Database on the structure of large ribosomal subunit RNA.


:Our database on large ribosomal subunit RNA contained 334 sequences in July, 1995. All sequences in the database are aligned, taking into account secondary structure. The aligned sequences are provided, together with incorporated secondary structure information, in several computer-readable formats. These data can easily be obtained through the World Wide Web. The files in the database are also available via anonymous ftp.


Nucleic Acids Res


Nucleic acids research


De Rijk P,Van de Peer Y,De Wachter R




Has Abstract


1996-01-01 00:00:00














  • Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase.

    abstract::The methyltransferase, M.EcoKI, recognizes the DNA sequence 5'-AACNNNNNNGTGC-3' and methylates adenine at the underlined positions. DNA methylation has been shown by crystallography to occur via a base flipping mechanism and is believed to be a general mechanism for all methyltransferases. If no structure is available...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Su TJ,Connolly BA,Darlington C,Mallin R,Dryden DT

    更新日期:2004-04-23 00:00:00

  • IS3 can function as a mobile promoter in E. coli.

    abstract::We had shown previously (3) that the E. coli argE gene could be turned-on by an IS3 element inserted in orientation II near the 5' end of the gene. Here we show that this effect is due to the presence of an outward promoter located on IS3. The exact site of insertion of IS3 was determined by DNA sequencing. Using the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Charlier D,Piette J,Glansdorff N

    更新日期:1982-10-11 00:00:00

  • HIV-1 Tat directly binds to NFkappaB enhancer sequence: role in viral and cellular gene expression.

    abstract::HIV-1 Tat protein reprograms cellular gene expression of infected as well as uninfected cells apart from its primary function of transactivating HIV-1 long terminal repeat (LTR) promoter by binding to a nascent RNA stem-loop structure known as the transactivator response region (TAR). Tat also induces chromatin remode...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Dandekar DH,Ganesh KN,Mitra D

    更新日期:2004-02-23 00:00:00

  • Coding capacity of complementary DNA strands.

    abstract::A Fortran computer algorithm has been used to analyze the nucleotide sequence of several structural genes. The analysis performed on both coding and complementary DNA strands shows that whereas open reading frames shorter than 100 codons are randomly distributed on both DNA strands, open reading frames longer than 100...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Casino A,Cipollaro M,Guerrini AM,Mastrocinque G,Spena A,Scarlato V

    更新日期:1981-03-25 00:00:00

  • Structural organization of Staf-DNA complexes.

    abstract::The transactivator Staf, which contains seven contiguous zinc fingers of the C(2)-H(2)type, exerts its effects on gene expression by binding to specific targets in vertebrate small nuclear RNA (snRNA) and snRNA-type gene promoters. Here, we have investigated the interaction of the Staf zinc finger domain with the opti...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Schaub M,Krol A,Carbon P

    更新日期:2000-05-15 00:00:00

  • The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis.

    abstract::We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Cur...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rampp M,Soddemann T,Lederer H

    更新日期:2006-07-01 00:00:00

  • Sequences of human immunoglobulin switch regions: implications for recombination and transcription.

    abstract::We have sequenced the entire human S mu and S gamma 4 immunoglobulin heavy chain class switch regions, and have also completed the sequence of human S epsilon. S mu is composed predominantly of GAGCT and GGGCT pentameric repeats, with these units also being found in S epsilon at a much lower density. S mu-S gamma 4 ma...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mills FC,Brooker JS,Camerini-Otero RD

    更新日期:1990-12-25 00:00:00

  • Fission yeast with DNA polymerase delta temperature-sensitive alleles exhibits cell division cycle phenotype.

    abstract::DNA polymerases alpha and delta are essential enzymes believed to play critical roles in initiation and replication of chromosome DNA. In this study, we show that the genes for Schizosaccharomyces pombe (S.pombe) DNA polymerase alpha and delta (pol alpha+ and pol delta+) are essential for cell viability. Disruption of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Francesconi S,Park H,Wang TS

    更新日期:1993-08-11 00:00:00

  • Specifically alkylated DNA fragments. Synthesis and physical characterization of d[CGC(O6Me)GCG] and d[CGT(O6Me)GCG].

    abstract::Two hexamer DNA fragments containing a carcinogenic modified base, O6-methyl guanine, have been synthesized by a solid-phase phosphotriester method, in which the unmodified guanine residues present were O6 protected with the 4-nitrophenylethyl group. These two alkylated oligonucleotides were found to have similar Tm's...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kuzmich S,Marky LA,Jones RA

    更新日期:1983-05-25 00:00:00

  • A yeast transcription system for the 5S rRNA gene.

    abstract::A cell-free extract of yeast nuclei that can specifically transcribe cloned yeast 5S rRNA genes has been developed. Optima for transcription of 5S rDNA were determined and conditions of extract preparation leading to reproducible activities and specificities established. The major in vitro product has the same size an...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: van Keulen H,Thomas DY

