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Dna-encoded library

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https://www.readbyqxmd.com/read/29648439/development-and-synthesis-of-dna-encoded-benzimidazole-library
#1
Yun Ding, Jing Chai, Paolo A Centrella, Chenaimwoyo Gondo, Jennifer L DeLorey, Matthew A Clark
Encoded library technology (ELT) is an effective approach to the discovery of novel small-molecule ligands for biologi-cal targets. A key factor for the success of the technology is the chemical diversity of the libraries. Here we report the development of DNA-conjugated benzimidazoles. Using 4-fluoro-3-nitrobenzoic acid as a key synthon, we synthesized a 320 million-member DNA-encoded benzimidazole library using Fmoc-protected amino acids, amines and aldehydes as diversity elements. Affinity selection of the library led to the discovery of a novel, potent and specific antagonist of the NK3 receptor...
April 12, 2018: ACS Combinatorial Science
https://www.readbyqxmd.com/read/29610462/second-generation-dna-templated-macrocycle-libraries-for-the-discovery-of-bioactive-small-molecules
#2
Dmitry L Usanov, Alix I Chan, Juan Pablo Maianti, David R Liu
DNA-encoded libraries have emerged as a widely used resource for the discovery of bioactive small molecules, and offer substantial advantages compared with conventional small-molecule libraries. Here, we have developed and streamlined multiple fundamental aspects of DNA-encoded and DNA-templated library synthesis methodology, including computational identification and experimental validation of a 20 × 20 × 20 × 80 set of orthogonal codons, chemical and computational tools for enhancing the structural diversity and drug-likeness of library members, a highly efficient polymerase-mediated template library assembly strategy, and library isolation and purification methods...
April 2, 2018: Nature Chemistry
https://www.readbyqxmd.com/read/29578681/solid-phase-synthesis-of-%C3%AE-hydroxy-ketones-via-dna-compatible-organocatalytic-aldol-reactions
#3
Keitou Shu, 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 aldol reaction between immobilized aldehydes and soluble ketones. These reaction conditions do not compromise the amplification of DNA by the polymerase chain reaction...
March 26, 2018: ACS Combinatorial Science
https://www.readbyqxmd.com/read/29556050/versatile-protein-recognition-by-the-encoded-display-of-multiple-chemical-elements-on-a-constant-macrocyclic-scaffold
#4
Yizhou Li, Roberto De Luca, Samuele Cazzamalli, Francesca Pretto, Davor Bajic, Jörg Scheuermann, Dario Neri
In nature, specific antibodies can be generated as a result of an adaptive selection and expansion of lymphocytes with suitable protein binding properties. We attempted to mimic antibody-antigen recognition by displaying multiple chemical diversity elements on a defined macrocyclic scaffold. Encoding of the displayed combinations was achieved using distinctive DNA tags, resulting in a library size of 35,393,112. Specific binders could be isolated against a variety of proteins, including carbonic anhydrase IX, horseradish peroxidase, tankyrase 1, human serum albumin, alpha-1 acid glycoprotein, calmodulin, prostate-specific antigen and tumour necrosis factor...
April 2018: Nature Chemistry
https://www.readbyqxmd.com/read/29505267/direct-selection-of-fluorescence-enhancing-rna-aptamers
#5
Michael Gotrik, Gurpreet Sekhon, Saumya Saurabh, Margaret Nakamoto, Michael Eisenstein, H Tom Soh
RNA aptamers that generate a strong fluorescence signal upon binding a nonfluorescent small-molecule dye offer a powerful means for the selective imaging of individual RNA species. Unfortunately, conventional in vitro discovery methods are not efficient at generating such fluorescence-enhancing aptamers, because they primarily exert selective pressure based on target affinity-a characteristic that correlates poorly with fluorescence enhancement. Thus, only a handful of fluorescence-enhancing aptamers have been reported to date...
