Detection of conformational and net charge differences in DNA-protein complexes by quantitative electrophoresis on polyacrylamide-agarose copolymer gels

The Galactosidase repressor (GalR) of Escherichia coli modulates the expression of the gal operon by binding to two DNA operators, OE and O1. The OE and O1 elements are 16 bp pallindromic DNA sequences, differing in four of the base pairs. OE and O1 DNA fragments, both free and complexed with repressor, were analyzed by "quantitative gel electrophoresis". By the criteria of that method, applied to the linear Ferguson plots of both DNA fragments and the linear ranges of those of the DNA-GalR complexes, it was shown that the apparent size of DNA increases upon repressor binding. Moreover, this size increase is greater for the complex with the O1 operator than for the complex with the OE operator in the case that GalR is located in the center of a 155 bp DNA fragment. This is not the case when GalR is located in a peripheral position. By contrast with their size differences, the centrally located GalR-O1 and GalR-OE complexes appear to possess indistinguishable net surface charge densities as judged from the intercepts with the mobility axis. The larger size of the complex with centrally located O1 fragment, as compared with that bearing the OE fragment, is interpreted as being due to bending of the DNA-protein complex, since an authentically bent fragment of a plasmid with bent upstream activator sequence also exhibits a larger slope of the Ferguson plot, and thus the larger size, than predicted on the basis of its DNA chain length (bp).(ABSTRACT TRUNCATED AT 250 WORDS)     

Thermal studies on copper(II)-5,5′-thiodisalicylic acid complexes

Aquo, ammonia and pyridine complexes of copper(II) with 5,5-thiodisalicylic acid have been investigated by TG and DTG. All these complexes decompose in three distinct steps, viz. dehydration, loss of axial bases and decarboxylation of the aromatic ligand. The thermal curves of the aquo and pyridine complexes show water loss in two distinct steps. The decreasing order of thermal stability of the complexes is py > NH₃ > H₂O.

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Zusammenfassung Aquo-, Ammoniak- und Pyridinkomplexe von Kupfer(II) mit 5,5-Thiodisalicylsäure wurden durch TG und DTG untersucht. Diese Komplexe werden in den drei Stufen, Dehydratisierung, Verlust axialer Basen und Decarboxylierung des aromatischen Liganden zersetzt. Die Abbaukurven der Aquo- und Pyridinkomplexe zeigen einen Wasserverlust in zwei Stufen. Die abnehmende Reihenfolge der Thermostabilität der Komplexe ist py > NH₃ > H₂O.

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, (II) 5,5- . , : , . - , . : > NH₃ > ₂.

     

Lasing without population inversion in molecules

We have described here the physical basis for lasing without population inversion (LWOPI). This type of amplification is obtained basically by two mechanisms: (i) one is based on atomic interference and (ii) the other is based on Fano-type interference. We have shown here, in H₂ molecules, amplification without population inversion is feasible by considering both the mechanisms.     

Spectroscopic and DFT investigation of [M{HB(3,5-iPr2pz)3}(SC6F5)] (M = Mn, Fe, Co, Ni, Cu, and Zn) model complexes: periodic trends in metal-thiolate bonding

A series of metal-varied [ML(SC6F5)] model complexes (where L = hydrotris(3,5-diisopropyl-1-pyrazolyl)borate and M = Mn, Fe, Co, Ni, Cu, and Zn) related to blue copper proteins has been studied by a combination of absorption, MCD, resonance Raman, and S K-edge X-ray absorption spectroscopies. Density functional calculations have been used to characterize these complexes and calculate their spectra. The observed variations in geometry, spectra, and bond energies are interpreted in terms of changes in the nature of metal-ligand bonding interactions. The metal 3d-ligand orbital interaction, which contributes to covalent bonding in these complexes, becomes stronger going from Mn(II) to Co(II) (the sigma contribution) and to Cu(II) (the pi contribution). This change in the covalency results from the increased effective nuclear charge of the metal atom in going from Mn(II) to Zn(II) and the change in the 3d orbital populations (d5-->d10). Ionic bonding also plays an important role in determining the overall strength of the ML(+)-SC6F5(-) interaction. However, there is a compensating effect: as the covalent contribution to the metal-ligand bonding increases, the ionic contribution decreases. These results provide insight into the Irving-Williams series, where it is found that the bonding of the ligand being replaced by the thiolate makes a major contribution to the observed order of the stability constants over the series of metal ions.     

Shorter argentophilic interaction than aurophilic interaction in a pair of dimeric {(NHC)MCl}(2) (M = Ag, Au) complexes supported over a N/O-functionalized N-heterocyclic carbene (NHC) ligand

Synthesis, structure, bonding, and photoluminescence studies of a pair of neutral dimeric silver and gold complexes of a N/O-functionalized N-heterocyclic carbene ligand exhibiting closed-shell d10...d10 argentophilic and aurophilic interactions, are reported. In particular, dimeric complexes of the type {[1-(benzyl)-3-(N-tert-butylacetamido)imidazol-2-ylidene]MCl}2 [M = Ag (2); Au (3)] displayed attractive metallophilic interaction in the form of a close ligand-unsupported metal...metal contact [3.1970(12) A in 2; 3.2042(2) A in 3] as observed from X-ray diffraction study and also was further verified by low temperature photoluminescence study at 77 K that showed the characteristic emission [527 nm for 2; 529 nm for 3] owing to the metal...metal interaction. The nature of the metallophilic interaction in these complexes was further probed using computational studies that estimated the metal...metal interaction energy to be 12.8 (2) and 8.6 kcal/mol (3). Notably, the argentophilic interaction was found to be stronger than the aurophilic interaction in this series of neutral dimeric complexes. The complexes 2 and 3 were synthesized sequentially, with the silver 2 complex prepared by the reaction of the 1-(benzyl)-3-(N-tert-butylacetamido)imidazolium chloride with Ag2O in 66% yield, while the gold 3 complex was obtained by the transmetallation reaction of the silver 2 complex with (SMe2)AuCl in 86% yield.     

