Stability and structural features of DNA intercalation with ethidium bromide, acridine orange and methylene blue

Chitosan promotes ROS-mediated apoptosis and S phase cell cycle arrest in triple-negative breast cancer cells: evidence for intercalative interaction with genomic DNA

Chitosan (CS) is a semi-synthetic bio-based polysaccharide with promising biological and antitumor properties.

Granulosa cell apoptosis by impairing antioxidant defense system and cellular integrity in caprine antral follicles post malathion exposure

Toxicological studies have demonstrated the exposure-risk relationship of several pesticides on reproduction of living organisms. To evaluate the role of malathion as a reproductive toxicant, this study aims at assessing the cytological and biochemical changes in the granulosa cells after malathion exposure in dose (1 nM, 10 nM, 100 nM) and time (4 h, 6 h, 8 h) dependent manner. Histomorphological analysis, fluorescence assay, apoptosis quantification, and terminal deoxynucleotidyl transferase d-UTP mediated nick end labeling (TUNEL) assay were done to determine cytological changes, whereas antioxidant enzyme assays were done to measure the oxidative stress in malathion treated ovarian antral follicles. Histological studies exhibited the occurrence of highly condensed or marginated chromatin with fragmented nucleus, pyknosis, loss of membrane integrity, increased empty spaces, and vacuolization in malathion treated granulosa cells. Ethidium bromide/acridine orange (EB/AO) fluorescence staining demonstrated a significant increase in incidence and percentage of apoptosis after malathion exposure (p < 0.001), both between and within the groups. Malathion exposure also resulted in increased DNA fragmentation and decline in both antioxidant enzymes activity namely catalase (CAT) and superoxide dismutase (SOD) in granulosa cells of antral follicles. Moreover, there was found a significant negative correlation between the apoptosis incidence and the level of antioxidant enzymes activity, SOD (r = -0.73 p < 0.01) and CAT (r = -0.80 p < 0.01), in malathion treated ovarian antral follicles. Thus, highlighting the role of DNA fragmentation and declining antioxidant level as a possible mechanism underlying malathion induced reproductive toxicity. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 1944-1954, 2016.

Genotoxic assessment of the copper chelated compounds Casiopeinas: Clues about their mechanisms of action

Casiopeinas is the generic name of a group of copper chelated complexes designed to be used as antineoplastic. Some of these compounds have shown promising results, and in fact, one of them named Casiopeina III-ia has completed preclinical trials and is ready to start clinical phase I in Mexico. As part of the tests that have to be done to every molecule intended to be used in humans, bacterial assays are required because of their sensitivity, speed and reproducibility and among them, Ames test and the SOS Chromotest are widely used to evaluate DNA damage. With the aim to contribute to complete safety information related to genotoxicity and support the hypothesis about their mode of action, four different Casiopeinas (Cas II-gly, Cas III-Ea, Cas III-ia and Cas III-Ha) were tested for genotoxicity with these assays, as well as differential cytotoxicity upon Escherichia coli mutants defectives in some DNA repair mechanisms. However, although it is well known that these molecules produce DNA breakage, the results of the Chromotest and Ames test were negative. Despite this is controversial, a possible explanation is that there is a direct interaction between DNA and the Casiopeinas tested.

Synthesis and characterization of azo-guanidine based alcoholic media naked eye DNA sensor

DNA sensing always has an open meadow of curiosity for biotechnologists and other researchers. Recently, in this field, we have introduced an emerging class of molecules containing azo and guanidine functionalities. In this study, we have synthesized three new compounds (UA1, UA6 and UA7) for potential application in DNA sensing in alcoholic medium. The synthesized materials were characterized by elemental analysis, FTIR, UV-visible, 1H NMR and 13C NMR spectroscopies. Their DNA sensing potential were investigated by UV-visible spectroscopy. The insight of interaction with DNA was further investigated by electrochemical (cyclic voltammetry) and hydrodynamic (viscosity) studies. The results showed that compounds have moderate DNA binding properties, with the binding constants range being 7.2 × 103, 2.4 × 103 and 0.2 × 103 M-1, for UA1, UA6 and UA7, respectively. Upon binding with DNA, there was a change in colour (a blue shift in the λmax value) which was observable with a naked eye. These results indicated the potential of synthesized compounds as DNA sensors with detection limit 1.8, 5.8 and 4.0 ng µl-1 for UA1, UA6 and UA7, respectively.

