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Dna-encoded library

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https://www.readbyqxmd.com/read/29457795/random-access-in-large-scale-dna-data-storage
#1
Lee Organick, Siena Dumas Ang, Yuan-Jyue Chen, Randolph Lopez, Sergey Yekhanin, Konstantin Makarychev, Miklos Z Racz, Govinda Kamath, Parikshit Gopalan, Bichlien Nguyen, Christopher N Takahashi, Sharon Newman, Hsing-Yeh Parker, Cyrus Rashtchian, Kendall Stewart, Gagan Gupta, Robert Carlson, John Mulligan, Douglas Carmean, Georg Seelig, Luis Ceze, Karin Strauss
Synthetic DNA is durable and can encode digital data with high density, making it an attractive medium for data storage. However, recovering stored data on a large-scale currently requires all the DNA in a pool to be sequenced, even if only a subset of the information needs to be extracted. Here, we encode and store 35 distinct files (over 200 MB of data), in more than 13 million DNA oligonucleotides, and show that we can recover each file individually and with no errors, using a random access approach. We design and validate a large library of primers that enable individual recovery of all files stored within the DNA...
February 19, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29454942/cloning-molecular-modeling-and-characterization-of-acidic-cellulase-from-buffalo-rumen-and-its-applicability-in-saccharification-of-lignocellulosic-biomass
#2
Tripti Dadheech, Ravi Shah, Ramesh Pandit, Ankit Hinsu, Prakram Singh Chauhan, Subhash Jakhesara, Anju Kunjadiya, Dharamshibhai Rank, Chaitanya Joshi
Cellulase hydrolyses the cellulose by cleaving the β-1,4-linkages to produce mono-, oligo- and shorter polysaccharide units. These enzymes have applications in various industries such as pulp and paper, laundry, food and feed, textile, brewing industry and in biofuel production. In the present study we have cloned acid-cellulase gene (Cel-1) from the fosmid library of buffalo rumen metagenomic DNA and functionally expressed it in Escherichia coli. The ORF encoding cellulase consisted of 1176-bp, corresponding to protein of 391 amino acid and has catalytic domain belonging to glycosyl hydrolase family 5...
February 15, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29437521/randomness-in-dna-encoded-library-selection-data-can-be-modeled-for-more-reliable-enrichment-calculation
#3
Letian Kuai, Thomas O'Keeffe, Christopher Arico-Muendel
DNA Encoded Libraries (DELs) use unique DNA sequences to tag each chemical warhead within a library mixture to enable deconvolution following affinity selection against a target protein. With next-generation sequencing, millions to billions of sequences can be read and counted to report binding events. This unprecedented capability has enabled researchers to synthesize and analyze numerically large chemical libraries. Despite the common perception that each library member undergoes a miniaturized affinity assay, selections with higher complexity libraries often produce results that are difficult to rank order...
February 1, 2018: SLAS Discovery
https://www.readbyqxmd.com/read/29432181/three-classes-of-recurrent-dna-break-clusters-in-brain-progenitors-identified-by-3d-proximity-based-break-joining-assay
#4
Pei-Chi Wei, Cheng-Sheng Lee, Zhou Du, Bjoern Schwer, Yuxiang Zhang, Jennifer Kao, Jeffrey Zurita, Frederick W Alt
We recently discovered 27 recurrent DNA double-strand break (DSB) clusters (RDCs) in mouse neural stem/progenitor cells (NSPCs). Most RDCs occurred across long, late-replicating RDC genes and were found only after mild inhibition of DNA replication. RDC genes share intriguing characteristics, including encoding surface proteins that organize brain architecture and neuronal junctions, and are genetically implicated in neuropsychiatric disorders and/or cancers. RDC identification relies on high-throughput genome-wide translocation sequencing (HTGTS), which maps recurrent DSBs based on their translocation to "bait" DSBs in specific chromosomal locations...
