Interactions of antitumor drug daunomycin with DNA in solution and at the surface

Candidate drug molecule-DNA interaction and molecular modelling of candidate drug molecule

Aim: 1,4-dihydropyridine derivative, 1-(3-phenyl propyl)-4-(2-(2-hydroxybenzylidene) hydrazone)-1,4-dihydropyridine (abbreviated as DHP) was synthesized as potential agent for Alzheimer’s disease which is a progressive neurodegenerative brain disorder affecting millions of elderly people. With this study, the electrochemical properties of DHP were investigated and its interaction with DNA was analyzed by differential pulse voltammetry (DPV) and cyclic voltammetry (CV) measurements. In addition, this study aims to determine degradation mechanism of the DHP molecule by Density-functional theory (DFT) in gas and in aqueous phase. Material and Method: Experimental conditions such as immobilization time, the effect of the scan rate, concentration, and the effect of pH were optimized. The method was validated according to validation parameters such as range, precision, linearity, limit of detection (LOD), limit of quantitation (LOQ) and inter/intraday. Results: Linearity study for the calibration curve of DNA and DHP with DPV was calculated in the calibration range 10-100 µg/mL. The LOD and LOQ values were calculated as 3 and 10 µg/mL and intra-day and inter-day repeatability (RSD %) were 1.85 and 3.64 µg/mL, respectively. After the DHP-DNA interaction, the oxidation currents of guanine decreased as a proof of interaction. The activation energy of the most possible path of reaction was calculated, and their thermodynamically most stable state was determined in gas phase. Conclusion: We developed to improve a sensitive, fast and easy detection process for determination of interaction between DHP and DNA.

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.

Interaction of two peptide drugs with biomacromolecules analyzed by molecular docking and multi-spectroscopic methods

Peptide drugs, which are mainly used for the treatment of AIDS, myeloma, and breast cancer, have evolved rapidly owing to their high efficacy and low side effects. The interaction mechanisms of two peptide drugs with two biological macromolecules (protein and DNA), which are of great significance in disease prevention and drug design, were investigated using molecular docking, fluorescence spectroscopy, circular dichroism (CD) spectroscopy, UV-visible spectroscopy and viscosity measurements. The interaction between a series of common drugs and ovalbumin (OVA) was simulated by molecular docking, and two peptide drugs with the highest energy values, namely atazanavir and carfilzomib, were selected; the binding energy values of these drugs with OVA were -59.20 and -55.93 kcal/mol, respectively. The K_b values of the interaction of the two drugs with OVA/DNA were in the range of 10⁴-10⁷ M^-1, and the binding affinity of the drugs was stronger with OVA than with DNA. Hydrogen bonds and van der Waals forces were very important for the binding between drugs and OVA through molecular docking studies, and it was consistent with experimental results (ΔH < 0, ΔH < 0). The synchronous fluorescence spectrum showed that the interaction caused a change to the original structure of OVA, and atazanavir had a greater effect on OVA than carfilzomib. CD spectrum analysis also demonstrated that the conformation of OVA changed slightly. The interaction between atazanavir and DNA was mainly driven by hydrophobic forces (ΔH > 0 and ΔH > 0), whereas the major interaction forces involved in the binding of carfilzomib with DNA were hydrogen bonds and van der Waals forces. DNA melting studies, UV-visible spectroscopy, CD spectroscopy and viscosity measurements established that the interaction between the drugs and DNA was groove binding.

Electrochemical Biosensor for Polycyclic Organic Compounds Screening Based on a Methylene Blue-incorporated DNA Polyion Complex Modified Electrode

A reagent-less electrochemical DNA biosensor for rapid non-electroactive polycyclic organic compounds (POCs) screening and detection was proposed. In this method, methylene blue (MB) was incorporated into DNA/chitosan polyion complex membrane and then modified onto a glassy carbon electrode (GCE). The electrochemical analysis for the prepared DNA-MB/chitosan/GCE showed that the modified electrode exhibited high electrochemical activity and stability. The addition of tetracycline hydrochloride (TC), a model analyte of non-electroactive POCs, resulted in an obvious peak current decrease in DNA-MB/chitosan/GCE, and this electrochemical response was affected by the DNA type and MB/DNA ratio in the modified electrodes. Ultraviolet-visible (UV-Vis) absorption spectroscopy was utilized to furthermore investigate the interaction between TC and DNA-MB/chitosan/GCE. As a result, a competitive interaction and displacement effect between TC and the intercalated MB was proposed. In our condition, the prepared DNA-MB/chitosan/GCE showed high sensitivity to POCs and had almost no response to common interferences. Besides, the good stability and reproducibility of the prepared electrode made it suitable for practical use.

