Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq.

abstract：:Cancer-associated somatic mutations outside protein-coding regions remain largely unexplored. Analyses of the TERT locus have indicated that non-coding regulatory mutations can be more frequent than previously suspected and play important roles in oncogenesis. Using a computational method called SASE-hunter, developed...

journal_title：Nucleic acids research

authors： Smith KS,Yadav VK,Pedersen BS,Shaknovich R,Geraci MW,Pollard KS,De S

更新日期：2015-06-23 00:00:00

abstract：:The chicken erythroid proteins binding to the histone H5 5' promoter and 3' erythroid-specific enhancer regions were identified. In DNase I footprinting and gel mobility shift experiments with immature adult erythrocyte nuclear extracts, we have demonstrated the binding of proteins to the GC-box, a high affinity Sp1 b...

journal_title：Nucleic acids research

authors： Sun JM,Penner CG,Davie JR

更新日期：1992-12-11 00:00:00

abstract：:The σ subunit of bacterial RNA polymerase (RNAP) has been implicated in all steps of transcription initiation, including promoter recognition and opening, priming of RNA synthesis, abortive initiation and promoter escape. The post-promoter-recognition σ functions were proposed to depend on its conserved region σ3.2 th...

journal_title：Nucleic acids research

authors： Pupov D,Kuzin I,Bass I,Kulbachinskiy A

更新日期：2014-04-01 00:00:00

abstract：:The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct...

journal_title：Nucleic acids research

authors： Schudoma C,May P,Nikiforova V,Walther D

更新日期：2010-01-01 00:00:00

abstract：:We have developed an effective, easy-to-use two-step system for the site-directed insertion of large genetic constructs into arbitrary positions in the Escherichia coli chromosome. The system uses lambda-Red mediated recombineering accompanied by the introduction of double-strand DNA breaks in the chromosome and a don...

journal_title：Nucleic acids research

authors： Kuhlman TE,Cox EC

更新日期：2010-04-01 00:00:00

abstract：:The mitochondrial DNA of Neurospora crassa has a heterogeneous intramolecular base distribution. A contiguous piece, representing at least 30% of the total genome, has a G+C content that is 6% lower than the overall G+C content of the DNA. The genes for both ribosomal RNAs are contained in the remaining, relatively G+...

journal_title：Nucleic acids research

authors： Terpstra P,Holtrop M,Kroon A

更新日期：1977-01-01 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：:Proteins that bind to DNA are found in all areas of genetic activity within the cell. To help understand how these proteins perform their various functions, it is useful to analyse which residues are involved in binding to the DNA and how they interact with the bases and sugar-phosphate backbone of nucleic acids. Here...

journal_title：Nucleic acids research

authors： Luscombe NM,Laskowski RA,Thornton JM

更新日期：1997-12-15 00:00:00

abstract：:We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar struc...

journal_title：Nucleic acids research

authors： Cabaj MK,Dominiak PM

更新日期：2020-09-04 00:00:00

abstract：:The Gene Expression Atlas (http://www.ebi.ac.uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, ...

journal_title：Nucleic acids research

authors： Kapushesky M,Emam I,Holloway E,Kurnosov P,Zorin A,Malone J,Rustici G,Williams E,Parkinson H,Brazma A

更新日期：2010-01-01 00:00:00

abstract：:We report here the different ways in which four subunits of the basal transcription/repair factor TFIIH (XPB, XPD, p62 and p44) and the damage recognition XPC repair protein can enter the nucleus. We examined their nuclear localization by transiently expressing the gene products tagged with the enhanced green fluoresc...

journal_title：Nucleic acids research

authors： Santagati F,Botta E,Stefanini M,Pedrini AM

更新日期：2001-04-01 00:00:00

abstract：:The adenovirus late region 1 (L1) represents an example of an alternatively spliced gene where one 5' splice site is spliced to two alternative 3' splice sites, to produce two mRNAs; the 52,55K and IIIa mRNAs, respectively. Accumulation of the L1 mRNAs is temporally regulated during the infectious cycle. Thus, the pro...

