Water-mediated interactions in the CRP–cAMP–DNA complex: Does water mediate sequence-specific binding at the DNA primary-kink site?

The cyclic AMP receptor protein (CRP) of Escherichia coli binds preferentially to DNA sequences possessing a T:A base pair at position 6 (at which the DNA becomes kinked), but with which it does not form any direct interactions. It has been proposed that indirect readout is involved in CRP-DNA binding, in which specificity for this base pair is primarily related to sequence effects on the energetic susceptibility of the DNA to kink formation. In the current study, the possibility of contributions to indirect readout by water-mediated hydrogen bonding of CRP with the T:A base pair was investigated. A 1.0 ns molecular dynamics simulation of the CRP-cAMP-DNA complex in explicit solvent was performed, and assessed for water-mediated CRP-DNA hydrogen bonds; results were compared to several X-ray crystal structures of comparable complexes. While several water-mediated CRP-DNA hydrogen bonds were identified, none of these involved the T:A base pair at position 6. Therefore, the sequence specificity for this base pair is not likely enhanced by water-mediated hydrogen bonding with the CRP.     

Synthesis and Characterization of the Orthorhombic Sn3O4 Polymorph

An unexplored tin oxide crystal phase (Sn₃O₄) was experimentally synthesized via a facile hydrothermal method. After tuning the often-neglected parameters for the hydrothermal synthesis, namely the degree of filling of the precursor solution and the gas composition in the reactor head space, an unreported X-ray diffraction pattern was discovered. Through various characterization studies, such as Rietveld analysis, energy dispersive X-ray spectroscopy, and first-principles calculations, this novel material was characterized as orthorhombic mixed-valence tin oxide with the composition Sn^II₂Sn^IVO₄. This orthorhombic tin oxide is a new polymorph of Sn₃O₄, which differs from the reported conventional monoclinic structure. Computational and experimental analyses showed that orthorhombic Sn₃O₄ has a smaller band gap (2.0 eV), enabling greater absorption of visible light. This study is expected to improve the accuracy of hydrothermal synthesis and aid the discovery of new oxide materials.     

Supported lipid bilayer self-spreading on a nanostructured silicon surface

We report on the self-spreading behavior of a supported lipid bilayer (SLB) on a silicon surface with various 100 nm nanostructures. SLBs have been successfully grown from a small spot of a lipid molecule source both on a flat surface and uneven surfaces with 100 nm up-and-down nanostructures. After an hour, the self-spreading SLB forms a large circle or an ellipse depending on the nanostructure pattern. The results are explained by a model that shows that a single-layer SLB grows along the nanostructured surfaces. The model is further supported by a quantitative analyses of our data. We also discuss the stability of the SLB on nanostructured surfaces in terms of the balance between its bending and adhesion energies.     

A new morphology of copper 7,7,8,8-tetracyano-p-quinodimethane

Morphology control is a long-standing problem that needs to be solved for making the switching mechanism of copper 7,7,8,8-tetracyano-p-quinodimethane (CuTCNQ) understood all the time, but up till now how many morphologies CuTCNQ possesses and which morphology should be responsible for the on/off switching phenomenon are still unclear. A new morphology of CuTCNQ, namely the tubular structure, has been obtained and characterized in our experiment, whose formation mechanism has also been investigated. Through characterizing, we can conclude that the tubular structure belongs to the phase I, which can be further confirmed by the electrical measurements. From the I-V plots, the carrier mobility of the tubular structure is estimated to be approximately 0.1 cm2 V-1 s-1, which suggests the potential application of CuTCNQ in devices.     

Anomalous reinforcing effects in cellulose gel-based polymeric nanocomposites

Cellulose-synthetic polymer nanocomposite films were prepared by immersion of cellulose gel in polymer solutions followed by dry casting. The cellulose hydrogel was prepared from aqueous alkali-urea solution. As the synthetic polymer, polystyrene (PS) and poly(methyl methacrylate) (PMMA) were used. The polymer content could be changed between 10 and 80% by changing polymer concentration of immersing solution. While the mechanical properties of the cellulose-PMMA composite films showed a nearly linear dependence on PMMA content, those of cellulose-PS composites showed an anomalous behavior; both tensile strength and Young’s modulus showed prominent maxima at 15–30 wt% PS contents. This anomaly may have resulted from the specific interaction between the aromatic ring of PS and the hydrophobic plane of the glucopyranoside. Both PMMA and PS composite films showed significant improvements in dimensional thermal stability; up to 25 wt% synthetic polymer content, the coefficient of thermal expansion (CTE) was as low as ca. 30 ppm/K, about 1/3 of the pure polymers. This indicates that the regenerated cellulose network is effective in suppressing thermal expansion of the synthetic polymers.     

