Electrochemical Detection of DNA Hybridization via Bis-Intercalation of a Naphthylimide-Functionalized Viologen Dimer

Synthesis, DNA binding of bis-naphthyl ferrocene derivatives and the application as new electroactive indicators for DNA biosensor

A series of bis-naphthyl ferrocene derivatives were synthesized and characterized. Based on the results obtained from UV-visible absorption titration and ethidium bromide (EB) displacement experiments, it was observed that the synthesized compounds exhibited a strong binding ability to dsDNA. In comparison to the viscosity curve of EB, the tested compounds demonstrated a bisintercalation binding mode when interacting with CT-DNA. Differential pulse voltammetry (DPV) was employed to assess the binding specificity of these indicators towards ssDNA and dsDNA. All tested indicators displayed more pronounced signal differences before and after hybridization between probe nucleic acids and target nucleic acids compared to Methylene Blue (MB). Among the evaluated compounds, compound 3j containing an ether chain showed superior performance as an indicator, making it suitable for constructing DNA-based biosensors. Under optimized conditions including probe ssDNA concentration and indicator concentration, this biosensor exhibited good sensitivity, reproducibility, stability, and selectivity. The limit of detection was calculated as 4.53 × 10-11 mol/L. Furthermore, when utilizing 3j as the indicator in serum samples, the biosensor achieved satisfactory recovery rates for detecting the BRCA1 gene.

A planar and uncharged copper(II)-picolinic acid chelate: Its intercalation to duplex DNA by experimental and theoretical studies and electrochemical sensing application

Using an external redox-active molecule as a DNA hybridization indicator is still a popular strategy in electrochemical DNA biosensors because it is label-free and the multi-site binding can enhance the response signal. A planar and uncharged transition metal complex, Cu(PA)₂ (PA = picolinic acid) with excellent electrochemical activity has been synthesized and its interaction with double-stranded DNA (dsDNA) is studied by experimental electrochemical methods and theoretical molecular docking technology. The experimental results reveal that the copper complex interacts with dsDNA via specific intercalation, which is verified by the molecular docking result. The surface-based voltammetric analysis demonstrates that the planar Cu(PA)₂ can effectively accumulate within the electrode-confined hybridized duplex DNA rather than the single-stranded probe DNA. Based on this phenomenon, the Cu(PA)₂ is utilized as an electrochemical hybridization indicator for the detection of oligonucleotides. The sensing assays show that upon incubation in Cu(PA)₂ solution, the probe electrode does not display any Faraday signal, but the hybridized one has a pair of strong redox peaks corresponding to the electrochemistry of Cu(PA)₂, showing excellent hybridization indicating function of Cu(PA)₂ without background interference. The signal intensity of Cu(PA)₂ is dependent on the concentrations of the target oligonucleotide ranging from 1 fM to 100 nM with an experimental detection limit of 1.0 fM. Due to the specific intercalation of Cu(PA)₂ with dsDNA, the biosensor also exhibits good ability to recognize oligonucleotide with different base mismatching degree.

Development of an electrochemical surface-enhanced Raman spectroscopy (EC-SERS) aptasensor for direct detection of DNA hybridization

Rapid detection of disease biomarkers at the patient point-of-care is essential to timely and effective treatment. The research described herein focuses on the development of an electrochemical surface-enhanced Raman spectroscopy (EC-SERS) DNA aptasensor capable of direct detection of tuberculosis (TB) DNA. Specifically, a plausible DNA biomarker present in TB patient urine was chosen as the model target for detection. Cost-effective screen printed electrodes (SPEs) modified with silver nanoparticles (AgNP) were used as the aptasensor platform, onto which the aptamer specific for the target DNA was immobilized. Direct detection of the target DNA was demonstrated through the appearance of SERS peaks characteristic for adenine, present only in the target strand. Modulation of the applied potential allowed for a sizeable increase in the observed SERS response and the use of thiol back-filling prevented non-specific adsorption of non-target DNA. To our knowledge, this work represents the first EC-SERS study of an aptasensor for the direct, label-free detection of DNA hybridization. Such a technology paves the way for rapid detection of disease biomarkers at the patient point-of-care.

A DNA hybridization sensor based on catalytic response by platinum deposition

We report a novel electrochemical sensing system for single-stranded DNA (ssDNA) with a specific sequence based on the catalytic reduction of protons with platinum deposited by the electrochemical reduction of chloro-2,2':6',2''-terpyridine platinum(II) chloride dihydrate (Pt complex) on a glassy carbon (GC) electrode. There was no catalytic property observed for proton reduction at the GC electrode, while the platinum deposited by the reduction of the Pt complex shows the catalytic activity of proton reduction. The intercalation of the Pt complex with double-stranded DNA (dsDNA) decreased the concentration of the free Pt complex with a concomitant diminution in the electrochemical catalytic current due to steric hindrance and a decrease in the diffusion coefficient of the intercalated Pt complex. Thus, the catalytic current of proton reduction by platinum deposited on a GC electrode decreased with an increase in the concentration of target ssDNA, when capture DNA with a complementary sequence was present in the solution to form the hybrid dsDNA. A detectable concentration range was estimated and found to be 0.1-1.0 μM. The catalytic current was significantly larger than the reduction current of the Pt complex, resulting in the sensitive detection of ssDNA. Furthermore, the present method is simply due to the immobilization of capture DNA being unnecessary.