Electrochemical monitoring of the interaction between anticancer drug and DNA in the presence of antioxidant

The aim of this work is to find out the effect of antioxidant onto the interaction of DNA-anticancer drug, daunorubicin. Daunorubicin (DNR) is an anti-cancer drug which is used for the treatment of certain cancers including the treatment of leukemia. The treatments of patients, who suffer from cancer, become generally complicated if they take some antioxidant-containing supplement during chemotherapy. In this study, the interaction performance between DNR and DNA was investigated both in the presence and absence of antioxidant, caffeic acid, as the first time in the literature. Interaction performances were evaluated by observing both guanine (1.0V) and DNR (0.5V) oxidation signal in the same potential window.

Emerging Loop-Mediated Isothermal Amplification-Based Microchip and Microdevice Technologies for Nucleic Acid Detection

Rapid, sensitive, and selective pathogen detection is of paramount importance in infectious disease diagnosis and treatment monitoring. Currently available diagnostic assays based on polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) are time-consuming, complex, and relatively expensive, thus limiting their utility in resource-limited settings. Loop-mediated isothermal amplification (LAMP) technique has been used extensively in the development of rapid and sensitive diagnostic assays for pathogen detection and nucleic acid analysis and hold great promise for revolutionizing point-of-care molecular diagnostics. Here, we review novel LAMP-based lab-on-a-chip (LOC) diagnostic assays developed for pathogen detection over the past several years. We review various LOC platforms based on their design strategies for pathogen detection and discuss LAMP-based platforms still in development and already in the commercial pipeline. This review is intended as a guide to the use of LAMP techniques in LOC platforms for molecular diagnostics and genomic amplifications.

Using DNA devices to track anticancer drug activity

It is beneficial to develop systems that reproduce complex reactions of biological systems while maintaining control over specific factors involved in such processes. We demonstrated a DNA device for following the repair of DNA damage produced by a redox-cycling anticancer drug, beta-lapachone (β-lap). These chips supported ß-lap-induced biological redox cycle and tracked subsequent DNA damage repair activity with redox-modified DNA monolayers on gold. We observed drug-specific changes in square wave voltammetry from these chips at therapeutic ß-lap concentrations of high statistical significance over drug-free control. We also demonstrated a high correlation of this change with the specific ß-lap-induced redox cycle using rational controls. The concentration dependence of ß-lap revealed significant signal changes at levels of high clinical significance as well as sensitivity to sub-lethal levels of ß-lap. Catalase, an enzyme decomposing peroxide, was found to suppress DNA damage at a NQO1/catalase ratio found in healthy cells, but was clearly overcome at a higher NQO1/catalase ratio consistent with cancer cells. We found that it was necessary to reproduce key features of the cellular environment to observe this activity. Thus, this chip-based platform enabled tracking of ß-lap-induced DNA damage repair when biological criteria were met, providing a unique synthetic platform for uncovering activity normally confined to inside cells.

Pharmacogenomic study using bio- and nanobioelectrochemistry: Drug-DNA interaction

Small molecules that bind genomic DNA have proven that they can be effective anticancer, antibiotic and antiviral therapeutic agents that affect the well-being of millions of people worldwide. Drug-DNA interaction affects DNA replication and division; causes strand breaks, and mutations. Therefore, the investigation of drug-DNA interaction is needed to understand the mechanism of drug action as well as in designing DNA-targeted drugs. On the other hand, the interaction between DNA and drugs can cause chemical and conformational modifications and, thus, variation of the electrochemical properties of nucleobases. For this purpose, electrochemical methods/biosensors can be used toward detection of drug-DNA interactions. The present paper reviews the drug-DNA interactions, their types and applications of electrochemical techniques used to study interactions between DNA and drugs or small ligand molecules that are potentially of pharmaceutical interest. The results are used to determine drug binding sites and sequence preference, as well as conformational changes due to drug-DNA interactions. Also, the intention of this review is to give an overview of the present state of the drug-DNA interaction cognition. The applications of electrochemical techniques for investigation of drug-DNA interaction were reviewed and we have discussed the type of qualitative or quantitative information that can be obtained from the use of each technique.

