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














  • The site-specific DNA endonuclease encoded by a group I intron in the Chlamydomonas pallidostigmatica chloroplast small subunit rRNA gene introduces a single-strand break at low concentrations of Mg2+.

    abstract::Two group I introns (CpSSU.1 and CpSSU.2) that each potentially encode a protein with two copies of the LAGLI-DADG motif were identified in the Chlamydomonas pallidostigmatica chloroplast small subunit rRNA gene. They both belong to subgroup IA3 and represent novel insertion positions in this gene (sites 508 and 793 i...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Turmel M,Mercier JP,Côté V,Otis C,Lemieux C

    更新日期:1995-07-11 00:00:00

  • Determination of affinity, stoichiometry and sequence selectivity of minor groove binder complexes with double-stranded oligodeoxynucleotides by electrospray ionization mass spectrometry.

    abstract::Electrospray mass spectrometry was evaluated regarding the reliability of the determination of the stoichiometries and equilibrium association constants from single spectra. Complexes between minor groove binders (Hoechst 33258, Hoechst 33342, DAPI, netropsin and berenil) and 12mer oligonucleotide duplexes with a cent...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rosu F,Gabelica V,Houssier C,De Pauw E

    更新日期:2002-08-15 00:00:00

  • A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing.

    abstract::Correlation of motif occurrences with gene expression intensity is an effective strategy for elucidating transcriptional cis-regulatory logic. Here we demonstrate that this approach can also identify cis-regulatory elements for alternative pre-mRNA splicing. Using data from a human exon microarray, we identified 56 ca...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Das D,Clark TA,Schweitzer A,Yamamoto M,Marr H,Arribere J,Minovitsky S,Poliakov A,Dubchak I,Blume JE,Conboy JG

    更新日期:2007-01-01 00:00:00

  • Absolute configuration of Rp-uridine 3',5'-cyclic phosphorothioate.

    abstract::Triethylammonium uridine-3',5'-cyclic phosphorothioate crystallizes in space group P2(1)2(1)2(1), a = 7.177(1), b = 13.155(6), c = 21.114(7) A, C15H26N3O7PS, MW 423.4, Z = 4, dx = 1.41g/cm3. The crystal structure was solved by direct methods on the basis of 1493 counter X-ray diffraction data (CuK alpha) and refined t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hinrichs W,Steifa M,Saenger W,Eckstein F

    更新日期:1987-06-25 00:00:00

  • GenBank.

    abstract::GenBank (R) is a comprehensive sequence database that contains publicly available DNA sequences for more than 119 000 different organisms, obtained primarily through the submission of sequence data from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


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

    更新日期:2003-01-01 00:00:00

  • Carboxy terminal modifications of the P0 protein reveal alternative mechanisms of nuclear ribosomal stalk assembly.

    abstract::The P0 scaffold protein of the ribosomal stalk is mainly incorporated into pre-ribosomes in the cytoplasm where it replaces the assembly factor Mrt4. In analyzing the role of the P0 carboxyl terminal domain (CTD) during ribosomal stalk assembly, we found that its complete removal yields a protein that is functionally ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Francisco-Velilla R,Remacha M,Ballesta JP

    更新日期:2013-10-01 00:00:00

  • Two step binding of HIV-1 reverse transcriptase to nucleic acid substrates.

    abstract::The interactions of HIV-1 reverse transcriptase (HIV-1 RT) with a synthetic 53/19-mer DNA substrate was investigated. For this template-primer HIV-1 RT displayed a Km value of 20 nM. The 53/19-mer competitively inhibited DNA synthesis performed on poly (rC).oligo(dG) with Ki value of 260 nM. This corresponded well to ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kruhøffer M,Urbanke C,Grosse F

    更新日期:1993-08-25 00:00:00

  • Sequence-specific interactions of the tight-binding I12-X86 lac repressor with non-operator DNA.

    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

    pub_type: 杂志文章


    authors: Schmitz A,Galas DJ

    更新日期:1980-02-11 00:00:00

  • FREP: a database of functional repeats in mouse cDNAs.

    abstract::The FREP database ( contains 31 396 RepeatMasker-identified non-redundant variant repeat sequences derived from 16,527 mouse cDNAs with protein-coding potential. The repeats were computationally associated with potential effects on transcriptional variation, translation, protein func...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Nagashima T,Matsuda H,Silva DG,Petrovsky N,Konagaya A,Schönbach C,Kasukawa T,Arakawa T,Carninci P,Kawai J,Hayashizaki Y,RIKEN GER Group.,Genome Science Laoratory Members.