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.

Detection of Ligand-Induced Conformational Changes in Oligonucleotides by Second-Harmonic Generation at a Supported Lipid Bilayer Interface

There is a high demand for characterizing oligonucleotide structural changes associated with binding interactions as well as identifying novel binders that modulate their structure and function. In this study, second-harmonic generation (SHG) was used to study RNA and DNA oligonucleotide conformational changes associated with ligand binding. For this purpose, we developed an avidin-based biotin capture surface based on a supported lipid bilayer membrane. The technique was applied to two well-characterized aptamers, both of which undergo conformational changes upon binding either a protein or a small molecule ligand. In both cases, SHG was able to resolve conformational changes in these oligonucleotides sensitively and specifically, in solution and in real time, using nanogram amounts of material. In addition, we developed a competition assay for the oligonucleotides between the specific ligands and known, nonspecific binders, and we demonstrated that intercalators and minor groove binders affect the conformation of the DNA and RNA oligonucleotides in different ways upon binding and subsequently block specific ligand binding in all cases. Our work demonstrates the broad potential of SHG for studying oligonucleotides and their conformational changes upon interaction with ligands. As SHG offers a powerful, high-throughput screening approach, our results here also open an important new avenue for identifying novel chemical probes or sequence-targeted drugs that disrupt or modulate DNA or RNA structure and function.

Modeling and Analysis of Intercalant Effects on Circular DNA Conformation

The large-scale conformation of DNA molecules plays a critical role in many basic elements of cellular functionality and viability. By targeting the structural properties of DNA, many cancer drugs, such as anthracyclines, effectively inhibit tumor growth but can also produce dangerous side effects. To enhance the development of innovative medications, rapid screening of structural changes to DNA can provide important insight into their mechanism of interaction. In this study, we report changes to circular DNA conformation from intercalation with ethidium bromide using all-atom molecular dynamics simulations and characterized experimentally by translocation through a silicon nitride solid-state nanopore. Our measurements reveal three distinct current blockade levels and a 6-fold increase in translocation times for ethidium bromide-treated circular DNA as compared to untreated circular DNA. We attribute these increases to changes in the supercoiled configuration hypothesized to be branched or looped structures formed in the circular DNA molecule. Further evidence of the conformational changes is demonstrated by qualitative atomic force microscopy analysis. These results expand the current methodology for predicting and characterizing DNA tertiary structure and advance nanopore technology as a platform for deciphering structural changes of other important biomolecules.

Unraveling multiple binding modes of acridine orange to DNA using a multispectroscopic approach

The interaction of acridine orange (AOH(+)) with calf thymus DNA (ct-DNA) under different dye-DNA conditions has been investigated in detail using multispectroscopic techniques, unraveling a number of hitherto unexplored intricacies of dye-DNA binding. The observed results intriguingly show contrasting binding features when low (2.4 μM) and significantly high (23 μM) dye concentrations are used. It is conclusively inferred from absorption, steady-state fluorescence, circular dichroism, fluorescence decay and anisotropy decay studies that at low [DNA] to [dye] ratio, especially with higher dye concentration, dimeric AOH(+) predominantly binds externally to DNA surfaces through electrostatic interactions. At sufficiently high [DNA] to [dye] ratios, however, the interaction intriguingly changes to monomeric AOH(+) bound to DNA, predominantly in the intercalative mode between DNA base pairs, with partly an electrostatic binding on DNA surfaces. With very low initial dye concentration, monomeric (AOH(+)) mostly binds to DNA through intercalative and electrostatic modes for most DNA to dye ratios. The present study demonstrates a systematic correlation of the striking changes in the photophysical properties of the dye upon multimode binding with DNA. The observed results are of great significance in understanding the fundamental insights of dye/drug binding to DNA hosts, of use in the design of effective therapeutic agents.

