Formation of DNA Complexes with Actinomycins in Aqueous Solutions and Films

The mechanisms of DNA interaction with actinomycin D (AMD), 7-amino-actinomycin D (7-AAMD), and ethidium bromide (EtBr) were studied in aqueous solutions and in the condensed state (films coating plates). The use of the methods of absorption (UV, IR, and visible spectral ranges) and fluorescence (steady-state, polarization, and phase-modulation) spectroscopy revealed that (1) the formation of DNA complexes with 7-AAMD in solution was not accompanied by energy transfer from photoexcited nucleotides to phenoxazone chromophore and (2) the mechanism of ligand incorporation was distinct from stacking. In the film of the DNA–7-AAMD complex, which simulated the native state in a biological cell, the energy transfer efficiency was high. This indicates that a stacking-type mechanism underlies actinomycin intercalation into DNA. In the presence of high concentrations of 7-AAMD in the film, DNA denatured and its double-helical structure degraded. In the DNA–AMD complex, the native B-form of DNA molecule was conserved both in films and in solution.     

Non stacking binding of 7-amino-actinomycin D and actinomycin D to DNA and model nucleotide systems in solutions

Mechanism of actinomycin D (AMD) and 7-aminoactinomycin D (7AAMD) interaction with DNA and model nucleotide compounds was studied by absorption and fluorescence spectroscopy (steady-state, phase-modulation, and polarization). It was shown that complex formation does not result in energy transfer from photoexcited nucleotides to phenoxazone chromophore of 7AAMD that indicates the absence of stacking-like intercalation. This fact is fundamentally important to explain the biological effect of actinomycin on cells. It was revealed a fundamental difference in the complex-forming properties of AMD and 7AAMD. Thus AMD is capable of binding to guanine micelles to destroy them. 7AAMD forms complexes neither guanine micelles nor polyguanilic acid. 7AAMD binding sites on DNA can differ substantially from AMD binding sites. However, a strong competition is observed between AMD and 7AAMD for binding site in oligonucleotide HP1 used as DNA hairpin model. The efficient diameters of 7AAMD-HP1 complex and free 7AAMD were determined using the Levshin-Perren equation.     

Nonstacking Binding of 7-Aminoactinomycin D and Actinomycin D to DNA and Model Nucleotide Systems in Solutions

The mechanism of actinomycin D (AMD) and 7-aminoactinomycin D (7AAMD) interaction with DNA and model nucleotide compounds was studied by absorption and fluorescence spectroscopy (steady-state, phase-modulation, and polarization). It was shown that complex formation does not result in energy transfer from photoexcited nucleotides to the phenoxazone chromophore of 7AAMD, which indicates the absence of stacking-like intercalation. This fact is fundamentally important to explain the biological effect of actinomycin on cells. A basic difference was revealed in the complex-forming properties of AMD and 7AAMD. Thus AMD is capable of binding to guanine micelles to destroy them; 7AAMD forms no complexes with either guanine micelles or polyguanylic acid. 7AAMD binding sites on DNA can differ substantially from AMD binding sites. However, strong competition is observed between AMD and 7AAMD for the binding site in oligonucleotide HP1 used as a DNA hairpin model. The effective diameters of 7AAMD–HP1 complex and free 7AAMD were determined using the Levshin–Perren equation.     

A stereocomplex platform efficiently detecting antigen-antibody interactions

Ultrathin poly(methyl methacrylate) (PMMA) stereocomplex films with macromolecularly double-stranded regular nanostructures were prepared by layer-by-layer assembly of isotactic and syndiotactic PMMAs on solid surfaces. Antibodies were immobilized through the Fc region-capturing protein A, which had been physically adsorbed on the complex film, and the binding of antigens to immobilized antibodies was quantitatively investigated by the quartz crystal microbalance technique. Greater amounts of protein A with native forms were adsorbed on the complex film than those on conventional single-component PMMA films. Antibodies with high target-binding activities were also immobilized on the complex film. A greater amount of antigens could be detected on the complex film. The activity of protein A was maintained on the complex for a long time even within a dried state. The mechanism for the preservation of protein native forms on the complex surface was speculated by analyzing the physical adsorption of proteins with various secondary structures. Stereocomplex films can be utilized as novel coating nanomaterials for efficiently detecting protein-protein interactions.     