February 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29395976/screening-one-bead-one-compound-libraries-against-serum-using-a-flow-cytometer-determination-of-the-minimum-antibody-concentration-required-for-ligand-discovery
#5
Osayemwenre Erharuyi, Scott Simanski, Patrick J McEnaney, Thomas Kodadek
One bead one compound (OBOC) libraries can be screened against serum samples to identify ligands to antibodies in this mixture. In this protocol, hit beads are identified by staining with a fluorescent labeled secondary antibody. When screens are conducted against two different sets of serum, antibodies, and ligands to them, can be discovered that distinguish the two populations. The application of DNA-encoding technology to OBOC libraries has allowed the use of 10 µm beads for library preparation and screening, which pass through a standard flow cytometer, allowing the fluorescent hit beads to be separated from beads displaying non-ligands easily...
January 29, 2018: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/29385567/elucidating-the-small-regulatory-rna-repertoire-of-the-sea-anemone-anemonia-viridis-based-on-whole-genome-and-small-rna-sequencing
#6
Ilona Urbarova, Hardip Patel, Sylvain Forêt, Bård Ove Karlsen, Tor Erik Jørgensen, Jason M Hall-Spencer, Steinar D Johansen
Cnidarians harbour a variety of small regulatory RNAs that include microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), but detailed information is limited. Here we report the identification and expression of novel miRNAs and putative piRNAs, as well as their genomic loci, in the symbiotic sea anemone Anemonia viridis. We generated a draft assembly of the A. viridis genome with putative size of 313 Mb that appeared to be composed of about 36% repeats, including known transposable elements. We detected approximately equal fractions of DNA transposons and retrotransposons...
January 27, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29365249/towards-a-microparticle-based-system-for-pooled-assays-of-small-molecules-in-cellular-contexts
#7
Carrie E Yozwiak, Tal Hirschhorn, Brent R Stockwell
Experimental approaches to the discovery of small molecule probes and drug candidates often use biochemical or cell-based screening of large libraries (>105) of small molecules. Small molecules of interest are tested one at a time in individual wells of a microtiter plate, at a significant cost in time and resources. Furthermore, evaluation of large numbers of compounds in such assays requires robust cellular or biochemical screening formats that may not be relevant to the contexts found in human patients...
January 24, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29361864/tagfinder-a-novel-tag-analysis-methodology-that-enables-detection-of-molecules-from-dna-encoded-chemical-libraries
#8
Jorge Amigo, Ramón Rama-Garda, Xabier Bello, Beatriz Sobrino, Jesús de Blas, María Martín-Ortega, Theodore C Jessop, Ángel Carracedo, María Isabel García Loza, Eduardo Domínguez
Available tools to analyze sequencing data coming from DNA-encoded chemical libraries (DELs) are often limited to in-house methods, which usually rely on strictly looking for the particular DEL structure used. Current methods do not take into account technological errors, such as library codification and sequencing errors, when detecting the sequences. The vast amount of data produced by next-generation sequencing of DEL screens is usually enough to extract the minimum information needed for compound identification...
January 1, 2018: SLAS Discovery
https://www.readbyqxmd.com/read/29361863/design-and-development-of-a-technology-platform-for-dna-encoded-library-production-and-affinity-selection
#9
José Pablo Román, Rubén Haro, Jesús de Blas, Theodore C Jessop, Jesús Castañón
DNA-encoded libraries (DELs) have emerged as an efficient and cost-effective drug discovery tool for the exploration and screening of very large chemical space using small-molecule collections of unprecedented size. Herein, we report an integrated automation and informatics system designed to enhance the quality, efficiency, and throughput of the production and affinity selection of these libraries. The platform is governed by software developed according to a database-centric architecture to ensure data consistency, integrity, and availability...
