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Dna-encoded library

Stefan Matysiak, Klaus Hellmuth, Afaf H El-Sagheer, Arun Shivalingam, Yavuz Ariyurek, Marco de Jong, Martine J Hollestelle, Ruud Out, Tom Brown
DNA encoded ligands are self-assembled into bivalent complexes and chemically ligated to link their identities. To demonstrate their potential as a combinatorial screening platform for avidity interactions, the optimal bivalent aptamer design (examplar ligands) for human alpha-thrombin is determined in a single round of selection and the DNA scaffold replaced with minimal impact on the final design.
December 7, 2017: Organic & Biomolecular Chemistry
Zhengrong Zhu, Alex Shaginian, LaShadric C Grady, Thomas O'Keeffe, Xiangguo E Shi, Christopher P Davie, Graham L Simpson, Jeffrey A Messer, Ghotas Evindar, Robert N Bream, Praew P Thansandote, Naomi R Prentice, Andrew M Mason, Sandeep Pal
A DNA-encoded macrocyclic peptide library was designed and synthesized with 2.4×(10^12) members composed of 4-20 natural and non-natural amino acids. Affinity-based selection was performed against two therapeutic targets, VHL and RSV N protein. Based on selection data some peptides were selected for resynthesis without DNA tag and their activity was confirmed.
November 29, 2017: ACS Chemical Biology
Marella D Canny, Nathalie Moatti, Leo C K Wan, Amélie Fradet-Turcotte, Danielle Krasner, Pedro A Mateos-Gomez, Michal Zimmermann, Alexandre Orthwein, Yu-Chi Juang, Wei Zhang, Sylvie M Noordermeer, Eduardo Seclen, Marcus D Wilson, Andrew Vorobyov, Meagan Munro, Andreas Ernst, Timothy F Ng, Tiffany Cho, Paula M Cannon, Sachdev S Sidhu, Frank Sicheri, Daniel Durocher
Programmable nucleases, such as Cas9, are used for precise genome editing by homology-dependent repair (HDR). However, HDR efficiency is constrained by competition from other double-strand break (DSB) repair pathways, including non-homologous end-joining (NHEJ). We report the discovery of a genetically encoded inhibitor of 53BP1 that increases the efficiency of HDR-dependent genome editing in human and mouse cells. 53BP1 is a key regulator of DSB repair pathway choice in eukaryotic cells and functions to favor NHEJ over HDR by suppressing end resection, which is the rate-limiting step in the initiation of HDR...
November 27, 2017: Nature Biotechnology
Stéphanie Caby, Lucile Pagliazzo, Julien Lancelot, Jean-Michel Saliou, Nicolas Bertheaume, Raymond J Pierce, Emmanuel Roger
BACKGROUND: Histone deacetylase 8 from Schistosoma mansoni (SmHDAC8) is essential to parasite growth and development within the mammalian host and is under investigation as a target for the development of selective inhibitors as novel schistosomicidal drugs. Although some protein substrates and protein partners of human HDAC8 have been characterized, notably indicating a role in the function of the cohesin complex, nothing is known of the partners and biological function of SmHDAC8. METHODOLOGY/PRINCIPAL FINDINGS: We therefore employed two strategies to characterize the SmHDAC8 interactome...
November 20, 2017: PLoS Neglected Tropical Diseases
K Delaney Hook, John T Chambers, Ryan Hili
We have developed a novel high-throughput screening platform for the discovery of small-molecules catalysts for bond-forming reactions. The method employs an in vitro selection for bond-formation using amphiphilic DNA-encoded small molecules charged with reaction substrate, which enables selections to be conducted in a variety of organic or aqueous solvents. Using the amine-catalysed aldol reaction as a catalytic model and high-throughput DNA sequencing as a selection read-out, we demonstrate the 1200-fold enrichment of a known aldol catalyst from a library of 16...
October 1, 2017: Chemical Science
Nan Hao, Keith E Shearwin
Bacterial sigma54 (σ(54)) promoters are the DNA-binding motif for σ(54)-containing RNA polymerase (RNAP) holoenzymes. A recent study using a combination of synthetic oligonucleotide library screening, biochemical characterization, and bioinformatics has uncovered a new and unexpected role for σ(54) promoters, encoding a form of bacterial 'insulator sequence' to dampen unwanted translation.
November 7, 2017: Trends in Biochemical Sciences
Wesley Cochrane, Amber L Hackler, Valerie J Cavett, Alexander K Price, Brian M Paegel
Reaction incubation is ubiquitous in high-throughput screening workflows, including those at the microfluidic droplet scale. Fully integrated microfluidic processors that generate, incubate, and sort droplets for continuous droplet screening must passively handle a flowing emulsion such that droplet-droplet incubation time variation is minimized. Here, we disclose an integrated microfluidic emulsion creamer that close packs assay droplets by draining away excess oil through microfabricated drain channels. The drained oil co-flows with creamed emulsion and then reintroduces the oil to disperse the droplets at the circuit terminus for analysis...
