De novo metallonucleases based on helix-loop-helix motifs

Three new 42-mer peptides (PR I-III) designed to fold into a hairpin helix-loop-helix motif have been prepared. In the peptide sequence two (PR II-III) or four (PR I) copies of an unnatural amino acid bearing a triazacyclononane metal-ion binding site (ATANP) have been inserted in appropriate positions to allow the ligand subunits to face each other either within the same helix or between the two helices of the hairpin motif. Circular dichroism (CD) studies in solution have shown that the apopeptides adopt a well-defined helix-loop-helix tertiary structure that dimerizes in solution at concentrations above 200 microM to form a four-helix bundle. However, the helical content is strongly dependent on pH and metal-ion binding. Both protonation of the amines of the triazacyclononane units present in the ATANP lateral arm and complexation with Zn(II) ions cause a significant decrease of the helical content of the sequences. The Zn(II) complexes of the three peptides catalyze the transesterification of the RNA model substrate 2-hydroxypropyl-p-nitrophenyl phosphate (HPNP) with different efficiency. The best catalyst appears to be PR I-4 Zn(II), that is, the peptide incorporating four ATANP units. Michaelis-Menten saturation kinetics allowed us to estimate that substrate fully bound to the catalyst reacts 380 times faster than in its absence. The kinetic evidence suggests cooperativity between (at least two) metal ions: one activating the nucleophilic species (directly or indirectly) and the other facilitating nucleophilic attack by coordination of the phosphate.     

最优特征子集预测蛋白质与蛋白质的相互作用

蛋白质与蛋白质相互作用的识别有助于研究蛋白质功能和发现潜在的药物靶标。本研究采用氨基酸组成、二肽组成、三联子组成、组成、转变、分布和自相关特征对蛋白质与蛋白质相互作用对进行表征。基于最小冗余最大相关方法选择最优特征子集,结合支持向量机对酵母蛋白质与蛋白质相互作用进行了预测研究。通过采用最优特征子集,训练集和测试集的预测精度分别比二肽组成的提高了4%和2%,表明了当前方法的有效性。     

A solution-processable electron acceptor based on diketopyrrolopyrrole and naphthalenediimide motifs for organic solar cells

A novel, solution-processable small molecular electron acceptor (HP1) based on diketopyrrolopyrrole and naphthalenediimide fragments was designed and synthesized via a Stille coupling reaction, characterized by spectroscopic means, and exhibited excellent solubility and thermal stability. HP1 exerted strong and very broad absorption tailing into the near infra-red region, with appropriate energy levels matching with the archetypal electron donor, poly(3-hexylthiophene) (P3HT), and afforded 1.02% power conversion efficiency with a high open-circuit voltage (1.05 V) when tested in solution-processable bulk-heterojunction devices.     

An improved poly(A) motifs recognition method based on decision level fusion

Polyadenylation is the process of addition of poly(A) tail to mRNA 3′ ends. Identification of motifs controlling polyadenylation plays an essential role in improving genome annotation accuracy and better understanding of the mechanisms governing gene regulation. The bioinformatics methods used for poly(A) motifs recognition have demonstrated that information extracted from sequences surrounding the candidate motifs can differentiate true motifs from the false ones greatly. However, these methods depend on either domain features or string kernels. To date, methods combining information from different sources have not been found yet. Here, we proposed an improved poly(A) motifs recognition method by combing different sources based on decision level fusion. First of all, two novel prediction methods was proposed based on support vector machine (SVM): one method is achieved by using the domain-specific features and principle component analysis (PCA) method to eliminate the redundancy (PCA–SVM); the other method is based on Oligo string kernel (Oligo-SVM). Then we proposed a novel machine-learning method for poly(A) motif prediction by marrying four poly(A) motifs recognition methods, including two state-of-the-art methods (Random Forest (RF) and HMM-SVM), and two novel proposed methods (PCA–SVM and Oligo-SVM). A decision level information fusion method was employed to combine the decision values of different classifiers by applying the DS evidence theory. We evaluated our method on a comprehensive poly(A) dataset that consists of 14,740 samples on 12 variants of poly(A) motifs and 2750 samples containing none of these motifs. Our method has achieved accuracy up to 86.13%. Compared with the four classifiers, our evidence theory based method reduces the average error rate by about 30%, 27%, 26% and 16%, respectively. The experimental results suggest that the proposed method is more effective for poly(A) motif recognition.     