Synthesis of panchromatic Ru(II) thienyl-dipyrrin complexes and evaluation of their light-harvesting capacity

Ru(II) complexes with 5-(3-thienyl)-4,6-dipyrrin (3-TDP), containing 2,2'-bipyridine (bpy) or 4,4'-bis(methoxycarbonyl)-2,2'-bipyridine (dcmb) as coligands, have been prepared and extensively characterized. Crystal structure determination of [Ru(bpy)(2)(3-TDP)]PF(6) (1a) and [Ru(bpy)(3-TDP)(2)] (2) reveals that the 3-thienyl substituent is rotated with respect to the plane of the dipyrrinato moiety. These complexes, as well as [Ru(dcmb)(2)(3-TDP)]PF(6) (1b), act as panchromatic light absorbers in the visible range, with two strong absorption bands observable in each case. A comparison to known Ru(II) complexes and quantum-chemical calculations at the density functional theory (DFT) level indicate that the lower-energy band is due to metal-to-ligand charge transfer (MLCT) excitation, although the frontier occupied metal-based molecular orbitals (MOs) contain significant contributions from the 3-TDP moiety. The higher energy band is assigned to the π-π* transition of the 3-TDP ligand. Each complex exhibits an easily accessible one-electron oxidation. According to DFT calculations and spectroelectrochemical experiments, the first oxidation takes place at the Ru(II) center in 1a, but is shifted to the 3-TDP ligand in 1b. An analysis of MO energy diagrams suggests that complex 1b has potential to be used for light harvesting in the dye-sensitized (Gr?tzel) solar cell.     

Spectroscopic studies of the Met182Thr mutant of nitrite reductase: role of the axial ligand in the geometric and electronic structure of blue and green copper sites

A combination of spectroscopic methods and density functional calculations has been used to describe the electronic structure of the axial mutant (Met182Thr) of Rhodobacter sphaeroides nitrite reductase in which the axial methionine has been changed to a threonine. This mutation results in a dramatic change in the geometric and electronic structure of the copper site. The electronic absorption data imply that the type 1 site in the mutant is like a typical blue copper site in contrast to the wild-type site, which is green. Similar ligand field strength in the mutant and the wild type (from MCD spectra) explains the similar EPR parameters for very different electronic structures. Resonance Raman shows that the Cu-S(Cys) bond is stronger in the mutant relative to the wild type. From a combination of absorption, CD, MCD, and EPR data, the loss of the strong axial thioether (present in the wild-type site) results in an increase of the equatorial thiolate-Cu interaction and the site becomes less tetragonal. Spectroscopically calibrated density functional calculations were used to provide additional insight into the role of the axial ligand. The calculations reproduce well the experimental ground-state bonding and the changes in going from a green to a blue site along this coupled distortion coordinate. Geometry optimizations at the weak and strong axial ligand limits show that the bonding of the axial thioether is the key factor in determining the structure of the ground state. A comparison of plastocyanin (blue), wild-type nitrite reductase (green), and the Met182Thr mutant (blue) sites enables evaluation of the role of the axial ligand in the geometric and electronic structure of type 1 copper sites, which can affect the electron-transfer properties of these sites.     

Thermal behaviour of copper oxalate and its mixed ligand complexes with amines

The thermal decomposition behaviour of copper oxalate hemihydrate and its complexes with different amines has been studied by TG and DTA methods in nitrogen and air atmospheres. The complexes CuC₂O4 · 0.5 H₂O, CuC₂O₄(NH₃)₂ and CuC₂O₄(py) produced Cu₂O as final residue after decomposition, whereas, another group of complexes, CuC₂O₄(EtNH₂)₂, CuC₂O₄(MeNH₂)₂, CuC₂O₄(en)₂ and CuC₂O₄(An)₂, gave a final residue of CuO. All the complexes decomposed without forming any isolable stable intermediate; an exception was CuC₂O₄(en)₂, which formed a binuclear intermediate complex, [CuC₂O₄en]₂.     

Spectroscopic and density functional theory studies of the blue-copper site in M121SeM and C112SeC azurin: Cu-Se versus Cu-S bonding

S K-edge X-ray absorption, UV-vis absorption, magnetic circular dichroism (MCD), and resonance Raman spectroscopies are used to investigate the electronic structure differences among WT, M121SeM, and C112SeC Pseudomonas aeruginosa (P.a) azurin. A comparison of S K-edge XAS of WT and M121SeM azurin and a CuII-thioether model complex shows that the 38% S character in the ground state wave function of the blue-copper (BC) sites solely reflects the Cu-SCys bond. Resonance Raman (rR) data on WT and C112SeC azurin give direct evidence for the kinematic coupling between the Cu-SCys stretch and the cysteine deformation modes in WT azurin, which leads to multiple features in the rR spectrum of the BC site. The UV-vis absorption and MCD data on WT, M121SeM, and C112SeC give very similar C0/D0 ratios, indicating that the C-term MCD intensity mechanism involves Cu-centered spin-orbit coupling (SOC). The spectroscopic data combined with density functional theory (DFT) calculations indicate that SCys and SeCys have similar covalent interactions with Cu at their respective bond lengths of 2.1 and 2.3 A. This reflects the similar electronegativites of S and Se in the thiolate/selenolate ligand fragment and explains the strong spectroscopic similarities between WT and C112SeC azurin.