Pierre Colson

G-quadruplex DNA assemblies: loop length, cation identity, and multimer formation.

G-rich DNA sequences are able to fold into structures called G-quadruplexes. To obtain general trends in the influence of loop length on the structure and stability of G-quadruplex structures, we studied oligodeoxynucleotides with random bases in the loops. Sequences studied are dGGGW(i)GGGW(j)GGGW(k)GGG, with W = thymine or adenine with equal probability, and i, j, and k comprised between 1 and 4. All were studied by circular dichroism, native gel electrophoresis, UV-monitored thermal denaturation, and electrospray mass spectrometry, in the presence of 150 mM potassium, sodium, or ammonium cations. Parallel conformations are favored by sequences with short loops, but we also found that sequences with short loops form very stable multimeric quadruplexes, even at low strand concentration. Mass spectrometry reveals the formation of dimers and trimers. When the loop length increases, preferred quadruplex conformations tend to be more intramolecular and antiparallel. The nature of the cation also has an influence on the adopted structures, with K(+) inducing more parallel multimers than NH4(+) and Na(+). Structural possibilities are discussed for the new quadruplex higher-order assemblies.

Well Shaped Mn 3 O 4 Nano-octahedra with Anomalous Magnetic Behavior and Enhanced Photodecomposition Properties

Very uniform and well shaped Mn₃O₄ nano-octahedra are synthesized using a simple hydrothermal method under the help of polyethylene glycol (PEG200) as a reductant and shape-directing agent. The nano-octahedra formation mechanism is monitored. The shape and crystal orientation of the nanoparticles is reconstructed by scanning electron microscopy and electron tomography, which reveals that the nano-octahedra only selectively expose {101} facets at the external surfaces. The magnetic testing demonstrates that the Mn₃O₄ nano-octahedra exhibit anomalous magnetic properties: the Mn₃O₄ nano-octahedra around 150 nm show a similar Curie temperature and blocking temperature to Mn₃O₄ nanoparticles with 10 nm size because of the vertical axis of [001] plane and the exposed {101} facets. With these Mn₃O₄ nano-octahedra as a catalyst, the photodecomposition of rhodamine B is evaluated and it is found that the photodecomposition activity of Mn₃O₄ nano-octahedra is much superior to that of commercial Mn₃O₄ powders. The anomalous magnetic properties and high superior photodecomposition activity of well shaped Mn₃O₄ nano-octahedra should be related to the special shape of the nanoparticles and the abundantly exposed {101} facets at the external surfaces. Therefore, the shape preference can largely broaden the application of the Mn₃O₄ nano-octahedra.

Nanosphere lithography: a powerful method for the controlled manufacturing of nanomaterials

The never-ending race towards miniaturization of devices induced an intense research in the manufacturing processes of the components of those devices. However, the complexity of the process combined with high equipment costs makes the conventional lithographic techniques unfavorable formany researchers. Through years, nanosphere lithography (NSL) attracted growing interest due to its compatibility with wafer-scale processes as well as its potential to manufacture a wide variety of homogeneous one-, two-, or three-dimensional nanostructures. This method combines the advantages of both top-down and bottom-up approaches and is based on a two-step process: (1) the preparation of a colloidal crystal mask (CCM) made of nanospheres and (2) the deposition of the desired material through the mask. The mask is then removed and the layer keeps the ordered patterning of the mask interstices. Many groups have been working to improve the quality of the CCMs. Throughout this review, we compare the major deposition techniques to manufacture the CCMs (focusing on 2D polystyrene nanospheres lattices), with respect to their advantages and drawbacks. In traditional NSL, the pattern is usually limited to triangular structures. However, new strategies have been developed to build up more complex architectures and will also be discussed.

