Structural organization of mRNA complexes with major core mRNP protein YB-1.

abstract：:Allostery is the most direct, rapid and efficient way of regulating protein function, ranging from the control of metabolic mechanisms to signal-transduction pathways. However, an enormous amount of unsystematic allostery information has deterred scientists who could benefit from this field. Here, we present the AlloS...

journal_title：Nucleic acids research

authors： Huang Z,Zhu L,Cao Y,Wu G,Liu X,Chen Y,Wang Q,Shi T,Zhao Y,Wang Y,Li W,Li Y,Chen H,Chen G,Zhang J

更新日期：2011-01-01 00:00:00

abstract：:The study of pathogenic mitochondrial DNA mutations has, in most cases, relied on the production of transmitochondrial cybrids. Although the procedure to produce such cybrids is well established, it is laborious and cumbersome. Moreover, the mechanical enucleation procedure is inefficient and different techniques have...

journal_title：Nucleic acids research

authors： Bayona-Bafaluy MP,Manfredi G,Moraes CT

更新日期：2003-08-15 00:00:00

abstract：:Gut-enriched Krüppel-like factor (GKLF or KLF4) is a pleiotropic (activating and repressive) transcription factor. This study characterizes the mechanisms of transactivation by GKLF. Using a GAL4 fusion assay, the activating domain of murine GKLF was localized to the 109 amino acid residues in the N-terminus. Site-dir...

journal_title：Nucleic acids research

authors： Geiman DE,Ton-That H,Johnson JM,Yang VW

更新日期：2000-03-01 00:00:00

abstract：:Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of RNAs is often linked to their innate internal motions poses the question of whet...

journal_title：Nucleic acids research

authors： Pinamonti G,Bottaro S,Micheletti C,Bussi G

更新日期：2015-09-03 00:00:00

abstract：:In mammalian cells, DNA double-strand breaks (DSBs) are repaired by three pathways, nonhomologous end-joining (NHEJ), gene conversion (GC) and single-strand annealing (SSA). These pathways are distinct with regard to repair efficiency and mutagenic potential and must be tightly controlled to preserve viability and gen...

journal_title：Nucleic acids research

authors： Mansour WY,Schumacher S,Rosskopf R,Rhein T,Schmidt-Petersen F,Gatzemeier F,Haag F,Borgmann K,Willers H,Dahm-Daphi J

更新日期：2008-07-01 00:00:00

abstract：:Structural information on interacting proteins is important for understanding life processes at the molecular level. Genome-wide docking database is an integrated resource for structural studies of protein-protein interactions on the genome scale, which combines the available experimental data with models obtained by ...

journal_title：Nucleic acids research

authors： Kundrotas PJ,Zhu Z,Vakser IA

更新日期：2010-01-01 00:00:00

abstract：:Exposure of Schizosaccharomyces pombe cells to UV light results in increased uvi15(+) gene expression at both the mRNA and protein levels, leading to elevated cell survival. This UV-induced expression of the uvi15(+) gene was reduced in Deltasty1 and Deltawis1 cells lacking the stress-activated protein kinase pathway,...

journal_title：Nucleic acids research

authors： Kim M,Lee W,Park J,Kim JB,Jang YK,Seong RH,Choe SY,Park SD

更新日期：2000-09-01 00:00:00

abstract：:The crystal structure is reported of a complex between an ethyl derivative of the minor-groove drug furamidine and the dodecanucleotide duplex d(CGCGAATTCGCG)2, which has been refined to 1.85 A resolution and an R factor of 16.6% for data collected at -173 degreesC. An exceptionally large number (220) of water molecul...

journal_title：Nucleic acids research

authors： Guerri A,Simpson IJ,Neidle S

更新日期：1998-06-15 00:00:00

abstract：:PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points...

journal_title：Nucleic acids research

authors： Jendele L,Krivak R,Skoda P,Novotny M,Hoksza D

更新日期：2019-07-02 00:00:00

abstract：:The deoxyoctanucleotide 5'd (AAGGAGGT) which is complementary to the 3' terminus of 16S RNA has been used as a probe to measure the potential of this rRNA region to engage in intermolecular basepairing. The site specific binding of the octanucleotide is shown by labeling 16S RNA in situ at its 3' end with [32P]pCp and...

journal_title：Nucleic acids research

authors： Backendorf C,Ravensbergen CJ,Van der Plas J,van Boom JH,Veeneman G,Van Duin J