Electrochemical study on the effects of epigenetic cytosine methylation on anti-benzo[a]pyrene diol epoxide damage at TP53 oligomers

Anti-benzo[a]pyrene-r-7,t-8-dihydrodiol-t-9,10-epoxide (anti-BPDE) is a known carcinogen that damages DNA, and this damage is influenced by the DNA sequence and epigenetic factors. The influence of epigenetic cytosine methylation on the reaction with anti-BPDE at a known hotspot DNA damage site was studied electrochemically. Gold electrodes were modified with thiolated DNA oligomers spanning codons 270-276 of the TP53 gene. The oligomers exhibited 5-carbon cytosine methylation at the codon 273 location on the bound probe, the acquired complementary target, or both. Redox active diviologen compounds of the form C(12)H(25)V(2+)C(6)H(12)V(2+)C(12)H(25) (V(2+) = 4,4'-bipyridyl or viologen, C12-Viologen) were employed to detect anti-BPDE damage to DNA. DNA was exposed to racemic (±)- or enantiomerically pure (+)-anti-BPDE solutions followed by electrochemical interrogation in the presence of C12-Viologen. Background subtracted square wave voltammograms (SWV) showed the appearance of two peaks at approximately -0.38 V and -0.55 V vs Ag/AgCl upon anti-BPDE exposure. The acquired voltammetry is consistent with singly reduced C12-Viologen dimers bound at two different DNA environments, which arise from BPDE damage and are influenced by cytosine methylation and BPDE stereochemical considerations. UV spectroscopic and mass spectrometric methods employed to validate the electrochemical responses showed that (+)-anti-BPDE primarily adopts a minor groove bound orientation within the oligomers while selectively targeting the nontranscribed ssDNA sequence within the duplexes.

Electrochemical detection of anti-benzo[a]pyrene diol epoxide DNA damage on TP53 codon 273 oligomers

DNA damage from (+/-)-anti-benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE) at a hotspot TP53 gene sequence was electrochemically detected. BPDE was exposed to gold electrode immobilized double-stranded DNA oligomers followed by voltammetric measurements in the presence of redox-active C(12)H(25)V(2+)C(6)H(12)V(2+)C(12)H(25) (V(2+) = 4,4'-bipyridyl or viologen, C12-viologen). Square wave voltammograms from BPDE-exposed DNA-modified electrodes showed the emergence of a C12-viologen-DNA complex at -0.37 V versus Ag/AgCl. The peak current intensity of this redox wave was dependent on both BPDE concentration and exposure time. Controls with alternate xenobiotics and DNA sequences showed this redox wave to be primarily due to BPDE damage at the wild-type DNA sequence. The detection limit was determined to be approximately 170 nM BPDE. Mass spectrometry and UV thermal melting experiments provided insight into the BPDE reaction and mirrored the sensor results. This report demonstrates that an electrochemical hybridization sensor can be used to detect sequence-related xenobiotic DNA damage.

Characterization of mismatched DNA hybridization via a redox-active diviologen bound in the PNA-DNA minor groove

Diviologen molecules of the general formula CH3(CH2)11V2+(CH2)6V2+(CH2)11CH3 (C12VC6VCI2, V2+ = 4,4'-bipyridinium or viologen) were employed to electrochemically assay DNA hybridization to PNA probes immobilized at Au electrodes. Immobilized 15-mer PNA probes were exposed to 25-mer DNA oligonucleotides containing either complementary or single base mismatched sequences. In the presence of complementary PNA-DNA hybrids, the V2+/+ redox couple of C12VC6VC12 exhibited a unique double-wave cyclic voltammogram, with a formal potential shifted -100 mV from the E(f) in the presence of single base mismatched DNA hybrids or PNA probes alone. Integration of the CVs demonstrated that C12VC6VC12 exhibited binding cooperativity to the complementary PNA-DNA hybrids and saturated at a ratio of 2:1 (C12VC6VC12:hybrid). Reduced C12VC6VC12 (V+) absorption spectra showed a significant lambda(max) blue shift (22 nm) in the presence of complementary hybrids compared to the lambda(max) in the presence of PNA or mismatched DNA hybrids. Chronocoulometry was employed to assay surface populations and obtain thermodynamics for C12VC6VC12 binding. These data are consistent with C12VC6VC12 bound in the minor groove of complementary hybrids as face-to-face pi-dimers. This approach to distinguishing complementary hybrids from mismatched hybrids is novel, with potential applications involving detection of DNA damage or single nucleotide polymorphism (SNP) analysis.