Characterization of a Novel DNA Minor-Groove Complex

Many dicationic amidine compounds bind in the DNA minor groove and have excellent biological activity against a range of infectious diseases. Para-substituted aromatic diamidines such as furamidine, which is currently being tested against trypanosomiasis in humans, and berenil, which is used in animals, are typical examples of this class. Recently, a meta-substituted diamidine, CGP 40215A, has been found to have excellent antitrypanosomal activity. The compound has a linear, conjugated linking group that can be protonated under physiological conditions when the compound interacts with DNA. Structural and molecular dynamics analysis of the DNA complex indicated an unusual AT-specific complex that involved water-mediated H-bonds between one amidine of the compound and DNA bases at the floor of the minor groove. To investigate this unique system in more detail DNase I footprinting, surface plasmon resonance biosensor techniques, linear dichroism, circular dichroism, ultraviolet-visible spectroscopy, and additional molecular dynamics simulations have been conducted. Spectrophotometric titrations of CGP 40215A binding to poly(dAT)(2) have characteristics of DNA-binding-induced spectral changes as well as effects due to binding-induced protonation of the compound linker. Both footprinting and surface plasmon resonance results show that this compound has a high affinity for AT-rich sequences of DNA but very weak binding to GC sequences. The dissociation kinetics of the CGP 40215A-DNA complex are much slower than with similar diamidines such as berenil. The linear dichroism results support a minor-groove complex for the compound in AT DNA sequences. Molecular dynamics studies complement the structural analysis and provide a clear picture of the importance of water in mediating the dynamic interactions between the ligand and the DNA bases in the minor groove.

Electric linear dichroism as a new tool to study sequence preference in drug binding to DNA

An original approach using electric linear dichroism (ELD) and natural DNAs and polynucleotides of differing base composition has been developed with the aim to investigate the sequence-dependent recognition of DNA by drugs. Both intercalators and minor groove binders have been studied as well as certain hybrid molecules. The results indicate that the orientation of drugs upon binding to nucleic acids can change markedly according to the target sequence. Among the intercalators tested, only actinomycin D and hycanthone show a clear preference for GC- and AT-rich sequences, respectively. For minor groove binders, the linear dichroism showing a strong dependence on base composition of the DNA and polynucleotides is most pronounced. Netropsin and distamycin bind to DNA with a marked AT specificity. Hoechst 33258, berenil and DAPI exhibit positive and negative dichroism signals at AT and GC sites respectively, suggesting that at least two types of drug-DNA interaction are involved depending on the AT/GC content of the DNA. Further investigations using polynucleotides with inosine substituted for guanosine, and competition experiments with intercalative drugs suggest that Hoechst 33258, berenil and DAPI interact with GC sequences via a non-classical intercalation process.

Experimental Design applied to spin coating of 2D colloidal crystal masks : a relevant method?

Monolayers of colloidal spheres are used as masks in nanosphere lithography (NSL) for the selective deposition of nanostructured layers. Several methods exist for the formation of self-organized particle monolayers, among which spin coating appears to be very promising. However, a spin coating process is defined by several parameters like several ramps, rotation speeds, and durations. All parameters influence the spreading and drying of the droplet containing the particles. Moreover, scientists are confronted with the formation of numerous defects in spin coated layers, limiting well-ordered areas to a few micrometers squared. So far, empiricism has mainly ruled the world of nanoparticle self-organization by spin coating, and much of the literature is experimentally based. Therefore, the development of experimental protocols to control the ordering of particles is a major goal for further progress in NSL. We applied experimental design to spin coating, to evaluate the efficiency of this method to extract and model the relationships between the experimental parameters and the degree of ordering in the particles monolayers. A set of experiments was generated by the MODDE software and applied to the spin coating of latex suspension (diameter 490 nm). We calculated the ordering by a homemade image analysis tool. The results of partial least squares (PLS) modeling show that the proposed mathematical model only fits data from strictly monolayers but is not predictive for new sets of parameters. We submitted the data to principal component analysis (PCA) that was able to explain 91% of the results when based on strictly monolayered samples. PCA shows that the ordering was positively correlated to the ramp time and negatively correlated to the first rotation speed. We obtain large defect-free domains with the best set of parameters tested in this study. This protocol leads to areas of 200 μm(2), which has never been reported so far.

Terbium(3+) as a probe of nucleic acids structure. Does it alter the DNA conformation in solution?

At low ionic strength, Tb3+ binding strongly alters the secondary structure of DNA. Circular dichroism and electro-optical techniques are more sensitive than fluorescence to study these alterations in double-stranded DNA, at low Tb3+/DNA phosphate (I/P) ratios. Both techniques yield the following conclusion: as I/P is increased, native and sonicated DNA undergo a transition from the B- to psi-form, the latter being a compact structure characteristic of aggregated DNA. Our study of alkylated DNA establishes that the accessibility of N-7 guanine to Tb3+ is clearly required for structural alterations in an aggregated state to occur. The chelation of the phosphate group and of the N-7 guanine by Tb3+ simultaneously alters the geometry of the sugar-phosphate backbone and the stacking interaction between the bases in double-stranded DNA.

