Structure-function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop-loop interaction motif conserved in most natural hammerheads.

abstract：:Uridylation-dependent RNA decay is a widespread eukaryotic pathway modulating RNA homeostasis. Terminal uridylyltransferases (Tutases) add untemplated uridyl residues to RNA 3'-ends, marking them for degradation by the U-specific exonuclease Dis3L2. In Schizosaccharomyces pombe, Cid1 uridylates a variety of RNAs. In t...

journal_title：Nucleic acids research

authors： Chung CZ,Jaramillo JE,Ellis MJ,Bour DYN,Seidl LE,Jo DHS,Turk MA,Mann MR,Bi Y,Haniford DB,Duennwald ML,Heinemann IU

更新日期：2019-04-08 00:00:00

abstract：:Circular DNA can arise from all parts of eukaryotic chromosomes. In yeast, circular ribosomal DNA (rDNA) accumulates dramatically as cells age, however little is known about the accumulation of other chromosome-derived circles or the contribution of such circles to genetic variation in aged cells. We profiled circular...

journal_title：Nucleic acids research

authors： Prada-Luengo I,Møller HD,Henriksen RA,Gao Q,Larsen CE,Alizadeh S,Maretty L,Houseley J,Regenberg B

更新日期：2020-08-20 00:00:00

abstract：:A small library of 49 peptide-oligonucleotide conjugates were synthesized to explore the influence of various peptide side chains on the hybridization properties of the DNA. An invariant 8mer oligonucleotide was coupled to a peptide portion that contained a five residue variable region composed of the cationic amino a...

journal_title：Nucleic acids research

authors： Harrison JG,Balasubramanian S

更新日期：1998-07-01 00:00:00

abstract：:Spliced leader (SL) trans-splicing is a critical element of gene expression in a number of eukaryotic groups. This process is arguably best understood in nematodes, where biochemical and molecular studies in Caenorhabditis elegans and Ascaris suum have identified key steps and factors involved. Despite this, the preci...

journal_title：Nucleic acids research

authors： Philippe L,Pandarakalam GC,Fasimoye R,Harrison N,Connolly B,Pettitt J,Müller B

更新日期：2017-08-21 00:00:00

abstract：:IS200 is found throughout Enterobacteriaceae and transposes at a notoriously low frequency. In addition to the transposase protein (TnpA), IS200 encodes an uncharacterized Hfq-binding sRNA that is encoded opposite to the tnpA 5'UTR. In the current work we asked if this sRNA represses tnpA expression. We show here that...

journal_title：Nucleic acids research

authors： Ellis MJ,Trussler RS,Haniford DB

更新日期：2015-07-27 00:00:00

abstract：:We have determined the nucleotide sequence at the 3' end of the vesicular stomatitis virus (VSV) polymerase or L gene and compared it to that obtained from a defective interfering particle (DI) RNA generated by this virus. The latter (DI 0.50) contains a large internal deletion within this gene. The deletion begins ex...

journal_title：Nucleic acids research

authors： De BK,Perrault J

更新日期：1982-11-11 00:00:00

abstract：:(19)F NMR spectroscopy has proved to be a valuable tool to monitor functionally important conformational transitions of nucleic acids. Here, we present a systematic investigation on the application of 5-fluoro pyrimidines to probe DNA and RNA secondary structures. Oligonucleotides with the propensity to adapt secondar...

journal_title：Nucleic acids research

authors： Puffer B,Kreutz C,Rieder U,Ebert MO,Konrat R,Micura R

更新日期：2009-12-01 00:00:00

abstract：:The gene, rpb2, encoding the second largest subunit, subunit 2, of RNA polymerase II has been cloned from Schizosaccharomyces pombe using the corresponding gene, RPB2, of Saccharomyces cerevisiae as a probe for cross-hybridization. We have determined the complete nucleotide sequence of rpb2, and parts of the PCR-ampli...

journal_title：Nucleic acids research

authors： Kawagishi M,Yamagishi M,Ishihama A

更新日期：1993-02-11 00:00:00

abstract：:A system for the tetracycline-inducible regulation of gene expression in mycobacteria has been developed. We have sub-cloned the tetRO region from the Corynebacterium glutamicum TetZ locus into a mycobacterial shuttle plasmid, making expression of genes cloned downstream of tetRO responsive to tetracycline. Using the ...

journal_title：Nucleic acids research

authors： Blokpoel MC,Murphy HN,O'Toole R,Wiles S,Runn ES,Stewart GR,Young DB,Robertson BD

更新日期：2005-02-01 00:00:00

abstract：:To investigate the mechanism of N4-aminocytidine-induced mutagenesis, N'-alkyl-N4-aminocytidines and N4-alkyl-N4-aminocytidines were prepared and their mutagenicity on bacteria were assayed. N'-Methyl-N4-aminocytidine, N'-(2-hydroxyethyl)-N4-aminocytidine and N',N'-dimethyl-N4-aminocytidine showed direct-acting mutage...

