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Dna-encoded library

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https://www.readbyqxmd.com/read/29043777/isoform-selective-atad2-chemical-probe-with-novel-chemical-structure-and-unusual-mode-of-action
#1
Amaury E Fernández-Montalván, Markus Berger, Benno Kuropka, Seong Joo Koo, Volker Badock, Joerg Weiske, Vera Puetter, Simon J Holton, Detlef Stöckigt, Antonius Ter Laak, Paolo A Centrella, Matthew A Clark, Christoph E Dumelin, Eric A Sigel, Holly H Soutter, Dawn M Troast, Ying Zhang, John W Cuozzo, Anthony D Keefe, Didier Roche, Vincent Rodeschini, Apirat Chaikuad, Laura Díaz-Sáez, James M Bennett, Oleg Fedorov, Kilian V M Huber, Jan Huebner, Hilmar Weinmann, Ingo V Hartung, Matyas Gorjanacz
ATAD2 (ANCCA) is an epigenetic regulator and transcriptional co-factor, whose over-expression has been linked to the progress of various cancer types. Here we report a DNA-encoded library screen leading to the discovery of BAY-850, a potent and isoform selective inhibitor that specifically induces ATAD2 bromodomain dimerization, and prevents interactions with acetylated histones in vitro, as well as with chromatin in cells. These features qualify BAY-850 as chemical probe to explore ATAD2 biology.
October 18, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29033289/foldability-of-a-natural-de-novo-evolved-protein
#2
Dixie Bungard, Jacob S Copple, Jing Yan, Jimmy J Chhun, Vlad K Kumirov, Scott G Foy, Joanna Masel, Vicki H Wysocki, Matthew H J Cordes
The de novo evolution of protein-coding genes from noncoding DNA is emerging as a source of molecular innovation in biology. Studies of random sequence libraries, however, suggest that young de novo proteins will not fold into compact, specific structures typical of native globular proteins. Here we show that Bsc4, a functional, natural de novo protein encoded by a gene that evolved recently from noncoding DNA in the yeast S. cerevisiae, folds to a partially specific three-dimensional structure. Bsc4 forms soluble, compact oligomers with high β sheet content and a hydrophobic core, and undergoes cooperative, reversible denaturation...
October 7, 2017: Structure
https://www.readbyqxmd.com/read/29032547/genome-wide-mutagenesis-in-borrelia-burgdorferi
#3
Tao Lin, Lihui Gao
Signature-tagged mutagenesis (STM) is a functional genomics approach to identify bacterial virulence determinants and virulence factors by simultaneously screening multiple mutants in a single host animal, and has been utilized extensively for the study of bacterial pathogenesis, host-pathogen interactions, and spirochete and tick biology. The signature-tagged transposon mutagenesis has been developed to investigate virulence determinants and pathogenesis of Borrelia burgdorferi. Mutants in genes important in virulence are identified by negative selection in which the mutants fail to colonize or disseminate in the animal host and tick vector...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29029697/the-identification-of-transcriptional-regulation-related-gene-of-laccase-poxc-through-yeast-one-hybrid-screening-from-pleurotus-ostreatus
#4
Yuancheng Qi, Chao Liu, Xiankai Sun, Liyou Qiu, Jinwen Shen
Pleurotus ostreatus laccase gene poxc is transcriptionally induced by copper, and several putative MREs have been found and confirmed in its promoter region. However, the related transcription factors mediating copper response via MREs have not been reported. To isolate MRE binding proteins, we carried out yeast one-hybrid screens. Reporter genes containing two trimers of the cMRE2 and cMRE3 element were prepared and introduced into a yeast strain. The yeast was transformed with library cDNA that represents RNA isolated from CuSO4-treated fungi of P...
