Electrochemical behaviour of anticancer drug lomustine and in situ evaluation of its interaction with DNA.

Electrochemical techniques were used to investigate the behavior of lomustine (CCNU) and its degradation in aqueous solution at a glassy carbon electrode (GCE). The in situ interaction of CCNU and chemically degraded CCNU (cdCCNU) with dsDNA was then investigated in dsDNA incubated solutions, using dsDNA electrochemical biosensors and comet assays. CCNU undergoes electrochemical reduction in two irreversible, diffusion-controlled, and pH-dependent redox processes, each with transfer of two electrons and one proton. At pH ≥ 10.1, the peak potential for the two processes was essentially pH-independent and involved only one electron. A mechanism was proposed for the reduction of CCNU in a neutral medium. In addition, it was found that CCNU underwent spontaneous degradation during incubation in aqueous solution, without the formation of electroactive degradation products. The degradation process was faster in basic media. Moreover, this pro-drug interacted with the DNA. Its metabolite(s) initially caused condensation of the double helix chains, followed by the unwinding of these chains. In addition, free guanine (Gua) was released from the dsDNA and oxidative damage to the DNA by the CCNU metabolite(s) was evidenced from the detection of 8-oxoGua and 2,8-oxoAde. These results were confirmed by the poly(dA)- and poly(dG)-polyhomonucleotide biosensors, which revealed the oxidative damage caused to both bases (guanine and adenine) of the dsDNA by the CCNU metabolite(s). The comet assay indicated breaks in the single strand DNA, complementing the results of the studies using differential pulse voltammetry. Conformational changes of dsDNA caused by CCNU and cdCCNU were confirmed using comet assays.

Effects of caffeine on the structure and conformation of DNA: A force spectroscopy study.

Here, we use single molecule force spectroscopy performed with optical tweezers in order to investigate the interaction between Caffeine and the DNA molecule for various different concentrations of the alkaloid and under two distinct ionic strengths of the surrounding buffer. We were able to determine the mechanical changes induced on the double-helix structure due to Caffeine binding, the binding mode and the binding parameters of the interaction. The results obtained show that Caffeine binds to DNA by outside the double-helix with a higher affinity at lower ionic strengths. On the other hand, a considerable cooperativity was found only for sufficient high ionic strengths, suggesting that Caffeine may binding forming dimers and/or trimers along the double-helix under this condition. Finally, it was also shown that Caffeine stabilizes the DNA double-helix upon binding, preventing force-induced DNA melting.

Force spectroscopy unravels the role of ionic strength on DNA-cisplatin interaction: Modulating the binding parameters.

In the present work we have gone a step forward in the understanding of the DNA-cisplatin interaction, investigating the role of the ionic strength on the complexes formation. To achieve this task, we use optical tweezers to perform force spectroscopy on the DNA-cisplatin complexes, determining their mechanical parameters as a function of the drug concentration in the sample for three different buffers. From such measurements, we determine the binding parameters and study their behavior as a function of the ionic strength. The equilibrium binding constant decreases with the counterion concentration ([Na]) and can be used to estimate the effective net charge of cisplatin in solution. The cooperativity degree of the binding reaction, on the other hand, increases with the ionic strength, as a result of the different conformational changes induced by the drug on the double-helix when binding under different buffer conditions. Such results can be used to modulate the drug binding to DNA, by appropriately setting the ionic strength of the surrounding buffer. The conclusions drawn provide significant new insights on the complex cooperative interactions between the DNA molecule and the class of platinum-based compounds, much used in chemotherapies.

In situ evaluation of gemcitabine-DNA interaction using a DNA-electrochemical biosensor.

