Abstract:
:Recently published alignments of available 5 S rRNA sequences have shown that a rigid base pairing pattern, pointing to the existence of a universal five-helix secondary structure for all 5 S RNAs, can be superimposed on such alignments. For a few species, the alignment and the base pairing pattern show distortions with respect to the large majority of sequences. Their 5 S RNAs may form exceptional secondary structures, or there may just be errors in the published sequences. We have examined such a case, Pseudomonas fluorescens, and found the sequence to be in error. The corrected sequence, as well as those of the related species Azotobacter vinelandii and Pseudomonas aeruginosa, fit perfectly in the 5 S RNA sequence alignment and in the five-helix secondary structure model. There exists comparative evidence for the frequent presence of non-standard base pairs at several points of the 5 S RNA secondary structure.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Dams E,Vandenberghe A,De Wachter Rdoi
10.1093/nar/11.5.1245subject
Has Abstractpub_date
1983-03-11 00:00:00pages
1245-52issue
5eissn
0305-1048issn
1362-4962journal_volume
11pub_type
杂志文章abstract::The extent of base pairing in Escherichia coli and Bacillus stearothermophilus 5S RNAs was determined by infrared spectroscopy. From the infrared spectra taken at 20 degrees and 52 degrees C it is concluded that E. coli and B. stearothermophlius 5S RNAs possess a large number of base pairs (Table I). Comparison of our...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.4.1043
更新日期:1979-10-25 00:00:00
abstract::The nucleoplasm is not homogenous; it consists of many types of nuclear bodies, also known as nuclear domains or nuclear subcompartments. These self-organizing structures gather machinery involved in various nuclear activities. Nuclear speckles (NSs) or splicing speckles, also called interchromatin granule clusters, w...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkx759
更新日期:2017-10-13 00:00:00
abstract::The bacteriophage Mu A and B genes, which lie adjacent to each other and are colinear on the phage genome, encode proteins that catalyze efficient transposition of Mu DNA. We show that the molar ratio of A and B proteins is approximately 1:20 in extracts prepared after induction of cells containing a Mu lysogen or a p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.23.11285
更新日期:1988-12-09 00:00:00
abstract::RBD-1 is the Caenorhabditis elegans homolog of Mrd1p, which was recently shown to be required for 18S ribosomal RNA (rRNA) processing in yeast. To gain insights into the relationship between ribosome biogenesis and the development of multicellular organisms, we examined the expression and function of RBD-1. Maternal R...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh264
更新日期:2004-02-10 00:00:00
abstract::We have developed an end-labelling approach to map the positions of nucleosomes and protein binding sites at nucleotide resolution by footprinting micrococcal nuclease (MNase)-sensitive sites. Using this approach we determined that the MFA2 gene and its upstream control regions have four positioned nucleosomes when tr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.13.e64
更新日期:2001-07-01 00:00:00
abstract::The cis-requirements for the first editing site in the atp9 mRNA from pea mitochondria were investigated in an in vitro RNA editing system. Template RNAs deleted 5' of -20 are edited correctly, but with decreased efficiency. Deletions between -20 and the edited nucleotide abolish editing activity. Substitution of the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh763
更新日期:2004-08-04 00:00:00
abstract::MDg3 is a family of mobile dispersed genetic elements represented by 15 copies in the haploid genome of D. melanogaster and flanked, like other similar elements, by the regions of homology. In the present work, these regions of mdg3 have been sequenced. The existence of perfect direct repeats 268 base pairs long has b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.15.3263
更新日期:1980-08-11 00:00:00
abstract::The Gene Context Tool (GeConT) allows users to visualize the genomic context of a gene or a group of genes and their orthologous relationships within fully sequenced bacterial genomes. The new version of the server incorporates information from the COG, Pfam and KEGG databases, allowing users to have an integrated gra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn330
更新日期:2008-07-01 00:00:00
abstract::It has been inferred from DNA sequence analyses that in echinoderm mitochondria not only the usual asparagine codons AAU and AAC, but also the usual lysine codon AAA, are translated as asparagine by a single mitochondrial (mt) tRNAAsn with the anticodon GUU. Nucleotide sequencing of starfish mt tRNAAsn revealed that t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.7.1683
更新日期:1999-04-01 00:00:00
abstract::We show herein the transcription of a processed gene that originated from a spliced transcript. Recently, we isolated the human and murine homologues of the yeast chromatin protein, SPT4. The Supt4h gene is spliced normally from five exons encoded by chromosome 11. Here we show that a related sequence on chromosome 10...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.21.4960
更新日期:1998-11-01 00:00:00
abstract::Synchronous plasmodia of cycloheximide-sensitive and cycloheximide-resistant strains of Physarum polycephalum were labelled with 3[H]-deoxyadenosine in pulse and pulse-chase experiments in presence and absence of cycloheximide. The replication products were studied with alkaline sucrose gradient sedimentation analysis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.2.405
更新日期:1977-02-01 00:00:00
abstract::Several lines of evidence indicate that differences in DNA repair capacity are an important source of variability in cancer risk. However, traditional assays for measurement of DNA repair activity in human samples are laborious and time-consuming. DNA glycosylases are the first step in base excision repair of a variet...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni166
更新日期:2005-10-21 00:00:00
abstract::O-GLYCBASE is a revised database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the sequence databases. Entries include information about species, sequence, glycosylation sites and glycan type and is fully cross-referenced. Compare...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.1.387
更新日期:1998-01-01 00:00:00