November 2017: Fungal Biology
https://www.readbyqxmd.com/read/29019965/molecular-cloning-recombinant-expression-and-antifungal-activity-of-bncpi-a-cystatin-in-ramie-boehmeria-nivea-l
#5
Yongting Yu, Gang Zhang, Zhimin Li, Yi Cheng, Chunsheng Gao, Liangbin Zeng, Jia Chen, Li Yan, Xiangping Sun, Litao Guo, Zhun Yan
Phytocystatins play multiple roles in plant growth, development and resistance to pests and other environmental stresses. A ramie (Boehmeria nivea L.) phytocystatin gene, designated as BnCPI, was isolated from a ramie cDNA library and its full-length cDNA was obtained by rapid amplification of cDNA ends (RACE). The full-length cDNA sequence (691 bp) consisted of a 303 bp open reading frame (ORF) encoding a protein of 100 amino acids with deduced molecular mass of 11.06 kDa and a theoretical isoelectric point (pI) of 6...
October 11, 2017: Genes
https://www.readbyqxmd.com/read/29018427/human-cytomegalovirus-ie2-86-kda-protein-induces-sting-degradation-and-inhibits-cgamp-mediated-ifn-%C3%AE-induction
#6
Jung-Eun Kim, Young-Eui Kim, Mark F Stinski, Jin-Hyun Ahn, Yoon-Jae Song
Stimulator of interferon genes (STING) is a critical signaling molecule in the innate immune response against DNA viruses by either directly sensing intracellular DNA or functioning as an adaptor molecule to activate the type I interferon (IFN) signaling pathway. We determined the functional interaction between STING and human cytomegalovirus (HCMV). A cDNA library containing 133 HCMV ORFs was screened to identify viral genes that inhibit STING-induced IFN-β promoter activation. Among the screened ORFs, UL122, which encodes the immediate-early 2 86 kDa (IE86) protein, strongly abolished STING-induced IFN-β promoter activation...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28994778/creation-of-a-dense-transposon-insertion-library-using-bacterial-conjugation-in-enterobacterial-strains-such-as-escherichia-coli-or-shigella-flexneri
#7
Nikki E Freed
Transposon mutagenesis is a method that allows gene disruption via the random genomic insertion of a piece of DNA called a transposon. The protocol below outlines a method for high efficiency transfer between bacterial strains of a plasmid harboring a transposon containing a kanamycin resistance marker. The plasmid-borne transposase is encoded by a variant tnp gene that inserts the transposon into the genome of the recipient strain with very low insertional bias. This method thus allows the creation of large mutant libraries in which transposons have been inserted into unique genomic positions in a recipient strain of either Escherichia coli or Shigella flexneri bacteria...
September 23, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28977762/lung-cancer-heterogeneity-and-new-strategies-for-drug-therapy
#8
Diane C Wang, William Wang, Bijun Zhu, Xiangdong Wang
Lung cancer heterogeneity plays an important role in the development of drug resistance. Comprehensive molecular characterizations of lung cancer can describe hereditary and somatic gene changes, mutation, and heterogeneity. We discuss heterogeneity specificity, characterization, and roles of PIK3CD, TP53, and KRAS, as well as target-driven therapies and strategies applied in clinical trials based on a proposed precise self-validation system. The system is a specifically selected strategy of treatment for patients with cancer gene mutations and heterogeneity based on gene sequencing, following validation of the strategies in the patient's own cancer cells or in patientderived xenografts using their own cancer cells isolated during surgery or biopsies...
October 4, 2017: Annual Review of Pharmacology and Toxicology
https://www.readbyqxmd.com/read/28967572/validation-and-application-of-quantitative-pcr-assays-using-host-specific-bacteroidales-genetic-markers-for-swine-fecal-pollution-tracking
#9
Lihua Fan, Jiangbing Shuai, Ruoxue Zeng, Hongfei Mo, Suhua Wang, Xiaofeng Zhang, Yongqiang He
Genome fragment enrichment (GFE) method was applied to identify host-specific bacterial genetic markers that differ among different fecal metagenomes. To enrich for swine-specific DNA fragments, swine fecal DNA composite (n = 34) was challenged against a DNA composite consisting of cow, human, goat, sheep, chicken, duck and goose fecal DNA extracts (n = 83). Bioinformatic analyses of 384 non-redundant swine enriched metagenomic sequences indicated a preponderance of Bacteroidales-like regions predicted to encode metabolism-associated, cellular processes and information storage and processing...
