Reusable, label-free electrochemical aptasensor for sensitive detection of small molecules

We report a sensitive electrochemical aptasensor for adenosine based on electrochemical impedance spectroscopy measurement, which gives not only a label-free but also a reusable platform to make the detection of small molecules simple and convenient.

Microarray-based kinase inhibition assay by gold nanoparticle probes

We report on the development of a new class of kinase microarray for the detection of kinase inhibition based on marking peptide phosphorylation/biotinylation events by attachment of gold nanoparticles followed by silver deposition for signal enhancement. The alpha-catalytic subunit of cyclic adenosine 5'-monophosphate-dependent protein kinase (PKA), and its well-known substrate, kemptide, were used for the purpose of monitoring phosphorylation and inhibition. As expected, highly selective inhibition of PKA is demonstrated with the four inhibitors: H89, HA1077, mallotoxin, and KN62. Furthermore, an inhibition assay demonstrates the ability to detect kinase inhibition as well as derive IC50 (half-maximal inhibitory concentration) plots.

DNA与生物碱类化合物非共价作用的负离子电喷雾质谱研究(Ⅰ)

目前 ,临床上使用的许多抗病毒药物均是通过与 DNA,RNA发生相互作用破坏其结构 ,进而影响基因调控与表达的功能 ,表现出抗病毒活性 [1,2 ] .因此 ,核酸与药物分子相互作用的研究对阐述抗病毒药物的作用机理 ,以及对药物的体外筛选都具有重要的意义 .电喷雾电离质谱作为一种软电离手段 ,可将溶液中生物分子与药物分子的非共价复合物转为气相进行分析 ,再现其生理状态 ,使其成为分子水平上进行药物筛选的最佳方法 [3～ 6 ] 和在分子水平上筛选中药抗病毒活性成分的理想工具 .本文选择合成了与 SARS病毒相关的 DNA片段作为抗病毒药物筛选的靶分子 ,用电喷雾质谱技术 ,通过对靶分子与 5种生物碱的非共价复合作用 ,探讨了生物质谱方法用于药物筛选的可行性 .1　实验部分1 .1　材料及样品制备　 DNA分子系人工合成 ,由 1 5个碱基组成 ,分子量为 470 4 ,结构为 GGTAA-GATGGAGAGC( 1 5 - mer) ;腺苷 ( Adenosine,Mw=2 67)、鸟苷 ( Guanosine,Mw=2 83)和胞苷 ( Cyti-dine,Mw=2 4 3)购自 Sigma公司 ;小檗碱、...

Cleavage of nucleotides by Ce4+ and the lanthanide metal complexes

The cleavage of adenosine-5'-monophosphate (5'-AMP) and guanosine-5'-monophosphate (S-GMP) by Ce4+ and lanthanide complex of 2-carboxyethylgermanium sesquioxide (Ge-132) in acidic and near neutral conditions was investigated by NMR, HPLC and measuring the liberated inorganic phosphate at 37 degrees C and 50 degrees C, The results showed that 5'-GMP and 5'-AMP was converted to guanine (G), 5'-monophosphate (depurination of 5'-GMP), ribose (depurination and dephosphorylation of 5'-GMP), phosphate and adenine (A), 5'-monophosphate (depurination of 5'-AMP), ribose (depurination and dephosphorylation of 5'-AMP), phosphate respectively by Ce4+. In presence of lanthanide complexes, 5'-GMP and 5'-AMP were converted to guanosine (Guo) and phosphate and adenosine (Ado) and phosphate respectively. The mechanism of cleaving 5'-GMP and 5'-AMP is hydrolytic scission.

Cleavage of nucleotides by lanthanide metal complexes

The present work revealed that the praseodymium( II ) complex of 2-carboxyethylgermanium sesquioxide (Ge-132) promotes the hydrolysis of the phosphodiester linkages of 3',5'-cyclic adenosine monophosphate (cAMP), 3' , 5'-cyclic deoxyadenosine monophosphate (dcAMP), 5'-adenosine monophosphate(5'-AMP) and 5'-deoxyadenosine monophosphate (5'-dAMP) under mild conditions. Both cAMP and dcAMP were hydrolyzed site-specifically, yielding predominantly 3'-monophosphates, the main products of the cleavage of 5'-AMP and 5'-dAMP included adenosine (Ado). deoxyadenosine (dAdo) and free phosphates respectively. A hydrolytic mechanism was proposed for cAMP, dcAMP, 5'-AMP and 5'-dAMP.