Roles of K151 and D180 in L‐2‐haloacid dehalogenase from Pseudomonas sp. YL: Analysis by molecular dynamics and ab initio fragment molecular orbital calculations

L ‐2‐haloacid dehalogenase (L ‐DEX) catalyzes the hydrolytic dehalogenation of L ‐2‐haloalkanoic acids to produce the corresponding D ‐2‐hydroxyalkanoic acids. This enzyme is expected to be applicable to the bioremediation of environments contaminated with halogenated organic compounds. We analyzed the reaction mechanism of L ‐DEX from Pseudomonas sp. YL (L ‐DEX YL) by using molecular modeling. The complexes of wild‐type L ‐DEX YL and its K151A and D180A mutants with its typical substrate, L ‐2‐chloropropionate, were constructed by docking simulation. Subsequently, molecular dynamics (MD) and ab initio fragment molecular orbital (FMO) calculations of the complexes were performed. The ab initio FMO method was applied at the MP2/6‐31G level to estimate interfragment interaction energies. K151 and D180, which are experimentally shown to be important for enzyme activity, interact particularly strongly with L ‐2‐chloropropionate, catalytic water, nucleophile (D10), and with each other. Our calculations suggest that K151 stabilizes substrate orientation and balances the charge around the active site, while D180 stabilizes the rotation of the nucleophile D10, fixes catalytic water around D10, and prevents K151 from approaching D10. Further, D180 may activate catalytic water on its own or with K151, S175, and N177. These roles are consistent with the previous results. Thus, MD and ab initio FMO calculations are powerful tools for the elucidation of the mechanism of enzymatic reaction at the molecular level and can be applied to other catalytically important residues. The results obtained here will play an important role in elucidating the reaction mechanism and rational design of L ‐DEX YL with improved enzymatic activity or substrate specificity. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

A self-assembled nano optical switch and transistor based on a rigid conjugated polymer, thioacetyl-end-functionalized poly(para-phenylene ethynylene)

A nanometer-scale optical switch and transistor were fabricated with thioacetyl-end-functionalized poly(para-phenylene ethynylene)s and Au nanogap electrodes by self-assembly. With photoirradiation, the switch can be switched on/off quickly with a switching ratio as high as 1000. Moreover, the device works well as a p-type transistor. With an increase in gate bias, strong conductance oscillation was observed in this self-assembled transistor (under low temperature 147 K), which is very likely due to single-electron charging oscillations arising from electron tunneling through the nanometer-scale transistor.     

Flow-injection chemiluminescent determination of vanadium(IV) and total vanadium by means of catalysis on the periodate oxidation of purpurogallin

A flow-injection chemiluminescent (CL) method is proposed for the successive determination of nanogram levels of vanadium(IV) and total vanadium. The method is based on the catalytic effect of vanadium(IV) on the oxidation of purpurogallin by periodate to produce light emission at 4 °C. The presence of hydrogen carbonate enhanced the light emission arising from the vanadium(IV)-catalyzed reaction. Since vanadium(V) did not catalyze the CL reaction of purpurogallin, vanadium(V) was determined after being reduced to vanadium(IV) by using an on-line silver-reducing column. Calibration curves for vanadium(IV) and (V) were linear in the range 0.1–10 ng ml⁻¹ with sampling rate of about 50 h⁻¹. The limit of detection for signal-to-noise ratio of 2 was 0.05 ng ml⁻¹ and the relative standard deviations were 1.4 and 1.6% for ten determinations of 2.0 ng ml⁻¹ vanadium(IV) and (V), respectively. Interferences from metal ions could be eliminated by the use of O,O′-bis(2-aminoethyl)ethyleneglycol- N,N,N′,N′-tetraacetic acid and diphosphate as masking agents. The proposed method was successfully applied to the determination of vanadium(IV) and total vanadium in fresh water samples.