Prompt non-stacking binding of actinomycin D to hairpin oligonucleotide HP1 and slow redistribution from HP1 to DNA

Complexes of actinomycin D (AMD) and 7-amino-actinomycin D (7AAMD) with model hairpin oligonucleotide HP1 and various types of DNA in aqueous solutions were investigated by steady-state, polarized, time-resolved and stopped-flow fluorimetry, and photometry. Prompt non-stacking binding of the actinomycins inside HP1 was observed. No energy transfer from nucleotides to 7AAMD in the complex was detected, most likely because of the absence of stacking intercalation. Complex formation of AMD or 7AAMD and HP1 was followed by the transition from a random flexible conformation of the hairpin to a more compact rigid structure, and subsequently to hypochromism. Strong competition between AMD and 7AAMD for a cavity in HP1 was observed. The decrease in the 7AAMD emission after addition of DNA to the 7AAMD/HP1 complex indicates that actinomycins can be redistributed from HP1 to DNA, i.e. hairpin oligonucleotides can serve as molecular carriers of actinomycins.     

Single-strand DNA binding of actinomycin D with a chromophore 2-amino to 2-hydroxyl substitution

A modified actinomycin D was prepared with a hydroxyl group that replaced the amino group at the chromophore 2-position, a substitution known to strongly reduce affinity for double-stranded DNA. Interactions of the modified drug on single-stranded DNAs of the defined sequence were investigated. Competition assays showed that 2-hydroxyactinomycin D has low affinity for two oligonucleotides that have high affinities (K(a) = 5-10 x 10(6) M(-1) oligomer) for 7-aminoactinomycin D and actinomycin D. Primer extension inhibition assays performed on several single-stranded DNA templates totaling around 1000 nt in length detected a single high affinity site for 2-hydroxyactinomycin D, while many high affinity binding sites of unmodified actinomycin D were found on the same templates. The sequence selectivity of 2-hydroxyactinomycin D binding is unusually high and approximates the selectivity of restriction endonucleases. Binding appears to require a complex structure, including residues well removed from the polymerase pause site.     

A study of interaction of 7-aminoactinomycin D with DNA by fluorescence correlation spectroscopy

The investigation of interaction of 7-aminoactinomycin D with DNA is hampered at nanomolar concentrations by low quantum yield of the dye fluorescence and high adsorbability of the dye. It was found that, instead of the increase in the fluorescence of 7-aminoactinomycin D after binding with DNA, a decrease in the fluorescence takes place, because 7-aminoactinomycin D complexed with DNA exists in two states: photochemically active and inactive. The presence of the photochemically active state of 7-aminoactinomycin D causes an apparent increase in the diffusion coefficient upon embedding of 7-aminoactinomycin D into DNA. The data obtained allow one to state that 7-aminoactinomycin D: (1) forms dimers at micromolar concentration, (2) has two specific photodestruction times, and (3) binds with DNA more effectively than actinomycin D. Polarization measurements made it possible to estimate numerically the adsorption of 7-aminoactinomycin D on the walls of the measuring cell.     

The interaction of 7-substituted actinomycin D analogs with DNA

The interaction of actinomycin D and three new 7-substituted analogs with calf thymus DNA has been studied by a number of physical techniques. The methods utilized in this investigation include visible absorption spectrometry and ultrafiltration methodology for the determination of equilibrium binding constants; viscometry; and circular dichroism. The studies show that the 7-substituted actinomycin D analogs retain the G . C base pair specific DNA binding demonstrated by actinomycin D. The mode of binding to native DNA, despite substitution at position 7, is practically unaltered. The retention of this binding specificity by these analogs seems to be unaffected by changes in the electon properties of the chromophore.     

Mechanical properties of DNA films

The Young's dynamical modulus (E) and the DNA film logarithmic decrement (theta) at frequencies from 50 Hz to 20 kHz are measured. These values are investigated as functions of the degree of hydration and temperature. Isotherms of DNA film hydration at 25 degrees C are measured. The process of film hydration changing with temperature is studied. It is shown that the Young's modulus for wet DNA films (E = 0.02-0.025 GN m-2) strongly increases with decreasing hydration and makes E = 0.5-0.7 GN m-2. Dependence of E on hydration is of a complex character. Young's modulus of denatured DNA films is larger than that of native ones. All peculiarities of changing of E and theta of native DNA films (observed at variation of hydration) vanish in the case of denatured ones. The native and denatured DNA films isotherms are different and depend on the technique of denaturation. The Young's modulus of DNA films containing greater than 1 g H2O/g dry DNA is found to decrease with increasing temperature, undergoing a number of step-like changes accompanied by changes in the film hydration. At low water content (less than 0.3 g H2O/g dry DNA), changing of E with increasing temperature takes place smoothly. The denaturation temperature is a function of the water content.     

Melting of DNA-actinomycin clusters

Differential methods of scanning micro-calorimetry and UV spectrophotometry were used for understanding the interaction of natural anti-tumour antibiotic actinomycin D with cluster sites of native and fragmented DNA during thermal melting. At low (micro-molar) concentrations, the actinomycin molecules penetrate into unwound regions of DNA, but not into the double helix. Moreover, they stabilize the fragmented DNA and increase a total melting point. Actinomycin D interacts with fractions of native DNA even at very low concentrations (at the antibiotic/nucleotide ratio of 1:868) and stabilizes the most loose clusters. At high concentrations, it destabilizes the double helix.     

