Structural and mechanistic insights into Helicobacter pylori NikR activation.

abstract：:Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb (http://www.ebi.ac.uk/RHdb/RHdb.html ), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. Recently, CORBA access has been added to Rhdb. The EBI is an Out...

journal_title：Nucleic acids research

authors： Lijnzaad P,Helgesen C,Rodriguez-Tomé P

更新日期：1998-01-01 00:00:00

abstract：:Stress response mechanisms that modulate the dynamics of tRNA degradation and accumulation from the cytoplasm to the nucleus have been studied in yeast, the rat hepatoma and human cells. In the current study, we investigated tRNA degradation and accumulation in HeLa cells under various forms of stress. We found that i...

journal_title：Nucleic acids research

authors： Watanabe K,Miyagawa R,Tomikawa C,Mizuno R,Takahashi A,Hori H,Ijiri K

更新日期：2013-04-01 00:00:00

abstract：:Small disulfide-bonded proteins (SDPs) are rich sources for therapeutic drugs. Designing drugs from these proteins requires three-dimensional structural information, which is only available for a subset of these proteins. SDPMOD addresses this deficit in structural information by providing a freely available automated...

journal_title：Nucleic acids research

authors： Kong L,Lee BT,Tong JC,Tan TW,Ranganathan S

更新日期：2004-07-01 00:00:00

abstract：:A 5',7-methylguanosine cap is a quintessential feature of RNA polymerase II-transcribed RNAs, and a textbook aspect of co-transcriptional RNA processing. The cap is bound by the cap-binding complex (CBC), canonically consisting of nuclear cap-binding proteins 1 and 2 (NCBP1/2). Interest in the CBC has recently renewed...

journal_title：Nucleic acids research

authors： Dou Y,Kalmykova S,Pashkova M,Oghbaie M,Jiang H,Molloy KR,Chait BT,Rout MP,Fenyö D,Jensen TH,Altukhov I,LaCava J

更新日期：2020-10-09 00:00:00

abstract：:The gene encoding myelin basic protein (MBP) contains multiple activator sequences spanning upstream of its transcriptional initiation site which differentially promote transcription in glial cells. The proximal activator sequence, designated MB1, activates transcription in a glial cell type specific manner. This sequ...

journal_title：Nucleic acids research

authors： Devine-Beach K,Haas S,Khalili K

更新日期：1992-02-11 00:00:00

abstract：:It has been proposed that phage lambda site-specific recombination proceeds via two independent strand exchanges: the first exchange forming a Holliday-structure which is then converted into complete recombinant products by the second strand exchange. If this hypothesis is correct, one should be able to trap the putat...

journal_title：Nucleic acids research

authors： Kitts PA,Nash HA

更新日期：1988-07-25 00:00:00

abstract：:Augmented biological activity in vitro has been demonstrated in oligonucleotides (oligos) modified to provide nuclease resistance, to enhance cellular uptake or to increase target affinity. How chemical modification affects the duration of effect of an oligo with potent activity has not been investigated directly. We ...

journal_title：Nucleic acids research

authors： Tam RC,Li Y,Noonberg S,Hwang DG,Lui G,Hunt CA,Garovoy MR

更新日期：1994-03-25 00:00:00

abstract：:A reporter assay was developed to detect and quantify nonsense codon suppression by chemically aminoacylated tRNAs in mammalian cells. It is based on the cellular expression of the enhanced green fluorescent protein (EGFP) as a reporter for the site-specific amino acid incorporation in its sequence using an orthogonal...

journal_title：Nucleic acids research

authors： Ilegems E,Pick HM,Vogel H

更新日期：2002-12-01 00:00:00

abstract：:Gene finding is complicated in organisms that exhibit insertional RNA editing. Here, we demonstrate how our new algorithm Predictor of Insertional Editing (PIE) can be used to locate genes whose mRNAs are subjected to multiple frameshifting events, and extend the algorithm to include probabilistic predictions for site...

journal_title：Nucleic acids research

authors： Gott JM,Parimi N,Bundschuh R

更新日期：2005-09-07 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：:HbVar (http://globin.bx.psu.edu/hbvar) is one of the oldest and most appreciated locus-specific databases launched in 2001 by a multi-center academic effort to provide timely information on the genomic alterations leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records incl...