场效应管药物传感器

将场效应管与药物敏感膜结合,以硅钨酸或四苯硼钠未转型的定域体试剂为电活性物质的药物传感器.该传感器制作简单,线性范围宽于或检测下限低于文献值.并对器件的影响因素进行了详尽的讨论.     

A reversible microarray immobilization strategy based on thiol-quinone reaction

Microarray technology has been widely applied in biomedical research. The key to microarray study is to develop efficient immobilization method. In this study, we designed a new reversible microarray immobilization method based on thiol-quinone reaction. A quinone-functionalized slide was fabricated through H₂O₂ treatment of dopamine-coated slides. Various thiol-containing molecules can be anchored onto the quinone-functionalized slides via thioether linker, which could be ...     

Targeting the proangiogenic VEGF-VEGFR protein-protein interface with drug-like compounds by in silico and in vitro screening

Protein-protein interactions play a central role in medicine, and their modulation with small organic compounds remains an enormous challenge. Because it has been noted that the macromolecular complexes modulated to date have a relatively pronounced binding cavity at the interface, we decided to perform screening experiments over the vascular endothelial growth factor receptor (VEGFR), a validated target for antiangiogenic treatments with a very flat interface. We focused the study on the VEGFR-1 D2 domain, and 20 active compounds were identified. These small compounds contained a (3-carboxy-2-ureido)thiophen unit and had IC₅₀ values in the low micromolar range. The most potent compound inhibited the VEGF-induced VEGFR-1 transduction pathways. Our findings suggest that our best hit may be a promising scaffold to probe this macromolecular complex and for the development of treatments of VEGFR-1-dependent diseases.     

Identifying DNA motifs based on match and mismatch alignment information

The conventional way of identifying DNA motifs, solely based on match alignment information, is susceptible to a high number of spurious sites. A novel scoring system has been introduced by taking both match and mismatch alignment information into account. The mismatch alignment information is useful to remove spurious sites encountered in DNA motif searching. As an example, a correct TATA box site in Homo sapiens $H4/g$ gene has successfully been identified based on match and mismatch alignment information.     

Efficient hydrogen sorption in 8-connected MOFs based on trinuclear pinwheel motifs

Two new metal-organic frameworks based on trinuclear pinwheel motifs are prepared using dicarboxylate and diamine ligands. The structure of [Co3(bdc)3(dabco)] (1) (bdc = 1,4-benzenedicarboxylate; dabco = 1,4-diazabicyclo[2.2.2]octane) is described as pillared layers, whereas [Co3(ndc)3(dabco)] (2) (ndc = 2,6-naphthalenedicarboxylate) forms a variation of primitive cubic net with 3D connected pores. The two 8-connected MOFs are thermally stable at 160 and 250 degrees C for 1 and 2 respectively in the air and possess corrugated channels owing to the high connectivities of the secondary building unit. As a result, they show highly efficient hydrogen sorption capabilities. Especially, a high hydrogen uptake (2.45 wt % at 77 K and 1 bar) is observed for 2 that has the unique combination of high surface area and small portals.     

HADDOCK: a protein-protein docking approach based on biochemical or biophysical information

The structure determination of protein-protein complexes is a rather tedious and lengthy process, by both NMR and X-ray crystallography. Several methods based on docking to study protein complexes have also been well developed over the past few years. Most of these approaches are not driven by experimental data but are based on a combination of energetics and shape complementarity. Here, we present an approach called HADDOCK (High Ambiguity Driven protein-protein Docking) that makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments or mutagenesis data. This information is introduced as Ambiguous Interaction Restraints (AIRs) to drive the docking process. An AIR is defined as an ambiguous distance between all residues shown to be involved in the interaction. The accuracy of our approach is demonstrated with three molecular complexes. For two of these complexes, for which both the complex and the free protein structures have been solved, NMR titration data were available. Mutagenesis data were used in the last example. In all cases, the best structures generated by HADDOCK, that is, the structures with the lowest intermolecular energies, were the closest to the published structure of the respective complexes (within 2.0 A backbone RMSD).     