更新日期：1981-03-25 00:00:00

abstract：:The mutation patterns at Cas9 targeted sites contain unique information regarding the nuclease activity and repair mechanisms in mammalian cells. However, analytical framework for extracting such information are lacking. Here, we present a novel computational platform called Rational InDel Meta-Analysis (RIMA) that en...

journal_title：Nucleic acids research

authors： Taheri-Ghahfarokhi A,Taylor BJM,Nitsch R,Lundin A,Cavallo AL,Madeyski-Bengtson K,Karlsson F,Clausen M,Hicks R,Mayr LM,Bohlooly-Y M,Maresca M

更新日期：2018-09-19 00:00:00

abstract：:Vitamin C breaks DNA only in the presence of oxygen. Superoxide dismutase has no effect on the reaction but catalase suppresses it. Superoxide also gives rise to breaks in DNA suppressible by both superoxide dismutase and catalase. The hydroxyl radical seems to be the agent responsible for strand cleavage itself. ...

journal_title：Nucleic acids research

authors： Morgan AR,Cone RL,Elgert TM

更新日期：1976-05-01 00:00:00

abstract：:Gene losses provide an insightful route for studying the morphological and physiological adaptations of species, but their discovery is challenging. Existing genome annotation tools focus on annotating intact genes and do not attempt to distinguish nonfunctional genes from genes missing annotation due to sequencing an...

journal_title：Nucleic acids research

authors： Turakhia Y,Chen HI,Marcovitz A,Bejerano G

更新日期：2020-09-18 00:00:00

abstract：:We report here spectroscopic and biochemical data of a novel series of sugar-modified oligodeoxy-nucleotides, the carbocyclic oligothymidylates, c(dT)3-20. In c(dT)n a methylene group has been substituted for the oxygen atom of the deoxyribose ring of the natural thymidylate unit. c(dT)10-20 form helical structures, i...

journal_title：Nucleic acids research

authors： Sági J,Szemzõ A,Szécsi J,Otvös L

更新日期：1990-04-25 00:00:00

abstract：:Next-generation sequencing allows now the sequencing of small RNA molecules and the estimation of their expression levels. Consequently, there will be a high demand of bioinformatics tools to cope with the several gigabytes of sequence data generated in each single deep-sequencing experiment. Given this scene, we deve...

journal_title：Nucleic acids research

authors： Hackenberg M,Sturm M,Langenberger D,Falcón-Pérez JM,Aransay AM

更新日期：2009-07-01 00:00:00

abstract：:Four phage clones which hybridize with U1 small nuclear RNA were obtained from a rat gene library. Two clones contain a presumed pseudogene. A third clone includes two gene candidates that are co-linear with the rat U1-RNA, 3.6kb apart and in the opposite orientation. The two genes are surrounded by identical sequence...

journal_title：Nucleic acids research

authors： Watanabe-Nagasu N,Itoh Y,Tani T,Okano K,Koga N,Okada N,Ohshima Y

更新日期：1983-03-25 00:00:00

abstract：:In apurinic acid, a single-stranded polydeoxyribonucleotide easily obtained upon depurination of DNA, the proton resonances arising from thymine and cytosine are readily observable in aqueous solution of 25 degrees C. Two methyl thymine resonances, centered at 1.88 ppm and separated by 0.045 ppm, are observed. We attr...

journal_title：Nucleic acids research

authors： Rahn RO,Schleich T

更新日期：1974-08-01 00:00:00

abstract：:Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency of microRNA (miRNA) ...

journal_title：Nucleic acids research

authors： Wu X,Kim TK,Baxter D,Scherler K,Gordon A,Fong O,Etheridge A,Galas DJ,Wang K

更新日期：2017-12-01 00:00:00

abstract：:Anti-microRNA (miRNA) oligonucleotides (AMOs) with 2'-O-Methyl (2'OMe) residues are commonly used to study miRNA function and can achieve high potency, with low cytotoxicity. Not withstanding this, we demonstrate the sequence-dependent capacity of 2'OMe AMOs to inhibit Toll-like receptor (TLR) 7 and 8 sensing of immun...

journal_title：Nucleic acids research

authors： Sarvestani ST,Stunden HJ,Behlke MA,Forster SC,McCoy CE,Tate MD,Ferrand J,Lennox KA,Latz E,Williams BR,Gantier MP

更新日期：2015-01-01 00:00:00

abstract：:Abasic sites are common DNA lesions resulting from spontaneous depurination and excision of damaged nucleobases by DNA repair enzymes. However, the influence of the local sequence context on the structure of the abasic site and ultimately, its recognition and repair, remains elusive. In the present study, duplex DNAs ...