journal_title：Nucleic acids research

authors： Kreivi JP,Akusjärvi G

更新日期：1994-02-11 00:00:00

abstract：:GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or st...

journal_title：Nucleic acids research

authors： Benson DA,Karsch-Mizrachi I,Lipman DJ,Ostell J,Wheeler DL

更新日期：2008-01-01 00:00:00

abstract：:In the filamentous cyanobacterium Anabaena sp. PCC 7120, the ferric uptake regulator FurA functions as a global transcriptional regulator. Despite several analyses have focused on elucidating the FurA-regulatory network, the number of target genes described for this essential transcription factor is limited to a handf...

journal_title：Nucleic acids research

authors： González A,Angarica VE,Sancho J,Fillat MF

更新日期：2014-04-01 00:00:00

abstract：:DNA target recognizing domains of different multispecific DNA-cytosine-methyltransferases can be rearranged through engineering of the corresponding genes to generate enzymes with novel combinations of target recognition. ...

journal_title：Nucleic acids research

authors： Trautner TA,Balganesh TS,Pawlek B

更新日期：1988-07-25 00:00:00

abstract：:Dlx2, Lymphoid Enhancer Factor (Lef-1) and Msx2 transcription factors are required for several developmental processes. To understand the control of gene expression by these factors, chromatin immunoprecipitation (ChIP) assays identified Msx2 as a downstream target of Dlx2 and Lef-1. Dlx2 activates the Msx2 promoter i...

journal_title：Nucleic acids research

authors： Diamond E,Amen M,Hu Q,Espinoza HM,Amendt BA

更新日期：2006-01-01 00:00:00

abstract：:Current DNA assembly methods for preparing highly purified linear subassemblies require complex and time-consuming in vitro manipulations that hinder their ability to construct megabase-sized DNAs (e.g. synthetic genomes). We have developed a new method designated 'CasHRA (Cas9-facilitated Homologous Recombination Ass...

journal_title：Nucleic acids research

authors： Zhou J,Wu R,Xue X,Qin Z

更新日期：2016-08-19 00:00:00

abstract：:It has been proposed that DNA multiply damaged sites (MDS), where more than one moiety in a local region ( approximately 1 helical turn, 10 bp) of the DNA is damaged, are lesions of enhanced biological significance. However, other than indirect measures, there are few analytical techniques that allow direct detection ...

journal_title：Nucleic acids research

authors： Bowman KJ,Pla RL,Guichard Y,Farmer PB,Jones GD

更新日期：2001-10-15 00:00:00

abstract：:Selenoproteins contain the amino acid selenocysteine which is encoded by a UGA Sec codon. Recoding UGA Sec requires a complex mechanism, comprising the cis-acting SECIS RNA hairpin in the 3'UTR of selenoprotein mRNAs, and trans-acting factors. Among these, the SECIS Binding Protein 2 (SBP2) is central to the mechanism...

journal_title：Nucleic acids research

authors： Takeuchi A,Schmitt D,Chapple C,Babaylova E,Karpova G,Guigo R,Krol A,Allmang C

更新日期：2009-04-01 00:00:00

abstract：:Two triple helix structures (15-mers containing only T.A-T triplets or containing mixed T.A-T and C.G-C triplets) have been studied by uranyl mediated DNA photocleavage to probe the accessibility of the phosphates of the DNA backbone. Whereas the phosphates of the pyrimidine strand are at least as accessible as in dou...

journal_title：Nucleic acids research

authors： Nielsen PE

更新日期：1992-06-11 00:00:00

abstract：:Enzymes that form transient DNA-protein covalent complexes are targets for several potent classes of drugs used to treat infectious disease and cancer, making it important to establish robust and rapid procedures for analysis of these complexes. We report a method for isolation of DNA-protein adducts and their identif...