March 5, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29503702/acid-resistant-genes-of-oral-plaque-microbiome-from-the-functional-metagenomics
#6
Meng Zhang, Yuqiao Zheng, Yuhong Li, Han Jiang, Yuping Huang, Minquan Du
Acid resistance is one of key properties assisting the survival of cariogenic bacteria in a dental caries environment, but only a few genes conferring acid resistance have been identified to data. Functional metagenomics provides a systematic method for investigating commensal DNA to identify genes that encode target functions. Here, the host strain Escherichia coli DH10B and a constructed bidirectional transcription vector pSKII+ -lacZ contributed to the construction of a metagenomic library, and 46.6 Mb of metagenomic DNA was cloned from carious supragingival plaque of 8children along with screening for lethal functionality...
2018: Journal of Oral Microbiology
https://www.readbyqxmd.com/read/29497412/metagenomic-analysis-of-a-biphenyl-degrading-soil-bacterial-consortium-reveals-the-metabolic-roles-of-specific-populations
#7
Daniel Garrido-Sanz, Javier Manzano, Marta Martín, Miguel Redondo-Nieto, Rafael Rivilla
Polychlorinated biphenyls (PCBs) are widespread persistent pollutants that cause several adverse health effects. Aerobic bioremediation of PCBs involves the activity of either one bacterial species or a microbial consortium. Using multiple species will enhance the range of PCB congeners co-metabolized since different PCB-degrading microorganisms exhibit different substrate specificity. We have isolated a bacterial consortium by successive enrichment culture using biphenyl (analog of PCBs) as the sole carbon and energy source...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29492372/the-use-of-agrobacterium-mediated-insertional-mutagenesis-sequencing-to-identify-novel-genes-of-humicola-insolens-involved-in-cellulase-production
#8
Chao Fan, Xinxin Xu, Liya Song, Weishi Guan, Jinyang Li, Bo Liu, Pengjun Shi, Wei Zhang
A transfer DNA (T-DNA)-tagged mutant library of Humicola insolens was screened for mutants with altered cellulase production using the plate-clearing zone assay. Three selected mutants (5-A7, 5-C6, and 13-B7) exhibited significantly depressed FPase, CMCase and xylanase activities compared with the wild-type strain upon shake-flask fermentation, while the pNPCase and pNPGase activities of the three mutants were relatively higher than those of the parental strain. Combined with the results of SDS-PAGE and mass spectrometry, we suggest that expression of the CMCases Cel6B, Cel7B, CMC3, and XynA/B/C was reduced in the mutant strains...
March 2018: 3 Biotech
https://www.readbyqxmd.com/read/29483632/the-chejuenolide-biosynthetic-gene-cluster-harboring-an-iterative-trans-at-pks-system-in-hahella-chejuensis-strain-mb-1084
#9
Bee Gek Ng, Jae Woo Han, Dong Wan Lee, Gyung Ja Choi, Beom Seok Kim
Hahella chejuensis MB-1084 is a Gram-negative marine bacterial strain that produces unusual 17-membered carbocyclic tetraenes, chejuenolide A and B. Two fosmid clones responsible for chejuenolide production were identified from the genomic DNA library of the MB-1084 strain. Systematic inactivation of the open reading frames (ORFs) in the sequenced region defines the boundaries of the chejuenolide (che) biosynthetic gene cluster (24.9 kbp) that encodes one non-ribosomal peptide synthase (NRPS)-polyketide synthase (PKS) hybrid protein, three modular PKSs, two PKS domains, and an amine oxidase homolog...
February 26, 2018: Journal of Antibiotics
https://www.readbyqxmd.com/read/29476983/draft-genome-sequence-of-a-kpc-2-producing-klebsiella-pneumoniae-st340-carrying-bla-ctx-m-15-and-bla-ctx-m-59-concomitantly
#10
Tiago Casella, Andressa Batista Zequini de Morais, Diego Diniz de Paula Barcelos, Fernanda Modesto Tolentino, Louise Teixeira Cerdeira, Maria Fernanda Campagnari Bueno, Gabriela Rodrigues Francisco, Leonardo Neves de Andrade, Ana Lucia da Costa Darini, Doroti de Oliveira Garcia, Nilton Lincopan, Mara Corrêa Lelles Nogueira
OBJECTIVES: Klebsiella pneumoniae is considered an opportunistic pathogen and important agent of nosocomial and community infections. It presents the ability to capture and harbor several antimicrobial resistance genes, and in this context, the extensive use of carbapenems to treat serious infections was responsible for selection of several resistance genes. In this study, we report the draft genome sequence of a KPC-2-procuding K. pneumoniae strain (Kp10) simultaneously harboring the blaCTX-M-15 and blaCTX-M-59 genes, isolated from urine culture of a patient with Parkinson's disease...