January 1, 2018: SLAS Discovery
https://www.readbyqxmd.com/read/29352178/compositional-bias-in-na%C3%A3-ve-and-chemically-modified-phage-displayed-libraries-uncovered-by-paired-end-deep-sequencing
#10
Bifang He, Katrina F Tjhung, Nicholas J Bennett, Ying Chou, Andrea Rau, Jian Huang, Ratmir Derda
Understanding the composition of a genetically-encoded (GE) library is instrumental to the success of ligand discovery. In this manuscript, we investigate the bias in GE-libraries of linear, macrocyclic and chemically post-translationally modified (cPTM) tetrapeptides displayed on the M13KE platform, which are produced via trinucleotide cassette synthesis (19 codons) and NNK-randomized codon. Differential enrichment of synthetic DNA {S}, ligated vector {L} (extension and ligation of synthetic DNA into the vector), naïve libraries {N} (transformation of the ligated vector into the bacteria followed by expression of the library for 4...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29332216/characteristics-of-arg-carrying-plasmidome-in-the-cultivable-microbial-community-from-wastewater-treatment-system-under-high-oxytetracycline-concentration
#11
Yanhong Shi, Hong Zhang, Zhe Tian, Min Yang, Yu Zhang
Studies on antibiotic production wastewater have shown that even a single antibiotic can select for multidrug resistant bacteria in aquatic environments. It is speculated that plasmids are an important mechanism of multidrug resistance (MDR) under high concentrations of antibiotics. Herein, two metagenomic libraries were constructed with plasmid DNA extracted from cultivable microbial communities in a biological wastewater treatment reactor supplemented with 0 (CONTROL) or 25 mg/L of oxytetracycline (OTC-25)...
January 13, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29328784/dna-encoded-chemical-libraries-a-selection-system-based-on-endowing-organic-compounds-with-amplifiable-information
#12
Dario Neri, Richard A Lerner
The discovery of organic ligands that bind specifically to proteins is a central problem in chemistry, biology, and the biomedical sciences. The encoding of individual organic molecules with distinctive DNA tags, serving as amplifiable identification bar codes, allows the construction and screening of combinatorial libraries of unprecedented size, thus facilitating the discovery of ligands to many different protein targets. Fundamentally, one links powers of genetics and chemical synthesis. After the initial description of DNA-encoded chemical libraries in 1992, several experimental embodiments of the technology have been reduced to practice...
January 12, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29316408/agonists-and-antagonists-of-protease-activated-receptor-2-discovered-within-a-dna-encoded-chemical-library-using-mutational-stabilization-of-the-target
#13
Dean G Brown, Giles A Brown, Paolo Centrella, Kaan Certel, Robert M Cooke, John W Cuozzo, Niek Dekker, Christoph E Dumelin, Andrew Ferguson, Cédric Fiez-Vandal, Stefan Geschwindner, Marie-Aude Guié, Sevan Habeshian, Anthony D Keefe, Oliver Schlenker, Eric A Sigel, Arjan Snijder, Holly T Soutter, Linda Sundström, Dawn M Troast, Giselle Wiggins, Jing Zhang, Ying Zhang, Matthew A Clark
The discovery of ligands via affinity-mediated selection of DNA-encoded chemical libraries is driven by the quality and concentration of the protein target. G-protein-coupled receptors (GPCRs) and other membrane-bound targets can be difficult to isolate in their functional state and at high concentrations, and therefore have been challenging for affinity-mediated selection. Here, we report a successful selection campaign against protease-activated receptor 2 (PAR2). Using a thermo-stabilized mutant of PAR2, we conducted affinity selection using our >100-billion-compound DNA-encoded library...
January 1, 2018: SLAS Discovery
https://www.readbyqxmd.com/read/29316387/solid-phase-synthesis-of-%C3%AE-amino-ketones-via-dna-compatible-organocatalytic-mannich-reactions
#14
Nam Tran Hoang, Thomas Kodadek
One-bead-one-compound (OBOC) libraries constructed by solid-phase split-and-pool synthesis are a valuable source of protein ligands. Most OBOC libraries are comprised of oligoamides, particularly peptides, peptoids and peptoid-inspired molecules. Further diversification of the chemical space covered by OBOC libraries is desirable. Towards this end, we report here the efficient proline-catalyzed asymmetric Mannich reaction between immobilized aldehydes and soluble ketones and anilines. The reaction conditions do not compromise the amplification of DNA by the PCR...