Interactions of a biocompatible water-soluble anthracenyl polymer derivative with double-stranded DNA

We have studied the interaction of a polymeric water soluble anthracenyl derivative () with salmon testes DNA. The results from UV-Vis, fluorescence, Fourier transform infrared (FT-IR) and circular dichroism spectroscopies indicate that the groove binding process regulates the interaction between and DNA. The binding constants, calculated by absorption spectroscopy at 298, 304 and 310 K, were equal to 3.2 × 10(5) M(-1), 4.7 × 10(5) M(-1), and 6.6 × 10(5) M(-1) respectively, proving a relatively high affinity of for salmon testes DNA. Results of Hoechst 33258 displacement assays strongly support the groove binding mode of to DNA. The association stoichiometry of the :DNA adduct was found to be 1 for every 5 base pairs. FT-IR spectra, recorded at different /DNA molar ratios, indicate the involvement of the phosphate groups and adenine and thymine DNA bases in the association process. Thermodynamic results suggest that hydrophobic forces regulate the binding of with DNA without excluding some extent of involvement of van der Waals forces and hydrogen bonding arising due to surface binding between the hydrophilic polymeric arms of the ligand and the functional groups positioned on the edge of the groove. The resulting composite biomaterial could constitute a valuable candidate for future biological and/or photonic applications.

A New Organic Dye-Based Staining for The Detection of Plant DNA in Agarose Gels

Ethidium bromide (EtBr) is used to stain DNA in agarose gel electrophoresis, but this dye is mutagenic and carcinogenic. We investigated N-719, which is a visible, reliable and organic Ruthenium-based dye, and five fluorescent alternatives for staining plant DNA. For prestaining and poststaining, N-719, GelRed, and SYBR Safe stained both DNA and PCR product bands as clearly as EtBr. SYBR Green I, methylene blue, and crystal violet were effective for poststaining only. The organic dye N-719 stained DNA bands as sensitively and as clearly as EtBr. Consequently, organic dyes can be used as alternatives to EtBr in plant biotechnology studies.

Pendant-drop method coupled to ultraviolet-visible spectroscopy: A useful tool to investigate interfacial phenomena

UV-vis spectroscopy is a powerful tool to investigate surface phenomena. Surface tension measurements coupled to spectroscopic techniques can help to elucidate how the interface organization influences the electronic properties of molecules. However, appreciable sample volumes are usually necessary to achieve strong signals during conduction of experiments. This study reports on the simultaneous acquisition of surface tension data and UV-vis spectra by axisymmetric drop shape analysis (ADSA) coupled to diffuse reflectance (DRUV) spectrophotometry using a pendant microliter-drop that requires small sample volumes and low analyte concentrations. Three example systems gave evidence of the applicability of this technique: (a) disaggregation of an organic dye driven by surfactant as a function of the surface tension and alterations in the UV-vis spectra, (b) activity of a glycosylphosphatidylinositol anchored enzyme estimated from formation of a colored product, and (c) interaction between this enzyme and biomimetic membrane systems consisting of dipalmitoylphosphaditylcholine and cholestenone. Apart from using smaller sample volume, this coupled technique allowed to investigate interfacial organization in the light of electronic spectra obtained in loco within a shorter acquisition time. This procedure provided precise interfacial information about static and dynamic systems. This has been the first study describing the kinetic activity of an enzyme in the presence of phospholipid monolayers through simultaneous determination of the surface tension and UV-vis spectra.

Supra-molecular inter-actions in a 1:1 co-crystal of acridine and 3-chloro-thio-phene-2-carb-oxy-lic acid

In the title co-crystal, C5H3ClO2S·C13H9N, the components inter-act with each other via an O-H⋯N hydrogen bond. Acridine-acridine stacking, thio-phene-thio-phene stacking and acridine-thio-phene C-H⋯π inter-actions also occur in the crystal.

