Energetic basis of molecular recognition in a DNA aptamer

The thermal stability and ligand binding properties of the L-argininamide-binding DNA aptamer (5'-GATCGAAACGTAGCGCCTTCGATC3') were studied by spectroscopic and calorimetric methods. Differential calorimetric studies showed that the uncomplexed aptamer melted in a two-state reaction with a melting temperature T-m = 50.2 +/- 0.2 degrees C and a folding enthalpy Delta H degrees(fold) = -49.0 +/- 2.1 kcal mol(-1). These values agree with values of T-m = 49.6 degrees C and Delta H degrees(fold) = -51.2 kcal mol(-1) predicted for a simple hairpin structure. Melting of the uncomplexed aptamer was dependent upon salt concentration, but independent of strand concentration. The T of aptamer melting was found to increase as L-argininamide concentrations increased. Analysis of circular dichroism titration data using a single-site binding model resulted in the determination of a binding free energy Delta G degrees(bind) = -5.1 kcal mol(-1). Isothermal titration calorimetry studies revealed an exothermic binding reaction with Delta H degrees(bind) = -8.7 kcal mol(-1). Combination of enthalpy and free energy produce ail unfavorable entropy of -T Delta S degrees = +3.6 kcal mol(-1). A molar heat capacity change of -116 cal mol(-1) K-1 was determined from calorimetric measurements at four temperatures over the range of 15-40 degrees C. Molecular dynamics simulations were used to explore the structures of the unligated and ligated aptamer structures.

Structural diversity of lanthanide-amino acid complexes under near physiological pH conditions and their recognition of single-stranded DNA

We reported here four structures of lanthanide-amino acid complexes obtained under near physiological pH conditions and their individual formula can be described as [Tb-2(DL-Cys)(4)(H2O)(8)]Cl-2 (1), [Eu-4(mu(3)-OH)(4)(L-Asp)(2)(L-HAsp)(3)(H2O)(7)] Cl center dot 11.5H(2)O (2), [Eu-8-(L-HVal) (16)(H2O)(32)]Cl-24 center dot 12.5H(2)O (3), and [Tb-2(DL-HVal)(4)(H2O)(8)]Cl-6 center dot 2H(2)O (4). These complexes showed diverse structures and have shown potential application in DNA detection. We studied the interactions of the complexes with five single-stranded DNA and found different fluorescence enhancement, binding affinity and binding stoichiometry when the complexes are bound to DNA.

Synthesis, structure and electrochemical property of calixarene potassium polyoxometalates

One inorganic-organic hybrid and two host-guest complexes were synthesized from calix[4] arene tetra acetic ether derivative( C60H80O12, L) and potassium polyoxometalates. The structures of the complexes were characterized with the elemental analysis, IR, TG-DTA and X-crystallographic. X-ray crystallographic studies reveal the formation of an ionic crystal, which contains a calix-cluster and calix-cluster-calix line array, and belongs to a typical inorganic-organic hybrid ( complex 1) or has a host-guest structure ( complex 2 and 3). The results of cyclic voltammograms at different scanning rates showed that the anode peak current of complex 1 was proportional to the square root of the scanning rate and the charge transfer process was controlled by pervasion. The anode peak current of complexes 2 and 3 was proportional to the scanning rate and the charge transfer process was controlled by the surface. The results suggest that there are consanguineous relationship between the anode reaction and the structure.

The first polyoxometalate polymer constructed by assembly of the heptamolybdic anion and copper coordination groups

The first example of one-dimensional organic-inorganic polymetallic coordination polymer based on heptamolybdate anions, formulated (NH4)[Cu(en)(2)][Na(en)Cu(en)(2)(H2O)(Mo7O24)].4H(2)O (en = ethylenediamine) (1) has been hydrothermally synthesized and characterized by element analysis, IR, EPR, CV and single crystal X-ray diffraction. The structure of 1 is fabricated by self-assembly of integrated heptamolybdic anions without collapse of primary structure and copper-ethylenediamine(en) coordination groups into one-dimensional zigzag-shaped chains.

