” fluorescent sensor for cytosine in aqueous media was prepared.

Use of Electrocatalysis for Differentiating DNA Polymorphisms and Enhancing the Sensitivity of Electrochemical Nucleic Acid-Based Sensors with Covalent Redox Tags-Part II

Single-nucleotide polymorphisms (SNPs), insertion/deletion (indel) polymorphisms, and DNA methylation are the most frequent types of genetic variations. As such, DNA polymorphisms play significant roles in genetic mapping and diagnostics. Thus, analytical methods enabling DNA polymorphism detection will provide an invaluable means for early disease diagnosis. However, no single electrochemical nucleic acid-based sensor has achieved the detection of the three major polymorphisms (SNPs, indel polymorphisms, and DNA methylation) with sufficient specificity and sensitivity. In response, we explore the utilization of a catalytic reaction between methylene blue (MB) covalently linked to surface-bound nucleic acid and freely diffusing ferricyanide (Fe(CN)₆^3-) to improve specificity and sensitivity of DNA polymorphism detection. We find that the dynamics of the nucleic acid tether is an additional rate-limiting factor for the electrocatalytic reaction, in addition to the more traditional kinetic and excess factors. Our proof-of-concept experiments demonstrate that the use of electrocatalysis enables differentiation of the three polymorphisms when target sequences are present at 10 nM. We hypothesize that this ability is a result of the distinct dynamics of the DNA probe with each respective polymorphism. In addition to the specificity the sensor displays, the sensor achieves a 20 pM limit of detection. We believe that the electrocatalysis between nucleic acid-tethered MB and Fe(CN)₆^3- is highly promising for electrochemical nucleic acid-based sensors to achieve better specificity and sensitivity.

Label-Free DNA Biosensor Using Modified Reduced Graphene Oxide Platform as a DNA Methylation Assay

This work reports the use of modified reduced graphene oxide (rGO) as a platform for a label-free DNA-based electrochemical biosensor as a possible diagnostic tool for a DNA methylation assay. The biosensor sensitivity was enhanced by variously modified rGO. The rGO decorated with three nanoparticles (NPs)—gold (AuNPs), silver (AgNPs), and copper (CuNPs)—was implemented to increase the electrode surface area. Subsequently, the thiolated DNA probe (single-stranded DNA, ssDNA−1) was hybridized with the target DNA sequence (ssDNA-2). After the hybridization, the double-stranded DNA (dsDNA) was methylated by M.SssI methyltransferase (MTase) and then digested via a HpaII endonuclease specific site sequence of CpG (5′-CCGG-3′) islands. For monitoring the MTase activity, differential pulse voltammetry (DPV) was used, whereas the best results were obtained by rGO-AuNPs. This assay is rapid, cost-effective, sensitive, selective, highly specific, and displays a low limit of detection (LOD) of 0.06 U·mL⁻¹. Lastly, this study was enriched with the real serum sample, where a 0.19 U·mL⁻¹ LOD was achieved. Moreover, the developed biosensor offers excellent potential in future applications in clinical diagnostics, as this approach can be used in the design of other biosensors.

Direct DNA Methylation Profiling with an Electric Biosensor

DNA methylation is one of the principal epigenetic mechanisms that control gene expression in humans, and its profiling provides critical information about health and disease. Current profiling methods require chemical modification of bases followed by sequencing, which is expensive and time-consuming. Here, we report a direct and rapid determination of DNA methylation using an electric biosensor. The device consists of a DNA-tweezer probe integrated on a graphene field-effect transistor for label-free, highly sensitive, and specific methylation profiling. The device performance was evaluated with a target DNA that harbors a sequence of the methylguanine-DNA methyltransferase, a promoter of glioblastoma multiforme, a lethal brain tumor. The results show that we successfully profiled the methylated and nonmethylated forms at picomolar concentrations. Further, fluorescence kinetics and molecular dynamics simulations revealed that the position of the methylation site(s), their proximity, and accessibility to the toe-hold region of the tweezer probe are the primary determinants of the device performance.

