ESI-MS characterization of a novel pyrrole-inosine nucleoside that interacts with guanine bases

Based on binding studies undertaken by electrospray ionization-mass spectrometry, a synthetic pyrrole-inosine nucleoside, 1, capable of forming an extended three-point Hoogsteen-type hydrogen-bonding interaction with guanine, is shown to form specific complexes with two different quadruplex DNA structures [dTG₄T]₄ and d(T₂G₄)₄ as well as guanine-rich duplex DNA. The binding interactions of two other analogs were evaluated in order to unravel the structural features that contribute to specific DNA recognition. The importance of the Hoogsteen interactions was confirmed through the absence of specific binding when the pyrrole NH hydrogen-bonding site was blocked or removed. While 2, with a large blocking group, was not found to interact with virtually any form of DNA, 3, with the pyrrole functionality missing, was found to interact non-specifically with several types of DNA. The specific binding of 1 to guanine-rich DNA emphasizes the necessity of careful ligand design for specific sequence recognition.     

Synthesis and binding studies of novel diethynyl-pyridine amides with genomic promoter DNA G-quadruplexes

Herein, we report the design, synthesis and biophysical evaluation of novel 1,2,3-triazole-linked diethynyl-pyridine amides and trisubstituted diethynyl-pyridine amides as promising G-quadruplex binding ligands. We have used a Cu(I)-catalysed azide-alkyne cycloaddition click reaction to prepare the 1,2,3-triazole-linked diethynyl-pyridine amides. The G-quadruplex DNA binding properties of the ligands have been examined by using a F?rster resonance energy transfer (FRET) melting assay and surface plasmon resonance (SPR) experiments. The investigated compounds are conformationally flexible, having free rotation around the triple bond, and exhibit enhanced G-quadruplex binding stabilisation and specificity between intramolecular promoter G-quadruplex DNA motifs compared to the first generation of diaryl-ethynyl amides (J. Am. Chem. Soc. 2008, 130, 15950-15956). The ligands show versatility in molecular recognition and promising G-quadruplex discrimination with 2-50-fold selectivity exhibited between different intramolecular promoter G-quadruplexes. Circular dichroism (CD) spectroscopic analysis suggested that at higher concentration these ligands disrupt the c-kit2 G-quadruplex structure. The studies validate the design concept of the 1,3-diethynyl-pyridine-based scaffold and demonstrate that these ligands exhibit not only significant selectivity over duplex DNA but also variation in G-quadruplex interaction properties based on small chemical changes in the scaffold, leading to unprecedented differential recognition of different DNA G-quadruplex sequences.     

Diarylethynyl amides that recognize the parallel conformation of genomic promoter DNA G-quadruplexes

We report bis-phenylethynyl amide derivatives as a potent G-quadruplex binding small molecule scaffold. The amide derivatives were efficiently prepared in 3 steps by employing Sonogashira coupling, ester hydrolysis and a chemoselective amide coupling. Ligand-quadruplex recognition has been evaluated using a fluorescence resonance energy transfer (FRET) melting assay, surface plasmon resonance (SPR), circular dichroism (CD) and (1)H nuclear magnetic resonance (NMR) spectroscopy. While most of the G-quadruplex ligands reported so far comprise a planar, aromatic core designed to stack on the terminal tetrads of a G-quadruplex, these compounds are neither polycyclic, nor macrocyclic and have free rotation around the triple bond enabling conformational flexibility. Such molecules show very good binding affinity, excellent quadruplex:duplex selectivity and also promising discrimination between intramolecular promoter quadruplexes. Our results indicate that the recognition of the c-kit2 quadruplex by these ligands is achieved through groove binding, which favors the formation of a parallel conformation.     

