Metal-salen-base-pair complexes inside DNA: complexation overrides sequence information

Two isomeric salicylic aldehyde nucleobases have been prepared and incorporated into various DNA duplexes. Reaction with ethylenediamine leads to formation of the well-known salen ligand inside the DNA double helix. Addition of transition-metal ions such as Cu(2+), Mn(2+), Ni(2+), Fe(2+), or VO(2+) results in the formation of metal-salen-base-pair complexes, which were studied by using UV and circular dichroism (CD) spectroscopy. HPLC and ESI mass spectrometric measurements reveal an unusually high stability of the DNA-metal system. These metal-salen complexes act as interstrand cross-links and thereby lead to a strong stabilization of the DNA duplexes, as studied by thermal de- and renaturing experiments. Complex formation is strong enough to override sequence information even when the preorganization of the ligand precursors is unfavorable and the DNA duplex is distorted by the metal complexation. Furthermore, melting-point studies show that the salen complex derived from ligand 2 fits better into the DNA duplex, in accordance with results obtained from the crystal structure of the corresponding copper-salen complex 8.     

Synthesis and characterization of chromium(I) bis(η-toluene) derivatives containing sterically demanding anions

The reaction of Cr(η⁶-CH₃C₆H₅)₂ with 1-benzoyl-6-hydroxy-6-phenyl fulvene, dbcpH, and with pentakis(methoxycarbonyl)cyclopentadiene, pcmcpH, proceeds with evolution of dihydrogen and the formation of the ionic derivatives [Cr(η⁶-CH₃C₆H₅)₂][X] ([X]⁻ = 1,2-dibenzoylcyclopentadienyl, [dbcp]⁻, pentakis(methoxycarbonyl)cyclopentadienyl, [pcmcp]⁻), which have been characterized by IR and EPR spectroscopies, X-ray diffraction and electrochemical techniques. The sterically demanding anions do not affect the structural and electronic properties of the cations in solution but strongly influence crystal packing. In fact, a rare cis-eclipsed conformation of the toluene rings is found for [Cr(η⁶-CH₃C₆H₅)₂][dbcp] · THF, whereas two independent complexes are observed in the unit cell of [Cr(η⁶-CH₃C₆H₅)₂][pcmcp], one with toluene rings in a cis-eclipsed conformation and the other in a staggered conformation (projections of methyl groups form an angle of 151°).     

Structure determination of protein-ligand complexes by transferred paramagnetic shifts

Rational drug design depends on the knowledge of the three-dimensional (3D) structure of complexes between proteins and lead compounds of low molecular weight. A novel nuclear magnetic resonance (NMR) spectroscopy strategy based on the paramagnetic effects from lanthanide ions allows the rapid determination of the 3D structure of a small ligand molecule bound to its protein target in solution and, simultaneously, its location and orientation with respect to the protein. The method relies on the presence of a lanthanide ion in the protein target and on fast exchange between bound and free ligand. The binding affinity of the ligand and the paramagnetic effects experienced in the bound state are derived from concentration-dependent (1)H and (13)C spectra of the ligand at natural isotopic abundance. Combined with prior knowledge of the crystal or solution structure of the protein and of the magnetic susceptibility tensor of the lanthanide ion, the paramagnetic data define the location and orientation of the bound ligand molecule with respect to the protein from simple 1D NMR spectra. The method was verified with the ternary 30 kDa complex between the lanthanide-labeled N-terminal domain of the epsilon exonuclease subunit from the Escherichia coli DNA polymerase III, the subunit theta, and thymidine. The binding mode of thymidine was found to be very similar to that of thymidine monophosphate present in the crystal structure.     