journal_title：Nucleic acids research

authors： Chen J,Dupradeau FY,Case DA,Turner CJ,Stubbe J

更新日期：2008-01-01 00:00:00

abstract：:Rap1 is an essential DNA-binding factor from the yeast Saccharomyces cerevisiae involved in transcription and telomere maintenance. Its binding to DNA targets Rap1 at particular loci, and may optimize its ability to form functional macromolecular assemblies. It is a modular protein, rich in large potentially unfolded ...

journal_title：Nucleic acids research

authors： Matot B,Le Bihan YV,Lescasse R,Pérez J,Miron S,David G,Castaing B,Weber P,Raynal B,Zinn-Justin S,Gasparini S,Le Du MH

更新日期：2012-04-01 00:00:00

abstract：:The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and re...

journal_title：Nucleic acids research

authors： NCBI Resource Coordinators.

更新日期：2018-01-04 00:00:00

abstract：:Nucleotide sequences of large T1 ribonuclease fragments of 18S ribosomal RNA of Novikoff rat ascites hepatoma cells and chicken lymphoblastoid cells were determined and compared. Among the 19 large T1 ribonuclease fragments examined of rat 18S ribosomal RNA, 12 fragments were found to be the same in chicken 18S riboso...

journal_title：Nucleic acids research

authors： Fuke M,Busch H

更新日期：1979-11-10 00:00:00

abstract：:NF-IL6beta regulates gene expression and plays function roles in many tissues. The EGF-regulated cyclooxygenase-2 (cox-2) expression is mediated through p38(MAPK) signaling pathway and positively correlates with NF-IL6beta expression in A431 cells. NF-IL6beta coordinated with c-Jun on cox-2 transcriptional activation ...

journal_title：Nucleic acids research

authors： Wang JM,Ko CY,Chen LC,Wang WL,Chang WC

更新日期：2006-01-05 00:00:00

abstract：:The prokaryotic beta recombinase catalyzes site-specific recombination between two directly oriented minimal six sites in chromatin-integrated substrates. Here, we demonstrate that an enhanced green fluorescent protein (EGFP)-fused version of beta recombinase (beta-EGFP) is fully active, retaining most specific activi...

journal_title：Nucleic acids research

authors： Servert P,Garcia-Castro J,Díaz V,Lucas D,Gonzalez MA,Martínez-A C,Bernad A

更新日期：2006-01-03 00:00:00

abstract：:Eukaryotic cells possess several distinct mismatch repair pathways. A mismatch can be introduced in retroviral double-stranded DNA by a pre-existing mutation within the primer binding site (PBS) of the viral RNA genome. In order to evaluate mismatch repair of retroviral double-stranded DNA, Moloney leukemia virus (MLV...

journal_title：Nucleic acids research

authors： Tang LY,Zhang J

更新日期：2000-06-15 00:00:00

abstract：:Au (III) reacts with DNA at pH 5.6 to form a complex which is sensitive to mid-UV radiation. Cyclobutane pyrimidine dimers are produced at some 15 to 30 times the rate that they are in untreated DNA. The mechanism of photosensitization appears to involve energy absorption by Au-urine and Au-cytosine adducts which can ...

journal_title：Nucleic acids research

authors： Wilkins RJ

更新日期：1978-10-01 00:00:00

abstract：:A new series of DNA bis-intercalators is reported in which acridine moieties are connected by rigid and extended pyridine-based linkers of varied length. Cross-linking of DNA by bis-intercalation is inferred from the unwinding and folding of linear DNA induced by the compounds; after ligation and removal of the bis-in...

journal_title：Nucleic acids research

authors： Annan NK,Cook PR,Mullins ST,Lowe G

更新日期：1992-03-11 00:00:00

abstract：:Cellular RNA labeling strategies based on bioorthogonal chemical reactions are much less developed in comparison to glycan, protein and DNA due to its inherent instability and lack of effective methods to introduce bioorthogonal reactive functionalities (e.g. azide) into RNA. Here we report the development of a simple...

journal_title：Nucleic acids research

authors： Sawant AA,Tanpure AA,Mukherjee PP,Athavale S,Kelkar A,Galande S,Srivatsan SG

更新日期：2016-01-29 00:00:00

abstract：:The positions of the trfA and trfB promoters of broad host range IncP plasmid RK2 (identical to RP1, RP4, R68 and R18 ) were identified by RNA polymerase protection studies, and the nucleotide sequences of the promoter regions determined. A mutation within the trfA promoter sequence is associated with loss of kilD act...

journal_title：Nucleic acids research

authors： Smith CA,Shingler V,Thomas CM

更新日期：1984-04-25 00:00:00