一种新型呋喃香豆素类似物: 呋喃并萘并吡喃酮的合成及DNA嵌入活性

1,5-萘二酚经Pechmann缩合，烯丙基醚化，Claisen重排，乙酰化，溴加成，闭环六步反应，合成了一个新型的呋喃香豆素类似物，2H-4,8-二甲基呋喃并[2',3':5,6]萘并[1,2-b]吡喃-2-酮(6)。所得2～6的5个新化合物的结构均经^1H NMR，MS，IR，元素分析确证，测试了化合物6的紫外及荧光光谱。在DMSO-Tris HCl体系中，用荧光淬灭技术考察了6和7的DNA嵌入活性，求取了Scatchard表观嵌入常数，发现6和7都能有效地嵌入小牛胸腺DNA中，6的嵌入活性小于7。     

Nonspecific protein-DNA interactions: complexation of alpha-chymotrypsin with a genomic DNA

In this contribution, we report studies on nonspecific protein-DNA interactions of an enzyme protein bovine pancreatic alpha-chymotrypsin (CHT) with genomic DNA (from salmon testes) using two biologically common fluorescent probes: 1-anilinonaphthalene-8-sulfonate (ANS) and 2,6-p-toluidinonaphthalene sulfonate (TNS). TNS molecules that are nonspecifically bound to positively charged basic residues at the surface sites, not in the hydrophobic cavities of the protein, are preferentially displaced upon complexation of TNS-labeled CHT with DNA. The time-resolved fluorescence anisotropy of TNS molecules bound to hydrophobic cavities/clefts of CHT reveals that global tumbling motion of the protein is almost frozen in the protein-DNA complex. A control study on TNS-labeled human serum albumin (HSA) upon interaction with DNA clearly indicates that the ligands in the deep pockets of the protein cannot be displaced by interaction with DNA. We have also found that ANS, which binds to a specific surface site of CHT, is not displaced by DNA. The intactness of the ANS binding in CHT upon complexation with DNA offers the opportunity to measure the distance between the ANS binding site and the contact point of the ethidium bromide (EB)-labeled DNA using the F?rster resonance energy transfer (FRET) technique. Enzymatic activity studies on CHT on a substrate (Ala-Ala-Phe 7-amido-4-methyl coumarin) reveal that the active site of the enzyme remains open for the substrate even in the protein-DNA complex. Circular dichroism (CD) studies on CHT upon complexation with DNA confirm the structural integrity of CHT in the complex. Our studies have attempted to explore an application of nonspecific protein-DNA interactions in the characterization of ligand binding of a protein in solution.     

来源于类芽孢杆菌属新型耐有机溶剂脂肪酶的克隆、表达与性质研究（英文）

脂肪酶(EC 3.1.1.3)全称为三酰基甘油水解酶,是一类能够将长链脂肪酸甘油酯水解成脂肪酸和二甘酯、单甘酯或甘油的酯键水解酶.它除了能够水解脂肪外,还具有催化酯化反应、酯交换反应、酸解反应、醇解反应以及氨解等反应的性质.在脂肪酶催化的反应中,通常用有机溶剂代替水.有机溶剂可以转移合成反应的平衡方向,通过溶剂工程修饰酶的选择性能够提高底物的溶解度、有机相产物的回收率、酶的热稳定性.但有机溶剂对酶活性和稳定性有不同程度的影响.因此,寻找在有机溶剂中表现出高活性和稳定性的脂肪酶是一个亟待解决的重要课题.由于微生物种类多、作用底物专一性强,且微生物来源的脂肪酶一般分泌到胞外,因此微生物脂肪酶是工业用脂肪酶的重要来源.目前,微生物脂肪酶的研究主要集中于根霉属(Rhizopus)、曲霉属(Aspergillus)、青霉属(Penicillium)、毛霉属(Mucor)、地霉属(Geotrichum)、假丝酵母属(Candida)、假单胞菌属(Pseudomonas)、伯克霍尔德菌属(Burkholderia)等具有工业应用价值的菌株.很少有类芽孢杆菌属所产脂肪酶进行相关酶学性质的研究.我们以Paenibacillus pasadenensis CS0611为出发菌株,在全基因序列草图中得到了一个新型脂肪酶基因lp2252.以Paenibacillus pasadenensis CS0611基因组为模板,设计特异性引物对目标序列进行扩增,并成功将其插入到表达载体p ET-28a中得到含有目的基因的重组质粒.在E.coli BL21(DE3)中,脂肪酶lp2252经0.1mmol/L的IPTG诱导后在20°C实现了高水平表达.重组脂肪酶的活性约为野生型的1631倍.用镍离子亲和层析柱快速、高效地纯化了两端带有组氨酸标签的重组脂肪酶,回收率为63.5%,纯化因子为10.78.纯化后的脂肪酶最适温度为50°C,在20-40°C范围内具有良好的稳定性.最适pH值为7,属于中性脂肪酶,同时在pH 3.0-8.0间具有较高稳定性.在金属离子如钙、镁离子和一些非离子表面活性剂的作用下,其活性有所提高.此外,纯化后的脂肪酶可被一系列水溶性有机溶剂激活,例如一些短链醇.而对某些水不溶性有机溶剂,其也具有高度的耐受性.综上所述,本文所涉新型脂肪酶在非水相催化领域具有广泛的应用和前景.     