    更新日期:2004-01-01 00:00:00

  • The BCL2 gene is regulated by a special AT-rich sequence binding protein 1-mediated long range chromosomal interaction between the promoter and the distal element located within the 3'-UTR.

    abstract::The 279-bp major breakpoint region (mbr) within the 3'-untranslated region (3'-UTR) of the BCL2 gene is a binding site of special AT-rich sequence binding protein 1 (SATB1) that is well known to participate in the long-range regulation of gene transcription. Our previous studies have revealed that the mbr could regula...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gong F,Sun L,Wang Z,Shi J,Li W,Wang S,Han X,Sun Y

    更新日期:2011-06-01 00:00:00

  • Glycosyl conformational and inductive effects on the acid catalysed hydrolysis of purine nucleosides.

    abstract::The log kobs vs. pH profiles were determined in the intermediate acidity region for the glycosyl hydrolysis of guanosine and its 8-amino, 8-monomethylamino, 8-dimethylamino and 8-bromo derivatives. The decreased rate of the 8-amino and enhanced rate of the 8-bromo compound compared to guanosine support an A type mecha...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Jordan F,Niv H

    更新日期:1977-03-01 00:00:00

  • The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.

    abstract::We report the latest release (version 3.0) of the CATH protein domain database ( There has been a 20% increase in the number of structural domains classified in CATH, up to 86 151 domains. Release 3.0 comprises 1110 fold groups and 2147 homologous superfamilies. To cope with the increases in di...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Greene LH,Lewis TE,Addou S,Cuff A,Dallman T,Dibley M,Redfern O,Pearl F,Nambudiry R,Reid A,Sillitoe I,Yeats C,Thornton JM,Orengo CA

    更新日期:2007-01-01 00:00:00

  • Enhancing multiplex genome editing by natural transformation (MuGENT) via inactivation of ssDNA exonucleases.

    abstract::Recently, we described a method for multiplex genome editing by natural transformation (MuGENT). Mutant constructs for MuGENT require large arms of homology (>2000 bp) surrounding each genome edit, which necessitates laborious in vitro DNA splicing. In Vibrio cholerae, we uncover that this requirement is due to cytopl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Dalia TN,Yoon SH,Galli E,Barre FX,Waters CM,Dalia AB

    更新日期:2017-07-07 00:00:00

  • Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA.

    abstract::The satellite RNA of tobacco ringspot virus (STobRV RNA) replicates and becomes encapsidated in association with tobacco ringspot virus. Previous results show that the infected tissue produces multimeric STobRV RNAs of both polarities. RNA that is complementary to encapsidated STobRV RNA, designated as having the (-) ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Buzayan JM,Hampel A,Bruening G

    更新日期:1986-12-22 00:00:00

  • Selective disruption of the DNA polymerase III α-β complex by the umuD gene products.

    abstract::DNA polymerase III (DNA pol III) efficiently replicates the Escherichia coli genome, but it cannot bypass DNA damage. Instead, translesion synthesis (TLS) DNA polymerases are employed to replicate past damaged DNA; however, the exchange of replicative for TLS polymerases is not understood. The umuD gene products, whic...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Silva MC,Nevin P,Ronayne EA,Beuning PJ

    更新日期:2012-07-01 00:00:00

  • JBP1 and JBP2 are two distinct thymidine hydroxylases involved in J biosynthesis in genomic DNA of African trypanosomes.

    abstract::Genomic DNA of African trypanosomes contains a hypermodified thymidine residue termed base J (beta-d-glucosyl-HOMedU). This modified base is localized primarily to repetitive DNA, namely the telomeres, and is implicated in the regulation of antigenic variation. The base is synthesized in a two-step pathway. Initially,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Cliffe LJ,Kieft R,Southern T,Birkeland SR,Marshall M,Sweeney K,Sabatini R

    更新日期:2009-04-01 00:00:00

  • Conservative site-specific and single-copy transgenesis in human LINE-1 elements.

    abstract::Genome engineering of human cells plays an important role in biotechnology and molecular medicine. In particular, insertions of functional multi-transgene cassettes into suitable endogenous sequences will lead to novel applications. Although several tools have been exploited in this context, safety issues such as cyto...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Vijaya Chandra SH,Makhija H,Peter S,Myint Wai CM,Li J,Zhu J,Ren Z,D'Alcontres MS,Siau JW,Chee S,Ghadessy FJ,Dröge P

    更新日期:2016-04-07 00:00:00

  • PRODORIC2: the bacterial gene regulation database in 2018.

    abstract::Bacteria adapt to changes in their environment via differential gene expression mediated by DNA binding transcriptional regulators. The PRODORIC2 database hosts one of the largest collections of DNA binding sites for prokaryotic transcription factors. It is the result of the thoroughly redesigned PRODORIC database. PR...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Eckweiler D,Dudek CA,Hartlich J,Brötje D,Jahn D

    更新日期:2018-01-04 00:00:00

  • Fine mapping of replication origins (ori A and ori B) in Nicotiana tabacum chloroplast DNA.

    abstract::Using a partially purified replication complex from tobacco chloroplasts, replication origins have been localized to minimal sequences of 82 (pKN8, positions 137 683-137 764) and 243 bp (pKN3, positions 130 513-130 755) for ori A and ori B respectively. Analysis of in vitro replication products by two-dimensional agar...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kunnimalaiyaan M,Nielsen BL

    更新日期:1997-09-15 00:00:00

  • Transcriptional and post-transcriptional regulation of storage protein gene expression in sulfur-deficient pea seeds.

