Abstract:
:RNArchitecture is a database that provides a comprehensive description of relationships between known families of structured non-coding RNAs, with a focus on structural similarities. The classification is hierarchical and similar to the system used in the SCOP and CATH databases of protein structures. Its central level is Family, which builds on the Rfam catalog and gathers closely related RNAs. Consensus structures of Families are described with a reduced secondary structure representation. Evolutionarily related Families are grouped into Superfamilies. Similar structures are further grouped into Architectures. The highest level, Class, organizes families into very broad structural categories, such as simple or complex structured RNAs. Some groups at different levels of the hierarchy are currently labeled as 'unclassified'. The classification is expected to evolve as new data become available. For each Family with an experimentally determined three-diemsional (3D) structure(s), a representative one is provided. RNArchitecture also presents theoretical models of RNA 3D structure and is open for submission of structural models by users. Compared to other databases, RNArchitecture is unique in its focus on structure-based RNA classification, and in providing a platform for storing RNA 3D structure predictions. RNArchitecture can be accessed at http://iimcb.genesilico.pl/RNArchitecture/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Boccaletto P,Magnus M,Almeida C,Zyla A,Astha A,Pluta R,Baginski B,Jankowska E,Dunin-Horkawicz S,Wirecki TK,Boniecki MJ,Stefaniak F,Bujnicki JMdoi
10.1093/nar/gkx966subject
Has Abstractpub_date
2018-01-04 00:00:00pages
D202-D205issue
D1eissn
0305-1048issn
1362-4962pii
4561639journal_volume
46pub_type
杂志文章abstract::Precursor tRNAAsp molecules, containing a 26-base 5' leader, were treated with diethylpyrocarbonate, 50% hydrazine or anhydrous hydrazine/3M NaCl and then subjected to processing by RNase P RNAs from Escherichia coli or Bacillus subtilis. Fully processed tRNAs and material not successfully cleaved by the catalytic RNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.4.885
更新日期:1991-02-25 00:00:00
abstract::We demonstrate compaction of DNA with nanoscale biomimetic constructs which are robust synthetic analogs of globular proteins. These constructs are approximately 15 nm in diameter, shell crosslinked knedel-like (SCKs) nanoparticles, which are prepared by covalent stabilization of amphiphilic di-block co-polymer micell...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.14.2966
更新日期:1999-07-15 00:00:00
abstract::Toscana virus (TOSV) is an arthropod-borne human pathogen responsible for seasonal outbreaks of fever and meningoencephalitis in the Mediterranean basin. TOSV is a segmented negative-strand RNA virus (sNSV) that belongs to the genus phlebovirus (family Phenuiviridae, order Bunyavirales), encompassing other important h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz838
更新日期:2019-11-18 00:00:00
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
doi:10.1093/nar/28.10.2114
更新日期:2000-05-15 00:00:00
abstract::Twenty AdoMet-dependent methyltransferases (MTases) have been characterized structurally by X-ray crystallography and NMR. These include seven DNA MTases, five RNA MTases, four protein MTases and four small molecule MTases acting on the carbon, oxygen or nitrogen atoms of their substrates. The MTases share a common co...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/29.18.3784
更新日期:2001-09-15 00:00:00
abstract::A new approach has been developed for the rapid fragmentation and fractionation of DNA into a size suitable for shotgun cloning and sequencing. The restriction endonuclease CviJI normally cleaves the recognition sequence PuGCPy between the G and C to leave blunt ends. Atypical reaction conditions which alter the speci...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.14.3753
更新日期:1992-07-25 00:00:00
abstract::The shape of the chromosomal DNA of the sulfur-dependent archaebacterium Sulfolobus acidocaldarius was analyzed by the pulsed-field gel electrophoresis(PFGE). S.acidocaldarius DNA digested with Notl showed two DNA bands at around 1.0 Mbp and 2.1 Mbp. Notl-linking clones were isolated from the library of S.acidocaldari...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.5.1133
更新日期:1990-03-11 00:00:00
