Structural insights into catalysis and dimerization enhanced exonuclease activity of RNase J.

abstract：:The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these ...

journal_title：Nucleic acids research

authors： Bult CJ,Eppig JT,Blake JA,Kadin JA,Richardson JE,Mouse Genome Database Group.

更新日期：2016-01-04 00:00:00

abstract：:We recently developed a new type of pyrrole (Py)-imidazole (Im) polyamide-tetrahydrocyclopropabenzindolone (CBI) conjugate with an indole linker as a stable sequence-specific alkylating agent. In this study, we investigated the gene silencing activities of polyamides A, B and C, which selectively alkylate specific seq...

journal_title：Nucleic acids research

authors： Shinohara K,Sasaki S,Minoshima M,Bando T,Sugiyama H

更新日期：2006-02-25 00:00:00

abstract：:Gene promoters are enriched in guanine clusters that potentially fold into quadruplex structures. Such quadruplexes were implicated in the regulation of gene expression, plausibly by interacting with transcription factors. We showed previously that homodimers of the myogenic transcription factor MyoD bound in vitro mo...

journal_title：Nucleic acids research

authors： Shklover J,Weisman-Shomer P,Yafe A,Fry M

更新日期：2010-04-01 00:00:00

abstract：:Post-translational modifications (PTMs) regulate many aspects of protein function and are indispensable for the spatio-temporal regulation of cellular processes. The proteome-wide identification of PTM targets has made significant progress in recent years, as has the characterization of their writers, readers, modifie...

journal_title：Nucleic acids research

authors： Teloni F,Altmeyer M

更新日期：2016-02-18 00:00:00

abstract：:Using peptide arrays and binding to native histone proteins, we show that the ADD domain of Dnmt3a specifically interacts with the H3 histone 1-19 tail. Binding is disrupted by di- and trimethylation of K4, phosphorylation of T3, S10 or T11 and acetylation of K4. We did not observe binding to the H4 1-19 tail. The ADD...

journal_title：Nucleic acids research

authors： Zhang Y,Jurkowska R,Soeroes S,Rajavelu A,Dhayalan A,Bock I,Rathert P,Brandt O,Reinhardt R,Fischle W,Jeltsch A

更新日期：2010-07-01 00:00:00

abstract：:Sequencing by hybridization (SBH) approaches to DNA sequencing face two conflicting constraints. First, in order to ensure that the target DNA binds reliably, the oligonucleotide probes that are attached to the chip array must be >15 bp in length. Secondly, the total number of possible 15 bp oligonucleotides is too la...

journal_title：Nucleic acids research

authors： Fedrigo O,Naylor G

更新日期：2004-02-18 00:00:00

abstract：:Hereditary persistence of fetal hemoglobin (HPFH) is a condition characterized by the continued expression of the fetal globin gene in adulthood. Both deletional and nondeletional forms have been described. We studied one Japanese family with two different nondeletional forms of HPFH. Analysis of polymorphic restricti...

journal_title：Nucleic acids research

authors： Fucharoen S,Shimizu K,Fukumaki Y

更新日期：1990-09-11 00:00:00

abstract：:The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provide...

journal_title：Nucleic acids research

authors： Markowitz VM,Chen IM,Palaniappan K,Chu K,Szeto E,Grechkin Y,Ratner A,Jacob B,Huang J,Williams P,Huntemann M,Anderson I,Mavromatis K,Ivanova NN,Kyrpides NC

更新日期：2012-01-01 00:00:00

abstract：:A frequently used method of comparing large RNA molecules employs the two-dimensional display of oligonucleotides generated through the action of specific RNases (oligonucleotide mapping, fingerprinting). Using computer simulations and simple analytic expressions the number of large RNase T1-resistant oligonucleotides...

journal_title：Nucleic acids research

authors： Aaronson RP,Young JF,Palese P

更新日期：1982-01-11 00:00:00

abstract：:Using a human interferon-alpha probe we have isolated recombinant phages containing murine interferon-alpha (Mu IFN-alpha) genes from a genomic library. One of these phages contained two complete Mu IFN-alpha genes and part of a third gene. The insert of a second phage held two IFN genes. This indicates that the Mu IF...

journal_title：Nucleic acids research

authors： Zwarthoff EC,Mooren AT,Trapman J

更新日期：1985-02-11 00:00:00

abstract：:Argonaute (Ago) proteins function in RNA silencing as components of the RNA-induced silencing complex (RISC). In lower organisms, the small interfering RNA and miRNA pathways diverge due in part to sorting mechanisms that direct distinct small RNA (sRNA) duplexes onto specific Ago-RISCs. However, such sorting mechanis...