The electrochemical behaviour of the cytosine nucleoside analogue and anti-cancer drug gemcitabine (GEM) was investigated at glassy carbon electrode, using cyclic, differential pulse and square wave voltammetry, in different pH supporting electrolytes, and no electrochemical redox process was observed. The evaluation of the interaction between GEM and DNA in incubated solutions and using the DNA-electrochemical biosensor was studied. The DNA structural modifications and damage were electrochemically detected following the changes in the oxidation peaks of guanosine and adenosine residues and the occurrence of the free guanine residues electrochemical signal. The DNA-GEM interaction mechanism occurred in two sequential steps. The initial process was independent of the DNA sequence and led to the condensation/aggregation of the DNA strands, producing rigid structures, which favoured a second step, in which the guanine hydrogen atoms, participating in the C-G base pair, interacted with the GEM ribose moiety fluorine atoms.

On the effects of intercalators in DNA condensation: a force spectroscopy and gel electrophoresis study.

In this work we have characterized the effects of the intercalator ethidium bromide (EtBr) on the DNA condensation process by using force spectroscopy and gel electrophoresis. We have tested two condensing agents: spermine (spm(4+)), a tetravalent cationic amine which promotes cation-induced DNA condensation, and poly(ethylene glycol) (PEG), a neutral polymer which promotes DNA ψ-condensation. Two different types of experiments were performed. In the first type, bare DNA molecules disperse in solution are first treated with EtBr for intercalation, and then the condensing agent is added to the sample with the purpose of verifying the effects of the intercalator in hindering DNA condensation. In the second experiment type, the bare DNA molecules are first condensed, and then the intercalator is added to the sample in order to verify its influence on the previously condensed DNA. The results obtained with the two different experimental techniques used agree very well, indicating that previously intercalated EtBr can hinder both cation-induced and ψ-condensation, being more efficient in the first case. On the other hand, EtBr has little effect on the previously formed cation-induced condensates, but is efficient in unfolding the ψ-condensates.

Modeling the entropic structural transition of DNA complexes formed with intercalating drugs.

A first approach is presented to explain the entropic structural transition observed in the persistence length of DNA complexes formed with intercalating drug molecules. The proposed model is based on calculating the effective persistence length of two entropic springs associated in series, one intercalated with drug molecules and the other without drugs. As the total drug concentration in the sample increases, the lengths of the two entropic springs vary, modifying the effective persistence length. The theoretical predictions of this model are then compared to experimental results, and a good accordance was obtained.

Polymer induced condensation of DNA supercoils.

Macromolecular crowding is thought to be a significant factor driving DNA condensation in prokaryotic cells. Whereas DNA in prokaryotes is supercoiled, studies on crowding-induced DNA condensation have so far focused on linear DNA. Here we compare DNA condensation by poly(ethylene oxide) for supercoiled and linearized pUC18 plasmid DNA. It is found that supercoiling has only a limited influence on the critical amount of PEO needed to condense plasmid DNA. In order to pack DNA supercoils in condensates, it seems inevitable that they must be deformed in one way or another, to facilitate dense packing of DNA. Analytical estimates and Monte Carlo simulations indicate that packing of DNA supercoils in condensates is most likely facilitated by a decrease of the superhelical diameter rather than by unwinding of the supercoils.

Piplartine induces inhibition of leukemia cell proliferation triggering both apoptosis and necrosis pathways.

Piplartine {5,6-dihydro-1-[1-oxo-3-(3,4,5-trimethoxyphenyl)-2-propenyl]-2(1H)pyridinone} is an alkaloid/amide component of Piper species. The purpose of the present study was to examine the antiproliferative effects of piplartine on human leukemia cell lines HL-60, K562, Jukart, and Molt-4 using the trypan blue exclusion method, as well as the effect of piplartine on DNA synthesis. The viability of all human leukemia cell lines were not affected by piplartine after 6 h, 9 h, and 12 h exposure, whereas a steady decline was seen after an exposure time of 24 h. The antiproliferative activity of piplartine seemed to be related to the inhibition of DNA synthesis, as revealed by the reduction of 5-bromo-2'-deoxyuridine (BrdU) incorporation after 24h of incubation. Piplartine-mediated reduction in cell number was associated with an increasing number of dead cells at a concentration of 10 microg/ml. These findings were corroborated by morphologic analysis. However, at the lowest concentration (2.5 microg/ml), piplartine-treated cells exhibited typical apoptotic morphological changes. The increase in caspase-3 activity was also observed in lysates of piplartine-treated cells (2.5 microg/ml). Our findings suggest that piplartine can suppress leukemia growth and reduce cell survival, triggering both apoptosis and/or necrosis, depending on the concentration used.