journal_title：Nucleic acids research

authors： Nomura A,Negishi K,Hayatsu H

更新日期：1985-12-20 00:00:00

abstract：:The non-essential MGS1 gene of Saccharomyces cerevisiae is highly conserved in eukaryotes and encodes an enzyme containing both DNA-dependent ATPase and DNA annealing activities. MGS1 appears to function in post-replicational repair processes that contribute to genome stability. In this study, we identified MGS1 as a ...

journal_title：Nucleic acids research

authors： Kim JH,Kang YH,Kang HJ,Kim DH,Ryu GH,Kang MJ,Seo YS

更新日期：2005-10-26 00:00:00

abstract：:We have established a sensitive, monoclonal antibody (Mab)-based procedure permitting the selective enrichment of sequences containing the miscoding alkylation product O6-ethylguanine (O6-EtGua) from mammalian DNA. H5 rat hepatoma cells were reacted with the N-nitroso carcinogen N-ethyl-N-nitrosourea in vitro, to give...

journal_title：Nucleic acids research

authors： Hochleitner K,Thomale J,Nikitin AYu,Rajewsky MF

更新日期：1991-08-25 00:00:00

abstract：:The proposition that the 2-amino group of guanine plays a critical role in determining how antibiotics recognise their binding sites in DNA has been tested by relocating it, using tyrT DNA derivative molecules substituted with inosine plus 2,6-diaminopurine (DAP). Irrespective of their mode of interaction with DNA, su...

journal_title：Nucleic acids research

authors： Bailly C,Waring MJ

更新日期：1995-03-25 00:00:00

abstract：:Alternative splicing of pre-mRNA generates protein diversity. Dysfunction of splicing machinery and expression of specific transcripts has been linked to cancer progression and drug response. Exon microarray technology enables genome-wide quantification of expression levels of the majority of exons and facilitates the...

journal_title：Nucleic acids research

authors： Chen P,Lepikhova T,Hu Y,Monni O,Hautaniemi S

更新日期：2011-10-01 00:00:00

abstract：:The inducibility of the vir genes (virA, -B, -C, -D, -E, and -G) on pRiA4 was examined at the transcriptional level, and the RNA-starting sites were determined by S1-nuclease mapping and primer-extension experiments. All of these genes were inducible, while virA, -E, and -G were transcribed even under noninducing cond...

journal_title：Nucleic acids research

authors： Aoyama T,Takanami M,Oka A

更新日期：1989-11-11 00:00:00

abstract：:Acetyl-CoA Carboxylase catalyzes the first committed step in fatty acid synthesis. Escherichia coli acetyl-CoA carboxylase is composed of biotin carboxylase, carboxyltransferase and biotin carboxyl carrier protein functions. The accA and accD genes that code for the alpha- and beta-subunits, respectively, are not in a...

journal_title：Nucleic acids research

authors： Meades G Jr,Benson BK,Grove A,Waldrop GL

更新日期：2010-03-01 00:00:00

abstract：:The kinetics of PaeR7 endonuclease-catalysed cleavage reactions of fluorophor-labeled oligonucleotide substrates have been examined using fluorescence resonance energy transfer (FRET). A series of duplex substrates were synthesized with an internal CTCGAG PaeR7 recognition site and donor (fluorescein) and acceptor (rh...

journal_title：Nucleic acids research

authors： Ghosh SS,Eis PS,Blumeyer K,Fearon K,Millar DP

更新日期：1994-08-11 00:00:00

abstract：:Although Dicer is essential for general microRNA (miRNA) biogenesis, vertebrate mir-451 is Dicer independent. Instead, its short pre-miRNA hairpin is 'sliced' by Ago2, then 3'-resected into mature miRNAs. Here, we show that Drosophila cells and animals generate functional small RNAs from mir-451-type precursors. Howev...

journal_title：Nucleic acids research

authors： Yang JS,Smibert P,Westholm JO,Jee D,Maurin T,Lai EC

更新日期：2014-02-01 00:00:00

abstract：:Signaling pathways constitute a valuable source of information that allows interpreting the way in which alterations in gene activities affect to particular cell functionalities. There are web tools available that allow viewing and editing pathways, as well as representing experimental data on them. However, few metho...

journal_title：Nucleic acids research

authors： Sebastián-León P,Carbonell J,Salavert F,Sanchez R,Medina I,Dopazo J

更新日期：2013-07-01 00:00:00

abstract：:The Human Gene and Protein Database (HGPD; http://www.HGPD.jp/) is a unique database that stores information on a set of human Gateway entry clones in addition to protein expression and protein synthesis data. The HGPD was launched in November 2008, and 33,275 human Gateway entry clones have been constructed from the ...

