Interactions des ions métalliques avec le DNA. III. Stabilité et configuration des complexes Ag-DNA

A review of heavy metal cation binding to deoxyribonucleic acids for the creation of chemical sensors

Various human activities lead to the pollution of ground, drinking, and wastewater with toxic metals. It is well known that metal ions preferentially bind to DNA phosphate backbones or DNA nucleobases, or both. Foreman et al. (Environ Toxicol Chem 30(8):1810-1818, 2011) reported the use of a DNA-dye based assay suitable for use as a toxicity test for potable environmental water. They compared the results of this test with the responses of live-organism bioassays. The DNA-based demonstrated that the loss of SYBR Green I fluorescence dye bound to calf thymus DNA was proportional to the toxicity of the water sample. However, this report raised questions about the mechanism that formed the basis of this quasi-quantitatively test. In this review, we identify the unique and preferred DNA-binding sites of individual metals. We show how highly sensitive and selective DNA-based sensors can be designed that contain multiple binding sites for 21 heavy metal cations that bind to DNA and change its structure, consistent with the release of the DNA-bound dye.

Study of the antimicrobial and antifouling properties of different oxide surfaces

Membrane separation processes find applications in an array of fields as they use far less energy and chemical agents than competing processes. However, a major drawback of membrane technology is that biofilm formation alters membrane performances. Preventing biofilm formation is thus a pivotal challenge for larger-scale development of membrane processes. Here, we studied the comparative antibacterial activities of different inorganic membranes (ceramic and zeolite-coated ceramic with or without copper exchange) using several bacterial strains (Escherichia coli, Staphylococcus aureus, and Bacillus subtilis). In static conditions, alumina plates coated with Cu-exchanged zeolite showed significant bactericidal activity. In dynamic mode (circulation of a contaminated nutrient medium), there was no observable bacterial adhesion at the surface of the Cu-exchanged material. These results confirm the antifouling properties of the Cu-mordenite layer due to both the increased hydrophilicity and antibacterial properties of the active layer.Tests performed with tubular filtration membranes (without copper exchange) showed a significant decline in membrane hydraulic properties during filtration of culture media containing bacteria, whereas copper-exchanged membranes showed no decline in hydraulic permeability. Filtration tests performed with concentrated culture media containing spores of B. subtilis led to a significant decrease in membrane hydraulic permeabilities (but less so with Cu-exchanged membranes). The surfaces showed less effective global antifouling properties during the filtration of a concentrated culture medium due to competition between bacterial growth and the bactericidal effect of copper. Analyses of copper leached in solution show that after a conditioning step, the amount of copper released is negligible.

Recovery of an oligonucleotide using silver ions immobilized onto paramagnetic particles

A 3'-GCCCCTTTTTAAAAACCCCG-5' oligonucleotide can be recovered from aqueous solution using paramagnetic particles containing immobilized silver ions. Binding and elution experiments were conducted by attaching either fluorescein isothiocyanate (FITC) to the 3'-end or Texas Red or fluorescein phosphoramidite (FAM) to the 5'-end of the oligonucleotide. For the 5'-end FAM labeled oligonucleotide, a binding constant of 4.2 x 10(7) was measured at pH 7 using phosphate buffer. The percent of bound FAM labeled oligonucleotide eluted from the paramagnetic particles were found to be 97% using an aqueous solution of thiodiglycol. While the FAM molecule by itself does not bind to the silver activated paramagnetic particles, the choice of fluorescent label affects binding affinities and elution recoveries.

Fibre X-ray and conformational study of the binding of metal ions on DNA

Results obtained from X-ray diffraction as well as from conformational analysis of Ag-DNA fibres are presented. For small percentages of Ag+ bound and high humidity, the B-DNA form is maintained. As the percentage of Ag+ is increased, the helical parameters of the B-DNA are modified. These modifications are directly related to the percentage of G-C bases. The periodicity of the DNA fibres are perturbed as Ag+ is mainly bound to G-C pairs and, thus, only the equatorial diffracted intensities can be compared to values calculated from molecular models. It is shown, by this way, that the first binding site is located on N7 of G. A second site is situated between N3 and N1 of the G-C pair, at the place of a hydrogen bond. A molecular model of the Ag-DNA complex is proposed and shown to be in agreement with experimental data. Results obtained allow to get some information on the binding of other ions such as Cu2+ and Hg2+ which give very little modification of the fibre X-ray patterns.

Fine structure in the thermal denaturation of DNA: high temperature-resolution spectrophotometric studies

Fine structures which appear in the optical melting profile of DNA are examined from both the experimental and theoretical aspects. After a brief historical survey of the DNA melting experiments during the pre-fine-structure era in Section II, the high temperature-resolution experimental techniques which are essential to the investigation of fine structure are described in Section III. Then, the current status of the high-resolution study is reviewed first by a phenomenological description of the melting profile (Section IV) and then of the refolding profile (Section V), where a general idea about the cooperatively melting region and several factors affecting it is given. Sections VI and VII are devoted to the review of current theoretical works. Several well-established theoretical frameworks which correlate the base sequence with the melting phenomena are examined in terms of their rigorousness and usefulness. The molecular thermodynamic parameters concerning the DNA melting which have been evaluated by several research groups are compared and discussed. Finally, in Section VIII, current ideas on the correlation between the fine structure and genetic functions and genetic maps are reviewed. Some future problems relating to the fine structure are also discussed.

Effect of mercuric and silver ions on cesium sulfate equilibrium buoyant densities of synthetic polydeoxyribonucleotides

The effect of Hg2+ and Ag+ on the buoyant density (rho) of four synthetic DNA polymers, poly[d(A-T)]; poly(dA) - poly(dT); oikt[d(G-C)]; and poly(dG) - poly(dC), was investigated. The buoyant density of poly[d(A-T)] in Cs2SO4 increased dramatically after complexing with Hg2+, but little change in the buoyant density of other polymers resulted except at very high molar ratios of Hg2+/DNA-P (rf). Hg2+ raised the thermal transition temperature (Tm) of alternating polymers and lowered the Tm of homopolymers. Measurements in the preparative ultracentrifuge indicated that lowered Tm correlated with Hg2+-induced strand separation of one homopolymer [poly(dA) - poly(dT)], but strand separation was not observed with another homopolymer [poly(dG) - poly(dC)] complexed with Hg2+. When Ag+ was mixed with the polymers, the buoyant density of poly(dG) - poly(dC) increased most markedly. A substantial increase in the buoyant density of poly[d(A-T)] and a small increase in the buoyant density of poly[d(G-C)] were also observed. The Tm changes induced by Ag+ were not related in any obvious way to buoyant density changes. These findings indicate that nucleotide sequence as well as overall base composition is of importance in understanding the buoyant density changes induced by metal ions. Although these data do not allow construction of a detailed molecular model of polymer-metal ion interactions, they may be used to explain much of the behavior of naturally occurring DNA sequences, such as heterochromatic satellite sequences and 5 S and rRNA sequences, in Hg2+/Cs2SO4 and Ag+/Cs2SO4 gradients.