abstract::Starting from a crude E. coli extract, two activities which specifically protect highly repetitive bacterial DNA sequences (called PU for Palindromic Unit or REP for Repetitive Extragenic Palindromic sequence) against a digestion with Exonuclease III have been purified. We show that one of these activities is due to t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.13.3941
更新日期:1990-07-11 00:00:00
abstract::Gene trap vectors developed for genome-wide mutagenesis can be used to study factors governing the expression of exons inserted throughout the genome. For example, entrapment vectors consisting of a partial 3'-terminal exon [i.e. a neomycin resistance gene (Neo), a poly(A) site, but no 3' splice site] were typically e...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh604
更新日期:2004-05-20 00:00:00
abstract::The interaction of antibodies directed toward N6-(delta2-isopentenyl)adenosine, i6Ado, or its nucleotide with related bases, nucleosides, nucleotides and purified tRNAs is described. The selectivity of the antibody preparation was tested in inhibition experiments utilizing a sensitive radioimmunoassay to quantitate th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.9.3439
更新日期:1978-09-01 00:00:00
abstract::The laminin (LM)-database, hosted at http://www.lm.lncc.br, was published in the NAR database 2011 edition. It was the first database that provided comprehensive information concerning a non-collagenous family of extracellular matrix proteins, the LMs. In its first version, this database contained a large amount of in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt901
更新日期:2014-01-01 00:00:00
abstract::Histone H2B O-GlcNAcylation is an important post-translational modification of chromatin during gene transcription. However, how this epigenetic modification is regulated remains unclear. Here we found that the energy-sensing adenosine-monophosphate-activated protein kinase (AMPK) could suppress histone H2B O-GlcNAcyl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku236
更新日期:2014-05-01 00:00:00
abstract::The rat alpha- and bovine alpha s1-casein genes have been isolated and their 5' sequences determined. The rat alpha-, beta-, gamma- and bovine alpha s1-casein genes contain similar 5' exon arrangements in which the 5' noncoding, signal peptide and casein kinase phosphorylation sequences are each encoded by separate ex...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.4.1883
更新日期:1986-02-25 00:00:00
abstract::We have cloned and sequenced the lasR gene, which is involved in the transcriptional activation of several pathogenic factors, from Pseudomonas aeruginosa IFO3455 and PA103. These clones were predicted to be an open reading frame of 239 amino acids as reported for the PAO1 strain. There is only a single base change re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.18.3706
更新日期:1994-09-11 00:00:00
abstract::Defined DNA substrates containing discrete abasic sites or paired abasic sites set 1, 3, 5 and 7 bases apart on opposite strands were constructed to examine the reactivity of S1, mung bean and P1 nucleases towards abasic sites. None of the enzymes acted on the substrate containing discrete abasic sites. Under conditio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.19.3805
更新日期:1995-10-11 00:00:00
abstract::The S-adenosylmethionine (AdoMet) analog sinefungin is a natural product antibiotic that inhibits nucleic acid methyltransferases and arrests the growth of unicellular eukarya and eukaryal viruses. The basis for the particular sensitivity of fungi and protozoa to sinefungin is not known. Here we report the isolation a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm817
更新日期:2007-01-01 00:00:00
abstract::Initiation of Adenovirus (Ad) DNA replication occurs by a protein-priming mechanism in which the viral precursor terminal protein (pTP) and DNA polymerase (pol) as well as two nuclear DNA-binding proteins from uninfected HeLa cells are required. Biochemical studies on the pTP and DNA polymerase proteins separately hav...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.6.2431
更新日期:1988-03-25 00:00:00
abstract::A set of programs was developed for searching nucleic acid and protein sequence data bases for sequences similar to a given sequence. The programs, written in FORTRAN 77, were optimized for vector processing on a Hitachi S810-20 supercomputer. A search of a 500-residue protein sequence against the entire PIR data base...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.1.57
更新日期:1986-01-10 00:00:00
