Comparative analysis of non-autonomous effects of tasiRNAs and miRNAs in Arabidopsis thaliana.

abstract：:A physical mapping strategy has been developed to verify and accelerate the assembly and gap closure phase of a microbial genome shotgun-sequencing project. The protocol was worked out during the ongoing Pseudomonas putida KT2440 genome project. A macro-restriction map was constructed by linking probe hybridisation of...

journal_title：Nucleic acids research

authors： Weinel C,Tümmler B,Hilbert H,Nelson KE,Kiewitz C

更新日期：2001-11-15 00:00:00

abstract：:Comparative structural studies of ribosomes from various organisms keep offering exciting insights on how species-specific or environment-related structural features of ribosomes may impact translation specificity and its regulation. Although the importance of such features may be less obvious within more closely rela...

journal_title：Nucleic acids research

authors： Khusainov I,Vicens Q,Bochler A,Grosse F,Myasnikov A,Ménétret JF,Chicher J,Marzi S,Romby P,Yusupova G,Yusupov M,Hashem Y

更新日期：2016-12-01 00:00:00

abstract：:In general, synthetic RNA transcripts corresponding to the 3' ends of Saccharomyces cerevisiae genes appear to be accurately cleaved and polyadenylated in vitro under appropriate conditions in yeast cell extracts. Initially, however, the endpoints observed in vitro for the GAL7 gene failed to correlate adequately with...

journal_title：Nucleic acids research

authors： Sadhale PP,Sapolsky R,Davis RW,Butler JS,Platt T

更新日期：1991-07-11 00:00:00

abstract：:Holliday junction (HJ) resolving enzyme RecU is involved in DNA repair and recombination. We have determined the crystal structure of inactive mutant (D88N) of RecU from Bacillus subtilis in complex with a 12 base palindromic DNA fragment at a resolution of 3.2 Å. This structure shows the stalk region and the essentia...

journal_title：Nucleic acids research

authors： Khavnekar S,Dantu SC,Sedelnikova S,Ayora S,Rafferty J,Kale A

更新日期：2017-01-25 00:00:00

abstract：:Muscleblind-like proteins (MBNLs) are regulators of RNA metabolism. During tissue differentiation the level of MBNLs increases, while their functional insufficiency plays a crucial role in myotonic dystrophy (DM). Deep sequencing of RNA molecules cross-linked to immunoprecipitated protein particles (CLIP-seq) revealed...

journal_title：Nucleic acids research

authors： Konieczny P,Stepniak-Konieczna E,Taylor K,Sznajder LJ,Sobczak K

更新日期：2017-02-28 00:00:00

abstract：:DNA binding proteins that induce structural changes in DNA are common in both prokaryotes and eukaryotes. Integration host factor (IHF) is a multi-functional DNA binding and bending protein of Escherichia coli that can mediate protein-protein and protein-DNA interactions by bending DNA. Previously we have shown that t...

journal_title：Nucleic acids research

authors： Hales LM,Gumport RI,Gardner JF

更新日期：1996-05-01 00:00:00

abstract：:Chloroplast DNA, isolated from a synchronized culture of Chlamydomonas reinhardii, was digested with restriction endonucleases and examined in the electron microscope. Restriction fragments containing displacement loops (D-loop) were photographed and measured to determine the position of replicated sequences in relati...

journal_title：Nucleic acids research

authors： Waddell J,Wang XM,Wu M

更新日期：1984-05-11 00:00:00

abstract：:The Bcl-2 protein has an anti-apoptotic effect in neuronal and other cell types. We show for the first time that the Bcl-2 promoter is activated by the neuronal survival factor nerve growth factor (NGF) and that this effect is dependent on a region of the promoter from -1472 to -1414. This activation requires the Rap-...

journal_title：Nucleic acids research

authors： Liu YZ,Boxer LM,Latchman DS

更新日期：1999-05-15 00:00:00

abstract：:Module identification is a frequently used approach for mining local structures with more significance in global networks. Recently, a wide variety of bilayer networks are emerging to characterize the more complex biological processes. In the light of special topological properties of bilayer networks and the accompan...

journal_title：Nucleic acids research

authors： Xu Y,Guo M,Liu X,Wang C,Liu Y,Liu G

更新日期：2016-11-16 00:00:00

abstract：:The tight-binding I12-X86 lac repressor binds to non-operator DNA in a sequence-specific fashion. Using the DNA of the E. coli I gene we have investigated these sequence-specific interactions and compared them to the operator binding of wild-type repressor. The specific, non-operator DNA interactions are sensitive to ...