    更新日期:1982-09-11 00:00:00

  • Transcription and processing of the rodent ID repeat family in germline and somatic cells.

    abstract::ID elements comprise a rodent SINE (short interspersed DNA repetitive element) family that has amplified by retroposition of a few master genes. In order to understand the important factors of SINE amplification, we investigated the transcription of rat ID elements. Three different size classes of ID transcripts, BC1,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kim J,Kass DH,Deininger PL

    更新日期:1995-06-25 00:00:00

  • Preparation of base-modified nucleosides suitable for non-radioactive label attachment and their incorporation into synthetic oligodeoxyribonucleotides.

    abstract::A very mild and efficient procedure has been developed for the preparation of C-5 substituted deoxyuridines. The substituent carries a masked primary aliphatic amino group. These compounds are readily converted into their phosphoramidites and can be used to prepare oligonucleotides carrying one or more aliphatic amino...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Haralambidis J,Chai M,Tregear GW

    更新日期:1987-06-25 00:00:00

  • Large-scale profiling of microRNAs for The Cancer Genome Atlas.

    abstract::The comprehensive multiplatform genomics data generated by The Cancer Genome Atlas (TCGA) Research Network is an enabling resource for cancer research. It includes an unprecedented amount of microRNA sequence data: ~11 000 libraries across 33 cancer types. Combined with initiatives like the National Cancer Institute G...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chu A,Robertson G,Brooks D,Mungall AJ,Birol I,Coope R,Ma Y,Jones S,Marra MA

    更新日期:2016-01-08 00:00:00

  • Effects of hypoxanthine substitution on bleomycin-mediated DNA strand degradation in DNA-RNA hybrids.

    abstract::We have reported on the differences in site-specific cleavage between DNA and DNA-RNA hybrids by various prototypic DNA cleavers (accompanying paper). In the case of bleomycin (BLM), degradation at 5'-GC-3'sites was suppressed relative to the same sequence in double-stranded DNA, while 5'-GT-3' damage remained constan...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bansal M,Stubbe J,Kozarich JW

    更新日期:1997-05-01 00:00:00

  • The mechanism of DNA strand breakage by vitamin C and superoxide and the protective roles of catalase and superoxide dismutase.

    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

    pub_type: 杂志文章


    authors: Morgan AR,Cone RL,Elgert TM

    更新日期:1976-05-01 00:00:00

  • Enhancing identification of cancer types via lowly-expressed microRNAs.

    abstract::The primary function of microRNAs (miRNAs) is to maintain cell homeostasis. In cancerous tissues miRNAs' expression undergo drastic alterations. In this study, we use miRNA expression profiles from The Cancer Genome Atlas of 24 cancer types and 3 healthy tissues, collected from >8500 samples. We seek to classify the c...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rasnic R,Linial N,Linial M

    更新日期:2017-05-19 00:00:00

  • Nuclear poly(A) binding protein 1 (PABPN1) and Matrin3 interact in muscle cells and regulate RNA processing.

    abstract::The polyadenylate binding protein 1 (PABPN1) is a ubiquitously expressed RNA binding protein vital for multiple steps in RNA metabolism. Although PABPN1 plays a critical role in the regulation of RNA processing, mutation of the gene encoding this ubiquitously expressed RNA binding protein causes a specific form of mus...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Banerjee A,Vest KE,Pavlath GK,Corbett AH

    更新日期:2017-10-13 00:00:00

  • Structural requirements of polynucleotides for the activation of (2' - 5')An polymerase and protein kinase.

    abstract::Two enzymatic pathways are involved in the inhibitory effects of double-stranded (ds)RNA on protein synthesis in cell extracts derived from interferon-treated human fibroblasts or HeLa cells, an oligonucleotide polymerase that synthesizes (2'-5')An from ATP and a protein kinase that phosphorylates the alpha subunit of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Baglioni C,Minks MA,De Clercq E

    更新日期:1981-10-10 00:00:00

  • TFIIH is an elongation factor of RNA polymerase I.

    abstract::TFIIH is a multisubunit factor essential for transcription initiation and promoter escape of RNA polymerase II and for the opening of damaged DNA double strands in nucleotide excision repair (NER). In this study, we have analyzed at which step of the transcription cycle TFIIH is essential for transcription by RNA poly...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Assfalg R,Lebedev A,Gonzalez OG,Schelling A,Koch S,Iben S

    更新日期:2012-01-01 00:00:00

  • A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues.

    abstract::Histone proteins are synthesized in large amounts during S-phase to package the newly replicated DNA, and are among the most stable proteins in the cell. The replication-dependent (RD)-histone mRNAs expressed during S-phase end in a conserved stem-loop rather than a polyA tail. In addition, there are replication-indep...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lyons SM,Cunningham CH,Welch JD,Groh B,Guo AY,Wei B,Whitfield ML,Xiong Y,Marzluff WF

    更新日期:2016-11-02 00:00:00

  • SMART 6: recent updates and new developments.