journal_title：Nucleic acids research

authors： Maruyama Y,Kawamura Y,Nishikawa T,Isogai T,Nomura N,Goshima N

更新日期：2012-01-01 00:00:00

abstract：:We have isolated an eight kilobase fragment of Bacillus subtilis DNA by specific integration and excision of a plasmid containing a sequence adjacent to ribosomal operon rrn O. The genetic locus of the cloned fragment was verified by linkage of the integrated vector to nearby genetic markers using both transduction an...

journal_title：Nucleic acids research

authors： Lampe MF,Bott KF

更新日期：1984-08-10 00:00:00

abstract：:The Dnd (DNA degradation) phenotype, reflecting a novel DNA modification by sulfur in Streptomyces lividans 1326, was strongly aggravated when one (dndB) of the five genes (dndABCDE) controlling it was mutated. Electrophoretic banding patterns of a plasmid (pHZ209), reflecting DNA degradation, displayed a clear change...

journal_title：Nucleic acids research

authors： Liang J,Wang Z,He X,Li J,Zhou X,Deng Z

更新日期：2007-01-01 00:00:00

abstract：:The discovery of hydroxymethyl-, formyl- and carboxylcytosine, generated through oxidation of methylcytosine by TET dioxygenases, raised the question how these modifications contribute to epigenetic regulation. As they are subjected to complex regulation in vivo, we dissected links to gene expression with in vitro mod...

journal_title：Nucleic acids research

authors： Müller U,Bauer C,Siegl M,Rottach A,Leonhardt H

更新日期：2014-07-01 00:00:00

abstract：:Analysis of intergenic sequences for purposes such as the investigation of transcriptional signals or the identification of small RNA genes is frequently complicated by traditional biological database structures. Genome data is commonly treated as chromosome-length sequence records, detailed by gene calls demarcating ...

journal_title：Nucleic acids research

authors： Ray WC,Daniels CJ

更新日期：2003-01-01 00:00:00

abstract：:The locus control region is required for high-level, position-independent expression of mammalian beta-globin genes. It is marked by five major DNase hypersensitive sites (HSs) in a 16 kb region of chromatin, and the protein-DNA complexes that form these HSs may interact in a holocomplex that carries out the full func...

journal_title：Nucleic acids research

authors： Jackson JD,Miller W,Hardison RC

更新日期：1996-11-01 00:00:00

abstract：:Cell differentiation is a central process in development and in cancer growth and dissemination. OCT4 (POU5F1) and NANOG are essential for cell stemness and pluripotency; yet, the mechanisms that regulate their expression remain largely unknown. Repetitive elements account for almost half of the Human Genome; still, t...

journal_title：Nucleic acids research

authors： Morales-Hernández A,González-Rico FJ,Román AC,Rico-Leo E,Alvarez-Barrientos A,Sánchez L,Macia Á,Heras SR,García-Pérez JL,Merino JM,Fernández-Salguero PM

更新日期：2016-06-02 00:00:00

abstract：:MicroRNAs (miRNAs) are approximately 22 nucleotide (nt) long and play important roles in post-transcriptional regulation in both plants and animals. In animals, precursor (pre-) miRNAs are ∼70 nt hairpins produced by Drosha cleavage of long primary (pri-) miRNAs in the nucleus. Exportin-5 (XPO5) transports pre-miRNAs ...

journal_title：Nucleic acids research

authors： Sheng P,Fields C,Aadland K,Wei T,Kolaczkowski O,Gu T,Kolaczkowski B,Xie M

更新日期：2018-06-20 00:00:00

abstract：:The hammerhead self-cleaving motif occurs in a variety of RNAs that infect plants and consists of three non-conserved helices connected by a highly conserved central core. A variant hammerhead, called the extended hammerhead, is found in satellite 2 transcripts from a variety of caudate amphibians. The extended hammer...

journal_title：Nucleic acids research

authors： Mitrasinovic O,Epstein LM

更新日期：1997-06-01 00:00:00

abstract：:A simple, two-step method is described for the synthesis of the 5'-pyro- and triphosphate derivatives of 3'-5' ApA, ApG, GpA and GpG. The readily accessible 2'(3')-5' ApA, ApG, GpA and GpG were converted in one step to the corresponding 5'-phosphoramidate derivatives which were then transformed to the 5'-pyro- and tri...

journal_title：Nucleic acids research

authors： Tomasz J,Simoncsits A,Kajtár M,Krug RM,Shatkin AJ

更新日期：1978-08-01 00:00:00

abstract：:Despite the development of new high-throughput sequencing techniques, microarrays are still attractive tools to study small genome organisms, thanks to sample multiplexing and high-feature densities. However, the oligonucleotide design remains a delicate step for most users. A vast array of software is available to de...

journal_title：Nucleic acids research

authors： Jourdren L,Duclos A,Brion C,Portnoy T,Mathis H,Margeot A,Le Crom S

更新日期：2010-06-01 00:00:00