journal_title：Nucleic acids research

authors： Giardine B,Borg J,Viennas E,Pavlidis C,Moradkhani K,Joly P,Bartsakoulia M,Riemer C,Miller W,Tzimas G,Wajcman H,Hardison RC,Patrinos GP

更新日期：2014-01-01 00:00:00

abstract：:Primer design is a fundamental technique that is widely used for polymerase chain reaction (PCR). Although many methods have been proposed for primer design, they require a great deal of manual effort to generate feasible and valid primers, including homology tests on off-target sequences using BLAST-like tools. That ...

journal_title：Nucleic acids research

authors： Kim H,Kang N,Chon KW,Kim S,Lee N,Koo J,Kim MS

更新日期：2015-11-16 00:00:00

abstract：:Most small nucleolar RNAs (snoRNAs) guide rRNA nucleotide modifications, some participate in pre-rRNA cleavages, and a few have both functions. These activities involve direct base-pairing of the snoRNA with pre-rRNA using different domains. It is not known if the modification and processing functions occur independen...

journal_title：Nucleic acids research

authors： Liang XH,Liu Q,Liu Q,King TH,Fournier MJ

更新日期：2010-06-01 00:00:00

abstract：:An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA pr...

journal_title：Nucleic acids research

authors： Pokhrel N,Origanti S,Davenport EP,Gandhi D,Kaniecki K,Mehl RA,Greene EC,Dockendorff C,Antony E

更新日期：2017-09-19 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：:The modulation of GLI2, an oncogenic transcription factor commonly upregulated in cancer, is in many cases not due to genetic defects, suggesting dysregulation through alternative mechanisms. The identity of these molecular events remains for the most part unknown. Here, we identified TFII-I as a novel repressor of GL...

journal_title：Nucleic acids research

authors： McCleary-Wheeler AL,Paradise BD,Almada LL,Carlson AJ,Marks DL,Vrabel A,Vera RE,Sigafoos AN,Olson RL,Fernandez-Zapico ME

更新日期：2020-07-27 00:00:00

abstract：:Recently, a family of transcription factors structurally related to Sp1 has been described; thus, more than one activator may bind to the GC boxes present in a number of viral and cellular promoters. We have compared the transactivation potentials of Sp1, Sp3 and Sp4 proteins on the human immunodeficiency virus type 1...

journal_title：Nucleic acids research

authors： Majello B,De Luca P,Hagen G,Suske G,Lania L

更新日期：1994-11-25 00:00:00

abstract：:Current literature describes several methods for the design of efficient siRNAs with 19 perfectly matched base pairs and 2 nt overhangs. Using four independent databases totaling 3336 experimentally verified siRNAs, we compared how well several of these methods predict siRNA cleavage efficiency. According to receiver ...

journal_title：Nucleic acids research

authors： Matveeva O,Nechipurenko Y,Rossi L,Moore B,Saetrom P,Ogurtsov AY,Atkins JF,Shabalina SA

更新日期：2007-01-01 00:00:00

abstract：:Simple modular architecture research tool (SMART) is an online tool (http://smart.embl.de/) for the identification and annotation of protein domains. It provides a user-friendly platform for the exploration and comparative study of domain architectures in both proteins and genes. The current release of SMART contains ...

journal_title：Nucleic acids research

authors： Letunic I,Doerks T,Bork P

更新日期：2009-01-01 00:00:00

abstract：:Yeast tRNA Lys2 codes preferentially for AAA and contains a 2-thiouridine derivative (U) at the 5'-position of the anticodon. Removal of the 2-thio group from U by treatment with CNBr did not affect the amino acid accepting activity of the modified tRNA Lys2. CNBr treated tRNA Lys2 was active in protein synthesis but ...

journal_title：Nucleic acids research

authors： Sen GC,Ghosh HP

更新日期：1976-03-01 00:00:00

abstract：:Plant specialized metabolites are chemically highly diverse, play key roles in host-microbe interactions, have important nutritional value in crops and are frequently applied as medicines. It has recently become clear that plant biosynthetic pathway-encoding genes are sometimes densely clustered in specific genomic lo...