NMR and pattern recognition studies on the acute biochemical effects of Lu(NO3)(3)

Pattern recognition methods were applied to the analysis of 600 MHz H-1 NMR spectra of urine from rats dosed with compounds that induced organ-specific damage in the liver and kidney. Male Wistar rats were separated into groups (n=4) and each was treated with one of following compounds: HgCl2, CCl4, Lu(NO3)(3) and Changle (a kind of rare earth complex mixed with La, Ce, Pr and Nd). Urine samples from the rats dosed with HgCl2, CCl4 and Lu(NO3)(3) were collected over a 24 h time course and the samples from the rats administrated with Changle were gained after 3 months. These samples were measured by 600 MHz NMR spectroscopy. Each spectrum was data-processed to provide 223 intensity-related descriptors of spectra. Urine spectral data corresponding to the time intervals, 0-8 h (HgCl2 and CCl4), 4-8 (Lu(NO3)(3)) h and 90 d (Changle) were analyzed using principal component analysis (PCA). Successful classification of the toxicity and biochemical effects of Lu(NO3)(3) was achieved.

Quantifying the kinetic paths of flexible biomolecular recognition

Biomolecular recognition often involves large conformational changes, sometimes even local unfolding. The identification of kinetic pathways has become a central issue in understanding the nature of binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path-integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. The significant coupling between the binding and folding of biomolecules often exists in many important cellular processes. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. This implies that binding and folding happen concurrently. When the coupling between binding and folding is weak (strong), the kinetic process usually starts with significant folding (binding) first, with the binding (folding) later proceeding to the end. The kinetic rate can be obtained through the contributions from the dominant paths. The rate is shown to have a bell-shaped dependence on temperature in the concentration-saturated regime consistent with experiment. The changes of the kinetics that occur upon changing the parameters of the underlying binding-folding energy landscape are studied.

Observation of a water-anion layer constructed from water tetramers and nitrate anions in the crystal host of a cobalt complex

A novel self-assembled layer consisting of water tetramers and nitrate anions has been observed in the [Co(1,10-phenanthroline)(2)(NO3)]center dot(NO)(3)center dot 4H(2)O complex. X-ray crystallography and FT-IR spectroscopy indicate that although the water tetramers exist in an energetically less stable uudd configuration, the anionic host environments may play an important role in the formation and stabilization of the water clusters.

Discrimination of herbal medicines by molecular spectroscopy and chemical pattern recognition

The molecular spectroscopy (including near infrared diffuse reflection spectroscopy, Raman spectroscopy and infrared spectroscopy) with OPUS/Ident software was applied to clustering ginsengs according to species and processing methods. The results demonstrate that molecular spectroscopic analysis could provide a rapid, nondestructive and reliable method for identification of Chinese traditional medicine. It's found that the result of Raman spectroscopic analysis was the best one among these three methods. Comparing with traditional methods, which are laborious and time consuming, the molecular spectroscopic analysis is more effective.

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.

Anion coordination and molecular assembly in C2-substituted thiamine-anion systems: effects of the anion and molecular conformation

The compounds (het)(PtCl6)2H(2)O 1, (het)(HgI4).H2O 2 (het = 2-(alpha-hydroxyethyl)thiamine) and (hpt)(Hg2Br6) 3 (hpt = 2-(alpha-hydroxypropyl)thiamine) have been prepared and structurally characterized by X-ray crystallography in order to study the influence of the anion and molecular conformation on the formation of supramolecular architectures that adsorb anionic species. Both het and hpt molecules adopt the usual S conformation for C2-substituted thiamine but differ from the F conformation for C2-free thiamine derivatives. Two types of characteristic ligand-anion complexation are observed, being of the forms C(6')-H...anion...thiazolium-ring (in 1 and 2) and N(4'1)-H...anion...thiazolium-ring (in 3). The reaction of het with PtCl62- or HgI42- gives a 1-D double-chain in 1, consisting of two hydrogen-bonded het chains, which are cross-linked by anions through hydrogen bonding and anion...aromatic-ring interactions, or a cationic 3-D framework in 2 formed by the stacking of hydrogen-bonded sheets with anion-and-water-filled channels. In the case of 3, hydrogen-bonded hpt dimers and HgBr62- anions form alternate cation-anion columns. A comparison with the cases of C2-free thiamine-anion complexes indicates that the change in molecular conformation results in novel supramolecular assemblies in 1 and 2 and an analogous architecture in 3, which also depends on the nature of the anions.