1H-NMR analysis of heteroassociation of caffeine with antibiotic actinomycin D in the aqueous solution

The molecular basis of the action of caffeine as a complex forming agent, an interceptor of aromatic drugs intercalating into DNA was studied by the example of the an anticancer antibiotic actinomycin D examined. The hetero-association of caffeine and actionomycin D was studied by one- and two-dimensional 1H-NMR spectroscopy (500 MHz). Concentration and temperature dependences of the proton chemical shifts of molecules in aqueous solution were measured. The equilibrium reaction constant of hetero-association of caffeine with actinomycin D (K = 246 +/- 48 M-1), the limiting chemical shifts of caffeine protons in complexes were determined. The most favourable structure of the 1:1 caffeine-actinomycin D hetero-complex in aqueous solution was constructed using the calculated values of the induced proton chemical shifts of molecules and the quantum-mechanical iso-shielding curves for caffeine and actinomycin D. The thermo-dynamical parameters of the hetero-complex formation between caffeine and actinomycin D were also determined. The structural and thermo-dynamical analysis showed that dispersive forces and hydrophobic interactions play the major role in hetero-association of caffeine and actinomycin D in aqueous-salt solution. The relative content of different complexes in mixed solutions containing caffeine and actinomycin D was calculated and distinctive features of the dynamic equilibrium of caffeine-actinomycin D hetero-associates were revealed as a function of concentration and temperature. It is concluded that hetero-association of caffeine and actinomycin D molecules a lowers the effective concentration of the drug in solution and hence the pharmacological activity of actinomycin D.     

7-Amino-actinomycin D as a specific fluorophore for DNA content analysis by laser flow cytometry

A technique for DNA amount determination by flow cytometry based on the use of 7-amino-actinomycin D (7-amino-AMD), a fluorescent analogue of antibiotic actinomycin has been investigated, and a particular staining procedure has been developed. The procedure includes short fixation in 70% ethanol and staining for 20 min in 10(-5)M solution of 7-amino-AMD at pH7. The results of DNA content measurements are very reproducible. The histograms obtained have a coefficient of variation less than 3%. The absorption maximum of the complex of 7-amino-AMD with DNA is situated in the green spectrum region, making this stain particularly suitable for argon laser flow cytometry.     

Assessment of the DNA-binding properties of actinomycin and its derivatives by molecular dynamics simulation

A molecular dynamics simulation was used to assess the effect on the elasticity of a DNA fragment and the efficiency of DNA binding for actinomycins (antibiotics that are used in chemotherapy for certain oncology diseases). Hydroxyl and amino groups that were introduced as substituents in the phenoxazine ring of actinomycin were tested for their effect on the dynamic behavior and stability of antibiotic–DNA complexes. The Young modulus was calculated for DNA, DNA–actinomycin, DNA–7-hydroxyactinomycin, and DNA–7-aminoactinomycin. The free energy of complexation with DNA was calculated for actinomycin and its two analogs. The substituents were assumed to structurally stabilize the DNA fragment via additional hydrogen bonding.     

Impedance studies of a nano-structured conducting polymer and its application to the design of reliable scaffolds for impedimetric biosensors

Electrochemical impedance spectroscopy (EIS) as a powerful, non-invasive and informative technique was used to obtain important information about kinetics of doping process in conducting polymers. Polypyrrole (PPy) and its derivatives can form conducting polymer films which represent excellent charge transfer behaviors during doping processes. It can also have a wide range of applications in bioelectrochemistry. In the present study the conducting polymer of alpha-carboxy pyrrole (alpha-COOH-PPy), appended onto the underlying film of PPy, was prepared by electrochemical methods and its behavior was analyzed using EIS. From highly accurate fitting of impedance results it was found that the charging mechanism is governed by the diffusion process. In addition, the impedance analyses provided values for the bulk polymer parameters including diffusion coefficient (D), equilibrium capacitance (C(0)) and diffusion resistance (R(0)). The surface morphology of the polymeric film was characterized using scanning electron microscopy (SEM). The film was then used to immobilize the cytochrome C (cyt-C) and to perform its electrochemical studies. The modified cyt-C/alpha-COOH-PPy electrode was used for electrocatalytic reduction of H(2)O(2) in solution and its viability as a new impedimetric biosensor was examined. Based on the calibration curve obtained for the proposed impedimetric biosensor, the limit of detection and relative standard deviation were evaluated as 0.25mumolL(-1) and 7%, respectively. Finally, the prolonged stability test was performed and high stability and reproducibility of the new biosensor was confirmed.     

Actinomycin D-deoxynucleotide complexes as models for the actinomycin D-DNA complex. The use of nuclear magnetic resonance to determine the stoichiometry and the geometry of the complexes.