Use of lanthanide metal complexes for the hydrolysis of 3 ',5 '- and 2 ',3 ' cyclic nucleotides

Lutetium(III) and lanthanum(III) complexes of 2-carboxyethylgermanium sesquioxide (Ge-132) can hydrolyze the phosphodiester linkage of 3',5'-cyclic adenosine monophosphate (cAMP), 3',5'-cyclic deoxyadenosine monophosphate (dcAMP) and 2',3'-cyclic adenosine monophosphate (2',3'-cAMP). Both cAMP and dcAMP are hydrolyzed with high selectivity, yielding predominantly 3'-monophosphates. 2',3'-cAMP is converted to 3'-AMP and 2'-AMP, the ratio of 3'-AMP to 2'-AMP produced being 1.4.

Lanthanide ions for the hydrolysis of 5'-mononucleotides and 3'-mononucleotides

Cleavage of adenosine-5'-monophosphate (5'-AMP), guanosine-5'-monophosphate (5'-GMP), adenosine-3'-monophosphate (3'-AMP) and guanosine-3'-monophosphate (3'-GMP) by lanthanides was investigated by NMR and the method of measuring the liberated phosphates. Rapid cleavage of both 5'-mononucleotides and 3'-mononucleotides by Ce-III and Ce-IV under air at pH 9 and 37 degrees C was observed. Other lanthanides showed less efficiency for hydrolyzing 5'-mononucleotides but 3'-mononucleotides were catalyzed by a range of lanthanide ions. The mechanism for hydrolyzing 3'-mononucleotides by lanthanides was:investigated. The notable difference in reactivity between Ce-III and the other lanthanide ions under air was further studied showing that the cleavage is enhanced with increasing molar fraction of Ce-IV. The fast cleavage of mononucleotides by Ce-III under air at pH 9 is ascribed to the resultant Ce-IV in the reaction mixture. (C) 1997 Elsevier Science Ltd.

Lanthanide metal complexes for the hydrolysis of ribonucleoside 3',5'-cyclic phosphate and deoxyribonucleoside 3',5'-cyclic phosphate

Ytterbium(III) and praseodymium(III) complexes of 2-carboxyethylgermanium sesquioxide (Ge-132) can hydrolyze the phosphodiester linkage of 3',5'-cyclic adenosine monophosphate (cAMP) and 3',5'-cyclic deoxyadenosine monophosphate (dcAMP). Both cAMP and dcAMP are hydrolyzed with high selectivity, yielding predominantly 3'-monophosphates. The selectivity and activity for hydrolyzing cAMP and dcAMP by lanthanide metal(III) complexes and lanthanide metal ions are compared.

Efficient cleavage of ribonucleoside 3',5'-cyclic phosphates and deoxyribonucleoside 3',5'-cyclic phosphate by lanthanides

The cleavage of 3',5'-cAMP, 3',5'-cGMP and 3',5'-dcAMP by lanthanides has been investigated by HPLC and H-1 NMR. Rapid cleavage of cAMP, cGMP and dcAMP by Ce(III) under air at pH 8 and 37 degrees C has been observed. Regioselective cleavage of P-O(5') bond in cAMP, cGMP and dc;aMP tu give the corresponding 3'-AMP, 3'-GMP and 3'-dAMP by lanthanide chlorides has been achieved, and 3'-AMP and 3'-GMP are cleaved to adenosine(A) and guanosine(CT) more slowly, respectively, The notable difference in reactivity between Ce(III) and the other lanthanide ions under air has also been studied. The cleavage is enhanced with the increase in the molar fraction of Ce(IV). The fast cleavage of cAMP by Ce(III) under air at pH 8 is ascribed to the resultant Ce(IV) in the reaction mixture.

The chemical constituents from red alga Gymnogongrus flabelliformis Harv.

Eight compounds were isolated from red alga Gymnogongrus flabelliformis Harv. In normal phase silica gel, Sephadex LH-20 gel column chromatography, reverse phase HPLC, and recrystallization. Based on MS and 1D NMR spectroscopic data, their structures were determined as: stigmast-4-en-3-one (I), cholest-4-en-3-one (II), cholesterol (III), uracil (IV), uridine (V), adenosine (VI), succinic acid (VII), and 5-hydroxy-4-methyl-5-pentyl-2,5-dihydro-furan-2-on (VIII). All of them were obtained from this species for the first time. Cytotoxicity of these compounds was screened using standard MTT method, but all the compounds were inactive (IC50 > 10 mu g/ml).