Electrochemical recognition of alkali metal ions at the micro-water 1,2-dichloroethane interface using a calix[4]arene derivative

In this paper, a calix[4]arene derivative, 5,11,17,23-butyl-25,26,27,28-tetra-(ethanoxycarbonyl)-methoxy-calix[4]arene (L), is investigated as a host to recognize alkali metal ions (Li+, Na+, K+, Rb+ and Cs+) at the interface between two immiscible electrolyte solutions (ITIES). Well-defined cyclic voltammograms are obtained at the micro- and nano-water \ 1,2-dichloroethane (W \ DCE) interfaces supported at micro- and nano-pipets.

Determination of gold, platinum and palladium in geological samples by inductively coupled plasma-mass spectrometry after separation and preconcentration with C-410 anion exchange resin

A method for the determination of Au, Pt and Pd in geological samples is described. Au, Pt and Pd can be separated and concentrated quantitatively by C-410 anion-exchange resin in the condition of 1.5 mol/L HCl with the adsorption rates of 91.2%, 100.0% and 95.7% respectively. No interference exists from coexisting elements except for Ge(IV), Cr(VI),Ti(IV) in inductively coupled plasma-mass spectrometry. The detection limits are 0.27 mug/L, 0.40 mug/L and 0.19 mug/L for Au, Pt and Pd respectively. The results of these elements in standard geological materials are in agreement with certified values with precision of 19.2% RSD for Au (n = 8), 28.1% RSD for Pt (n=8), and 15.6% RSD for Pd (n=8).

Preparation and nonlinear optical properties of ultrathin composite films containing both a polyoxometalate anion and a binuclear phthalocyanine

An ultrathin composite film containing both polyoxometalate anion [PMo12O40](3-) ( PMo12) and a planar binuclear phthalocyanine, bi-CoPc, has been prepared by the electrostatic layer-by-layer self-assembly method. UV-vis measurements revealed regular film growth with each four-layer {PMo12/bi-CoPc/PSS/PAH} adsorption. The lm structure was characterized by small-angle X-ray reflectivity measurements, X-ray photoelectron spectra, and AFM images. The nanothick film shows a third-order nonlinear optical response of chi((3)) = 4.21 x 10(-12) esu. Experimental investigations also indicate that the combination of polyoxometalate anions [PMo12O40](3-) with the phthalocyanine bi-CoPc in multilayer films can enhance the third-order NLO susceptibility and modify the third-order NLO absorption of bi-CoPc.

Synthesis and crystal structure of 3-methoxycarbonylethyltin tetrachlorides anion

The anion of MeO2CCH2CH2SnCl4 - was obtained by decomposing the yellow solution of MeO2CCH2CH2SnCl3.(2-OHC6H4CH=NC6H5) by standing for 15 days, which is the product of 3-methoxy-carbonylethyltin trichlorides with Schiff base (2-OHC6H4CH=NC6H5). The title compound was characterized by elemental analysis, IR. H-1 NMR,C-13 NMR and X-ray diffraction analysis. The crystal of the title compound belongs to orthorhombic system, space group P2cn, a=7.852(2), b=12.236(1),c=16.952(4)Adegrees, V=1628.7 Angstrom(3), Z=4, D-c=1.79g/cm(3) F(000)=860, mu=22.2cm(-1), R=0.0449, Rw=0.0382. The title compound exists as a discrete molecule, and the tin atom attains a distorted octahedral geometry via the coordination of intramolecular carbonyl oxygen and chloride ion. The coordination number of tin atom is 6.