journal_title：Nucleic acids research

authors： Schmitz A,Galas DJ

更新日期：1980-02-11 00:00:00

abstract：:Preparation of large amount of single-stranded circular DNA in high selectivity is crucial for further developments of nanotechnology and other DNA sciences. Herein, a simple but practically useful methodology to prepare DNA rings has been presented. One of the essential factors is to use highly diluted T4 ligase buff...

journal_title：Nucleic acids research

authors： An R,Li Q,Fan Y,Li J,Pan X,Komiyama M,Liang X

更新日期：2017-09-06 00:00:00

abstract：:Since 2010, the Genomicus web server is available online at http://genomicus.biologie.ens.fr/genomicus. This graphical browser provides access to comparative genomic analyses in four different phyla (Vertebrate, Plants, Fungi, and non vertebrate Metazoans). Users can analyse genomic information from extant species, as...

journal_title：Nucleic acids research

authors： Nguyen NTT,Vincens P,Roest Crollius H,Louis A

更新日期：2018-01-04 00:00:00

abstract：:Organisms growing at elevated temperatures face the challenge of maintaining the integrity of their genetic materials. Archaea possess unique chromatin proteins for gene organization and information processing. We present the solution structure of Sso7c4 from Sulfolobus solfataricus, which has a homodimeric DNA-bindin...

journal_title：Nucleic acids research

authors： Hsu CH,Wang AH

更新日期：2011-08-01 00:00:00

abstract：:PsiB protein of plasmid R6-5 inhibits the induction of the SOS pathway. The F sex factor also carries a psiB gene homologous to that of R6-5. Yet, it fails to inhibit SOS induction. In order to solve this difference, we characterized the psiB genes of R6-5 and F. We found that (i) the sequences of the two psiB genes s...

journal_title：Nucleic acids research

authors： Dutreix M,Bäckman A,Célérier J,Bagdasarian MM,Sommer S,Bailone A,Devoret R,Bagdasarian M

更新日期：1988-11-25 00:00:00

abstract：:We have overproduced and purified wild type regA protein, a translational repressor encoded by bacteriophage T4. The repressor activity of the cloned regA protein has been tested on four known regA target genes (T4 genes: 44, 45, rpbA and regA) using in vitro coupled transcription-translation reactions. We have demons...

journal_title：Nucleic acids research

authors： Webster KR,Adari HY,Spicer EK

更新日期：1989-12-11 00:00:00

abstract：:A key issue when designing and using DNA-targeting nucleases is specificity. Ideally, an optimal DNA-targeting tool has only one recognition site within a genomic sequence. In practice, however, almost all designer nucleases available today can accommodate one to several mutations within their target site. The ability...

journal_title：Nucleic acids research

authors： Juillerat A,Dubois G,Valton J,Thomas S,Stella S,Maréchal A,Langevin S,Benomari N,Bertonati C,Silva GH,Daboussi F,Epinat JC,Montoya G,Duclert A,Duchateau P

更新日期：2014-04-01 00:00:00

abstract：:A library of three synthetic ribozymes with randomized arms, targeting NUX, GUX and NXG triplets, respectively, were used to identify ribozyme-accessible sites on the HIV-1 LTR transcript comprising positions -533 to 386. Three cleavable sites were identified at positions 109, 115 and 161. Ribozymes were designed agai...

journal_title：Nucleic acids research

authors： Bramlage B,Luzi E,Eckstein F

更新日期：2000-11-01 00:00:00

abstract：:In Trypanosoma brucei the genes are organised into long polycistronic transcription units and only three promoters for protein-encoding genes and a single terminator have been characterised. These promoters recruit a polI-like RNA polymerase for the transcription units encoding the two major stage-specific antigens of...

journal_title：Nucleic acids research

authors： Berberof M,Vanhamme L,Alexandre S,Lips S,Tebabi P,Pays E

更新日期：2000-01-15 00:00:00

abstract：:A soluble enzyme system that specifically initiates lambda dv plasmid DNA replication at a bacteriophage lambda replication origin [Wold et al. (1982) Proc. Natl. Acad. Sci. USA 79, 6176-6180] is also capable of replicating the single-stranded circular chromosomes of phages M13 and phi X174 to a duplex form. This chai...

journal_title：Nucleic acids research

authors： LeBowitz JH,McMacken R

更新日期：1984-04-11 00:00:00

abstract：:Negative superhelical strain induces the poly(dG)-poly(dC) sequence to adopt two totally different types of triple-helices, either a dG.dG.dC triplex in the presence of Mg(+)+ at both neutral and acidic pHs or a protonated dC+.dG.dC triplex in the absence of Mg(+)+ ions at acidic pH (1). To examine whether there are s...