    abstract::Simple modular architecture research tool (SMART) is an online tool ( 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

    pub_type: 杂志文章


    authors: Letunic I,Doerks T,Bork P

    更新日期:2009-01-01 00:00:00

  • Impact of CpG methylation on structure, dynamics and solvation of cAMP DNA responsive element.

    abstract::Methylation of CpG motifs in DNA is involved in the control of gene expression and in several other epigenic effects. It suppresses also the immuno-stimulation properties of bacterial or viral DNAs that contain CPGS: However, effects of methylation on the DNA structure and dynamics are not clear. Here we carried out a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Derreumaux S,Chaoui M,Tevanian G,Fermandjian S

    更新日期:2001-06-01 00:00:00

  • Target specificity of neuronal RNA-binding protein, Mel-N1: direct binding to the 3' untranslated region of its own mRNA.

    abstract::We have identified cDNAs encoding Mel-N1, the mouse homologue of a human nervous system-specific RNA-binding protein, Hel-N1. Two major mRNA transcripts of Mel-N1 were detected predominantly in the adult mouse brain by Northern blot analysis. To gain insight into the RNA binding specificity of Mel-N1, we performed ite...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Abe R,Yamamoto K,Sakamoto H

    更新日期:1996-06-01 00:00:00

  • Impact of target site distribution for Type I restriction enzymes on the evolution of methicillin-resistant Staphylococcus aureus (MRSA) populations.

    abstract::A limited number of Methicillin-resistant Staphylococcus aureus (MRSA) clones are responsible for MRSA infections worldwide, and those of different lineages carry unique Type I restriction-modification (RM) variants. We have identified the specific DNA sequence targets for the dominant MRSA lineages CC1, CC5, CC8 and ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Roberts GA,Houston PJ,White JH,Chen K,Stephanou AS,Cooper LP,Dryden DT,Lindsay JA

    更新日期:2013-08-01 00:00:00

  • Real-time analysis of single influenza virus replication complexes reveals large promoter-dependent differences in initiation dynamics.

    abstract::The viral RNA (vRNA) genome of influenza viruses is replicated by the RNA-dependent RNA polymerase (RNAP) via a complementary RNA (cRNA) intermediate. The vRNA promoter can adopt multiple conformations when bound by the RNAP. However, the dynamics, determinants, and biological role of these conformations are unknown; ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Robb NC,Te Velthuis AJW,Fodor E,Kapanidis AN

    更新日期:2019-07-09 00:00:00

  • Determinants of a transcriptionally competent environment at the GM-CSF promoter.

    abstract::Granulocyte macrophage-colony stimulating factor (GM-CSF) is produced by T cells, but not B cells, in response to immune signals. GM-CSF gene activation in response to T-cell stimulation requires remodelling of chromatin associated with the gene promoter, and these changes do not occur in B cells. While the CpG methyl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Brettingham-Moore KH,Sprod OR,Chen X,Oakford P,Shannon MF,Holloway AF

    更新日期:2008-05-01 00:00:00

  • Gene F of plasmid RSF1010 codes for a low-molecular-weight repressor protein that autoregulates expression of the repAC operon.

    abstract::The repAC operon of plasmid RSF1010 consists of the genes for proteins E, F, RepA (DNA helicase), and RepC (origin-binding initiator protein) and is transcriptionally initiated by a promoter called P4. We have studied the expression of the repAC operon in vivo by using fusions to the lacZ reporter gene. The results sh...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Maeser S,Scholz P,Otto S,Scherzinger E

    更新日期:1990-11-11 00:00:00

  • Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules.

    abstract::Using total internal reflection fluorescence microscopy, we directly visualize in real-time, the 1D Brownian motion and transcription elongation of T7 RNA polymerase along aligned DNA molecules bound to substrates by molecular combing. We fluorescently label T7 RNA polymerase with antibodies and use flow to convect th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kim JH,Larson RG

    更新日期:2007-01-01 00:00:00

  • Characterization of the 3' exonuclease subunit DP1 of Methanococcus jannaschii replicative DNA polymerase D.

    abstract::The B-subunits associated with the replicative DNA polymerases are conserved from Archaea to humans, whereas the corresponding catalytic subunits are not related. The latter belong to the B and D DNA polymerase families in eukaryotes and archaea, respectively. Sequence analysis places the B-subunits within the calcine...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Jokela M,Eskelinen A,Pospiech H,Rouvinen J,Syväoja JE

    更新日期:2004-04-30 00:00:00

  • Isolation and genome-wide characterization of cellular DNA:RNA triplex structures.

    abstract::RNA can directly bind to purine-rich DNA via Hoogsteen base pairing, forming a DNA:RNA triple helical structure that anchors the RNA to specific sequences and allows guiding of transcription regulators to distinct genomic loci. To unravel the prevalence of DNA:RNA triplexes in living cells, we have established a fast ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sentürk Cetin N,Kuo CC,Ribarska T,Li R,Costa IG,Grummt I

    更新日期:2019-03-18 00:00:00