    abstract::We have used in vitro transcription in isolated pea nuclei to determine whether the expression of genes for the seed storage proteins legumin and vicilin is regulated transcriptionally or post-transcriptionally in response to changing sulfur status in the developing seed. During the first 48 h of recovery from S defic...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Beach LR,Spencer D,Randall PJ,Higgins TJ

    更新日期:1985-02-11 00:00:00

  • The relationship of potential G-quadruplex sequences in cis-upstream regions of the human genome to SP1-binding elements.

    abstract::We have carried out a survey of potential quadruplex structure sequences (PQSS), which occur in the immediate upstream region (500 bp) of human genes. By examining the number and distribution of these we have established that there is a clear link between them and the occurrence of the SP1-binding element 'GGGCGG', su...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Todd AK,Neidle S

    更新日期:2008-05-01 00:00:00

  • A web-based genotyping resource for viral sequences.

    abstract::The Genotyping tool at the National Center for Biotechnology Information is a web-based program that identifies the genotype (or subtype) of recombinant or non-recombinant viral nucleotide sequences. It works by using BLAST to compare a query sequence to a set of reference sequences for known genotypes. Predefined ref...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rozanov M,Plikat U,Chappey C,Kochergin A,Tatusova T

    更新日期:2004-07-01 00:00:00

  • Transcription regulation of the type II restriction-modification system AhdI.

    abstract::The Restriction-modification system AhdI contains two convergent transcription units, one with genes encoding methyltransferase subunits M and S and another with genes encoding the controller (C) protein and the restriction endonuclease (R). We show that AhdI transcription is controlled by two independent regulatory l...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bogdanova E,Djordjevic M,Papapanagiotou I,Heyduk T,Kneale G,Severinov K

    更新日期:2008-03-01 00:00:00

  • In vitro optimization of 2'-OMe-4'-thioribonucleoside-modified anti-microRNA oligonucleotides and its targeting delivery to mouse liver using a liposomal nanoparticle.

    abstract::MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally. Previous studies, which characterized miRNA function, revealed their involvement in fundamental biological processes. Importantly, miRNA expression is deregulated in many human diseases. Specific inhibition of miRNAs usin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Takahashi M,Yamada N,Hatakeyama H,Murata M,Sato Y,Minakawa N,Harashima H,Matsuda A

    更新日期:2013-12-01 00:00:00

  • SITEHOUND-web: a server for ligand binding site identification in protein structures.

    abstract::SITEHOUND-web ( is a binding-site identification server powered by the SITEHOUND program. Given a protein structure in PDB format SITEHOUND-web will identify regions of the protein characterized by favorable interactions with a probe molecule. These regions correspond to putative ligand...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hernandez M,Ghersi D,Sanchez R

    更新日期:2009-07-01 00:00:00

  • Properties of a small transcribed poly A sequence in heterogeneous nuclear RNA of HeLa cells.

    abstract::A class of heterogeneous nuclear RNA (hnRNA) molecules contain an internal transcribed poly A sequence of close to 25 uninterrupted AMP residues. HnRNA molecules containing this sequence are separable from those containing the large 3' terminal poly A sequence on the basis of their differential affinity for oligo dT c...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Venkatesan S,Nakazato H,Kopp DW,Edmonds M

    更新日期:1979-03-01 00:00:00

  • CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures.

    abstract::Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and appli...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kuriata A,Gierut AM,Oleniecki T,Ciemny MP,Kolinski A,Kurcinski M,Kmiecik S

    更新日期:2018-07-02 00:00:00

  • Mediation of the A/B-DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG.

    abstract::The crystal structure of the DNA dodecamer duplex CATGGGCCCATG lies on a structural continuum along the transition between A- and B-DNA. The dodecamer possesses the normal vector plot and inclination values typical of B-DNA, but has the crystal packing, helical twist, groove width, sugar pucker, slide and x-displaceme...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ng HL,Dickerson RE

    更新日期:2002-09-15 00:00:00

  • Interaction of N-acetyl-phenylalanyl-tRNAPhe with 70S ribosomes of Escherichia coli.

    abstract::The interaction of N--Acetyl--Phe--tRNA Phe with 70 S ribosomes is a reversible process in the absence as well as in the presence of messenger. The equilibrium binding constants of these interactions were measured at different magnesium concentrations and temperatures and thermodynamical quantities computed. The entha...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Odinzov VB,Kirillov SV

    更新日期:1978-10-01 00:00:00

  • A promotor directing alpha-amanitin-sensitive transcription of GARP, the major surface antigen of insect stage Trypanosoma congolense.

    abstract::The major surface antigen of procyclic and epimastigote forms of Trypanosoma congolense in the tsetse fly is GARP (glutamic acid/alanine-rich protein), which is thought to be the analogue of procyclin/PARP in Trypanosoma brucei. We have studied two T.congolense GARP loci (the 4.3 and 4.4 loci) whose transcription is a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Graham SV,Jefferies D,Barry JD

    更新日期:1996-01-15 00:00:00