Exploitation of Ebola Virus VP35 Protein to identify new drugs counteracting its type I IFN antagonism

Ebolaviruses (EBOVs) are among the most virulent and deadly pathogens ever known, causing fulminant haemorrhagic fevers in humans and non-human primates. The 2014 outbreak of Ebola virus disease (EVD) in West Africa has claimed more lives than all previous EVD outbreaks combined. The EBOV high mortality rates have been related to the virus-induced impairment of the host innate immunity reaction due to two virus-coded proteins, VP24 and VP35. EBOV VP35 is a multifunctional protein, it is essential for viral replication as a component of the viral RNA polymerase and it also participates in nucleocapsid assembly. Early during EBOV infection, alpha-beta interferon (IFN-α/β) production would be triggered upon recognition of viral dsRNA products by cytoplasmic retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs). However, this recognition is efficiently prevented by the double-stranded RNA (dsRNA) binding activity of the EBOV VP35 protein, which hides RLRs binding sites on the dsRNA phosphate backbone as well the 5’-triphosphate (5’-ppp) dsRNA ends to RIG-I recognition. In addition to dsRNA binding and sequestration, EBOV VP35 inhibits IFN-α/β production preventing the activation of the IFN regulatory factor 3 (IRF-3) by direct interaction with cellular proteins. Previous studies demonstrated that single amino acid changes in the VP35 dsRNA binding domain reduce EBOV virulence, indicating that VP35 is an attractive target for antiviral drugs development. Within this context, here we report the establishment of a novel method to characterize the EBOV VP35 inhibitory function of the dsRNA-dependent RIG-I-mediated IFN-β signaling pathway in a BLS2 cell culture setting. In such system, a plasmid containing the promoter region of IFN-β gene linked with a luciferase reporter gene was transfected, together with a EBOV VP35 mammalian expression plasmid, into the IFN-sensitive A549 cell line, and the IFN-induction was stimulated through dsRNA transfection. Through alanine scanning mutational studies with biochemical, cellular and computational methods we highlighted the importance of some VP35 residues involved in dsRNA end-capping binding, such as R312, K282 and R322, that may serve as target for the development of small-molecule inhibitors against EBOV. Furthermore, we identified a synthetic compound that increased IFN-induction only under antiviral response stimulation and subverted VP35 inhibition, proving to be very attractive for the development of an antiviral drug. In conclusion, our results provide the establishment of a new assay as a straightforward tool for the screening of antiviral compounds that target i) dsRNA-VP35 or cellular protein-VP35 interaction and ii) dsRNA-dependent RIG-I-mediated IFN signaling pathway, in order to potentiate the IFN response against VP35 inhibition, setting the bases for further drug development.

Dynamic effects of cofactors and DNA on the oligomeric state of human mitochondrial DNA helicase

We examined the effects of cofactors and DNA on the stability, oligomeric state and conformation of the human mitochondrial DNA helicase. We demonstrate that low salt conditions result in protein aggregation that may cause dissociation of oligomeric structure. The low salt sensitivity of the mitochondrial DNA helicase is mitigated by the presence of magnesium, nucleotide, and increased temperature. Electron microscopic and glutaraldehyde cross-linking analyses provide the first evidence of a heptameric oligomer and its interconversion from a hexameric form. Limited proteolysis by trypsin shows that binding of nucleoside triphosphate produces a conformational change that is distinct from the conformation observed in the presence of nucleoside diphosphate. We find that single-stranded DNA binding occurs in the absence of cofactors and renders the mitochondrial DNA helicase more susceptible to proteolytic digestion. Our studies indicate that the human mitochondrial DNA helicase shares basic properties with the SF4 replicative helicases, but also identify common features with helicases outside the superfamily, including dynamic conformations similar to other AAA⁺ ATPases.

Identification of RNA editing in the human exome and development of DARNED DatabaseSF

RNA editing is a biological phenomena that alters nascent RNA transcripts by insertion, deletion and/or substitution of one or a few nucleotides. It is ubiquitous in all kingdoms of life and in viruses. The predominant editing event in organisms with a developed central nervous system is Adenosine to Inosine deamination. Inosine is recognized as Guanosine by the translational machinery and reverse-transcriptase. In primates, RNA editing occurs frequently in transcripts from repetitive regions of the genome. In humans, more than 500,000 editing instances have been identified, by applying computational pipelines on available ESTs and high-throughput sequencing data, and by using chemical methods. However, the functions of only a small number of cases have been studied thoroughly. RNA editing instances have been found to have roles in peptide variants synthesis by non-synonymous codon substitutions, transcript variants by alterations in splicing sites and gene silencing by miRNAs sequence modifications. We established the Database of RNA EDiting (DARNED) to accommo-date the reference genomic coordinates of substitution editing in human, mouse and fly transcripts from published literatures, with additional information on edited genomic coordinates collected from various databases e.g. UCSC, NCBI. DARNED contains mostly Adenosine to Inosine editing and allows searches based on genomic region, gene ID, and user provided sequence. The Database is accessible at http://darned.ucc.ie RNA editing instances in coding region are likely to result in recoding in protein synthesis. This encouraged me to focus my research on the occurrences of RNA editing specific CDS and non-Alu exonic regions. By applying various filters on discrepancies between available ESTs and their corresponding reference genomic sequences, putative RNA editing candidates were identified. High-throughput sequencing was used to validate these candidates. All predicted coordinates appeared to be either SNPs or unedited.

