Slow nucleic acid unzipping kinetics from sequence-defined barriers

Recent experiments on unzipping of RNA helix-loop structures by force have shown that ≈40-base molecules can undergo kinetic transitions between two well-defined “open” and “closed” states, on a timescale ≈1 sec [Liphardt et al., Science 297, 733-737 (2001)]. Using a simple dynamical model, we show that these phenomena result from the slow kinetics of crossing large free energy barriers which separate the open and closed conformations. The dependence of barriers on sequence along the helix, and on the size of the loop(s) is analyzed. Some DNA and RNA sequences that could show dynamics on different time scales, or three(or more)-state unzipping, are proposed. Our dynamical model is also applied to the unzipping of long (kilo-basepair) DNA molecules at constant force. Received 29 July 2002 / Received in final form 5 February 2003 Published online: 16 April 2003 RID="a" ID="a"e-mail: cocco@ldfc.u-strasbg.fr RID="b" ID="b"e-mail: jmarko@uic.edu RID="c" ID="c"e-mail: monasson@lpt.ens.fr     

Probing chromosome structure with dynamic force relaxation

We report measurements of the dynamics of force relaxation in single mitotic chromosomes, following step strains applied with micropipettes of force constant approximately 1 nN/microm. The force relaxes exponentially after an elongation (l/l(0)) to less than 3x native length, with a relaxation time approximately 2 sec. This relaxation time corresponds to an effective viscosity approximately 10(5) times that of water. We experimentally rule out solvent flow into the chromosome as the mechanism for the relaxation time. Instead, the relaxation can be explained in terms of the disentanglement dynamics of approximately 80 kb chromatin loop domains.     

Existence of weakly efficient solutions in vector optimization

In this paper, we present an existence result for weak efficient solution for the vector optimization problem. The result is stated for invex strongly compactly Lipschitz functions.     

A new material for hydrogen storage; ScAl0.8Mg0.2

A novel aluminium rich alloy for hydrogen storage has been discovered, ScAl_0.8Mg_0.2, which has very promising properties regarding hydrogen storage capacity, kinetics and stability towards air oxidation in comparison to hydrogen absorption in state-of-the-art intermetallic compounds. The absorption of hydrogen was found to be very fast, even without adding any catalyst, and reversible. The discovered alloy crystallizes in a CsCl-type structure, but decomposes to ScH₂ and Al(Mg) during hydrogen absorption. Detailed analysis of the hydrogen absorption in ScAl_0.8Mg_0.2 has been performed using in situ synchrotron radiation powder X-ray diffraction, neutron powder diffraction and quantum mechanical calculations. The results from theory and experiments are in good agreement with each other.     

Reconstitution of apomyoglobin with bile pigments

Summary Apomyoglobin was reconstituted with bile pigments of the verdinoid, 2,3-dihydroverdinoid, pterobilinoid, and violinoid type. Absorption and circular dichroism data as well as formation constants of the complexes were measured. From these results it was concluded that chromophore binding and induced chirality of these pigments are mainly governed by a lipophilic region opposite to the propionic side chain(s) and the asymmetric position of the hydrogen bonding acceptors of the propionic acid side chain(s) at the entrance of the protein pocket.Dedicated to Prof. Dr. A. Eschenmoser on occasion of his 65th birthday     

Pyridoxylidene aminoguanidine and its copper(II) complexes – Syntheses,structure, and DFT calculations

Two nitrate salts of the well-known, and due to its significant biological activity very important, compound pyridoxylidene aminoguanidine (PLAG) were obtained in the form of single crystals. Thus this ligand is structurally characterized for the first time. In addition, the first data on the structure of a Schiff base of aminoguanidine with the active form of vitamin B₆, i.e. pyridoxal-phosphate, of the formula PLPAG·HCl·2H₂O, are presented. Two new square-pyramidal Cu(II) complexes of PLAG were synthesized and their physicochemical and structural properties analyzed. In these complexes, PLAG is coordinated as a zwitter-ion, in a tridentate ONN manner, via the oxygen atom of the deprotonated phenolic OH-group and nitrogen atoms of the azomethine and imino group of the aminoguanidine moiety. For the first time it was possible to make a comparative analysis of the structural properties of ligand salts and the coordinated ligand, so the effects of coordination could be unequivocally pointed out. Common fragments encountered in ligand structures were compared by half-normal probability plots. Density functional theory calculations have been conducted in order to gain insight into reactive properties of the investigated molecules. Molecular electrostatic potential, average local ionization energy surfaces, and Fukui functions have been calculated in order to obtain further information on the reactive properties.