journal_title：Nucleic acids research

authors： Kohwi-Shigematsu T,Kohwi Y

更新日期：1991-08-11 00:00:00

abstract：:Helicase-nuclease systems dedicated to DNA end resection in preparation for homologous recombination (HR) are present in all kingdoms of life. In thermophilic archaea, the HerA helicase and NurA nuclease cooperate with the highly conserved Mre11 and Rad50 proteins during HR-dependent DNA repair. Here we show that HerA...

journal_title：Nucleic acids research

authors： Blackwood JK,Rzechorzek NJ,Abrams AS,Maman JD,Pellegrini L,Robinson NP

更新日期：2012-04-01 00:00:00

abstract：:Using a powerful computer-assisted analysis strategy, a large-scale search of small nucleolar RNA (snoRNA) genes in the recently released draft sequence of the rice genome was carried out. This analysis identified 120 different box C/D snoRNA genes with a total of 346 gene variants, which were predicted to guide 135 2...

journal_title：Nucleic acids research

authors： Chen CL,Liang D,Zhou H,Zhuo M,Chen YQ,Qu LH

更新日期：2003-05-15 00:00:00

abstract：:We previously found that the splicing of exon 5 to exon 6 in the rat beta-TM gene required that exon 6 first be joined to the downstream common exon 8 (Helfman et al., Genes and Dev. 2, 1627-1638, 1988). Pre-mRNAs containing exon 5, intron 5 and exon 6 are not normally spliced in vitro. We have carried out a mutationa...

journal_title：Nucleic acids research

authors： Tsukahara T,Casciato C,Helfman DM

更新日期：1994-06-25 00:00:00

abstract：:Several electrophoretic and chromatographic systems have been investigated and compared for sequence analysis of oligodeoxyribonucleotides. Three systems were found to be useful for the separation of a series of sequential degradation products resulting from a labeled oligonucleotide: (I) 2-D electrophoresisdagger; (I...

journal_title：Nucleic acids research

authors： Jay E,Bambara R,Padmanabhan R,Wu R

更新日期：1974-03-01 00:00:00

abstract：:With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; representing cellular processes or pathways is no exception. VISIBIOweb is a free, open-source, we...

journal_title：Nucleic acids research

authors： Dilek A,Belviranli ME,Dogrusoz U

更新日期：2010-07-01 00:00:00

abstract：:A nucleic acid affinity matrix containing a short oligodeoxynucleotide ligand has been prepared as an example of a material which can be used for the rapid and effective isolation of sequence specific DNA binding proteins. Two complementary oligodeoxynucleotides have been employed, one of which contains a small 5'-spa...

journal_title：Nucleic acids research

authors： Blanks R,McLaughlin LW

更新日期：1988-11-11 00:00:00

abstract：:Carbohydrate-binding proteins play crucial roles across all organisms and viruses. The complexity of carbohydrate structures, together with inconsistencies in how their 3D structures are reported, has led to difficulties in characterizing the protein-carbohydrate interfaces. In order to better understand protein-carbo...

journal_title：Nucleic acids research

authors： Copoiu L,Torres PHM,Ascher DB,Blundell TL,Malhotra S

更新日期：2020-01-08 00:00:00

abstract：:We have investigated the substrate specificity of the Ogg1 protein of Saccharomyces cerevisiae (yOgg1 protein) for excision of modified DNA bases from oxidatively damaged DNA substrates using gas chromatography/isotope dilution mass spectrometry. Four DNA substrates prepared by treatment with H2O2/Fe(III)-EDTA/ascorbi...

journal_title：Nucleic acids research

authors： Karahalil B,Girard PM,Boiteux S,Dizdaroglu M

更新日期：1998-03-01 00:00:00

abstract：:Aspartic acid residues comprising the -D-(aa) n -Y-L-D-D- DNA polymerase active site triad of reverse transcriptase from the Saccharomyces cerevisiae long terminal repeat-retrotransposon Ty3 (Asp151, Asp213 and Asp214) were evaluated via site-directed mutagenesis. An Asp151-->Glu substitution showed a dramatic decreas...

journal_title：Nucleic acids research

authors： Bibillo A,Lener D,Klarmann GJ,Le Grice SF

更新日期：2005-01-12 00:00:00

abstract：:The Galaxy HiCExplorer provides a web service at https://hicexplorer.usegalaxy.eu. It enables the integrative analysis of chromosome conformation by providing tools and computational resources to pre-process, analyse and visualize Hi-C, Capture Hi-C (cHi-C) and single-cell Hi-C (scHi-C) data. Since the last publicatio...

journal_title：Nucleic acids research

authors： Wolff J,Rabbani L,Gilsbach R,Richard G,Manke T,Backofen R,Grüning BA

更新日期：2020-07-02 00:00:00