journal_title：Nucleic acids research

authors： Kautsar SA,Suarez Duran HG,Blin K,Osbourn A,Medema MH

更新日期：2017-07-03 00:00:00

abstract：:We report that greA expression is driven by two strong, overlapping P1 and P2 promoters. The P1 promoter is sigma(70)-dependent and P2 is sigma(E)-dependent. Two-thirds of transcripts terminate within the leader region and the remaining third comprises greA mRNA. Termination efficiency seems to be unaffected by growth...

journal_title：Nucleic acids research

authors： Potrykus K,Murphy H,Chen X,Epstein JA,Cashel M

更新日期：2010-03-01 00:00:00

abstract：:We have previously shown that hedamycin, a GC-rich DNA-binding antitumor agent, downregulates survivin transcription (Wu et al. (2005) Molecular mechanism of inhibition of survivin transcription by the GC-rich sequence selective DNA-binding antitumor agent, hedamycin: evidence of survivin downregulation associated wit...

journal_title：Nucleic acids research

authors： Wu J,Apontes P,Song L,Liang P,Yang L,Li F

更新日期：2007-01-01 00:00:00

abstract：:Homo-oligomerization of proteins is abundant in nature, and is often intimately related with the physiological functions of proteins, such as in metabolism, signal transduction or immunity. Information on the homo-oligomer structure is therefore important to obtain a molecular-level understanding of protein functions ...

journal_title：Nucleic acids research

authors： Baek M,Park T,Heo L,Park C,Seok C

更新日期：2017-07-03 00:00:00

abstract：:Different pre-ribosomal complexes are formed during ribosome biogenesis, and the composition of these complexes is highly dynamic. Dbp4, a conserved DEAD-box RNA helicase implicated in ribosome biogenesis, interacts with nucleolar proteins Bfr2 and Enp2. We show that, like Dbp4, Bfr2 and Enp2 are required for the earl...

journal_title：Nucleic acids research

authors： Soltanieh S,Lapensée M,Dragon F

更新日期：2014-03-01 00:00:00

abstract：:Although a vast amount of life sciences data is generated in the form of images, most scientists still store images on extremely diverse and often incompatible storage media, without any type of metadata structure, and thus with no standard facility with which to conduct searches or analyses. Here we present a solutio...

journal_title：Nucleic acids research

authors： Gonzalez-Couto E,Hayes B,Danckaert A

更新日期：2001-01-01 00:00:00

abstract：:Microbial functional diversification is driven by environmental factors, i.e. microorganisms inhabiting the same environmental niche tend to be more functionally similar than those from different environments. In some cases, even closely phylogenetically related microbes differ more across environments than across tax...

journal_title：Nucleic acids research

authors： Zhu C,Mahlich Y,Miller M,Bromberg Y

更新日期：2018-01-04 00:00:00

abstract：:A series of unusual folding regions (UFR) immediately 3' to the cleavage site of the outer membrane protein (OMP) and transmembrane protein (TMP) were detected in the envelope gene RNA of the human immunodeficiency virus (HIV-1, HIV-2) and simian immunodeficiency virus (SIV) by an extensive Monte Carlo simulation. The...

journal_title：Nucleic acids research

authors： Le SY,Malim MH,Cullen BR,Maizel JV

更新日期：1990-03-25 00:00:00

abstract：:A new way of studying RNA-protein complexes, using neutron small angle scattering in solution, is described and was applied in the case of the system, yeast valyl-tRNA synthetase, interacting with its cognate and non cognate yeast tRNAs. It was shown that, when limited amounts of tRNA (either cognate or non cognate) a...

journal_title：Nucleic acids research

authors： Giegé R,Jacrot B,Moras D,Thierry JC,Zaccai G

更新日期：1977-07-01 00:00:00

abstract：:The GeneNet system is designed for collection and analysis of the data on gene and metabolic networks, signal transduction pathways and kinetic characteristics of elementary processes. In the past 2 years, the GeneNet structure was considerably improved: (i) the current version of the database is now implemented using...

journal_title：Nucleic acids research

authors： Ananko EA,Podkolodny NL,Stepanenko IL,Podkolodnaya OA,Rasskazov DA,Miginsky DS,Likhoshvai VA,Ratushny AV,Podkolodnaya NN,Kolchanov NA

更新日期：2005-01-01 00:00:00