Electrochemical examination of ability of dsDNA/PAM composites for storing and releasing of doxorubicin

Composites consisting of ss- and ds-DNA strands and polyacrylamide (PAM) hydrogel have been synthesized. DNA was entrapped non-covalently. The obtained DNA biomaterial exhibited a strong increase in guanine and adenine anodic currents when temperature reached the physiological level. This increase was related to the unique oligonucleotide structural changes in the composite. The structural alterations in the PAM lattices were employed for the release of the drug accumulated in the composite. Doxorubicin (Dox) was selected as the drug; it was accumulated by intercalation to dsDNA and was slowly released from the dsDNA/PAM system by using a minor temperature increase (up to 40÷45 °C) as it is routinely done in hyperthermia. The applied release temperature was either constant or oscillating. The binding strength, the rate of Dox release and the properties of the composite were examined using voltammetry, SEM and ICP-MS.

Gold nanoparticle/polymer nanocomposite for highly sensitive drug–DNA interaction

We demonstrate a gold nanaparticle/polyvinylferrocenium (AuNP/PVF⁺) coated platinum (Pt) electrode for sensing highly sensitive DNA–anticancer drug interactions.

Sensing conformational changes in DNA upon ligand binding using QCM-D. Polyamine condensation and Rad51 extension of DNA layers

Biosensors, in which binding of ligands is detected through changes in the optical or electrochemical properties of a DNA layer confined to the sensor surface, are important tools for investigating DNA interactions. Here, we investigate if conformational changes induced in surface-attached DNA molecules upon ligand binding can be monitored by the quartz crystal microbalance with dissipation (QCM-D) technique. DNA duplexes containing 59-184 base pairs were formed on QCM-D crystals by stepwise assembly of synthetic oligonucleotides of designed base sequences. The DNA films were exposed to the cationic polyamines spermidine and spermine, known to condense DNA molecules in bulk experiments, or to the recombination protein Rad51, known to extend the DNA helix. The binding and dissociation of the ligands to the DNA films were monitored in real time by measurements of the shifts in resonance frequency (Δf) and in dissipation (ΔD). The QCM-D data were analyzed using a Voigt-based model for the viscoelastic properties of polymer films in order to evaluate how the ligands affect thickness and shear viscosity of the DNA layer. Binding of spermine shrinks all DNA layers and increases their viscosity in a reversible fashion, and so does spermidine, but to a smaller extent, in agreement with its lower positive charge. SPR was used to measure the amount of bound polyamines, and when combined with QCM-D, the data indicate that the layer condensation leads to a small release of water from the highly hydrated DNA films. The binding of Rad51 increases the effective layer thickness of a 59 bp film, more than expected from the know 50% DNA helix extension. The combined results provide guidelines for a QCM-D biosensor based on ligand-induced structural changes in DNA films. The QCM-D approach provides high discrimination between ligands affecting the thickness and the structural properties of the DNA layer differently. The reversibility of the film deformation allows comparative studies of two or more analytes using the same DNA layer as demonstrated here by spermine and spermidine.

Spectroscopic and Modelling Analysis on the Interaction of 3'-Azidodaunorubicin Semicarbazone with ctDNA

The synthesis and characterisation of a new anthracycline, 3′-azidodaunorubicin semicarbazone (ADNRS) is reported. The interaction between ADNRS and calf thymus DNA (ctDNA) was investigated by absorption and fluorescence spectroscopy in combination with melting temperature (Tm) curves and molecular modelling in physiological buffer (pH 7.4). Evidence indicates that ADNRS binds in the groove of ctDNA and the fluorescence quenching mechanism is a static quenching type. Calculated thermodynamic parameters show that hydrophobic interactions may play a predominant role in the binding. Furthermore, molecular modelling results corroborate the spectroscopic investigations.

