Knots in Charged Polymers

The interplay of topological constraints and Coulomb interactions in static and dynamic properties of charged polymers is investigated by numerical simulations and scaling arguments. In the absence of screening, the long-range interaction localizes irreducible topological constraints into tight molecular knots, while composite constraints are factored and separated. Even when the forces are screened, tight knots may survive as local (or even global) equilibria, as long as the overall rigidity of the polymer is dominated by the Coulomb interactions. As entanglements involving tight knots are not easy to eliminate, their presence greatly influences the relaxation times of the system. In particular, we find that tight knots in open polymers are removed by diffusion along the chain, rather than by opening up. The knot diffusion coefficient actually decreases with its charge density, and for highly charged polymers the knot's position appears frozen.Comment: Revtex4, 9 pages, 9 eps figure

Evaluation intégrée des mesures agro-environnementales territorialisées à enjeu "qualité des eaux" sur la période 2007 à 2011 : le projet MAEVEAU

The MAEVEAU project has developed an approach for an integrated assessment of effectiveness of regionalized Agro-Environmental Measures (MAET) intended to preserve water quality in relation to pesticides. This approach investigates the concept of efficiency through a triple analysis: the impact (net effects), the environmental cost-effectiveness and the role of organizational factors in the contracting process. The impact is assessed by a quasi-experimental approach by counterfactuals and examines adaptation of the matching method to the regionalized MAET. Cost-effectiveness analysis is based on integrated modeling spatially distributed coupling the agro-hydrological SWAT model, pesticides pressure indicators and a bio-economic model optimizing gross margin. The effectiveness of organizational factors focuses on transaction costs, the role of collective action and preferences for alternative contracts.La recherche conduite dans le projet MAEVEAU a développé une démarche d'évaluation intégrée de l'efficacité des Mesures Agro-Environnementales Territorialisées (MAET) à enjeu préservation de la qualité de l'eau vis-à-vis des pesticides sur la période 2007 à 2011. La question scientifique traite le concept d'efficacité de la politique en s'appuyant sur une triangulation des approches: une évaluation de l'impact (c'est-à-dire des effets propres de la politique), une évaluation coût-efficacité environnementale et une évaluation du rôle des facteurs organisationnels dans le processus d'adhésion. L'impact est évalué par une approche quasi-expérimentale par contrefactuel et questionne l'adaptation de la méthode du matching à la territorialisation des MAET. L'analyse coût-efficacité s'appuie sur une modélisation intégrée spatialisée couplant modèle agro-hydrologique, indicateurs pesticides spatialisés et optimisation économique des marges brutes. L'efficacité des facteurs organisationnels s'est intéressée aux coûts de transaction, au rôle de l'action collective et aux préférences pour des contrats alternatifs

Measuring, in solution, multiple-fluorophore labeling by combining Fluorescence Correlation Spectroscopy and photobleaching

Determining the number of fluorescent entities that are coupled to a given molecule (DNA, protein, etc.) is a key point of numerous biological studies, especially those based on a single molecule approach. Reliable methods are important, in this context, not only to characterize the labeling process, but also to quantify interactions, for instance within molecular complexes. We combined Fluorescence Correlation Spectroscopy (FCS) and photobleaching experiments to measure the effective number of molecules and the molecular brightness as a function of the total fluorescence count rate on solutions of cDNA (containing a few percent of C bases labeled with Alexa Fluor 647). Here, photobleaching is used as a control parameter to vary the experimental outputs (brightness and number of molecules). Assuming a Poissonian distribution of the number of fluorescent labels per cDNA, the FCS-photobleaching data could be easily fit to yield the mean number of fluorescent labels per cDNA strand (@ 2). This number could not be determined solely on the basis of the cDNA brightness, because of both the statistical distribution of the number of fluorescent labels and their unknown brightness when incorporated in cDNA. The statistical distribution of the number of fluorophores labeling cDNA was confirmed by analyzing the photon count distribution (with the cumulant method), which showed clearly that the brightness of cDNA strands varies from one molecule to the other.Comment: 38 pages (avec les figures

Intramolecular Folding in Human ILPR Fragment with Three C-Rich Repeats

Enrichment of four tandem repeats of guanine (G) rich and cytosine (C) rich sequences in functionally important regions of human genome forebodes the biological implications of four-stranded DNA structures, such as G-quadruplex and i-motif, that can form in these sequences. However, there have been few reports on the intramolecular formation of non-B DNA structures in less than four tandem repeats of G or C rich sequences. Here, using mechanical unfolding at the single-molecule level, electrophoretic mobility shift assay (EMSA), circular dichroism (CD), and ultraviolet (UV) spectroscopy, we report an intramolecularly folded non-B DNA structure in three tandem cytosine rich repeats, 5'-TGTC4ACAC4TGTC4ACA (ILPR-I3), in the human insulin linked polymorphic region (ILPR). The thermal denaturation analyses of the sequences with systematic C to T mutations have suggested that the structure is linchpinned by a stack of hemiprotonated cytosine pairs between two terminal C4 tracts. Mechanical unfolding and Br2 footprinting experiments on a mixture of the ILPR-I3 and a 5′-C4TGT fragment have further indicated that the structure serves as a building block for intermolecular i-motif formation. The existence of such a conformation under acidic or neutral pH complies with the strand-by-strand folding pathway of ILPR i-motif structures