A novel strategy for developing yellow diarylethenes based on acid stimulus

A novel strategy for the preparation of yellow diarylethenes was established based on the acidichromism of two new diarylethenes with a bromopyridine moiety. The bromopyridine was connected directly to the central perfluorocyclopentene ring to participate in photoisomerization reaction. The two diarylethenes exhibited favorable photochromism and function as notable fluorescence switches in solution. The absorption maxima of their closed-ring isomers shifted dramatically to shorter wavelengths with notable color change from red to yellow upon the stimulation of trifluoroacetic acid.     

Assembly-controlled biocompatible interface on a microchip: strategy to highly efficient proteolysis

A biocompatible interface was constructed on a microchip by using the layer-by-layer (LBL) assembly of charged polysaccharides incorporating proteases for highly efficient proteolysis. The controlled assembly of natural polyelectrolytes and the enzyme-adsorption step were monitored by using a quartz-crystal microbalance and atomic force microscopy (AFM). Such a multilayer-assembled membrane provides a biocompatible interconnected network with high enzyme-loading capacity. The maximum digestion rate of the adsorbed trypsin in a microchannel was significantly accelerated to 1600 mM min(-1) microg(-1), compared with the tryptic digestion in solution. Based on the Langmuir isotherm model, the thermodynamic constant of adsorption K was calculated to be 1.6 x 10(5) M(-1) and the maximum adsorption loading Gammamax was 3.6 x 10(-6) mol m(-2), 30 times more than a monolayer of trypsin on the native surface. The tunable interface containing trypsin was employed to construct a microchip reactor for digestion of femtomoles of proteins and the produced peptides were analyzed by MALDI-TOF mass spectroscopy. The efficient on-chip proteolysis was obtained within a few seconds, and the identification of biological samples was feasible.     

A naked-eye based strategy for semiquantitative immunochromatographic assay

It is critical to develop a cost-effective quantitative/semiquantitative assay for rapid diagnosis and on-site detection of toxic or harmful substances. Here, a naked-eye based semiquantitative immunochromatographic strip (NSI-strip) was developed, on which three test lines (TLs, TL-I, TL-II and TL-III) were dispensed on a nitrocellulose membrane to form the test zone. Similar as the traditional strip assay for small molecule, the NSI-strip assay was also based on the competitive theory, difference was that the analyte competed three times with the capture reagent for the limited number of antibody binding sites. After the assay, the number of TLs developed in the test zone was inversely proportional to the analyte concentration, thus analyte content levels could be determined by observing the appeared number of TLs. Taking aflatoxin B₁ as the model analyte, visual detection limit of the NSI-strip was 0.06 ng mL⁻¹ and threshold concentrations for TL-I–III were 0.125, 0.5, and 2.0 ng mL⁻¹, respectively. Therefore, according to the appeared number of TLs, the following concentration ranges would be detectable by visual examination: 0–0.06 ng mL⁻¹ (negative samples), and 0.06–0.125 ng mL⁻¹, 0.125–0.5 ng mL⁻¹, 0.5–2.0 ng mL⁻¹ and >2.0 ng mL⁻¹ (positive samples). That was to say, compared to traditional strips the NSI-strip could offer more parameter information of the target analyte content. In this way, the NSI-strip improved the qualitative presence/absence detection of traditional strips by measuring the content (range) of target analytes semiquantitatively.     

Electrochemical sensor for bisphenol A based on a nanoporous polymerized ionic liquid interface

The ionic liquid 1-butyl -3-[3-(N-pyrrole)-propyl]imidazolium tetrafluoroborate was employed to fabricate a glassy carbon electrode (GCE) modified with a porous film of a polymerized ionic liquid. The resulting film electrode was treated with sodium dodecyl sulfonate solution to exchange the terafluoroborate anions by dodecyl sulfonate groups. This was confirmed by X-ray photoelectron spectroscopy. The morphology of the modified GCE was characterized by scanning electron microscopy and revealed a nanoporous surface. The electrochemical properties of this film electrode were studied by electrochemical impedance spectroscopy using the hexacyanoferrate(II/III) system as an electroactive probe. The response to bisphenol A was investigated by voltammetry. Compared to the unmodified GCE, the oxidation potential is positively shifted, and the oxidation peak current is strongly increased. Experimental conditions were optimized and resulted in an oxidation peak current that is linearly related to concentration of bisphenol A in the 10 nM to ~ 10 μM range. The detection limit is 8.0 nM (at S/N?=?3). The electrode was successfully applied to the determination of bisphenol A in leachates of plastic drinking bottles, and its accuracy was verified by independent assays via HPLC.