Effect of organic effectors on chromatin solubility, DNA-histone H1 interactions, DNA and histone H1 structures

We have extended our previous investigations on the effect of organic osmolytes (glycine, proline, taurine, mannitol, sorbitol and trimethylammonium oxide (TMAO)) on chromatin solubility, to the study of their influence on DNA stability and DNA-histone interactions. Our aim was to understand the molecular origin of the protection effects observed. To this end, we determined the amount of histone H1 required to precipitate DNA or H1-depleted chromatin, at various salt concentrations, in the presence of the above mentioned organic compounds. We found a shift of the H1/DNA ratio required to reach 50% precipitation, towards higher values. Taurine was the most efficient compound followed by mannitol and glycine, then sorbitol and proline. On the contrary, TMAO favoured the precipitation process. We attempted to interpret these results on the basis of Mannings counterion condensation theory. Changes in histone H1 structure folding and in DNA melting temperature Tm were also analyzed. Glycine, taurine, sorbitol and TMAO increased the degree of secondary structure folding of the protein while mannitol and sorbitol had no effect. Taurine, glycine and proline decreased the Tm of DNA, TMAO largely destabilized DNA, but mannitol and sorbitol had no effect. Measurements of NaCl activity in the presence of organic osmolytes did not reveal sufficiently large changes to account for their protection effect against chromatin precipitation. The osmotic coefficient j of the organic effectors solutions increased in the order: taurine < glycine < sorbitol < mannitol < proline << TMAO. For the two latter compounds, the j values increased above 1 at high concentration. We consider that the organic compounds investigated may be classified into three categories: (i) class I (zwitterionic compounds: glycine, proline, taurine) would produce sodium ions release from the DNA surface; (ii) class II (the very polar molecule TMAO) would increase sodium counterions condensation on DNA together with histone H1 folding; (iii) class III compounds (mannitol and sorbitol) would possibly produce a modification of NaCl activity but no definite explanation could be found for the complex behavior of these compounds.

Induction of unique structural changes in guanine-rich DNA regions by the triazoloacridone C-1305, a topoisomerase II inhibitor with antitumor activities

We recently reported that the antitumor triazoloacridone, compound C-1305, is a topoisomerase II poison with unusual properties. In this study we characterize the DNA interactions of C-1305 in vitro, in comparison with other topoisomerase II inhibitors. Our results show that C-1305 binds to DNA by intercalation and possesses higher affinity for GC- than AT-DNA as revealed by surface plasmon resonance studies. Chemical probing with DEPC indicated that C-1305 induces structural perturbations in DNA regions with three adjacent guanine residues. Importantly, this effect was highly specific for C-1305 since none of the other 22 DNA interacting drugs tested was able to induce similar structural changes in DNA. Compound C-1305 induced stronger structural changes in guanine triplets at higher pH which suggested that protonation/deprotonation of the drug is important for this drug-specific effect. Molecular modeling analysis predicts that the zwitterionic form of C-1305 intercalates within the guanine triplet, resulting in widening of both DNA grooves and aligning of the triazole ring with the N7 atoms of guanines. Our results show that C-1305 binds to DNA and induces very specific and unusual structural changes in guanine triplets which likely plays an important role in the cytotoxic and antitumor activity of this unique compound.

The Condensation of Chromatin and Histone Hl-Depleted Chromatin By Spermine

At low ionic strength, spermine induces aggregation of native and H1-depleted chromatin at spermine/phosphate (Sp/P) ratios of 0.15 and 0.3, respectively. Physico-chemical methods (electric dichroism, circular dichroism and thermal denaturation) show that spermine, at Sp/P less than 0.15, does not appreciably alter the conformation of native chromatin and interacts unspecifically with all parts of chromatin DNA (linker as well as regions slightly or tightly bound to histones). In chromatin, the role of spermine could be more important in the stabilization of higher-order structure than in the condensation of the 30 nm solenoid. The addition of spermine to H1-depleted chromatin revealed two important features: (i) spermine can partially mimic the role of histone H1 in the condensation of chromatin; (ii) the core histone octamer does not appear to play any role in the aggregation process by spermine as DNA and H1-depleted chromatin aggregate at the same Sp/P ratio.