The diffusion constant of a labeled protein sliding along DNA

Long ago inferred by biochemists, the linear diffusion of proteins along DNA has recently been observed at a single-molecule level using fluorescence microscopy. This imaging technique requires labeling the protein of interest with a fluorophore, usually an organic nanosized dye that is not supposed to impact the dynamics of the protein. Yet individual proteins can also be tracked using much larger labels, like quantum dots or beads. We investigate here the impact of such a large label on the protein diffusion along DNA. Solving a Fokker-Planck equation, we estimate the diffusion constant of a protein-label complex diffusing in a periodic potential that mimics the DNA-protein interaction, the link between the protein and the label being modeled as a Hookean spring. Our results indicate that the diffusion constant can generally be calculated by considering that the motion of the protein in the DNA potential is decoupled from the Brownian motion of the label. Our conclusions are in good agreement with the experimental results we obtained with the restriction enzyme EcoRV, assuming a rotation-coupled diffusion of the enzyme along DNA.     

Dissociation kinetics of Mn2+ complexes of NOTA and DOTA

The kinetics of transmetallation of [Mn(nota)](-) and [Mn(dota)](2-) was investigated in the presence of Zn(2+) (5-50-fold excess) at variable pH (3.5-5.6) by (1)H relaxometry. The dissociation is much faster for [Mn(nota)](-) than for [Mn(dota)](2-) under both experimental and physiologically relevant conditions (t(?) = 74 h and 1037 h for [Mn(nota)](-) and [Mn(dota)](2-), respectively, at pH 7.4, c(Zn(2+)) = 10(-5) M, 25 °C). The dissociation of the complexes proceeds mainly via spontaneous ([Mn(nota)](-)k(0) = (2.6 ± 0.5) × 10(-6) s(-1); [Mn(dota)](2-)k(0) = (1.8 ± 0.6) × 10(-7) s(-1)) and proton-assisted pathways ([Mn(nota)](-)k(1) = (7.8 ± 0.1) × 10(-1) M(-1) s(-1); [Mn(dota)](2-)k(1) = (4.0 ± 0.6) × 10(-2) M(-1) s(-1), k(2) = (1.6 ± 0.1) × 10(3) M(-2) s(-1)). The observed suppression of the reaction rates with increasing Zn(2+) concentration is explained by the formation of a dinuclear Mn(2+)-L-Zn(2+) complex which is about 20-times more stable for [Mn(dota)](2-) than for [Mn(nota)](-) (K(MnLZn) = 68 and 3.6, respectively), and which dissociates very slowly (k(3)～10(-5) M(-1) s(-1)). These data provide the first experimental proof that not all Mn(2+) complexes are kinetically labile. The absence of coordinated water makes both [Mn(nota)](-) and [Mn(dota)](2-) complexes inefficient for MRI applications. Nevertheless, the higher kinetic inertness of [Mn(dota)](2-) indicates a promising direction in designing ligands for Mn(2+) complexation.     

Tannin fingerprinting in vegetable tanned leather by solid state NMR spectroscopy and comparison with leathers tanned by other processes

Solid state 13C-NMR spectra of pure tannin powders from four different sources--mimosa, quebracho, chestnut and tara--are readily distinguishable from each other, both in pure commercial powder form, and in leather which they have been used to tan. Groups of signals indicative of the source, and type (condensed vs. hydrolyzable) of tannin used in the manufacture are well resolved in the spectra of the finished leathers. These fingerprints are compared with those arising from leathers tanned with other common tanning agents. Paramagnetic chromium (III) tanning causes widespread but selective disappearance of signals from the spectrum of leather collagen, including resonances from acidic aspartyl and glutamyl residues, likely bound to Cr (III) structures. Aluminium (III) and glutaraldehyde tanning both cause considerable leather collagen signal sharpening suggesting some increase in molecular structural ordering. The 2?Al-NMR signal from the former material is consistent with an octahedral coordination by oxygen ligands. Solid state NMR thus provides easily recognisable reagent specific spectral fingerprints of the products of vegetable and some other common tanning processes. Because spectra are related to molecular properties, NMR is potentially a powerful tool in leather process enhancement and quality or provenance assurance.     

Energy measurement and fragment identification using digital signals from partially depleted Si detectors

In this work we devise a new method to study quark-anti-quark interactions beyond simple ladder-exchange that yield massless pions in the chiral limit. The method is based on the requirement to have a representation of the quark-gluon vertex that is explicitly given in terms of quark dressings functions. We outline a general procedure to generate the Bethe-Salpeter kernel for a given vertex representation. Our method allows not only the identification of the mesons' masses but also the extraction of their Bethe-Salpeter wave functions exposing their internal structure. We exemplify our method with vertex models that are of phenomenological interest.     