November 10, 2017: Analytical Chemistry
Kevin A Henry
Immunogenetic analyses of expressed antibody repertoires are becoming increasingly common experimental investigations and are critical to furthering our understanding of autoimmunity, infectious disease, and cancer. Next-generation DNA sequencing (NGS) technologies have now made it possible to interrogate antibody repertoires to unprecedented depths, typically by sequencing of cDNAs encoding immunoglobulin variable domains. In this chapter, we describe simple, fast, and reliable methods for producing and sequencing multiplex PCR amplicons derived from the variable regions (VH, VHH or VL) of rearranged immunoglobulin heavy and light chain genes using the Illumina MiSeq platform...
2018: Methods in Molecular Biology
Marcio Zaccaron, Sandeep Sharma, Burton H Bluhm
Phomopsis longicolla (Hobbs) causes Phomopsis seed decay and stem lesions in soybean (Glycine max). In this study, a novel, high-throughput adaptation of RAD-seq termed MoNSTR-seq (Mutation analysis via Next-generation DNA Sequencing of T-DNA Regions) was developed to determine the genomic location of T-DNA insertions in P. longicolla mutants. Insertional mutants were created via ATMT, and one mutant, strain PL343, was further investigated due to impaired stem lesion formation. MoNSTR-seq, in which DNA libraries are created with two distinct restriction enzymes and customized adapters to simultaneously enrich both T-DNA insertion borders, was developed to characterize the genomic lesion in strain PL343...
November 6, 2017: Letters in Applied Microbiology
Huan Dong, Ling Bai, Jie Chang, Chun-Peng Song
The plant hormone abscisic acid (ABA) plays a crucial role in root architecture; however, the molecular mechanism of ABA-regulated lateral root (LR) growth is not well known. We screened an Arabidopsis thaliana mutant with LR growth that was sensitive to ABA from a T-DNA insertion mutant library, which was an allelic mutant of plgg1-1, termed plgg1-2. PLGG1 encodes a chloroplast protein that transports plastidic glycolate and glycerate. The length and number of LRs at the root-hypocotyl junction of plgg1-1 and plgg1-2 were significantly impaired under exogenous ABA treatment, and the transgenic plant complementary lines of plgg1-2 restored LR growth in response to ABA...
October 31, 2017: Biochemical and Biophysical Research Communications
Florence Arsène-Ploetze, Olfa Chiboub, Didier Lièvremont, Julien Farasin, Kelle C Freel, Stephanie Fouteau, Valérie Barbe
Several studies have suggested the existence of a close relationship between antibiotic-resistant phenotypes and resistance to other toxic compounds such as heavy metals, which involve co-resistance or cross-resistance mechanisms. A metagenomic library was previously constructed in Escherichia coli with DNA extracted from the bacterial community inhabiting an acid mine drainage (AMD) site highly contaminated with heavy metals. Here, we conducted a search for genes involved in antibiotic resistance using this previously constructed library...
October 31, 2017: Environmental Science and Pollution Research International
Martin Moder, Georgia Velimezi, Michel Owusu, Abdelghani Mazouzi, Marc Wiedner, Joana Ferreira da Silva, Lydia Robinson-Garcia, Fiorella Schischlik, Rastislav Slavkovsky, Robert Kralovics, Michael Schuster, Christoph Bock, Trey Ideker, Stephen P Jackson, Jörg Menche, Joanna I Loizou
Maintenance of genome integrity via repair of DNA damage is a key biological process required to suppress diseases, including Fanconi anemia (FA). We generated loss-of-function human haploid cells for FA complementation group C (FANCC), a gene encoding a component of the FA core complex, and used genome-wide CRISPR libraries as well as insertional mutagenesis to identify synthetic viable (genetic suppressor) interactions for FA. Here we show that loss of the BLM helicase complex suppresses FANCC phenotypes and we confirm this interaction in cells deficient for FA complementation group I and D2 (FANCI and FANCD2) that function as part of the FA I-D2 complex, indicating that this interaction is not limited to the FA core complex, hence demonstrating that systematic genome-wide screening approaches can be used to reveal genetic viable interactions for DNA repair defects...
November 1, 2017: Nature Communications
Cynthia Gomes, Jaemog Soh
Mammalian spermatogenesis occurs in a precise and coordinated manner in the seminiferous tubules. One of the attempts to understand the detailed biological process during mammalian spermatogenesis at the molecular level has been to identify the testis specific genes followed by study of the testicular expression pattern of the genes. From the subtracted cDNA library of rat testis prepared using representational difference analysis (RDA) method, a complimentary DNA clone encoding type III member of a DnaJ family protein, DnaJC18, was cloned (GenBank Accession No...
September 2017: Balsaeng'gwa Saengsig
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 Hübner, Hilmar Weinmann, Ingo V Hartung, Mátyás Gorjánácz
ATAD2 (ANCCA) is an epigenetic regulator and transcriptional cofactor, whose overexpression 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 a chemical probe to explore ATAD2 biology.
November 17, 2017: ACS Chemical Biology
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...
November 7, 2017: Structure
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
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
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
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
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
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