Synthesis and characterization of a novel thermosensitive gel with fast response

A gel is a kind of water-swellable but water-insoluble, crosslinked polymer. Some kinds of gels can respond to external temperature changes. This specific property is useful in biomedical and other technological fields. In this paper the synthesis of a novel, thermosensitive gel by the copolymerization of N-isopropylacrylamide or N,N- diethylacrylamide with 3-methacryloxypropyltrimethoxy silane (MPTMS) is reported. The formation of the gel is caused through the interaction of MPTMS under acidic condition. This thermosensitive gel can deswell and reswell quickly in response to the external temperature changes, this behavior probably being due to the heterogeneous structure of the gel produced. This fast-response gel may be useful both in biomedical and biotechnological fields. Received: 17 March 1999 Accepted on revised form: 9 June 1999     

Plant DNA fingerprinting with radioactive and digoxigenated oligonucleotide probes complementary to simple repetitive DNA sequences

The existence of hypervariable DNA sequences in nuclear genomes, and the use of appropriate "fingerprinting" probes to detect them, has gained widespread scientific interest, and also led to multiple applications in diverse areas. Two years ago, the new technique of "DNA fingerprinting" was also introduced into the analysis and characterization of plant genomes, initially by using human or M13 minisatellites as probes. In the present article, we demonstrate the applicability for plant DNA fingerprinting of oligonucleotide probes specific for simple repetitive DNA sequences. We show that various levels of intra- and interspecific polymorphisms can be detected; the information to be gained depends on the optimal combination of probe and species. Variety-specific patterns were obtained in several cases. Some probes revealed variability between individuals. Somatic variability was not observed. Different DNA isolation and purification procedures were tested in order to introduce a fast and easy-to-perform isolation method suitable for a large variety of plant species. Nonradioactive fingerprinting was performed using digoxigenated oligonucleotides as probes. Banding patterns obtained with radioactive and digoxigenin-based labeling techniques proved to be of similar quality.     

Spectroscopic characterization, crystal structure determination and interaction with DNA of novel cyano substituted benzimidazole derivative

Novel cyano-substituted benzimidazole derivatives 3 and 4 were synthesized from 4-N,N-dimethylamino-benzaldehyde and 2-cyanomethyl-benzimidazole. 2-(1H-benzimidazol-2-yl)-3-(4-N,N-dimethylamino-phenyl)-acrylonitrile hydrochloride monohydrate 4 has been studied by ¹H and ¹³C NMR, IR, MS, UV/Vis and fluorescence spectroscopy and confirmed by X-ray crystal structure analysis. The interaction of 4 with ct-DNA has also been investigated by fluorescence spectroscopy and melting temperature determination experiment. According to the emission spectra recorded in the absence and presence of ct-DNA at different ratios r ([compound]/[polynucleotide]), 4 showed marked decrease in the fluorescence intensity and very strong hypochromic effect. Melting temperature experiment showed weak stabilization of double helix. To determine binding mode of 4, other additional experiments are necessary. The molecules of 4 are almost planar with the dihedral angle between benzimidazole and phenyl rings of 6.99(6)°. The protonation of nitrogen atom of benzimidazole ring is followed by π-electrons delocalization in the region resulting in C–N bond distances equality [1.341(2) and 1.337(2) Å]. Both NH groups of benzimidazole ring form intermolecular hydrogen bonds, one with the oxygen atom of water molecule [N···O 2.689(2) Å] and the other with Cl^? ion (N···Cl^? 3.051(1) Å). Except proton acceptor, water molecule acts as double proton donor in the formation of intermolecular hydrogen bonds with Cl^? ion [O···Cl^? 3.126(2) and 3.169(2) Å]. In that way, infinite chains along [110] direction are formed.     