September 26, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28963711/novel-archaeal-thermostable-cellulases-from-an-oil-reservoir-metagenome
#10
Anna Lewin, Jinglie Zhou, Vu Thuy Trang Pham, Tone Haugen, Mohamed El Zeiny, Olav Aarstad, Wolfgang Liebl, Alexander Wentzel, Mark R Liles
Microbial assemblages were sampled from an offshore deep sub-surface petroleum reservoir 2.5 km below the ocean floor off the coast of Norway, providing conditions of high temperature and pressure, to identify new thermostable enzymes. In this study, we used DNA sequences obtained directly from the sample metagenome and from a derived fosmid library to survey the functional diversity of this extreme habitat. The metagenomic fosmid library containing 11,520 clones was screened using function- and sequence-based methods to identify recombinant clones expressing carbohydrate-degrading enzymes...
September 29, 2017: AMB Express
https://www.readbyqxmd.com/read/28956406/-aide-encodes-an-n-acyl-homoserine-lactonase-in-acinetobacter
#11
Chunyan Liu, Song Guo, Ali Turak, Junwei Zhang, Liqun Zhang
Quorum sensing (QS) is a cell-cell communication mechanism that allows bacterial populations to coordinate gene expression in response to cell density. N-acylhomoserine lactones (AHL) are used as quorum-sensing signal molecules by many Gram negative bacteria. Acinetobacter sp. 77, an AHL-degrading bacterium, was isolated in our previous work. The gene aidE for AHL inactivation was cloned in this study by screening a genomic DNA library. The deduced protein AidE is 268 amino acids in length and shares a high identity (95%) with the beta-lactamase family protein in Acinetobacter gyllenbergii CIP110306, but low identities with known AHL-degrading enzymes...
September 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28948007/crosslinking-of-dna-linked-ligands-to-target-proteins-for-enrichment-from-dna-encoded-libraries
#12
Kyle E Denton, Casey J Krusemark
Achieving sufficient enrichment of ligands from DNA-encoded libraries for detection can be difficult, particularly for low affinity ligands within highly complex libraries. To address this challenge, we present an approach for crosslinking DNA-linked ligands to target proteins using electrophilic or photoreactive groups. The approach involves the teathering of a ssDNA oligonucleotide to a DNA-encoded molecule to enable attachment of a reactive group post-synthetically via DNA hybridization. Crosslinking traps ligand-protein complexes while in solution and allows for stringent washing conditions to be applied in the subsequent purification...
October 1, 2016: MedChemComm
https://www.readbyqxmd.com/read/28944578/impact-of-a-central-scaffold-on-the-binding-affinity-of-fragment-pairs-isolated-from-dna-encoded-self-assembling-chemical-libraries
#13
Martina Bigatti, Alberto Dal Corso, Sara Vanetti, Samuele Cazzamalli, Ulrike Rieder, Jörg Scheuermann, Dario Neri, Filippo Sladojevich
The screening of encoded self-assembling chemical libraries allows the identification of fragment pairs that bind to adjacent pockets on target proteins of interest. For practical applications, it is necessary to link these ligand pairs into discrete organic molecules, devoid of any nucleic acid component. Here we describe the discovery of a synergistic binding pair for acid alpha-1 glycoprotein and a chemical strategy for the identification of optimal linkers, connecting the two fragments. The procedure yielded a set of small organic ligands, the best of which exhibited a dissociation constant of 9...
September 24, 2017: ChemMedChem
https://www.readbyqxmd.com/read/28943871/global-screening-of-salmonella-enterica-serovar-typhimurium-genes-for-desiccation-survival
#14
Rabindra K Mandal, Young M Kwon
Salmonella spp., one of the most common foodborne bacterial pathogens, has the ability to survive under desiccation conditions in foods and food processing facilities for years. This raises the concerns of Salmonella infection in humans associated with low water activity foods. Salmonella responds to desiccation stress via complex pathways involving immediate physiological actions as well as coordinated genetic responses. However, the exact mechanisms of Salmonella to resist desiccation stress remain to be fully elucidated...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28935911/directing-evolution-the-next-revolution-in-drug-discovery
#15
REVIEW
Andrew M Davis, Alleyn T Plowright, Eric Valeur
The strong biological rationale to pursue challenging drug targets such as protein-protein interactions has stimulated the development of novel screening strategies, such as DNA-encoded libraries, to allow broader areas of chemical space to be searched. There has also been renewed interest in screening natural products, which are the result of evolutionary selection for a function, such as interference with a key signalling pathway of a competing organism. However, recent advances in several areas, such as understanding of the biosynthetic pathways for natural products, synthetic biology and the development of biosensors to detect target molecules, are now providing new opportunities to directly harness evolutionary pressure to identify and optimize compounds with desired bioactivities...
