Software note: using probe secondary structure information to enhance Affymetrix GeneChip background estimates

High-density short oligonucleotide microarrays are a primary research tool for assessing global gene expression. Background noise on microarrays comprises a significant portion of the measured raw data. A number of statistical techniques have been developed to correct for this background noise. Here, we demonstrate that probe minimum folding energy and structure can be used to enhance a previously existing model for background noise correction. We estimate that probe secondary structure accounts for up to 3% of all variation on Affymetrix microarrays.     

A partition function algorithm for nucleic acid secondary structure including pseudoknots

Nucleic acid secondary structure models usually exclude pseudoknots due to the difficulty of treating these nonnested structures efficiently in structure prediction and partition function algorithms. Here, the standard secondary structure energy model is extended to include the most physically relevant pseudoknots. We describe an O(N(5)) dynamic programming algorithm, where N is the length of the strand, for computing the partition function and minimum energy structure over this class of secondary structures. Hence, it is possible to determine the probability of sampling the lowest energy structure, or any other structure of particular interest. This capability motivates the use of the partition function for the design of DNA or RNA molecules for bioengineering applications.     

Synthesis,structure, DNA binding and cleavage ability of a new copper ciprofloxacin complex

The structure of 1 consists of [Cu(HCp)(phen)(H₂O)]²⁺ (HCp is ciprofloxacin and phen is 1,10-phenanthroline), two acetates, and four free water molecules. In each cation, copper displays a distorted square pyramid, coordinated to ring 3-carboxylate and 4-oxo oxygen from HCp, two nitrogens from phen, and one water molecule. There are five water molecules in each discrete complex with one coordinated to Cu center, and the other four linked to each other by intermolecular hydrogen bonds. Two uncoordinated acetates make the compound neutral. The complex exhibits higher DNA binding compared to HCp at the same conditions by fluorescence and viscosity measurements. Combining its structure with the DNA-binding result, the binding mechanism may be explained by intercalation. Moreover, 1 shows significant cleavage of DNA in the presence of a reducing agent, such as ascorbate by gel electrophoresis using supercoiled pBR322 DNA in Tris-HCl buffer (pH 7.4). The complex also has a higher activity against Gram-positive bacteria Staphylococcus aureus and Gram-negative bacteria Klebsiella pneumoniae than HCp.     

TiCl4 assisted formation of nano-TiO2 secondary structure in photoactive electrodes for high efficiency dye-sensitized solar cells

A new kind of photoactive electrodes with nanocrystalline TiO2(nano-TiO2)secondary structure is successfully prepared via a simple method of adding a small amount of TiCl4 2-propanol solution in conventional nano-TiO2 paste to form micro-sized nano-TiO2 aggregates.The benefits of this special structure include improved optical absorption,increased light scattering ability,and enhanced electron transport and collection efficiency.Dye-sensitized solar cells(DSCs)based on these photoactive electrodes show improved performance.The power conversion efficiency of the cells can be increased from 5.03%to 7.30%by substituting 6μm conventional nano-TiO2 thin film with the same thickness of as-prepared nano-TiO2 aggregates film in the photoactive electrodes.A higher power conversion efficiency of the cells can be obtained by further increasing the thickness of the nano-TiO2 aggregates film.     

基于二级结构TiO_2纳米晶光阳极的高效染料敏化太阳能电池

本文报道了一种新型的二级结构TiO2纳米晶(nano-TiO2)光阳极的简单制备方法及其在高效染料敏化太阳能电池中的应用.通过添加适量TiCl4异丙醇溶液到传统nano-TiO2浆料中,可生成微米级nano-TiO2聚集体.该二级结构能有效提高光阳极光谱吸收和散射性能及电子传输和收集效率.基于这种结构光阳极的染料敏化太阳能电池光电性能有显著提高.在光阳极中将6μm厚传统nano-TiO2膜用相同厚度nano-TiO2聚集体替换,电池光电转换效率由5.03%提高到7.30%.进一步增加nano-TiO2聚集体的厚度能制备出更高光电转换效率的电池.     