abstract::Most RNA molecules collapse rapidly and reach the native state through a pathway that contains numerous traps and unproductive intermediates. The D135 group II intron ribozyme is unusual in that it can fold slowly and directly to the native state, despite its large size and structural complexity. Here we use hydroxyl ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki973
更新日期:2005-11-27 00:00:00
abstract::The nucleotide sequence of the faeD gene of Escherichia coli and the amino acid sequence of its product is presented. The faeD product is an outer membrane protein required for transport of K88ab fimbrial subunits across the outer membrane. The protein is synthesized as a precursor containing a signal peptide, and the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.6.2443
更新日期:1986-03-25 00:00:00
abstract::PROtein Domain Organization and Comparison (PRODOC) comprises several programs that enable convenient comparison of proteins as a sequence of domains. The in-built dataset currently consists of approximately 698 000 proteins from 192 organisms with complete genomic data, and all the SWISSPROT proteins obtained from th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki474
更新日期:2005-07-01 00:00:00
abstract::The CD spectra of twelve DNA restriction fragments ranging in size from 12 to 360 base pairs are reported. Since the sequences of these fragments are known, it is possible to calculate their CD spectra from a set of nearest neighbor contributions derived from a combination of synthetic polydeoxyribonucleotides. While ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.13.3029
更新日期:1981-07-10 00:00:00
abstract::ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org/modelle...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1091
更新日期:2011-01-01 00:00:00
abstract::The crystal structure of the RNA/DNA hybrid r(GAAGAGAAGC). d(GCTTCTCTTC) has been solved and refined at 2.5 A resolution. The refinement procedure converged at R = 0.181 for all reflections in the range 20.0-2.5 A. In the crystal, the RNA/DNA hybrid duplex has an A' conformation with all but one of the nucleotide suga...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.2.555
更新日期:1999-01-15 00:00:00
abstract::Many proteins of the SNF2 family, which share a similar DNA-dependent ATPase/putative helicase domain, are involved in global transcriptional control and processing of DNA damage. We report here the partial cloning and characterization of 89B helicase, a gene encoding a new Drosophila melanogaster member of the SNF2 f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.16.3121
更新日期:1996-08-15 00:00:00
abstract::We have determined the nucleotide sequence of the major species of E. coli tRNASer and of a minor species having the same GGA anticodon. These two tRNAs should recognize the UCC and UCU codons, the most widely used codons for serine in the highly expressed genes of E. coli. The two sequences differ in only one positio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.15.5697
更新日期:1985-08-12 00:00:00
abstract::The SeqA protein binds hemi-methylated GATC sites and forms structures that sequester newly replicated origins and trail the replication forks. Cells that lack SeqA display signs of replication fork disintegration. The broken forks could arise because of over-initiation (the launching of too many forks) or lack of dyn...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx263
更新日期:2017-06-20 00:00:00
abstract::Upon infection of Escherichia coli by bacteriophage Qβ, the virus-encoded β-subunit recruits host translation elongation factors EF-Tu and EF-Ts and ribosomal protein S1 to form the Qβ replicase holoenzyme complex, which is responsible for amplifying the Qβ (+)-RNA genome. Here, we use X-ray crystallography, NMR spect...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1212
更新日期:2015-12-15 00:00:00
abstract::Influenza A viruses are hosted by numerous avian and mammalian species, which have shaped their evolution into distinct lineages worldwide. The viral genome consists of eight RNA segments that are frequently exchanged between different viruses via a process known as genetic reassortment. A complete genotype nomenclatu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm365
更新日期:2007-07-01 00:00:00
abstract::The nucleotide sequence of a region located on the adenovirus type 5 genome between coordinates 59.9 and 62.5 has been determined. This region comprises the 3'-termini of mRNAs coding for the hexon and the DNA binding protein. The sequence reveals the presence of an open reading frame in r-strand transcripts downstrea...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.24.6033
更新日期:1980-12-20 00:00:00