Spectroscopic, viscositic and molecular modeling studies on the interaction of 3'-azido-daunorubicin thiosemicarbazone with DNA

A new daunorubicin has been synthesized and structurally characterized. The interaction of native calf thymus DNA (ctDNA) with 3′-azido-daunorubicin thiosemicarbazone (ADNRT) was investigated under simulated physiological conditions by multi-spectroscopic techniques, viscometric measurements and molecular modeling study. It concluded that ADNRT could intercalate into the base pairs of ctDNA, and the fluorescence quenching by ctDNA was static quenching type. Thermodynamic parameters calculated suggested that the binding of ADNRT to ctDNA was mainly driven by hydrophobic interactions. The relative viscosity of ctDNA increased with the addition of ADNRT, which confirmed the intercalation mode. Furthermore, molecular modeling studies corroborate the above experimental results.

Preclinical genotoxicology of nor-β-lapachone in human cultured lymphocytes and Chinese hamster lung fibroblasts

Nor-β-lapachone has shown several biological properties. Regarding cytotoxic activity against cancer cell lines, it has been recognized as an important prototype. However, quinonoid drugs present a major challenge because of their toxicity. In this study, we evaluated the cytotoxicity and genetic toxicity of nor-β-lapachone in human lymphocytes and HL-60 leukemia cells and murine V79 fibroblasts, to shed some light on its selectivity toward cancer cells. As measured by MTT test, exposure of V79 cells to nor-β-lapachone resulted in a weak cytotoxicity (IC(50) = 13.41 μM), and at a concentration up to 21.9 μM, no cytotoxic effect was observed in lymphocytes, while in HL-60 cells, nor-β-lapachone elicited significantly greater cytotoxicity (IC(50) = 1.89 μM). Cultures coexposed to GSH-OEt showed an increased viability, which may indicate a neutralization of ROS generated by quinonoid treatment. In fact, only the highest concentrations of nor-β-lapachone (10 or 20 μM) caused an increase in oxidative stress in nontumor levels cells as measured by TBARS and nitrite/nitrate detection. This was accompanied by an alteration in intracellular thiol content. However, NAC pre-exposure restored the redox equilibrium of the cells and the concentration of thiol levels to control values. Nor-β-lapachone at 2.5 and 5 μM failed to induce DNA damage in nontumor cells, but at the highest concentrations tested, it induced single and double DNA strand breaks and increased the frequency of chromosomal aberrations. Interestingly, these damages were prevented by NAC pretreatment or exacerbated by prior exposure to the GSH-depleting agent 1-bromoheptane. In electrochemical experiments, nor-β-lapachone at the same concentrations as those used in genotoxic tests did not damage DNA directly, but at the highest concentration tested (200 μM), it caused a very weak DNA interaction. Corroborating electrochemical data, oxidative modifications of DNA bases were observed, as checked by DNA repair enzymes EndoIII and FPG, which reinforced the indirect actions caused by nor-β-lapachone through ROS generation and not via DNA intercalation. The DNA repair capacities were higher for nontumor cells than for leukemia cells, which may be related to the selective cytoxicity of nor-β-lapachone toward cancer cells. Our data suggest that ROS play an important role in nor-β-lapachone toxicity and that its DNA-damaging effect occurs only at concentrations several times higher than that needed for its antiproliferative effect on cancer cells.

Detection of daunomycin using phosphatidylserine and aptamer co-immobilized on Au nanoparticles deposited conducting polymer

A highly sensitive and selective sensor for daunomycin was developed using phosphatidylserine (PS) and aptamer as bioreceptors. The PS and aptamer were co-immobilized onto gold nanoparticles modified/functionalized [2,2':5',2″-terthiophene-3'-(p-benzoic acid)] (polyTTBA) conducting polymer. Direct electrochemistry of daunomycin was used to fabricate a label free sensor that monitors current at -0.61 V. The formation of each layer was confirmed with XPS, SEM, and QCM. Response of the sensor was compared with and without PS in terms of sensitivity and selectivity. Interaction between the sensor probe and daunomycin was determined with DPV. The experimental parameters affecting sensor performance were optimized in terms of concentration of immobilized aptamer, PS:aptamer ratio, temperature, pH, and reaction times. The dynamic range for daunomycin analysis ranged between 0.1 and 60.0 nM with a detection limit of 52.3 ± 2.1 pM. Sensor was also examined for interference effect of other drugs. The present sensor exhibited long term stability and successfully detected daunomycin in a real human urine spiked with daunomycin.