RNA secondary structure alignment based on an extended binary coding method

Recently, we proposed a three‐dimensional cube representation of RNA secondary structure. An efficient method for mutation analysis has been proposed based on the introduced representation. According to the proposed three‐dimensional cube representations, we will introduce an extended binary coding method for RNA secondary structure alignment by converting the structure alignment to sequence alignment. Using our method, the result of structure alignment can be obtained quickly. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Synthesis,structure, DNA binding studies and nuclease activities of two luminescent neodymium complexes

Two neodymium(III) complexes, [Nd(Phen)(NO₃)₃(DMF)₂] (1) and [Nd(Phen)₂(NO₃)₃] (2) (phen = 1,10-phenanthroline; DMF = dimethylformamide), have been synthesized with a view to design artificial luminescent nucleases and nuclease mimics. The complexes were characterized by spectroscopic, powder, and single crystal XRD studies. The complexes, as expected, have luminescent properties. The DNA binding studies of both complexes have been carried out by spectroscopic studies e.g. electronic absorption (UV–Vis), fluorescence emission as well as viscosity measurements. The nuclease activity of the complexes has been established by gel electrophoresis using pUC19 circular plasmid DNA. The results of DNA binding as well as DNA cleavage activity and the model studies of interaction with pNPP indicate that both neodymium complexes demonstrate nuclease activity through phosphoester bond cleavage.     

八棱丝瓜蛋白1的二级结构及其生物活性

测定了八棱丝瓜蛋白1的N端顺序为Asp-Val-Ser-Phe-Ser-,用CD谱测定了八棱丝瓜蛋白 1的α螺旋,β-折叠和无规卷曲含量分别为37.1%,33.4%,29.5%。实验表明,八棱丝瓜蛋白 1具有RNA N-糖苷酶活性,体外抑制肿瘤细胞生长活性表明其对肿瘤细胞株B16,MGC,Bel的半数抑制浓度分别为1.78×10-7mol/L,2.11×10-7mol/L和4.21×10-7mol/L。并在N端顺序,二级结构和生物活性方面对八棱丝瓜蛋白 1和天花粉蛋白进行了比较。     

Prediction of glycoprotein secondary structure using ATR-FTIR

Glycoproteins are important biomolecules with a diverse array of structural and signaling functions in biology. Determination of glycoprotein secondary structure is becoming increasingly important in aiding the understanding of how these molecules function in biological environments and disease. Furthermore, glycoproteins such as mucins are being evaluated in various nano-engineering processes that require knowledge of how the underlying secondary structure might alter in different target environments. We have developed an analytical procedure for predicting the secondary structures of glycoprotein using ATR-FTIR on dry film. Using Bovine submaxillary mucin (BSM) as a glycoprotein model, we determined the additive infrared spectral pattern of acetyl amino sugars and amino acids that could contribute to the absorbance in the Amide I band of BSM through empirical data. We show through subtraction of these spectra how the absorbance pattern of the protein backbone can be determined in order to predict glycoprotein secondary structure. The analysis predicted a predominant pattern of random coil, beta sheet and beta turn secondary structure for BSM after carbohydrate and amino acid spectral subtraction in agreement with other methods. Our relatively simple approach can be applied to predict secondary structure in other glycoproteins.     

Erratum Study on the secondary structure and bioactivities of Luffaculin 1

The N-terminal sequence of Luffaculin 1 was determined to be Asp-Val-Ser-Phe-Ser- . The CD spectrum of Luffaculin 1 indicated that Luffaculin 1 contains the 37.1%α-helix , 33.4% β-sheet,and 29.5% random coil. N-glycosidase activity of Luffaculin 1 against animal rRNA is observed. The anti-tumor activity of Luffaculin 1 on cell strains B16, MGC, Bel were determined,giving IC50 of 1.78×10-7mol/L,2.11×10-7mol/L,and 4.21×10-7mol/L,respectively. We also discussed the N-terminal sequences, secondary structures, and bioactivities of Luffaculin 1 against Trichosanthin.     

蛋白质和变性蛋白质二级结构的FTIR分析进展

蛋白质结构的研究一直是人们研究的一个热点,蛋白质在发生变性后,二级结构会改变,从而导致生物活性丧失,这些与医药学及食品科学等领域密切相关。傅里叶变换红外光谱(FTIR)作为一种无损、快速的分析方法在蛋白质二级结构的研究中发挥重要的作用,本文就FTIR对于蛋白质二级结构的研究作一初步概述,主要介绍FTIR研究蛋白质结构的主要方法、红外光谱的谱学特点。     

Study of the effect of Cal-Red on the secondary structure of human serum albumin by spectroscopic techniques