Experimental and theoretical investigation for surface plasmon resonance biosensor based on graphene/Au film/D-POF

A D-shape plastic optical fiber (D-POF) surface plasmon resonance (SPR) biosensor based on the graphene/Au film (G/Au) was proposed and experimentally demonstrated for detection of DNA hybridization process. To improve the detection performance of SPR sensors, the Physical Vapor Deposition (PVD) method was used to evaporate the Au film directly onto the graphene grown on copper foil, and the Au film acted as a role of traditional Polymethyl Methacrylate (PMMA). The process made graphene and Au film form seamless contact. Next, the G/Au was transferred onto the D-shape fiber together. We explored the G/Au SPR sensor by using the finite element method (FEM) and obtained the optimum materials thickness to form configuration. Compared to other plastic optical fiber experiments, the proposed sensor's sensitivity was improved effectively and calculated as 1227 nm/RIU in a range of glucose solution. Meanwhile, our proposed sensor successfully distinguishes hybridization and single nucleotide polymorphisms (SNP) by observing the resonance wavelength change. It also exhibits a satisfactory linear response (R² = 0.996) to the target DNA liquids with respective concentrations of 0.1nM to1µM, which shows this method's wide potential in medical diagnostics.

Switchable conformational changes of DNA nanogel shells containing disulfide–DNA hybrids for controlled drug release and efficient anticancer action

Oligonucleotide strands containing dithiol (–SS–) groups were used as the co-crosslinkers in PNIPA–AAc based nanogels (NGs). They hybridized with PEG–oligonucleotides introduced into the gels. The specific DNA hybrid formed in the nanogel/nanocarrier was involved in highly efficient accumulation of intercalators. The presence of –SS– groups/bridges improved the storing efficiency of doxorubicin (Dox) in DNA hybrids by 53, 40 and 20% compared to regular, single stranded and regular double stranded DNA crosslinkers, respectively. The explicit arrangement of the hybrids in the carrier enabled their reduction by glutathione and an effective cancer treatment while the side toxicity could be reduced. Compared to the NGs with traditional crosslinkers and those containing typical dsDNA-based hybrids, an improved, switchable and controlled drug release occurred in the novel NGs. Since the novel NGs can release the oligonucleotide strands during their degradation, this gives an opportunity for a combined drug-gene therapy.

Switchable conformational changes of multiresponsive nanogels containing disulfide/DNA hybrid shells for pulsative drug release.

Guide to Selecting a Biorecognition Element for Biosensors

Biosensors are powerful diagnostic tools defined as having a biorecognition element for analyte specificity and a transducer for a quantifiable signal. There are a variety of different biorecognition elements, each with unique characteristics. Understanding the advantages and disadvantages of each biorecognition element and their influence on overall biosensor performance is crucial in the planning stages to promote the success of novel biosensor development. Therefore, this review will focus on selecting the optimal biorecognition element in the preliminary design phase for novel biosensors. Included is a review of the typical characteristics and binding mechanisms of various biorecognition elements, and how they relate to biosensor performance characteristics, specifically sensitivity, selectivity, reproducibility, and reusability. The goal is to point toward language needed to improve the design and development of biosensors toward clinical success.

Direct Writing and Characterization of Three-Dimensional Conducting Polymer PEDOT Arrays

Direct writing is an effective and versatile technique for three-dimensional (3D) fabrication of conducting polymer (CP) structures. It is precisely localized and highly controllable, thus providing great opportunities for incorporating CPs into microelectronic array devices. Herein we demonstrate 3D writing and characterization of poly(3,4-ethylenedioxythiophene)-polystyrenesulfonate (PEDOT:PSS) pillars in an array format, by using an in-house-constructed variant of scanning ion conductance microscopy (SICM). CP pillars with different aspect ratios were successfully fabricated by optimizing the writing parameters: pulling speed, pulling time, concentration of the polymer solution, and the micropipette tip diameter. Especially, super high aspect ratio pillars of around 7 μm in diameter and 5000 μm in height were fabricated, indicating a good capability of this direct writing technique. Additions of an organic solvent and a cross-linking agent contribute to a significantly enhanced water stability of the pillars, critical if the arrays were to be used in biologically relevant applications. Surface morphologies and structural analysis of CP pillars were characterized by scanning electron microscopy and Raman spectroscopy, respectively. Electrochemical properties of the individual pillars of different heights were examined by cyclic voltammetry using a double-barrel micropipette as an electrochemical cell. Exceptional mechanical properties of the pillars, such as high flexibility and robustness, were observed when bent by applying a force. The 3D pillar arrays are expected to provide versatile substrates for functionalized and integrated biological sensing and electrically addressable array devices.

