Dynamic imaging of single DNA-protein interactions using atomic force microscopy

Atomic force microscopy (AFM) imaging of static DNA-protein complexes, in air and in liquid, can be used to directly obtain quantitative and qualitative information on the structure of different complexes. For example, DNA length, the location of preferential binding sites for proteins and bending of DNA as a result of the complexation can all be measured. Recording consecutive AFM images of DNA and protein molecules under conditions that they are still able to move and interact, or dynamic AFM imaging, however, can reveal information on the dynamic aspects of the interactions between these molecules. Here, an overview is given of the technical challenges that need to be considered for successful dynamic AFM imaging studies of individual DNA-protein interactions. Necessary technical improvements to the AFM set-up and the development of new sample preparation methods are described in this paper.     

Solvating,manipulating, damaging,and repairing DNA in a computer

This work highlights four different topics in modeling of DNA: (i) the importance of water and ions together with the structure and function of DNA; the hydration structure around the ions appears to be the determining factor in the ion coordination to DNA, as demonstrated in the results of our MD simulations; (ii) how MD simulations can be used to simulate single molecule manipulation experiments as a complement to reveal the structural dynamics of the studied biomolecules; (iii) how damaged DNA can be studied in computer simulations; and (iv) how repair of damaged DNA can be studied theoretically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Supramolecular structures of macromolecules containing bipyridine–copper(I) complexes as revealed from transmission electron microscopy studies

Transmission electron microscopy (TEM) studies on bipyridine (bpy) containing block copolymer systems showed the formation of nanoscopic polymer–ion complexes through complexation with copper(I) ions which segregated to highly ordered columnar domains of mesoscopic dimensions. The domains, i.e. stacks of [(bpy)₂Cu(I)] complex moieties could be visualized by complementary TEM techniques. First, electron energy loss spectra (EELS) showed the absorption edges of copper and nitrogen, which are specific for the bipyridine copper complexes. The element spectroscopic imaging (ESI) technique allowed the imaging of the net copper and net nitrogen distribution, and the coinciding pictures exhibited a microphase separated system in the case of a 3-block copolymer with complexed end segments. High resolution elastic bright field images showed interference lines with a line to line distance of about 8 A which could be related to the Cu–Cu distance in staggered Cu(I)–bipyridine complexes. Received: 6 August 1997 Accepted: 28 April 1998     

Metabolomic-based investigation of Yinlan alleviating hyperlipidemia by inhibiting blood stasis and phlegm turbidity through the PXR-CYP3A4-ABCB1-FXR pathway

Yinlan lipid regulatory capsule (YL) is a composite traditional Chinese medicine (TCM) new drug to alleviate hyperlipidemia, while its therapeutic mechanism in vivo was not clarified with nontargeted metabolomics investigation. An animal model was established in rats fed a high-fat diet, and their body weights, body mass index (BMI) and blood cholesterol levels were measured. Serum, liver and kidney tissue samples were also extracted for PXR-CYP3A4-ABCB1-FXR signaling pathway research using PCR and UHPLC–MS. The obtained plasma samples were analyzed by UHPLC-Q-TOF-MS metabolomic investigation, which revealed PXR-CYP3A4-related metabolites and changes induced by YL. Finally, the key metabolites were chosen as index components, and their levels in the serum, liver, small intestine and bile were used for simultaneous UHPLC–MS-MS determination. The results indicated that YL was effective in rebalancing blood TG and TC levels (compared to controls). With respect to the PXR-CYP3A4-ABCB1 pathway, as a result of YL’s effect, gene expression or activity of the two targets decreased significantly in both the liver and kidney. The same trend was observed in the serum samples mentioned above. Metabolomics screening and data revealed that 44 metabolites can be regarded as biomarkers related to hyperlipidemia, fatty acids synthesis, and body energy consumption, as well as synthesis, transportation and exertion of cholesterol. YL’s treatment focused on 26 of them, primarily bile acids, indicating that the antihyperlipidemic effect of this drug lies in its inhibitory activity of cholesterol metabolism. Subsequent analysis of those in vivo components revealed that significant increases (compared to the model group) occurred in the blood, liver, small intestine and bile in groups that received medium and high doses of YL (while the low dose was relatively unchanged). Those target components exhibit a close relationship with PXR and/or CYP3A4. The use of YL repressed PXR expression and subsequently decreased CYP3A4 activity. As a result, synthesis of related bile acids increased, while cholesterol levels decreased, consequently leading to the attenuation of hyperlipidemia. This study comprehensively investigated the antihyperlipidemia mechanism of YL based on its repression of PXR-CYP3A4 activity and related metabolite yield, establishing an accurate method for evaluating the therapeutic effect of YL.     

Hydrothermal synthesis, crystal structures and luminescent properties of two new Ln(III)–succinate (Ln=Eu, Tb) complexes exhibiting three dimensional networks

Two new coordination polymers, [Eu₂(L)₃(H₂O)₂]_n 1 and {[Tb₂(L)₃(H₂O)₂]·H₂O}_n 2, (H₂L=succinic acid) have been synthesized by the reaction of H₂L with nitrate salts of Eu(III) or Tb(III) under hydrothermal conditions. The X-ray diffraction analysis reveals that the two complexes are constructed by L bridging the chains of edge-sharing EuO₈(H₂O) or TbO₈(H₂O) polyhedra to form 3D network structure. 1 and 2 possess different topological structures due to the difference in the conformations of L. The solid photoluminescence of 1 and 2 was also investigated in room temperature.     