Joint interaction of ethidium bromide and methylene blue with DNA. The effect of ionic strength on binding thermodynamic parameters

Large amount of data of experimental and theoretical studies have shown that ethidium bromide (EtBr) and methylene blue (MB) may bind to nucleic acids via three modes: intercalation between two adjacent base pairs, insertion into the plane between neighboring bases in the same strand (semi-intercalation), and outside binding with negatively charged backbone phosphate groups. The aim of the given research is to examine the behavior of these two ligands at both separate and joint DNA binding. The obtained experimental data show that the effect of simultaneous binding of EtBr and MB on double-stranded DNA has a non-additive effect of separate binding. The analyses of the melting thermodynamic parameters of DNA complexes with two bound ligands suggest competitive mechanism of interaction.

Review on the binding of anticancer drug doxorubicin with DNA and tRNA: Structural models and antitumor activity

In this review, we have compared the results of multiple spectroscopic studies and molecular modeling of anticancer drug doxorubicin (DOX) bindings to DNA and tRNA. DOX was intercalated into DNA duplex, while tRNA binding is via major and minor grooves. DOX-DNA intercalation is close to A-7, C-5, *C-19 (H-bonding with DOX NH2 group), G-6, T-8 and T-18 with the free binding energy of -4.99kcal/mol. DOX-tRNA groove bindings are near A-29, A-31, A-38, C-25, C-27, C-28, *G-30 (H-bonding) and U-41 with the free binding energy of -4.44kcal/mol. Drug intercalation induced a partial B to A-DNA transition, while tRNA remained in A-family structure. The structural differences observed between DOX bindings to DNA and tRNA can be the main reasons for drug antitumor activity. The results of in vitro MTT assay on SKC01 colon carcinoma are consistent with the observed DNA structural changes. Future research should be focused on finding suitable nanocarriers for delivery of DOX in vivo in order to exploit the full capacity of this very important anticancer drug.

Binding properties of pendimethalin herbicide to DNA: multispectroscopic and molecular docking approaches

Pendimethalin (PND) is a systemic herbicide widely used on rice, cotton, peas, wheat, potatoes, fruits, nuts and other residential and non-residential crops; however, it concurrently exerts toxic effects on beneficial organisms like earthworms, aquatic invertebrates and other non-targeted animals including humans. Most likely, the genotoxicity of agrochemicals/drugs is modulated through cellular distribution of bound DNA. Therefore, the in vitro interaction of PND with calf thymus DNA (ctDNA) has been investigated using various sensitive biophysical techniques to ascertain its binding mechanism. UV-visible absorption and fluorescence spectra suggested the formation of a complex between PND and ctDNA. The binding constant of the PND-ctDNA complex was found to be around 10(4) M(-1) using steady state fluorescence titration. The calculated positive values of enthalpy and entropy changes suggested that the binding reaction was predominantly driven by hydrophobic interactions. Competitive displacement studies using acridine orange (AO), ethidium bromide (EB) and Hoechst dye suggested intercalation of PND molecules into the double helix of ctDNA by replacing the bound AO and EB probes. An increase in the viscosity and melting temperature of ctDNA and a decrease in iodine-quenching also support the intercalative binding of PND with ctDNA. Molecular docking analysis further confirmed the specific binding mode of PND between adjacent 'G-C' base pairs of ctDNA.

Cytotoxicity and biodistribution studies of luminescent Au(i) and Ag(i) N-heterocyclic carbenes. Searching for new biological targets

Gold and silver NHC complexes have been developed as theranostic agents. The unexpected biodistribution opens the door to new biological targets for gold and silver complexes.