February 21, 2018: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29475401/corrigendum
#11
(no author information available yet)
Castañón, J.; Román, J. P.; Jessop, T. C.; et al. Design and Development of a Technology Platform for DNA-Encoded Library Production and Affinity Selection. SLAS Discovery. [Online early access]. (Original DOI: 10.1177/2472555217752091) In this article, the author order was incorrectly listed in the initial OnlineFirst version. The online and print versions have been updated to reflect the correct order: Jesús Castañón, José Pablo Román, Theodore C. Jessop, Jesús de Blas, and Rubén Haro.
February 1, 2018: SLAS Discovery
https://www.readbyqxmd.com/read/29470858/genes-affecting-progression-of-bacteriophage-p22-infection-in-salmonella-identified-by-transposon-and-single-gene-deletion-screens
#12
Kaitlynne Bohm, Steffen Porwollik, Weiping Chu, John A Dover, Eddie B Gilcrease, Sherwood R Casjens, Michael McClelland, Kristin N Parent
Bacteriophages rely on their hosts for replication, and many host genes critically determine either viral progeny production or host success via phage resistance. A random insertion transposon library of 240,000 mutants in Salmonella enterica serovar Typhimurium was used to monitor effects of individual bacterial gene disruptions on bacteriophage P22 lytic infection. These experiments revealed candidate host genes that alter the timing of phage P22 propagation. Using a False Discovery Rate of <0.1, mutations in 235 host genes either blocked or delayed progression of P22 lytic infection, including many genes for which this role was previously unknown...
February 22, 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/29462903/calcium-imaging-of-gpcr-activation-using-arrays-of-reverse-transfected-hek293-cells-in-a-microfluidic-system
#13
Margriet Roelse, Maurice G L Henquet, Harrie A Verhoeven, Norbert C A de Ruijter, Ron Wehrens, Marco S van Lenthe, Renger F Witkamp, Robert D Hall, Maarten A Jongsma
Reverse-transfected cell arrays in microfluidic systems have great potential to perform large-scale parallel screening of G protein-coupled receptor (GPCR) activation. Here, we report the preparation of a novel platform using reverse transfection of HEK293 cells, imaging by stereo-fluorescence microscopy in a flowcell format, real-time monitoring of cytosolic calcium ion fluctuations using the fluorescent protein Cameleon and analysis of GPCR responses to sequential sample exposures. To determine the relationship between DNA concentration and gene expression, we analyzed cell arrays made with variable concentrations of plasmid DNA encoding fluorescent proteins and the Neurokinin 1 (NK1) receptor...
February 16, 2018: Sensors
https://www.readbyqxmd.com/read/29459147/cycls-accurate-whole-library-sequencing-of-cyclic-peptides-using-tandem-mass-spectrometry
#14
Chad Townsend, Akihiro Furukawa, Joshua Schwochert, Cameron R Pye, Quinn Edmondson, R Scott Lokey
Cyclic peptides are of great interest as therapeutic compounds due to their potential for specificity and intracellular activity, but specific compounds can be difficult to identify from large libraries without resorting to molecular encoding techniques. Large libraries of cyclic peptides are often DNA-encoded or linearized before sequencing, but both of those deconvolution strategies constrain the chemistry, assays, and quantification methods which can be used. We developed an automated sequencing program, CycLS, to identify cyclic peptides contained within large synthetic libraries...
February 3, 2018: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/29457795/random-access-in-large-scale-dna-data-storage
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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