Synthesis and crystal structures of heterobimetallic Fe-Cd,Fe-Zn,and Fe-In complexes containing hemilabile phosphorus/oxygen and silicon/oxygen bridging ligands

The reactions of K[Fe{Si(OMe)₃}(CO)₃(PY)][PY=Ph₂PCH₂C(O)Ph, Ph₂PCH₂C(O)[(-C₅H₄)FeCp] (Cp=⁵-C₅H₅), Ph₂P(CH₂)₂CN] with CdCl₂·2.5H₂O, ZnX ₂ (X=Cl, I) or InCl₃ afforded Fe-Cd-Fe or Fe-M(-X)₂ M-Fe (M=Cd, Zn, In;X=Cl, I) and Fe-InCl₂ complexes. Some of them contain an unusual and labile -²-SiO alkoxysilyl bridge which may be associated with a bridging mode for the ketophosphine ligand (first such example structurally established), thus providing original results in bimetallic chemistry on the intramolecular coordination of oxygendonor functions ofchemically different hemilabile ligands firmly attached to a neighboring metal center. The structures of the trinuclear complex (3), of the chlorobenzene solvate of the tetranuclear complex (4a·C₆H₅Cl) and of [mer-(OC)₃{(EtO)₃Si} (4e) have been determined by X-ray diffraction. Crystals of 3 are orthorhombic, space groupPbcn, witha=19.010(4),b=11.766(5),c=26.998(7)Å, andZ=4. Crystals of4a·C₆H₅Cl are monoclinic, space groupC2/c witha=22.455(3),b=17.680(2),c=16.627(4)Å, =90.80(4)°, andZ=4. Crystals of4e are monoclinic, space groupC2/c witha=25.392(5),b=18.554(6),c=16.28(1)Å, =120.73(3)°, andZ=4. The structures were solved using direct methods and Fourier difference techniques and refined by blocked full-matrix least squares toR=0.035 (R _w =0.049) for 2719 observed reflections, toR=0.042 (R _w =0.056) for 3082 observed reflections, and toR=0.057 (R _w =0.075) for 1850 observed reflections for3, 4a·C₆H₅Cl and4e, respectively. The Fe-Zn complexes (9a), (9b) and (9c) were prepared and characterized by spectroscopic methods.Part 21 in the Series: Complexes with Functional Phosphines. Part 20: P. Braunstein, S. Coco Cea, A. DeCian, and J. Fischer (1992).Inorg. Chem. 31, 4203.     

Coordination modes of 2-hydroxynicotinic acid in second- and third-row transition metal complexes

The new Pd(II), Pt(II), Re(V), Mo(VI) and W(VI) complexes of 2-hydroxynicotinic acid (H₂nicO), trans-[PdCl(HnicO)(PPh₃)₂]·0.75CH₃CN (1), K[PdCl(HnicO)₂]·H₂O (2), [Pd(HnicO)₂(bipy)] (3), cis-[PtCl(HnicO)(PPh₃)₂]·0.75CH₃OH·0.5H₂O (4), [PtCl(HnicO)(bipy)] (5), cis-[ReOI₂(HnicO)(PPh₃)] (6), Na₂[Mo₂O₆(HnicO)₂]·5H₂O (7), Na₂[Mo₄O₁₂(HnicO)₂]·2H₂O (8) and Na₂[W₂O₆(HnicO)₂]·5H₂O (9) have been prepared. The crystal structures of 1 and 4, were determined by X-ray diffraction and show the HnicO⁻ ligand coordinated to palladium or platinum through the nitrogen atom only. Infrared, Raman, ¹H and ¹³C{¹H} NMR spectroscopic data for the complexes are presented and are in agreement with the crystallographic results.     

Chiral molecular glass: synthesis and characterization of enantiomerically pure thiophene-based [7]helicene

Synthesis of thiophene-based [7]helicenes, which are functionalized for both design of organic chiral glasses with strong chiroptical properties and for further homologation to higher [n]helicenes, is reported. The key synthetic transformations are kinetic resolution of the intermediate diketone and the annelation step forming the center benzene ring by means of an intramolecular McMurry reaction. Based upon X-ray crystallographic determinations of the absolute configurations for (+)-enantiomers of the diketone and the [7]helicene, stereochemical correlation between the (R) axial chirality of the diketone and the (M) helical chirality of the [7]helicene is established. One such enantiopure trimethylsilyl-substituted [7]helicene possesses enchanced chiroptical properties and forms a chiral molecular glass.     

Rapid biomass analysis

New, rapid, and inexpensive methods that monitor the chemical composition of corn stover and corn stover-derived samples are a key element to enabling the commercialization of processes that convert stover to fuels and chemicals. These new techniques combine near infrared (NIR) spectroscopy and projection to latent structures (PLS) multivariate analysis to allow the compositional analysis of hundreds of samples in 1 d at a cost of about $10 each. The new NIR/PLS rapid analysis methods can also be used to support a variety of research projects that would have been too costly to pursue by traditional methods.