PNA versus DNA in electrochemical gene sensing based on conducting polymers: study of charge and surface blocking effects on the sensor signal

In this communication, we present an in-depth study of DNA/DNA, DNA/PNA and PNA/PNA hybridisation on a conducting polymer-modified electrode, measured by means of electrochemical impedance spectroscopy (EIS). DNA or PNA nucleic base sequence probes (where DNA stands for deoxyribonucleic acid and PNA for peptide nucleic acid) were covalently attached onto the sensor surface. As PNA is a non-charged variant of DNA, we investigate the effects of the surface charge and surface blocking by the surface confined probe/target nucleic bases complexes onto the kinetics of redox reaction of Fe(CN)₆^3-/4- couple occurring at the electrode/solution interface that provides electrochemical readout for hybridisation. A range of hybridisation detection experiments were performed, where the surface charge and surface charge density were varied, through varying the charged nature of the probe and the target (i.e. PNA or DNA) and the density of surface-bound PNA and DNA probes. To further the understanding of these effects on the measured electrochemical signal, kinetic studies of the hybridisation reactions were undertaken, and the equilibrium binding constants and binding rate constants for the hybridisation reactions were obtained. The study provides valuable insights to guide future designs of biosensors.

Accurate Electrochemistry Analysis of Circulating Methylated DNA from Clinical Plasma Based on Paired-End Tagging and Amplifications

Circulating methylated DNA has been a new kind of cancer biomarker, yet its small fraction of trace total DNA from clinical samples impairs the accurate analysis. Though fluorescence methods based on quantitative methylation specific PCR (qMSP) have been adopted routinely, yet alternative electrochemistry assay of such DNA from clinical samples remains a great challenge. Herein, we report accurate electrochemistry analysis of circulating methylated DNA from clinical plasma samples based on a paired-end tagging and amplifications strategy. Two DNA primers each labeled with digoxigenin (Dig) and biotin are designed for the recognition and amplification of methylated DNA. Paired-end tagging amplicons and avidin-HRP molecules are successively captured on the electrode modified with Anti-Dig. Then HRP executes catalytic reaction to generate amplified signal. The design of paired-end tagging can readily integrate downstream electrochemical amplified reaction, and two heterogeneous amplifications enable high assay sensitivity. As little as 40 pg of methylated genomic DNA (∼10 genomic equivalents) is well identified, and our strategy can even distinguish as low as 1% methylation level. Tumor-specific methylated DNA is clearly detected in the plasma of 10 of 11 NSCLC patients. The high clinical sensitivity of 91% (10/11) indicates the good consistency with clinical diagnosis. Excellent spatial control of electrochemistry allows simpler detection of more methylation patterns compared to fluorescence methods. The developed electrochemical assay is a promising liquid biopsy tool for the analysis of tumor-specific circulating DNA.

Electrochemical biosensing strategies for DNA methylation analysis

DNA methylation is one of the key epigenetic modifications of DNA that results from the enzymatic addition of a methyl group at the fifth carbon of the cytosine base. It plays a crucial role in cellular development, genomic stability and gene expression. Aberrant DNA methylation is responsible for the pathogenesis of many diseases including cancers. Over the past several decades, many methodologies have been developed to detect DNA methylation. These methodologies range from classical molecular biology and optical approaches, such as bisulfite sequencing, microarrays, quantitative real-time PCR, colorimetry, Raman spectroscopy to the more recent electrochemical approaches. Among these, electrochemical approaches offer sensitive, simple, specific, rapid, and cost-effective analysis of DNA methylation. Additionally, electrochemical methods are highly amenable to miniaturization and possess the potential to be multiplexed. In recent years, several reviews have provided information on the detection strategies of DNA methylation. However, to date, there is no comprehensive evaluation of electrochemical DNA methylation detection strategies. Herein, we address the recent developments of electrochemical DNA methylation detection approaches. Furthermore, we highlight the major technical and biological challenges involved in these strategies and provide suggestions for the future direction of this important field.