QSAR and molecular modelling studies on B-DNA recognition of minor groove binders.

Aromatic bisamidines have been proved to be efficient compounds against Leishmania spp. and Pneumocystis carinii. Although the mode of action is still not known, these molecules are supposed to be DNA minor groove binders (MGBs). This paper describes a molecular modelling study for a set of MGBs in order to rank them through their complementarity to the Dickerson Drew Dodecamer (DDD) according to their interaction energies with B-DNA. A comparative molecular field analysis (CoMFA) has shown the importance of relatively bulky positively charged groups attached to the MGB aromatic rings, and small and negatively charged substituents into the middle chain. Models were obtained for DNA denaturation related to H-bonding processes of binding modes. Validation of the model demonstrated the robustness of CoMFA in terms of independent test set of similar MGBs. GRID results allotted bioisosteric substitution of z.sbnd;Oz.sbnd; by z.sbnd;NHz.sbnd; in furan ring of furamidine and related compounds as being capable to enhance the binding to DDD.

Damage induced by stannous chloride in plasmid DNA.

Stannous chloride (SnCl(2)) is widely used in daily human life, for example, to conserve soft drinks, in food manufacturing and biocidal preparations. In nuclear medicine, stannous chloride is used as a reducing agent of Technetium-99m, a radionuclide used to label different cells and molecules. In spite of this, stannous chloride is able to generate reactive oxygen species (ROS) which can damage DNA. In this work, plasmid DNA (pUC 9.1) was incubated with SnCl(2) under different conditions and the results analyzed through DNA migration in agarose gel electrophoresis. Our data reinforce the powerful damaging effect induced by stannous ion and suggest that this salt can play a direct role in inducing DNA lesions.

Electron microscopy and biological properties of pBR322 DNA condensed with the trivalent cations spermidine and hexammine cobalt (III).

Electron microscopy and the biological properties of susceptibility to DNase I, genetic transcription, and transformation of pBR322 DNA compacted with spermidine or hexammine cobalt (III), were analyzed in order to characterize the association of DNA in its compacted form with these two different trivalent cations. Spermidine and hexammine cobalt (III) produced an average 4-fold reduction of the DNA perimeter in compact DNA forms, which were doughnut-shaped toroids and cylinders. Both compacted DNAs were resistant to the hydrolytic activity of DNase I. However, spermidine-condensed pBR322 DNA was 10-fold and 4 to 6-fold more active in transcription and transformation, respectively, than naked pBR322. I. Hexammine cobalt (III)-condensed pBR322 was inactive in both biological properties. An inhibitory effect of hexammine cobalt (III) on RNA polymerase and genetic transformation activities was discarded because at higher ionic strength, in which DNA is not compacted by hexammine cobalt (III), transcription and transformation were similar to those observed with naked DNA. This information showed that the interaction of hexammine cobalt (III) with the DNA converted the pBR322 DNA into an inert molecule. In contrast, pBR322 did not loose its biological properties after its interaction with the polyamine spermidine; i.e., experimental condensation of pBR322 DNA by spermidine produced compacted DNA that is more similar to compact native genomes than relaxed DNA. These experiments led us to conclude that spermidine-condensed DNA can be used to study the roll of the native supercoiling of DNA in the regulation of genetic replication and transcription, as well as to study the mechanisms that allow the accessibility of the supercoiled or condensed DNA substrate for enzymes.