The effect of Cal-Red on the structure of human serum albumin (HSA) was studied using Resonance light scattering (RLS), Fourier transformed Infrared (FT-IR) and Circular dichroism (CD) spectroscopic methods. The RLS spectroscopic results show that the RLS intensity of HSA was significantly increased in the presence of Cal-Red. The binding parameters of HSA with Cal-Red were studied at different temperatures of 289, 299, 309 and 319 K at pH 4.1. It is indicated by the Scatchard plots that the binding constant K decreased from 4.03 × 10⁸ to 7.59 × 10⁷ l/mol and the maximum binding number N decreased from 215 to 152 with increasing the temperature, respectively. The binding process was exothermic and spontaneous, as indicated by the thermodynamic analyses, and the major part of the binding energy is hydrophobic interaction. The enthalpy change ΔH⁰, the free energy change ΔG⁰ and the entropy change ΔS⁰ of 289 K were calculated to be −42.75 kJ/mol, −47.56 kJ/mol and 16.66 J/mol K, respectively. The alterations of protein secondary structure in the presence of Cal-Red in aqueous solution were quantitatively calculated from FT-IR and CD spectroscopy with reductions of -helices content about 5%, β-turn from 10% to 2% and with increases of β-sheet from 38% to 51%.     

Dramatic change in the tertiary structure of giant DNA without distortion of the secondary structure caused by pteridine-polyamine conjugates

Pteridine-polyamine conjugates, such as 2-polyamine (1,3-diaminopropane and spermine) substituted 6,7-dimethyl-3H-pteridine-4-one, induce a folding transition of a giant DNA molecule more effectively than the corresponding polyamines. However, since neither a DNA high-temperature shift of denaturation (Tm) curve nor distortion of the UV/fluorescence spectra is observed in a mixture of these compounds with DNA, they do not interact with the DNA duplex strongly.     

Structural-Based Stability Enhancement of Antisense DNA Oligonucleotides

Antisense DNA oligonucleotide (AS) technology is a promising approach to regulate gene expression and cellular processes. For example, ASs can be used to capture the overexpressed, oncogenic miRNAs in tumors to suppress tumor growth. Among many challenges faced by AS approach is the degradation of ASs by nucleases under physiological conditions. Elongating the AS lifespan can substantially enhance the functions of AS. The paper reports a simple strategy to increase the stability of ASs. The authors discover that the ASs degrade quickly if their ends are in unpaired, single-stranded form, but much slower if their ends are in paired duplex form. It is conceivable to integrate this strategy with other strategies (such as chemical modification of ASs backbones) to maximally increase the ASs stabilities.     

Prediction of protein secondary structure content using support vector machine

In this paper, the support vector machine was trained to grasp the relationship between the pair-coupled amino acid composition and the content of protein secondary structural elements, including -helix, 3₁₀-helix, π-helix, β-strand, β-bridge, turn, bend and the rest random coil. Self-consistency and cross validation tests were made to assess the performance of our method. Results superior to or competitive with the popular theoretical and experimental methods have been obtained.     

2D representation of protein secondary structure sequences and its applications

In terms of the classification of the protein secondary structures, we propose a 2D representation of protein secondary structure sequences. The representation are used to display, analyze, and compare the secondary structure sequences. Based on this representation, we assign the structural class to the protein, and verify the advantage or disadvantage of the methods of predicted protein second structure.     

Synthesis,crystal structure,and DNA binding of a new oxalato-bridged binuclear zinc(II) complex

A new binuclear zinc(II) complex bridged by μ-oxalate, and end-capped with 2,2′-bipyridine (bpy), [Zn₂(ox)(bpy)₄](ClO₄)₂ · H₂O, has been synthesized and characterized by elemental analyses, molar conductance, IR, and electronic spectra and single-crystal X-ray diffraction. The single-crystal X-ray analysis reveals that the [Zn₂(ox)(bpy)₄]²⁺ cation has two zinc(II) centers bridged by a planar bis(bidentate) oxalate group with Zn···Zn distance of 5.482(3) Å; each zinc(II) is in a distorted octahedral environment. The crystal structure is stabilized by non-classical C–H···O hydrogen bonds and π–π stacking interactions to form a 3-D supramolecular structure. The interaction of the complex with calf-thymus DNA (CT-DNA) was explored by using electronic and fluorescence spectra and viscosity measurements. The results reveal that the complex intercalates with CT-DNA with intrinsic binding constant of 4.1 × 10⁴ M^?1.