abstract::PIWI-interacting RNAs (piRNAs) engage PIWI proteins to silence transposons and promote germ cell development in animals. In diverse species, piRNA biogenesis occurs near the mitochondrial surface, and involves mitochondrial membrane-anchored factors. In mice, two cytoplasmic PIWI proteins, MIWI and MILI, receive proce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1281
更新日期:2019-03-18 00:00:00
abstract::We report the isolation of a novel human POU domain encoding gene named RDC-1. The POU domain of the RDC-1 encoded protein is highly related to the POU domain potentially encoded by the rat brain-3 sequence and to that of the Drosophila I-POU protein; outside of the POU region, RDC-1 is unrelated to any previously cha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.18.4919
更新日期:1992-09-25 00:00:00
abstract::The DNA sequence of the spacer (plus flanking) regions separating the 16S rRNA and 23S rRNA genes of two presumptive rDNA operons of the archaebacterium Methanococcus vannielii was determined. The spacers are 156 and 242 base pairs in size and they share a sequence homology of 49 base pairs following the 3' terminus o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.21.7537
更新日期:1983-11-11 00:00:00
abstract::Ornithine decarboxylase (ODC) expression is important for proliferation and is elevated in many tumor cells. We previously showed that Sp1 is a major positive regulator of ODC transcription. In this paper we have investigated transcriptional regulation of rat ODC by the closely related factor Sp3. While over-expressio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.10.2012
更新日期:1997-05-15 00:00:00
abstract::3'-O-(5'-phosphoryldeoxycytidyl) phosphorothioate and fluorescent 3'-O-(5'-phosphoryldeoxycytidyl) S-bimane phosphorothioate can be ligated to tRNA by T4 RNA ligase. They are also efficient donors for the enzymatic ligation to oligodeoxynucleotides bearing a 3'-cytidine terminus. Cytidine 3',5'-bisphosphate is also a ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.4.1791
更新日期:1984-02-24 00:00:00
abstract::DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polym...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz653
更新日期:2019-09-19 00:00:00
abstract::The accuracy of a homology model based on the structure of a distant relative or other topologically equivalent protein is primarily limited by the quality of the alignment. Here we describe a systematic approach for sequence-to-structure alignment, called 'K*Sync', in which alignments are generated by dynamic program...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl480
更新日期:2006-01-01 00:00:00
abstract::The Central glycolytic genes Repressor (CggR) from Bacillus subtilis belongs to the SorC family of transcription factors that control major carbohydrate metabolic pathways. Recent studies have shown that CggR binds as a tetramer to its tandem operator DNA sequences and that the inducer metabolite, fructose 1,6-bisphos...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq334
更新日期:2010-09-01 00:00:00
abstract::Treatment of responsive cells by interferons (IFNs) induces within a few hours a rise in the concentration of several proteins and mRNAs. In order to characterize these IFN-induced mRNA species, we have cloned in E. coli the cDNA made from a 17-18S poly(A)+ RNA of human fibroblastoid cells (SV80) treated with IFN-beta...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.5.1213
更新日期:1983-03-11 00:00:00
abstract::Yeast Dna2 helicase/nuclease is essential for DNA replication and assists FEN1 nuclease in processing a subset of Okazaki fragments that have long single-stranded 5' flaps. It is also involved in the maintenance of telomeres. DNA2 is a gene conserved in eukaryotes, and a putative human ortholog of yeast DNA2 (ScDNA2) ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl070
更新日期:2006-04-04 00:00:00
abstract::The nucleotide sequences of the Streptomyces transposable element IS110 and its insertion site in the DNA of a derivative of the temperate phage luminal diameter C31 were determined. The element is inserted about 460 bp from the right-hand end of luminal diameter C31 DNA, in a region of apparently non-coding DNA. The ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.17.7053
更新日期:1987-09-11 00:00:00
abstract::A vast number of sweet tasting molecules are known, encompassing small compounds, carbohydrates, d-amino acids and large proteins. Carbohydrates play a particularly big role in human diet. The replacement of sugars in food with artificial sweeteners is common and is a general approach to prevent cavities, obesity and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq917
更新日期:2011-01-01 00:00:00
abstract::Eucaryotic ribosome biogenesis involves many cis-acting sequences and trans-acting factors, including snoRNAS: We have used directed mutagenesis of rDNA plasmids in yeast to identify critical sequence and structural elements within and flanking the ITS2-proximal stem. This base paired structure, present in the mature ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.10.2106
更新日期:2001-05-15 00:00:00
abstract::We have determined the three-dimensional structure of a non-selfcomplementary nonanucleotide duplex which contains an abasic (apyrimidinic) site in the centre, i.e. a deoxyribose residue opposite an adenosine. The majority of the base and sugar proton resonances were assigned by NOESY, COSY and 2DQF spectra in D2O and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.19.8003
更新日期:1987-10-12 00:00:00
abstract::Properties of a mutant bacteriophage T2 DNA [N:(6)-adenine] methyltransferase (T2 Dam MTase) have been investigated for its potential utilization in RecA-assisted restriction endonuclease (RARE) cleavage. Steady-state kinetic analyses with oligonucleotide duplexes revealed that, compared to wild-type T4 Dam, both wild...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.7.1484
更新日期:2001-04-01 00:00:00
abstract::RNA pseudoknots are functional structure elements with key roles in viral and cellular processes. Prediction of a pseudoknotted minimum free energy structure is an NP-complete problem. Practical algorithms for RNA structure prediction including restricted classes of pseudoknots suffer from high runtime and poor accura...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq021
更新日期:2010-04-01 00:00:00
abstract::A growing body of evidence suggests that genes transcribed by RNA polymerase III exhibit multiple functions within a chromosome. While the predominant function of these genes is the synthesis of RNA molecules, certain RNA polymerase III genes also function as genomic landmarks. Transfer RNA genes are known to exhibit ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh858
更新日期:2004-09-30 00:00:00