Electrochemistry of a novel monoruthenated porphyrin and its interaction with DNA

Interactions of an anisomerous ruthenated porphyrin [Ru(MPyTPP)(bpy)₂Cl]⁺ (where bpy = 2,2′-bipyridine, MPyTPP = 5-pyridyl-10,15,20-triphenyl porphyrin) with calf thymus DNA are studied using a tin-doped indium oxide (ITO) electrode. The Ru^III/II redox reaction for the complex exhibits a surface-controlled electron transfer process in buffer solutions. There exists an obvious interaction of the adsorbed [Ru(MPyTPP)(bpy)₂Cl]⁺ on an ITO electrode with DNA in the buffer solutions. The formal potential for [Ru(MPyTPP)(bpy)₂Cl]^2+/+ redox reaction is found to shift negatively in the presence of DNA compared with that in the absence of DNA. However, the current signals of [Ru(bpy)₃]^3+/2+ reaction exhibits a distinct catalytic enhancement to DNA, in contrast to the interactions of [Ru(MPyTPP)(bpy)₂Cl]⁺with DNA.     

Phylogenetic analysis of DNA sequences with a novel characteristic vector

In the basic biological research, one of major tasks is to compare biological sequences to infer evolutionary relations among sequences. In this paper, considering both the positions and numbers of a k-word and the random background, a novel characteristic vector of a DNA sequence is proposed to serve for genetic sequences comparison and phylogenetic analysis. The vector is composed of elements which characterize the relative difference of a DNA sequence from a sequence generated by a (k − 2)th order Markov process. Finally, we reconstruct the phylogenetic trees of 48 HEV (Hepatitis E virus) and 20 Eutherian mammals. The results show that this new method provides more information about k-word and improves the efficiency of sequence comparison.     

Synthesis and characterization of a novel unsymmetrical metal-free phthalocyanine with donor-acceptor substituents

A novel unsymmetrical metal-free phthalocyanine with a nitro group as an acceptor substituent and three t-butyl groups as donor groups, namely nitro-tri-t-butylphthalocyanine (NtBuPc) was synthesized for the first time by mixed condensation of two corresponding diiminoisoindolines. The NtBuPc can be separated by common column chromatography on silica gel using chloroform-hexane as the elution solvent. The structure was confirmed by elemental analysis, nmr, uv-vis, ir and mass spectroscopy. No contamination of either symmetrical or other related phthalocyanines was observed.     

Self-assembly and characterization of a novel hydrogen-bonded nanostructure

A novel hydrogen-bonded supramolecular system of a [60]fullerene derivative with perylene bisimide was synthesized and characterized. 1H NMR spectra confirmed the existence of strong hydrogen-bonding interaction between compounds 1 and 5. Transmission electron microscopy images of 1.5 aggregates showed spherical particles having a mean diameter of 50 nm. The photocurrent response of the film was measured, and a steady and rapid anodic photocurrent response was obtained.     

Synthesis and DNA binding studies of bis-intercalators with a novel spiro-cyclic linker

Threading polyintercalation has been demonstrated as a unique DNA binding mode in which a polyintercalating moiety threads back and forth through the DNA double helix. This binding topology necessitates linkers residing in both the minor and major grooves in an alternating fashion. In the present work, two novel, rigid, cis and trans oriented spiro-cyclic linkers were synthesized as potential groove binding elements in the context of threading bis-intercalation. Analysis of dissociation kinetics indicated that the cis oriented dimer has dramatically slower dissociation from poly(dGdC) and calf thymus (CT) DNA compared to the trans oriented dimer and a linear dimer control.     