Spectroscopic studies of the interaction of 3-(2-thienyl)-[1,2,3]triazolo[1,5-a]pyridine with 2,6-dimethyl-β-cyclodextrin and ctDNA

The studied effect of the inclusion complex on the ctDNA interaction indicates that the TTP-DMβCD complex binds similarly to ctDNA compared to free TTP.

A highly selective and sensitive photoinduced electron transfer (PET) based HOCl fluorescent probe in water and its endogenous imaging in living cells

A probe based on the phenothiazine–acridine orange conjugate (Ptz–AO) has been designed and synthesized for the sensitive and selective detection of HOCl.

Real-time electrochemical LAMP: a rational comparative study of different DNA intercalating and non-intercalating redox probes

The main objective of this study is provide guidelines in the search for ideal redox-active reporters in real-time electrochemical LAMP.

Spectral, electrochemical, and molecular docking evaluation of the interaction of the anti-hyperthyroid drug methimazole with DNA

The interaction of native calf thymus DNA with the anti-hyperthyroid drug methimazole was investigated by different spectroscopic (UV-Vis spectrophotometry, spectroflourimetry, and circular dichroism), electrochemical (cyclic voltammetry and chronoamperometry) methods, and molecular docking calculations. The binding constant (Kb) obtained from the spectrophotometric method was 9.67 × 103 L mol−1, comparable with that of groove binding molecules. The binding mode was further investigated by following the competition between Hoechst 33258 and methimazole for DNA grooves by spectrofluorimetry. Consistent results were obtained from all experimental methods used in this study. Finally, theoretical calculations using the molecular docking method confirmed the experimental results.

Pharmacological investigation of 2-aminobenzothiazolium-4-methylbenzenesulphonate: Synthesis, spectral characterization and structural elucidation

An organic charge transfer complex, 2-aminobenzothiazolium-4-methylbenzenesulphonate (ABPTS) was synthesized and single crystals grown by slow solvent evaporation solution growth technique at ambient temperature. The single crystal X-ray diffraction analysis was carried out to establish the molecular structure of the title crystal. FT-IR spectral study was carried out to identify the various functional groups present in the crystal. The (1)H and (13)C spectra were recorded to further confirm the molecular structure of the CT complex. The TG/DTA analyses were carried out to establish the thermal stability of the complex. The antibacterial and antifungal activities of synthesized complex were examined against various bacteria and fungi strains, to identify the antibacterial and antifungal activity. The DNA binding profile of the complex has been investigated through absorption spectroscopy and complex has intrinsic binding constant 3.6 × 10(4) M(-1). A gel electrophoresis assay demonstrated the ability of the complex to cleave the pBR322 DNA. The free radical scavenging activity of the complex has been determined against DPPH, OH and ABTS radicals.

Racemic R,S-venlafaxine hydrochloride-DNA interaction: experimental and computational evidence

The interaction of racemic R,S-venlafaxine hydrochloride (rac-VEN) drug with calf thymus deoxyribonucleic acid (ct-DNA) was studied using various physico-chemical techniques and molecular docking at simulated physiological conditions (pH=7.4). The fluorescence study shows that ct-DNA interacted with rac-VEN and quenched its intrinsic fluorescence in a static quenching process. These results are further supported by UV-Vis spectra. The binding constant of rac-VEN with ct-DNA (0.57 × 10(4)) obtained from the spectroscopic techniques, which is more in keeping with the groove binding with DNA. Furthermore, the competition experiment using Hoechst33258 indicated that rac-VEN may bind to ct-DNA by a minor groove binding mode. In addition, iodide quenching effect on the fluorescence of rac-VEN before and after the interaction with ct-DNA is another evidence to groove binding. The thermodynamic parameters are calculated by van't Hoff equation, which demonstrated that hydrogen bonds and van der Waals interactions played major roles in the binding reaction. Molecular simulation studies carried out by using the AutoDock4 and Spartan 10 programs. From the best docking map, we found that R and S-isomers fit in the A6T7T8/T19A18A17 region in minor groove of B-DNA. Finally, these results indicated that the docking of S-VEN-B-DNA is more stable than R-VEN-B-DNA.