A reversible adsorption-desorption interface of DNA based on nano-sized zirconia and its application

It is essential for the information storage in DNA-based bio-chips to construct a reversible exchange interface of DNA. Here, a highly reproducible and reversible adsorption–desorption interface of DNA based on the nano-sized zirconia in different pH solution was successfully fabricated. The results showed that DNA can be adsorbed onto the nano-sized zirconia from its solution, and can desorb from the nanoparticles in 0.10 M KOH solution. When the matrix with nanoparticles returns to the DNA solution again, DNA can be re-adsorbed onto them as initial state. Moreover, the interaction of DNA with non-electroactive molecules, 2,2′-bipyridine, has been studied by electrochemistry method in the aid of probe Co(phen)₃³⁺. The experiments showed that when 2,2′-bipyridine was added into the test solution, the voltammetric peak currents of Co(phen)₃³⁺ decreased; and the decrease value of peak current against the concentration of 2,2′-bipyridine has a good Langmuir relationship, by which the equilibrium constant of interaction between 2,2′-bipyridine and DNA was estimated to be 1.57×10⁴ M⁻¹.     

Progress on intelligent hydrogels based on RAFT polymerization: Design strategy,fabrication and the applications for controlled drug delivery

Although intelligent hydrogels have shown bright potential application in biomedical fields,they were prepared by conventional methods and still face many serious challenges,such as uncontrollable stimulus-response and low response sensitivity.Recently,RAFT polymerization provides a versatile strategy for the fabrication of intelligent hydrogels with improved stimulus-response properties,owing to the ability to efficiently construct hydrogel precursors with well-defined structure,such as block copolymer,graft copolymer,star copolymer.In this review,we summarized the recent progress on intelligent hydrogels based on RAFT polymerization with emphasis on their fabrication strategies and applications for controlled drug delivery.     

A strategy to sequence repetitive DNA based on partial restriction enzyme cleavage

The strategy to sequence repetitive DNA described in this article is based on partial restriction enzyme cleavage. It is an alternative to using nested deletion with exonuclease III or similar enzymes in which progressively more remote regions of the target DNA are brought into range for sequencing by universal primers.     

Realizing high-efficiency carrier separation in 3D hierarchical carbon nitride nanosheets via intramolecular donor-acceptor motifs strategy

The insufficient visible light responsive region and fast charge recombination probability are still the key obstacles for designing high-performance photocatalytic system. Herein, a “One Stone, Two Birds” strategy was reported in three-dimensional (3D) hierarchical graphitic carbon nitride (g-C₃N₄) nanosheet with intramolecular donor-acceptor (D-A) motifs (3D CN) photocatalyst, which solved two urgent problems simultaneously. The 3D hierarchical nanosheets structure endowed 3D CN with abundantly exposed reaction active sites and cross-plane diffusion channels. The formation of internal D-A system facilitated the light absorption and accelerated the transfer and separation of charge carriers. Furthermore, the introducing of D-A motifs optimized the bandgap of g-C₃N₄ and negative-shifted conduction band position. The as-prepared 3D CN showed excellent visible-light photocatalytic H₂ performance, with H₂ evolution rate of 2521.2 μmol h^?1/g, which was six times higher than the pristine CN. This outstanding performance was ascribed to the synergistic effect of 3D hierarchical nanosheets structure and intramolecular D-A motifs. This current work provides a novel insight to design and construct of 3D hierarchical CN nanostructures with D-A motifs simultaneously, which can be further promising applications for clean and sustainable energy conversion.     

A simple optimization strategy based on Rs-minimum and information theory of chromatography

Summary A simple optimization method based on the well-known Rs-minimum method and on the information theory of FUMI Φ is proposed. Resolution (Rs), peak area and height (or width) are the only parameters necessary for the calculation of the information Φ and information flow ϑ. The most precise analysis can be selected as the chromatogram having maximal ϑ. Mobile phase composition, column length, flow rate, detection wavelength, amount of internal standard, etc. can be optimized by this method.