On the use of different mass spectrometric techniques for characterization of sequence variability in genomic DNA

After completion of the human genome sequence the search for differences among individual genomes has become the centre of focus for geneticists. Two different types of polymorphism—single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs)—are major sources of genetic diversity and are of widespread use in genetic analysis. A plethora of genotyping techniques have been developed, and mass spectrometry (MS) is among the most widely used analytical platforms. The most striking advantage of mass spectrometric genotyping assays over others is the use of the measured molecular mass information for allele calling. The molecular mass is less error-prone than other sequence-specific parameters, including migration times, retention times, or hybridization yields, as it represents an intrinsic property of a nucleic acid molecule that is directly related to its nucleotide composition. Mass spectrometric assays can roughly be divided into two major groups—matrix-assisted laser desorption/ionization (MALDI)-based and electrospray ionization (ESI)-based assays. An important subdivision of ESI-based genotyping methods are approaches that originate from the hyphenation of liquid chromatography (LC) to MS. The principles of these three classes of mass spectrometric genotyping techniques are summarized in this review. Possibilities and limitations are critically discussed to assist scientists, especially non-experts in MS, in choosing the appropriate mass spectrometric assay for genotyping a genetic marker of interest. Figure Comparison of the principle workflows applied for the characterization of genetic markers by MALDI–MS, ESI–MS, and LC–MS     

Development and characterization of a DNA solar dosimeter

In this paper, we report the development and characterization of a solar ultraviolet (UV) dosimetry system that can be used as a film badge for radiation monitoring. DNA molecules are coated on a thin nylon membrane as a UV dosimeter. The membrane is sealed in a polyethylene filter envelope with silica gel to keep the humidity low. After exposure to UV or solar light, induced DNA damage is measured by an immunochemical reaction. The intensity of color developed during the immunological reaction can be correlated linearly with the irradiated UV dose delivered by an Oriel solar simulator within a limited dose range. We observe no effects of temperature on the level of damage induction. The membrane is proficient for measuring DNA damage for more than 21 days when stored at either 37 or 4°C. The induced damage remains stable on the membrane for at least 22 days at both 37 and 4°C. In addition to these indoor experiments, we report measurements of solar UV dose in outdoor experiments.     

Preparation and characterization of a novel stimuli-responsive nanocomposite hydrogel with improved mechanical properties

A novel stimuli-responsive organic/inorganic nanocomposite hydrogel (NC hydrogel) with excellent mechanical properties was synthesized by in situ polymerization of 2-(2-methoxyethoxy) ethyl methacrylate (MEO(2)MA), oligo (ethylene glycol) methacrylate (OEGMA) and acrylic acid (AAc), as the polymeric matrix (PMOA), and fibrillar attpulgite (AT), as the reinforcer and cross-linker. The effect of the AT content on the mechanical properties for the swollen and dried NC hydrogels was determined by tensile testing and dynamic mechanical analysis (DMA), respectively. The tensile testing results showed that the incorporation of AT nanoparticles significantly enhanced the mechanical properties of NC hydrogels. As the content of AT increased, the tensile strength, tensile modulus and effective cross-linked chain density increased. The DMA results showed that the storage modulus of AT/PMOA NC hydrogels was increased and the glass transition temperatures shifted to higher temperature compared to the pure PMOA hydrogel, which further indicated that the enhancement of mechanical property depended upon the presence and content of AT. In addition, the faster swelling rates of the NC hydrogels were observed in comparison with the corresponding physically cross-linked PMOA hydrogel, except for 1% AT/PMOA sample. However, the deswelling kinetics of NC hydrogels was obviously retarded.     

Synthesis and characterization of a novel imidazole cyclic trimer

A novel cyclic trimer of imidazole 1, in which imidazole rings are connected by amide bonds, has been synthesized with the help of LiCl as a template for the cyclization. The absorption spectra of 1 indicate the extension of conjugation between imidazole rings and amide bonds. The addition of 3 M equiv of MgCl₂ solubilizes 1 in polar organic solvent, suggesting the chelating ability of 1 to Mg cation.     

Synthesis and characterization of a novel well-defined comb-like ionomer

A novel well-defined comb-like ionomer with cations was synthesized by the combination of living anionic polymerization and atom transfer radical polymerization (ATRP). The synthetic approach involves the coupling reaction of polystyrene (PS) backbone bearing 1,1-diphenylethene (DPE) pendant groups with living polystyryllithium (PSLi), subsequent amine functionalization of the resulting 1,1-diphenylmethyl anions with 3-dimethylaminopropyl chloride (DMAPC), and quaternization of tertiary amino groups with hydrochloric acid. The comb-like ionomer was characterized by ¹H NMR, IR, GPC measurements and end-group titrition.