January 9, 2018: ACS Combinatorial Science
https://www.readbyqxmd.com/read/29313809/parp1-facilitates-ep300-recruitment-to-the-promoters-of-the-subset-of-rbl2-dependent-genes
#15
Agnieszka Robaszkiewicz, Ewelina Wiśnik, Zsolt Regdon, Kinga Chmielewska, László Virág
Differentiation of human monocytes is associated with proliferation arrest resulting from activation of the inter alia retinoblastoma protein family of gene repressors, which target gene promoters in an E2F-dependent manner. To investigate RBL2 contribution to defining monocyte phenotype and function, we used primer libraries. We identified genes encoding two surface receptors (CXCR1 and IL17RE) and two TLR signaling mediators (CD86 and NFKB2) that are repressed by the RBL2-E2F4-HDAC1-BRM complex. Surprisingly, PARP1 co-regulated 24 out of the 28 identified genes controlled by RBL2...
December 4, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29301959/multiplexed-gene-synthesis-in-emulsions-for-exploring-protein-functional-landscapes
#16
Calin Plesa, Angus M Sidore, Nathan B Lubock, Di Zhang, Sriram Kosuri
Improving our ability to construct and functionally characterize DNA sequences would broadly accelerate progress in biology. Here, we introduce DropSynth, a scalable, low-cost method to build thousands of defined gene-length constructs in a pooled (multiplexed) manner. DropSynth uses a library of barcoded beads that pull down the oligonucleotides necessary for a gene's assembly, which are then processed and assembled in water-in-oil emulsions. We used DropSynth to successfully build more than 7000 synthetic genes that encode phylogenetically diverse homologs of two essential genes in Escherichia coli We tested the ability of phosphopantetheine adenylyltransferase homologs to complement a knockout E...
January 19, 2018: Science
https://www.readbyqxmd.com/read/29298042/dna-compatible-solid-phase-combinatorial-synthesis-of-%C3%AE-cyanoacrylamides-and-related-electrophiles
#17
Kevin Pels, Paige Dickson, Hongchan An, Thomas Kodadek
We demonstrate that the Knoevenagel condensation can be exploited in combinatorial synthesis on the solid phase. Condensation products from such reactions were structurally characterized, and their Michael reactivity with thiol and phosphine nucleophiles is described. Cyanoacrylamides were previously reported to react reversibly with thiols, and notably, we show that dilution into low pH buffer can trap covalent adducts which are isolable via chromatography. Finally, we synthesized both traditional and DNA-encoded one-bead, one-compound libraries containing cyanoacrylamides as a source of cysteine-reactive, reversibly covalent protein ligands...
January 3, 2018: ACS Combinatorial Science
https://www.readbyqxmd.com/read/29261143/slbzip38-a-tomato-bzip-family-gene-downregulated-by-abscisic-acid-is-a-negative-regulator-of-drought-and-salt-stress-tolerance
#18
Yanglu Pan, Xin Hu, Chunyan Li, Xing Xu, Chenggang Su, Jinhua Li, Hongyuan Song, Xingguo Zhang, Yu Pan
The basic leucine zipper (bZIP) transcription factors have crucial roles in plant stress responses. In this study, the bZIP family gene SlbZIP38 (GenBank accession No: XM004239373) was isolated from a tomato (Solanum lycopersicum cv. Ailsa Craig) mature leaf cDNA library. The DNA sequence of SlbZIP38 encodes a protein of 484 amino acids, including a highly conserved bZIP DNA-binding domain in the C-terminal region. We found that SlbZIP38 was differentially expressed in various organs of the tomato plant and was downregulated by drought, salt stress, and abscisic acid (ABA)...
December 20, 2017: Genes
https://www.readbyqxmd.com/read/29215120/searching-for-avidity-by-chemical-ligation-of-combinatorially-self-assembled-dna-encoded-ligand-libraries
#19
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
https://www.readbyqxmd.com/read/29185700/design-and-application-of-a-dna-encoded-macrocyclic-peptide-library
#20
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
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