2‐Azido‐2‐deoxycellulose: Synthesis and 1,3‐Dipolar Cycloaddition

Chitosan ( 1 ) was prepared by basic hydrolysis of chitin of an average molecular weight of 70000 Da, ¹H‐NMR spectra indicating almost complete deacetylation. N‐Phthaloylation of 1 yielded the known N‐phthaloylchitosan ( 2 ), which was tritylated to provide 3a and methoxytritylated to 3b . Dephthaloylation of 3a with NH₂NH₂?H₂O gave the 6‐O‐tritylated chitosan 4a . Similarly, 3b gave the 6‐O‐methoxytritylated 4b . CuSO₄‐Catalyzed diazo transfer to 4a yielded 95% of the azide 5a , and uncatalyzed diazo transfer to 4b gave 82% of azide 5b . Further treatment of 5a with CuSO₄ produced 2‐azido‐2‐deoxycellulose ( 7 ). Demethoxytritylation of 5b in HCOOH gave 2‐azido‐2‐deoxy‐3,6‐di‐O‐formylcellulose ( 6 ), which was deformylated to 7 . The 1,3‐dipolar cycloaddition of 7 to a range of phenyl‐, (phenyl)alkyl‐, and alkyl‐monosubstituted alkynes in DMSO in the presence of CuI gave the 1,2,3‐triazoles 8 – 15 in high yields.     

Solid-phase organic tagging resins for labeling biomolecules by 1,3-dipolar cycloaddition: application to the synthesis of a fluorescent non-peptidic vasopressin receptor ligand

Two novel solid-phase organic tagging (SPOrT) resins were synthesized to facilitate the labeling of peptides and small organic compounds with a fluorescent probe. Both resins were obtained from the commercially available backbone amide linker (BAL) resin. Following the solid-phase synthesis of model compounds, a tripeptide and benzazepine, the fluorescent probe derived from Lissamine Rhodamine B was incorporated through CuI-catalyzed 1,3-dipolar cycloaddition. Final cleavage in acidic media enabled access to both types of molecules in good yield with high purity. The SPOrT resin was successfully applied to the preparation of the first non-peptidic fluorescent compound with a nanomolar affinity for the human vasopressin V2 receptor (V2R) subtype. This molecule will find application in binding assays that use polarization or fluorescence resonance energy-transfer (FRET) techniques. The SPOrT resins are also well suited for other tags and the parallel synthesis of a fluorescently tagged library for protein screening.     

A two-step spin crossover mononuclear iron(II) complex with a [HS-LS-LS] intermediate phase

The two-step spin crossover of a new mononuclear iron(ii) complex is studied by magnetic, crystallographic and calorimetric methods revealing two successive first-order phase transitions and an ordered intermediate phase built by the repetition of the unprecedented [HS-LS-LS] motif.     

Photochemistry synthesis. Part 2: Enantiomerically pure polyhydroxy-1,1,3-triarylpropan-2-ols

A new method to open the heterocyclic ring of flavan-3-ols via photolytic cleavage of the ether bond, with stereoselective trapping of the intermediates with phloroglucinol to obtain phloroglucinol grafted derivatives of flavan-3-ols, was developed. Photolysis of catechin and epicatechin, respectively, in the presence of phloroglucinol yielded the enantiomeric (1S,2S)- and (1R,2R)-1,3-di(2,4,6-trihydroxyphenyl)-1-(3,4-dihydroxyphenyl)propan-2-ols, respectively. The absolute configuration at C-1 and C-2 was determined by electronic circular dichroism (experimental and calculated) and these results confirmed that the trapping mechanism is controlled by the C-3 configuration of the flavan-3-ol.     

Dynamical study of H2 and D2 desorbing from a Cu(111) surface

A theoretical study of H(2) and D(2) desorbing from Cu(111) is reported. The study makes use of the LEPS PES of Dai and Zhang [J. Chem. Phys. 1995, 102, 6280]. The LEPS parameters have been modified in order to lower the barrier threshold in conformity with accurate ab initio electronic structure calculations. The topological study of the modified PES by the CHAIN method reveals unambiguously that the transition state (TS) is located at the top of a unique early barrier along the desorption path. The adsorbed H atoms are supposed to be in thermal equilibrium with the metal surface. Batches of classical trajectories (CT) are then carried out from the TS onto the products with their initial conditions canonically distributed and the effect of their possible recrossing of the TS taken into account according to Keck's method [Discuss. Faraday Soc. 1962, 33, 173]. Product state distributions are then calculated using the Gaussian weighting procedure [Chem. Phys. Lett. 2004, 397, 106] to account for the quantization of the vibration motion of the desorbed diatom. These distributions are in overall good agreement with experimental measurements. On average, the early barrier to desorption results in a significant vibrational excitation of the final diatom and a strong deexcitation of its rotational angular momentum J from the TS onto the products. Moreover, the orientation of the rotation plane is roughly random for low values of J (both cartwheel and helicopter motions are observed) while it is more likely parallel to the metal surface for large values of J (predominance for helicopter motion). These findings are analyzed in some details.