Binding of Net-Fla,a Netropsin-Flavin Hybrid Molecule,to DNA: Molecular Mechanics and Dynamics Studies in vacuo and in Water Solution

Abstract

We have studied the binding of the hybrid netropsin-flavin (Net-Fla) molecule onto four sequences containing four A.T base pairs. Molecular mechanics minimizations in vacuo show numerous minimal conformations separated by one base pair. 400 ps molecular dynamics simulations in vacuo have been performed using the lowest minima as the starting conformations. During these simulations, the flavin moiety of the drug makes two hydrogen bonds with an amino group of a neighboring guanine. A 200 ps molecular dynamics simulation in explicit water solution suggests that the binding of Net-Fla upon the DNA substrate is enhanced by water bridges. A water molecule bridging the amidinium of Net-Fla to the N3 atom of an adenine seems to be stuck in the dmg-DNA complex during the whole simulation. The fluctuations of the DNA helical parameters and of the torsion angles of the sugar-phosphate backbone are very similar in the simulations in vacuo and in water. The time auto-correlation functions for the DNA helical parameters decrease rapidly in the picosecond range in vacuo. The same functions computed from the water solution molecular dynamics simulations seem to have two modes: the rapid mode is similar to the behavior in vacuo, and is followed by a slower mode in the 10 ps range.     

Comparaisons des séquences d'ADN hautement répétées chez l'homme et diverses espèces de primates

Highly repeated DNA sequences from man, five other primate species and rat were compared using five restriction endonucleases. Calculations of a similarity index based on the mobility of various bands indicate that man, chimpanzee and baboons are very similar. The sequences of the genomes studied have apparently been reorganized during primate evolution.     

Interfacial Susceptibilities in Nanoplasmonics via Inversion of Fresnel Coefficients

The reflection coefficients of a nanoparticle film are driven to a large extent by perpendicular and parallel interfacial susceptibilities that have the meaning of “dielectric thicknesses” which combine the actual geometry of the film and its dielectric properties. The direct determination of these parameters faces the long-standing issue of the derivation of complex optical constants from Fresnel coefficients via a unique spectroscopic measurement. The present work sets up an iterative algorithm based on inversion of the reflection coefficients recorded in the UV–visible range for two polarization states s and p and Kramers–Kronig (KK) analysis. To calculate the KK integrals over a limited energy window, the strategy was to complement measurements by spectra calculated in the framework of the spheroidal dipole approximation. The algorithm has been successfully tested on synthetic data of differential reflectivity for supported truncated spheres. These were chosen to span different dielectric behaviors, involving (a) for the particles, metals whose optical response is dominated by plasmonic excitations with a noticeable Drude behavior (Ag and Au) and (b) for the substrate, either nonabsorbing wide bandgap (alumina) or semiconducting (zincite and titania) oxides. Unlike the thin plate model, the approach was proven to apply to “dielectric thicknesses” of several tens of nanometres in cases in which, even for geometric sizes of the order of the nanometer, the classical long-wavelength dielectric approximation fails because of strong plasmon resonances. Therefore, the disentanglement of dielectric behaviors along the parallel and perpendicular directions simplifies the understanding on the interface polarization process by removing substrate contribution. The present work that deals with plasmonics in nanoparticles can be easily generalized to different morphologies as well as to other combinations of Fresnel coefficients.     

Expression Patterns and Potential Biological Roles of Dip2a

Disconnected (disco)-interacting protein 2 homolog A is a member of the DIP2 protein family encoded by Dip2a gene. Dip2a expression pattern has never been systematically studied. Functions of Dip2a in embryonic development and adult are not known. To investigate Dip2a gene expression and function in embryo and adult, a Dip2a-LacZ mouse model was generated by insertion of β-Gal cDNA after Dip2a promoter using CRISPR/Cas9 technology. Dip2a-LacZ mouse was designed to be a lacZ reporter mouse as well as a Dip2a knockout mouse. Heterozygous mice were used to study endogenous Dip2a expression and homozygotes to study DIP2A-associated structure and function. LacZ staining indicated that Dip2a is broadly expressed in neuronal, reproductive and vascular tissues, as well as in heart, kidney, liver and lung. Results demonstrate that Dip2a is expressed in ectoderm-derived tissues in developing embryos. Adult tissues showed rich staining in neurons, mesenchymal, endothelial, smooth muscle cells and cardiomyocytes by cell types. The expression pattern highly overlaps with FSTL1 and supports previous report that DIP2A to be potential receptor of FSTL1 and its protective roles of cardiomyocytes. Broad and intense embryonic and adult expression of Dip2a has implied their multiple structural and physiological roles.     

Action de solvants basiques sur le spectre d'absorptiou des complexes pigmentes extraits de la bactérie pourpre Rhodospirillum rubrum

Absorption spectrum of Rhodospirillum rubout pigment complexes in basic solvents. — The adsorption and aggregation of bacteriochlorophyll are studied in various polar solvents, at different concentrations. It is shown that 3 absorption bands exist in these conditions, duplicating 3 of the absorption bands found in vivo: the 772 nin, the 830 nm and the 890 nm-bands. The 800 nm-band cannot be formed in vitro. The relations between the respective concentrations of the 3 states of bacteriochlorophyll found In vitro are calculated and discussed.