journal_title：Nucleic acids research

authors： Kiianitsa K,Maizels N

更新日期：2014-07-01 00:00:00

abstract：:The hydroxyl radical is a powerful oxidant that generates DNA lesions including the stereoisomeric R and S 5',8-cyclo-2'-deoxyadenosine (cdA) and 5',8-cyclo-2'-deoxyguanosine (cdG) pairs that have been detected in cellular DNA. Unlike some other oxidatively generated DNA lesions, cdG and cdA are repaired by the human ...

journal_title：Nucleic acids research

authors： Kropachev K,Ding S,Terzidis MA,Masi A,Liu Z,Cai Y,Kolbanovskiy M,Chatgilialoglu C,Broyde S,Geacintov NE,Shafirovich V

更新日期：2014-04-01 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 published in life science journals. The Entrez system provides search and re...

journal_title：Nucleic acids research

authors： Sayers EW,Beck J,Bolton EE,Bourexis D,Brister JR,Canese K,Comeau DC,Funk K,Kim S,Klimke W,Marchler-Bauer A,Landrum M,Lathrop S,Lu Z,Madden TL,O'Leary N,Phan L,Rangwala SH,Schneider VA,Skripchenko Y,Wang J,Ye J,

更新日期：2021-01-08 00:00:00

abstract：:A downstream G-rich sequence (GRS), GGGGGAGGUGUGGG, has been previously shown to influence the efficiency of 3' end processing of the SV40 late polyadenylation signal. We have now defined several important parameters for GRS-mediated polyadenylation. The ability of the GRS to influence 3' end processing efficiency was...

journal_title：Nucleic acids research

authors： Bagga PS,Ford LP,Chen F,Wilusz J

更新日期：1995-05-11 00:00:00

abstract：:Molecular Biology Database List (MBDL) includes brief descriptions and pointers to Web sites for the various databases described in this issue as well as other Web sites presenting data sets relevant to molecular biology. This information is compiled into a list (http://www.oup.co.uk/nar/Volume_27/Issue_01/summary/ gk...

journal_title：Nucleic acids research

authors： Burks C

更新日期：1999-01-01 00:00:00

abstract：:G-quadruplexes (G4s) are nucleic acid structure motifs that are of significance in chemistry and biology. The function of G4s is often governed by their interaction with G4-binding proteins. Few categories of G4-specific tools have been developed to inhibit G4-protein interactions; however, until now there is no aptam...

journal_title：Nucleic acids research

authors： Umar MI,Kwok CK

更新日期：2020-10-09 00:00:00

abstract：:Search of interrelationships between the structural-functional protein organization and exon structure of encoding gene provides insights into issues concerned with the function, origin and evolution of genes and proteins. The functions of proteins and their domains are defined mostly by functional sites. The relation...

journal_title：Nucleic acids research

authors： Medvedeva I,Demenkov P,Kolchanov N,Ivanisenko V

更新日期：2012-01-01 00:00:00

abstract：:Conditional gene targeting depends on tissue and time specificity of recombination events. Endogenous promoters are often used to drive various transgenic constructs. To avoid the problems associated with reconstituting a specific expression pattern in transgenic animals by this method, we tested the internal ribosome...

journal_title：Nucleic acids research

authors： Lindeberg J,Ebendal T

更新日期：1999-03-15 00:00:00

abstract：:During the formation of a transcriptionally active macronucleus, ciliated protozoa excise large numbers of interstitial segments of DNA (internal eliminated sequences; IESs) from their chromosomes. In this study we analyze the published sequences of 20 IESs that interrupt surface protein genes of Paramecium and identi...

journal_title：Nucleic acids research

authors： Klobutcher LA,Herrick G

更新日期：1995-06-11 00:00:00

abstract：:RJ2.2.5, a mutant derived from the human B-lymphoma cell, Raji, is unable to express the MHC class II genes because of a recessive transcriptional defect attributed to the lack of an activator function. We report the isolation of a RJ2.2.5 revertant, namely AR, in which the expression of the mRNAs encoded by these gen...

journal_title：Nucleic acids research

authors： Ombra MN,Perfetto C,Autiero M,Anzisi AM,Pasquinelli R,Maffei A,Del Pozzo G,Guardiola J

更新日期：1993-02-11 00:00:00