October 2017: Nature Reviews. Drug Discovery
https://www.readbyqxmd.com/read/28935108/discovery-of-new-glycosidases-from-metagenomic-libraries
#16
Zach Armstrong, Peter Rahfeld, Stephen G Withers
Microorganisms routinely perform complex enzymatic transformations of natural material; thus, their enzymes have the potential to tackle medical and industrial challenges. However, a vast number of microbes are recalcitrant to cultivation. Functional screening of environmental DNA allows us to tap into the seemingly boundless diversity of enzymes encoded by microbial populations. In this chapter, we describe methods for the isolation of environmental DNA, generation of metagenomic libraries, and the functional screening of these libraries for new glycosidases...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28934943/identification-of-new-corynebacterium-pseudotuberculosis-antigens-by-immunoscreening-of-gene-expression-library
#17
Cleber Eduardo Galvão, Stenio Perdigão Fragoso, Carina Elisei de Oliveira, Odinéia Forner, Renata Ribeiro Bastos Pereira, Cleber Oliveira Soares, Grácia Maria Soares Rosinha
BACKGROUND: Caseous lymphadenitis (CLA) is a disease that affects sheep, goats and occasionally humans. The etiologic agent is the Corynebacterium pseudotuberculosis bacillus. The objective of this study was to build a gene expression library from C. pseudotuberculosis and use immunoscreening to identify genes that encode potential antigenic proteins for the development of DNA and subunit vaccines against CLA. RESULTS: A wild strain of C. pseudotuberculosis was used for extraction and partial digestion of genomic DNA...
September 21, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28915003/the-evolution-of-dna-templated-synthesis-as-a-tool-for-materials-discovery
#18
Rachel K O'Reilly, Andrew J Turberfield, Thomas R Wilks
Precise control over reactivity and molecular structure is a fundamental goal of the chemical sciences. Billions of years of evolution by natural selection have resulted in chemical systems capable of information storage, self-replication, catalysis, capture and production of light, and even cognition. In all these cases, control over molecular structure is required to achieve a particular function: without structural control, function may be impaired, unpredictable, or impossible. The search for molecules with a desired function is often achieved by synthesizing a combinatorial library, which contains many or all possible combinations of a set of chemical building blocks (BBs), and then screening this library to identify "successful" structures...
October 17, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28903064/isolation-and-characterization-of-peroxiredoxin-1-gene-of-dunaliella-salina
#19
Fanghua Gong, Jing Wang, Jie Li
Peroxiredoxin 1 (Prdx1) is a ubiquitously expressed protein in eukaryotic cells, and plays an important role in cell proliferation, differentiation, apoptosis, and redox signaling. Although Prdx1 has been better studied in yeasts and humans, only few Prdx1 genes have been cloned in green algae. The microalga Dunaliella salina (D. salina) is a model for the study of a variety of human cilia-related diseases. In this study, a suppression subtractive hybridization cDNA library of D. salina was constructed, and 6 flagellum-associated genes including D...
November 30, 2017: Gene
https://www.readbyqxmd.com/read/28866120/identification-of-a-novel-single-chain-fragment-variable-antibody-targeting-cd24-expressing-cancer-cells
#20
Shirin Eyvazi, Bahram Kazemi, Mojgan Bandehpour, Siavoush Dastmalchi
CD24 is a heavy glycosylated protein that is overexpressed in numerous cancer and cancer stem cells. It is involved in the development, invasion, and metastasis of the cancer cells. CD24 can be considered in targeted cancer therapy as a new target. Here, phage display technology was used for the identification of novel scFv antibodies against CD24. To do so, the CD24 protein was expressed and purified from a stable transgenic CHO cell line. The cells were developed by using a CD24 encoding construct, which targets the 18S rRNA gene...
September 1, 2017: Immunology Letters
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