journal_title：Nucleic acids research

authors： Yamakawa N,Okuyama K,Ogata J,Kanai A,Helwak A,Takamatsu M,Imadome K,Takakura K,Chanda B,Kurosaki N,Yamamoto H,Ando K,Matsui H,Inaba T,Kotani A

更新日期：2014-04-01 00:00:00

abstract：:MDg3 is a family of mobile dispersed genetic elements represented by 15 copies in the haploid genome of D. melanogaster and flanked, like other similar elements, by the regions of homology. In the present work, these regions of mdg3 have been sequenced. The existence of perfect direct repeats 268 base pairs long has b...

journal_title：Nucleic acids research

authors： Bayev AA Jr,Krayev AS,Lyubomirskaya NV,Ilyin YV,Skryabin KG,Georgiev GP

更新日期：1980-08-11 00:00:00

abstract：:Replacement of alpha-, beta- and gamma-phosphate groups in 2'-deoxynucleoside 5'-triphosphates (dNTP) with phosphonate groups yields a new set of dNTP mimics with potential biological and therapeutic applications. Here, we describe the synthesis of 15 new dNTPs modified at alpha-, beta- and gamma-phosphates containing...

journal_title：Nucleic acids research

authors： Alexandrova LA,Skoblov AY,Jasko MV,Victorova LS,Krayevsky AA

更新日期：1998-02-01 00:00:00

abstract：:The three-dimensional Poisson-Boltzmann equation for the distribution of counterion charge density around double helical DNA has been solved by an iterative procedure. These computations have been performed for 0.01M monovalent salt solutions. A systematic study of the ten possible sequences found among adjacent nucle...

journal_title：Nucleic acids research

authors： Pack GR,Wong L,Prasad CV

更新日期：1986-02-11 00:00:00

abstract：:We present a tool for the prediction of mRNA 3'-processing (cleavage and polyadenylation) sites in the yeast Saccharomyces cerevisiae, based on a discrete state-space model or hidden Markov model. Comparison of predicted sites with experimentally verified 3'-processing sites indicates good agreement. All predicted or ...

journal_title：Nucleic acids research

authors： Graber JH,McAllister GD,Smith TF

更新日期：2002-04-15 00:00:00

abstract：:The aminoacylation kinetics of T7 transcripts representing defined regions of Escherichia coli serine tRNAs were determined using purified E.coli seryl-tRNA synthetase (SerRS) and the kinetic values were used to estimate the relative contribution of various tRNA(Ser) domains to recognition by SerRS. The analysis revea...

journal_title：Nucleic acids research

authors： Sampson JR,Saks ME

更新日期：1993-09-25 00:00:00

abstract：:To explain biochemical and genetic data on spontaneous nucleotide replacements in nucleic acid biosynthesis all the 8 mispairs in normal tautomeric forms have been considered. Possible B-conformations of DNA fragments containing each of such mispairs incorporated between Watson-Crick pairs have been found using comput...

journal_title：Nucleic acids research

authors： Chuprina VP,Poltev VI

更新日期：1985-01-11 00:00:00

abstract：:We have previously shown that the pyrimidine oligonucleotide 5'CTTCCTCCTCT (Y11) recognizes the double-helical stem of hairpin 5'GAAGGAGGAGA-T4-TCTCCTCCTTC (h26) by triple-helix formation (1). In this paper, we report the effect on triplex formation of substituting the cytosine residues of Y11 with 5-methylcytosines (...

journal_title：Nucleic acids research

authors： Xodo LE,Manzini G,Quadrifoglio F,van der Marel GA,van Boom JH

更新日期：1991-10-25 00:00:00

abstract：:In Pseudomonas aeruginosa the RNA chaperone Hfq and the catabolite repression control protein (Crc) act as post-transcriptional regulators during carbon catabolite repression (CCR). In this regard Crc is required for full-fledged Hfq-mediated translational repression of catabolic genes. RNAseq based transcriptome anal...

journal_title：Nucleic acids research

authors： Sonnleitner E,Wulf A,Campagne S,Pei XY,Wolfinger MT,Forlani G,Prindl K,Abdou L,Resch A,Allain FH,Luisi BF,Urlaub H,Bläsi U

更新日期：2018-02-16 00:00:00

abstract：:The HUGO Gene Nomenclature Committee (HGNC) based at EMBL's European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 42,000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. While we still update placeholder and problema...

journal_title：Nucleic acids research

authors： Tweedie S,Braschi B,Gray K,Jones TEM,Seal RL,Yates B,Bruford EA

更新日期：2021-01-08 00:00:00

abstract：:Accurate T-cell epitope prediction is a principal objective of computational vaccinology. As a service to the immunology and vaccinology communities at large, we have implemented, as a server on the World Wide Web, a partial least squares-based multivariate statistical approach to the quantitative prediction of peptid...