An electricity-fluorescence double-checking biosensor based on graphene for detection of binding kinetics of DNA hybridization

In this paper, an electricity-fluorescence double-checking biosensor based on graphene materials has been presented for detection of DNA hybridization kinetics.

Electrochemical immunosensor for N6-methyladenosine detection in human cell lines based on biotin-streptavidin system and silver-SiO2 signal amplification

N6-methyladenosine (m6A), a kind of RNA methylation form and important epigenetic event, plays crucial roles in many biological progresses. Thus it is essential to quantitatively detect m6A in complicated biological samples. Herein, a simple and sensitive electrochemical method was developed for m6A detection using N6-methyladenosine-5'-triphosphate (m6ATP) as detection target molecule. In this detection strategy, anti-m6A antibody was selected as m6A recognition and capture reagent, silver nanoparticles and amine-PEG3-biotin functionalized SiO₂ nanospheres (Ag@SiO₂) was prepared and used as signal amplification label, and phos-tag-biotin played a vital role of "bridge" to link m6ATP and Ag@SiO₂ through the two forms of specific interaction between phosphate group of m6ATP and phos-tag, biotin and streptavidin, respectively. Under the optimal experimental conditions, the immunosensor presented a wide linear range from 0.2 to 500nM and a low detection limit of 0.078nM (S/N=3). The reproducibility and specificity were acceptable. Moreover, the developed method was also validated for detect m6A content in human cell lines. Importantly, this detection strategy provides a promising immunodetection platform for ribonucleotides and deoxyribonucleotides with the advantages of simplicity, low-costing, specificity and sensitivity.

Label-free detection of missense mutations and methylation differences in the p53 gene using optically diffracting hydrogels

We have developed a novel approach for DNA detection as well as genetic screening of mutations by uniquely combining DNA-responsive and optically diffracting materials. This approach entails the polymerization of a photonic crystal within a hydrogel network that alters the diffraction of light in response to a target DNA strand. The utility of this approach, which permits label-free sensing, was demonstrated via the detection of a target sequence from the DNA binding domain of the major tumor suppressor protein p53. Using a complementary capture probe strand, we were able to detect down to picomole concentrations of the target p53 sequence. Moreover, we demonstrated that this approach could readily detect a single base pair mutation in the target strand, which corresponds to the hotspot cancer mutation R175H in p53. The sensitivity of detection was increased by lowering the rate of annealing of the target strand and adjusting the solution ionic strength during optical characterization. Changes in ionic strength during characterization impact the melting temperature of the bound target DNA and the Donnan potential between the hydrogel and solution, which influence detection. We further showed that this approach is sensitive to epigenetic changes via the detection of a fully methylated form of the target p53 sequence. Ultimately, this approach represents a new paradigm for DNA detection and specifically genetic screening of p53 as well as other disease markers and nucleotide modifications that alter the properties of DNA (e.g., epigenetic alterations and adducts with chemical carcinogens).

Environmentally sensitive nanohydrogels decorated with a three-strand oligonucleotide helix for controlled loading and prolonged release of intercalators

Biocompatible nanohydrogels modified with three-segment oligonucleotide hybrids were used for controlled loading and prolonged release of anticancer intercalators in hyperthermia treatment.

Conducting polymer based electrochemical biosensors

Conducting polymer (CP)-based electrochemical biosensors have gained great attention as such biosensor platforms are easy and cost-effective to fabricate, and provide a direct electrical readout of the presence of biological analytes with high sensitivity and selectivity.

A facile and highly sensitive impedimetric DNA biosensor with ultralow background response based on in situ reduced graphene oxide

A facile and highly sensitive impedimetric DNA biosensor with ultralow background response based on in situ reduced graphene oxide.