The use of proton and carbon-13 magnetic resonance spectroscopy for the determination of the geometry and the stoichiometry of the actinomycin D-deoxyguanosine 5'-monophosphate complex is outlined. The dimerization of actinomycin D has been reexamined by recording the proton magnetic resonance spectrum of actinomycin D to much lower concentrations through the use of Fourier transform nuclear magnetic resonance techniques. The effect of the actinomycin D dimerization on the observed chemical shifts that results from the additon of nucleotides to an actinomycin D solution is directly demonstrated by comparing the actinomycin D-nucleotide titrations at both low (approximately 0.3 mM) and high (approximately 12 mM) concentrations of actinomycin D. In the presence of excess nucleotide the chemical shifts of the actinomycin D groups were essentially the same for both the low and high concentration titrations. The complexes of actinomycin D with pdG-dC, dG-dC, deoxyguanosine 3'-monophosphate, G-C, C-G, dIMP(5'), 2, 6-diaminopurine deoxyribose, and other nucleotides were also investigated by proton magnetic resonance and visible spectral titrations. These data were interpreted in terms of the molecular geometry of the complexes and in terms of the effect of the structure of the nucleotide base on the relative binding affinity of the nucleotides for the two nucleotide binding sites of actinomycin D. The carbon-13 chemical shifts of dGMP(5') were measured as a function of concentration over the concentration range of 0.5-0.025 M. The infinite dilution carbon-13 chemical shifts were graphically estimated from the dilution curves. These values were used to calculate the changes in the chemical shifts of the dGMP carbons that result from the formation of an actinomycin D-(dGMP)2 complex. It was not possible to interpret these carbon-13 chemical shift changes in terms of only ring current effects, which thus rules out the use of carbon-13 spectroscopy in the determination of the geometries of the actinomycin D complexes with the mono- and dinucleotides. The induced chemical shifts in the proton spectra may be used in the determination of the geometries of the complexes. A consideration of these data for the above nucleotide series shows that the predominant complex formed is one in which the guanine rings in the two nucleotide binding sites of actinomycin D are oriented in a manner very similar to that observed in the cocrystalline complex of actinomycin D with deoxyguanosine.     

Atomic Layer Deposition of Functional Layers for on Chip 3D Li‐Ion All Solid State Microbattery

Nowadays, millimeter scale power sources are key devices for providing autonomy to smart, connected, and miniaturized sensors. However, until now, planar solid state microbatteries do not yet exhibit a sufficient surface energy density. In that context, architectured 3D microbatteries appear therefore to be a good solution to improve the material mass loading while keeping small the footprint area. Beside the design itself of the 3D microbaterry, one important technological barrier to address is the conformal deposition of thin films (lithiated or not) on 3D structures. For that purpose, atomic layer deposition (ALD) technology is a powerful technique that enables conformal coatings of thin film on complex substrate. An original, robust, and highly efficient 3D scaffold is proposed to significantly improve the geometrical surface of miniaturized 3D microbattery. Four functional layers composing the 3D lithium ion microbattery stacking has been successfully deposited on simple and double microtubes 3D templates. In depth synchrotron X‐ray nanotomography and high angle annular dark field transmission electron microscope analyses are used to study the interface between each layer. For the first time, using ALD, anatase TiO₂ negative electrode is coated on 3D tubes with Li₃PO₄ lithium phosphate as electrolyte, opening the way to all solid‐state 3D microbatteries. The surface capacity is significantly increased by the proposed topology (high area enlargement factor – “thick” 3D layer), from 3.5 μA h cm^?2 for a planar layer up to 0.37 mA h cm^?2 for a 3D thin film (105 times higher).     

AC impedance spectroscopy of native DNA and M-DNA

Monolayers of thiol-labeled DNA duplexes of 15, 20, and 30 basepairs were assembled on gold electrodes. Electron transfer was investigated by electrochemical impedance spectroscopy with Fe(CN)(6)(3-/4-) as a redox probe. The spectra, in the form of Nyquist plots, were analyzed with a modified Randles circuit which included an additional component in parallel, R(x), for the resistance through the DNA. For native B-DNA R(x) and R(ct), the charge transfer resistance, both increase with increasing length. M-DNA was formed by the addition of Zn(2+) at pH 8.6 and gave rise to characteristic changes in the Nyquist plots which were not observed upon addition of Mg(2+) or at pH 7.0. R(x) and R(ct) also increased with increasing duplex length for M-DNA but both were significantly lower compared to B-DNA. Therefore, electron transfer via the metal DNA film is faster than that of the native DNA film and certain metal ions can modulate the electrochemical properties of DNA monolayers. The results are consistent with an ion-assisted long-range polaron hopping mechanism for electron transfer.