VCP/p97 is essential for maturation of ubiquitin-containing autophagosomes and this function is impaired by mutations that cause IBMPFD.

VCP (VCP/p97) is a ubiquitously expressed member of the AAA(+)-ATPase family of chaperone-like proteins that regulates numerous cellular processes including chromatin decondensation, homotypic membrane fusion and ubiquitin-dependent protein degradation by the proteasome. Mutations in VCP cause a multisystem degenerative disease consisting of inclusion body myopathy, Paget disease of bone, and frontotemporal dementia (IBMPFD). Here we show that VCP is essential for autophagosome maturation. We generated cells stably expressing dual-tagged LC3 (mCherry-EGFP-LC3) which permit monitoring of autophagosome maturation. We determined that VCP deficiency by RNAi-mediated knockdown or overexpression of dominant-negative VCP results in significant accumulation of immature autophagic vesicles, some of which are abnormally large, acidified and exhibit cathepsin B activity. Furthermore, expression of disease-associated VCP mutants (R155H and A232E) also causes this autophagy defect. VCP was found to be essential to autophagosome maturation under basal conditions and in cells challenged by proteasome inhibition, but not in cells challenged by starvation, suggesting that VCP might be selectively required for autophagic degradation of ubiquitinated substrates. Indeed, a high percentage of the accumulated autophagic vesicles contain ubiquitin-positive contents, a feature that is not observed in autophagic vesicles that accumulate following starvation or treatment with Bafilomycin A. Finally, we show accumulation of numerous, large LAMP-1 and LAMP-2-positive vacuoles and accumulation of LC3-II in myoblasts derived from patients with IBMPFD. We conclude that VCP is essential for maturation of ubiquitin-containing autophagosomes and that defect in this function may contribute to IBMPFD pathogenesis.

Altered ultrasonic vocalization and impaired learning and memory in Angelman syndrome mouse model with a large maternal deletion from Ube3a to Gabrb3.

Angelman syndrome (AS) is a neurobehavioral disorder associated with mental retardation, absence of language development, characteristic electroencephalography (EEG) abnormalities and epilepsy, happy disposition, movement or balance disorders, and autistic behaviors. The molecular defects underlying AS are heterogeneous, including large maternal deletions of chromosome 15q11-q13 (70%), paternal uniparental disomy (UPD) of chromosome 15 (5%), imprinting mutations (rare), and mutations in the E6-AP ubiquitin ligase gene UBE3A (15%). Although patients with UBE3A mutations have a wide spectrum of neurological phenotypes, their features are usually milder than AS patients with deletions of 15q11-q13. Using a chromosomal engineering strategy, we generated mutant mice with a 1.6-Mb chromosomal deletion from Ube3a to Gabrb3, which inactivated the Ube3a and Gabrb3 genes and deleted the Atp10a gene. Homozygous deletion mutant mice died in the perinatal period due to a cleft palate resulting from the null mutation in Gabrb3 gene. Mice with a maternal deletion (m-/p+) were viable and did not have any obvious developmental defects. Expression analysis of the maternal and paternal deletion mice confirmed that the Ube3a gene is maternally expressed in brain, and showed that the Atp10a and Gabrb3 genes are biallelically expressed in all brain sub-regions studied. Maternal (m-/p+), but not paternal (m+/p-), deletion mice had increased spontaneous seizure activity and abnormal EEG. Extensive behavioral analyses revealed significant impairment in motor function, learning and memory tasks, and anxiety-related measures assayed in the light-dark box in maternal deletion but not paternal deletion mice. Ultrasonic vocalization (USV) recording in newborns revealed that maternal deletion pups emitted significantly more USVs than wild-type littermates. The increased USV in maternal deletion mice suggests abnormal signaling behavior between mothers and pups that may reflect abnormal communication behaviors in human AS patients. Thus, mutant mice with a maternal deletion from Ube3a to Gabrb3 provide an AS mouse model that is molecularly more similar to the contiguous gene deletion form of AS in humans than mice with Ube3a mutation alone. These mice will be valuable for future comparative studies to mice with maternal deficiency of Ube3a alone.