journal_title：Nucleic acids research

authors： Guan P,Doytchinova IA,Zygouri C,Flower DR

更新日期：2003-07-01 00:00:00

abstract：:A lac promotor mutant was constructed by filling in the protruding ends of the HpaII site located within the lac promotor. The mutation, named M42, is a two base pair insertion that changes the distance between the -10 and -35 regions from 18 to 20 residues. The activity of the mutant promotor measured in vivo is 15% ...

journal_title：Nucleic acids research

authors： Mandecki W,Reznikoff WS

更新日期：1982-02-11 00:00:00

abstract：:8-Oxo-7,8-dihydroguanine (8-oxoGua) is produced in cells by reactive oxygen species normally formed during cellular metabolic processes. This oxidized base can pair with both adenine and cytosine, and thus the existence of this base in messenger RNA would cause translational errors. The MutT protein of Escherichia col...

journal_title：Nucleic acids research

authors： Ishibashi T,Hayakawa H,Ito R,Miyazawa M,Yamagata Y,Sekiguchi M

更新日期：2005-07-07 00:00:00

abstract：:Using a combination of bioinformatic and molecular biology approaches a Drosophila melanogaster protein, DmTTF, has been identified, which exhibits sequence and structural similarity with two mitochondrial transcription termination factors, mTERF (human) and mtDBP (sea urchin). Import/processing assays indicate that D...

journal_title：Nucleic acids research

authors： Roberti M,Polosa PL,Bruni F,Musicco C,Gadaleta MN,Cantatore P

更新日期：2003-03-15 00:00:00

abstract：:Two types of different repetitive DNA sequences called RepMP1 and RepMP2 were identified in the genome of Mycoplasma pneumoniae. The number of these repeated elements, their nucleotide sequence and their localization on a physical map of the M. pneumoniae genome were determined. The results show that RepMP1 appears at...

journal_title：Nucleic acids research

authors： Wenzel R,Herrmann R

更新日期：1988-09-12 00:00:00

abstract：:This report documents the error rate in a commercially distributed subset of the IMAGE Consortium mouse cDNA clone collection. After isolation of plasmid DNA from 1189 bacterial stock cultures, only 62. 2% were uncontaminated and contained cDNA inserts that had significant sequence identity to published data for the o...

journal_title：Nucleic acids research

authors： Halgren RG,Fielden MR,Fong CJ,Zacharewski TR

更新日期：2001-01-15 00:00:00

abstract：:The RNA degradosome is a multi-enzyme assembly that contributes to key processes of RNA metabolism, and it engages numerous partners in serving its varied functional roles. Small domains within the assembly recognize collectively a diverse range of macromolecules, including the core protein components, the cytoplasmic...

journal_title：Nucleic acids research

authors： Tsai YC,Du D,Domínguez-Malfavón L,Dimastrogiovanni D,Cross J,Callaghan AJ,García-Mena J,Luisi BF

更新日期：2012-11-01 00:00:00

abstract：:The DNA damage response is vigorously activated by DNA double-strand breaks (DSBs). The chief mobilizer of the DSB response is the ATM protein kinase. We discovered that the COP9 signalosome (CSN) is a crucial player in the DSB response and an ATM target. CSN is a protein complex that regulates the activity of cullin ...

journal_title：Nucleic acids research

authors： Meir M,Galanty Y,Kashani L,Blank M,Khosravi R,Fernández-Ávila MJ,Cruz-García A,Star A,Shochot L,Thomas Y,Garrett LJ,Chamovitz DA,Bodine DM,Kurz T,Huertas P,Ziv Y,Shiloh Y

更新日期：2015-05-19 00:00:00

abstract：:An immunofluorescence assay was developed to identify proteins specifically binding to oligonucleoside phosphorodithioate (ODN) aptamers from a bead-bound ODN library. Accordingly, NF-kappaB p50 protein was incubated with either bead-bound NF-kappaB consensus sequence or a bead-bound ODN combinatorial library and adso...

journal_title：Nucleic acids research

authors： Yang X,Li X,Prow TW,Reece LM,Bassett SE,Luxon BA,Herzog NK,Aronson J,Shope RE,Leary JF,Gorenstein DG

更新日期：2003-05-15 00:00:00

abstract：:Pax-5, a member of the paired domain family of transcription factors, is a key regulator of B lymphocyte-specific transcription and differentiation. A major target of Pax-5-mediated activation is the mb-1 gene, which encodes the essential transmembrane signaling protein Ig-alpha. Pax-5 recruits three members of the Et...

journal_title：Nucleic acids research

authors： Maier H,Ostraat R,Parenti S,Fitzsimmons D,Abraham LJ,Garvie CW,Hagman J

更新日期：2003-10-01 00:00:00