Interactions of Isophorone Derivatives with DNA: Spectroscopic Studies

Interactions of three new isophorone derivatives, Isoa Isob and Isoc with salmon testes DNA have been investigated using UV-Vis, fluorescence and circular dichroism spectroscopic methods. All the studied compounds interact with DNA through intercalative binding mode. The stoichiometry of the isophorone/DNA adducts was found to be 1:1. The fluorescence quenching data revealed a binding interaction with the base pairs of DNA. The CD data indicate that all the investigated isophorones induce DNA modifications.

Synthesis, spectral, structural characterization and biological investigation of m-Xylylenediaminium-bis (p-toluenesulfonate) monohydrate

Novel organic charge transfer complex, m-xylylenediaminium-bis (p-toluenesulfonate) monohydrate (XDPTS) have been synthesized and crystallized to the triclinic system with space group P-1 and the lattice parameters obtained are a=9.9265(7) Å, b=9.9676(6) Å, c=13.4948(10) Å, α=71.95(6)°, β=77.02(6)°, γ=76.851(5)°. The synthesized complex structure was confirmed by IR, (1)H NMR and (13)C NMR spectral analysis. Pharmacology activities of charge transfer complex were evaluated through antimicrobial, DNA binding/cleavage, antioxidant and cytotoxicity studies. The results reveal that the compound shows good antimicrobial activity against various antibacterial and antifungal species. The DNA interaction indicated that the compound could interact with DNA through intercalation, which is further confirmed by viscosity measurements. The compound should have weak to moderate capacity of scavenging with DPPH, Hydroxyl and ABTS radicals. The cytotoxicity has been evaluated by MTT assay method against MCF-7 cancer cell line.

Spectroscopic and molecular docking studies on the interaction of troxerutin with DNA

Troxerutin (TXER) is a derivative of naturally occurring bioflavonoid rutin. It possesses different biological activities in rising clinical world. The biological activity possessed by most of the drugs mainly targets on macromolecules. Hence, in the current study we have examined the interaction mechanism of TXER with calf thymus DNA (CT-DNA) by using various spectroscopic methods, isothermal titration calorimetry (ITC) and molecular docking studies. Further, DNA cleavage study was carried out to find the DNA protection activity of TXER. UV-absorption and emission spectroscopy showed low binding constant values via groove binding. Circular dichroism study indicates that TXER does not modify native B-form of DNA, and it retains the native B-conformation. Furthermore, no effective positive potential peak shift was observed in TXER-DNA complex during electrochemical analysis by which it represents an interaction of TXER with DNA through groove binding. Molecular docking study showed thymine guanine based interaction with docking score -7.09 kcal/mol. This result was compared to experimental ITC value. The DNA cleavage study illustrates that TXER does not cause any DNA damage as well as TXER showed DNA protection against hydroxyl radical induced DNA damage. From this study, we conclude that TXER interacts with DNA by fashion of groove binding.

Phosphorescent quantum dots/ethidium bromide nanohybrids based on photoinduced electron transfer for DNA detection

Mercaptopropionic acid-capped Mn-doped ZnS quantum dots/ethidium bromide (EB) nanohybrids were constructed for photoinduced electron transfer (PIET) and then used as a room-temperature phosphorescence (RTP) probe for DNA detection. EB could quench the RTP of Mn-doped ZnS QDs by PIET, thereby forming Mn-doped ZnS QDs/EB nanohybrids and storing RTP. Meanwhile, EB could be inserted into DNA and EB could be competitively desorbed from the surface of Mn-doped ZnS QDs by DNA, thereby releasing the RTP of Mn-doped ZnS QDs. Based on this mechanism, a RTP sensor for DNA detection was developed. Under optimal conditions, the detection limit for DNA was 0.045 mg L(-1), the relative standard deviation was 1.7%, and the method linear ranged from 0.2 to 20 mg L(-1). The proposed method was applied to biological fluids, in which satisfactory results were obtained.