The lipidated membrane anchor of full length N-Ras protein shows an extensive dynamics as revealed by solid-state NMR spectroscopy

Many proteins involved in signal transduction are equipped with covalently attached lipid chains providing a hydrophobic anchor targeting these molecules to membranes. Despite the considerable biological significance of this membrane binding mechanism for 5-10% of all cellular proteins, to date very little is known about structural and dynamical features of lipidated membrane binding domains. Here we report the first comprehensive study of the molecular dynamics of the C-terminus of membrane-associated full-length lipidated Ras protein determined by solid-state NMR. Fully functional lipid-modified N-Ras protein was obtained by chemical-biological synthesis ligating the expressed water soluble N-terminus with a chemically synthesized (2)H or (13)C labeled lipidated heptapeptide. Dynamical parameters for the lipid chain modification at Cys 181 were determined from static (2)H NMR order parameter and relaxation measurements. Order parameters describing the amplitude of motion in the protein backbone and the side chain were determined from site-specific measurements of (1)H-(13)C dipolar couplings for all seven amino acids in the membrane anchor of Ras. Finally, the correlation times of motion were determined from temperature dependent relaxation time measurements and analyzed using a modified Lipari Szabo approach. Overall, the C-terminus of Ras shows a versatile dynamics with segmental fluctuations and axially symmetric overall motions on the membrane surface. In particular, the lipid chain modifications are highly flexible in the membrane.     

Synthesis of 3-substituted 2-fluoro- and 2,2-difluoroaziridines

A new route for the synthesis of stable 3-alkyl- and 3-aryl-2(,2)-(di)fluoroaziridines was developed by hydride reduction of novel alpha-bromo- and alpha-chloro-alpha(,alpha)-(di)fluoroketimines and subsequent ring closure of beta-fluorinated beta-chloro- and beta-bromoamines. This is the first report on the synthesis of 2,2-difluoroaziridines sensu stricto.     

Equilibrium dynamics of an associating polymer melt in narrow slits by computer simulation

Molecular dynamics simulations have been used to study the dynamics of a coarse-grained model of a melt of polymer chains with associating terminal groups, confined in a narrow slit by two layers of Lennard-Jones sites. Simulations were carried out as a function of wall separation and attracting strength. We found that confinement has an important effect on the overall dynamics of the system. Strongly attracting walls can significantly modify the dynamics of the melt, giving an aggregation structure with extremely long relaxation times. A noticeable degree of anisotropy was found for the dynamics of both the individual chains and the aggregates formed by the associating terminal groups.     

Single Drop Dynamics under Shearing Flow in Systems with a Viscoelastic Phase

In this article, we discuss the dynamics of a single drop immersed in an immiscible liquid, under an imposed shear flow. The two situations of a viscoelastic matrix with a Newtonian drop and of a viscoelastic drop in a Newtonian matrix are considered, both systems being characterized by a viscosity ratio equal to one, and by the same elasticity parameter. Experimental data are taken with a rheo-optical computer-assisted shearing device, allowing for drop observation from the vorticity direction of the shear flow. Data favourably compare with predictions of the recently proposed Maffettone-Greco model, where the drop is described as a deforming ellipsoid.     

Kinetics of the dehydrochlorination of poly(vinyl chloride) in the presence of NaOH and various diols as solvents

The dehydrochlorination of PVC in the presence of NaOH was investigated in different diols. Diethylene glycol (DEG), triethylene glycol (TEG), and propylene glycol (PG) were found to be effective in accelerating the dechlorination of PVC. The dehydrochlorination was promoted in the order TEG > DEG > PG, which was in agreement with the compatibility between PET and the diol. Compatibility resulted in an improved penetration of the PVC particle by the solvent, leading to the acceleration of the dehydrochlorination. The dehydrochlorination of PVC in NaOH/diol followed first-order kinetics, confirming the progress of the reaction under chemical reaction control. The apparent activation energies were 82 kJ mol⁻¹, 109 kJ mol⁻¹, and 151 kJ mol⁻¹ for TEG, DEG, and PG, respectively. The lower the activation energy became the faster the dehydrochlorination of PVC proceeded.