Abstract:
:Analysis of phylogenetically conserved secondary structure has been important in the development of models for the secondary structure of structural RNAs. In this paper, we apply this type of analysis to several families of informational RNAs to evaluate its usefulness in developing secondary structure models for mRNAs and mRNA precursors. We observed many conserved helices in all mRNA groups analyzed. Three criteria were used to identify potential helices which were not conserved solely because of coding sequence constraints, and may therefore be important for the structure and function of the RNA. These results suggest that this approach will be useful in deriving secondary structure models for informational RNAs when used in conjunction with other complementary techniques, and in designing experiments to determine the functional significance of conserved base pairing interactions.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Browner MF,Lawrence CBdoi
10.1093/nar/13.23.8645subject
Has Abstractpub_date
1985-12-09 00:00:00pages
8645-60issue
23eissn
0305-1048issn
1362-4962journal_volume
13pub_type
杂志文章abstract::We present evidence of formation of an intramolecular parallel triple helix with T*A.T and G*G.C base triplets (where * represents the hydrogen bonding interaction between the third strand and the duplex while. represents the Watson-Crick interactions which stabilize the duplex). The third GT strand, containing seven ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.18.3511
更新日期:2000-09-15 00:00:00
abstract::IL-2 gene expression in activated T-cells is initiated by chromatin remodeling at the IL-2 proximal promoter and conversion of a transcriptional repressor into a potent transcriptional activator. A purine-box regulator complex was purified from activated Jurkat T-cell nuclei based on sequence-specific DNA binding to t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm117
更新日期:2007-01-01 00:00:00
abstract::Recent advances in next-generation sequencing technologies and genome assembly algorithms have enabled the accumulation of a huge volume of genome sequences from various species. This has provided new opportunities for large-scale comparative genomics studies. Identifying and utilizing synteny blocks, which are genomi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw310
更新日期:2016-07-08 00:00:00
abstract::Human Silent Information Regulator Type 1 (SIRT1) is an NAD(+)-dependent deacetylase protein which is an intermediary of cellular metabolism in gene silencing and aging. SIRT1 has been extensively investigated and shown to delay senescence; however, less is known about the regulation of SIRT1 during aging. In this stu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq609
更新日期:2010-11-01 00:00:00
abstract::In Arabidopsis thaliana, endogenous trans-acting and exogenous siRNA pathways are initiated by the interaction of DRB4 with trigger dsRNA. Further, DCL4:DRB4 complex cleaves the dsRNA into 21 bp siRNA. Understanding molecular determinants and mechanistic details of dsRNA recognition by DRB4 is vital for inducing long-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx481
更新日期:2017-08-21 00:00:00
abstract::ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Information About a Microarray Experiment) requirements and stores well-annotated raw and normalized data. As of November 2004, ArrayExpress contains data from approximately 12,000 hybridizations covering 35 species. Data can be s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki056
更新日期:2005-01-01 00:00:00
abstract::DNA adenine methyltransferase (Dam) is widespread and conserved among the γ-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair and chromosome replication. Dam also controls virulence in many pathogenic Gram-negative bacteria. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv251
更新日期:2015-04-30 00:00:00
abstract::We have studied the effect of selenium on the expression of a cellular glutathione peroxidase, GSHPx-1, in transfected MCF-7 cells and in doxorubicin-resistant (Adrr) MCF-7 cells. A GSHPx-1 cDNA with a Rous Sarcoma virus promoter was transfected into a human mammary carcinoma cell line, MCF-7, which has very low endog...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.6.1531
更新日期:1990-03-25 00:00:00
abstract::Over 50 introns have been reported in archaeal rRNA genes (rDNAs), a subset of which nests putative homing endonuclease (HEase) genes. Here, we report the identification and characterization of a novel archaeal LAGLIDADG-type HEase, I-ApeKI [corrected], encoded by the ApeK1.S908 intron within the 16S rDNA of Aeropyrum...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni118
更新日期:2005-07-26 00:00:00
abstract::1731, a Drosophila retrotransposon was first described as having a transcription activity which was negatively regulated by 20-hydroxyecdysone (20-OH), the steroid molting hormone of insects. Using constructions expressing the bacterial chloramphenicol-acetyltransferase (CAT) gene under the control of the entire or de...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.20.5689
更新日期:1991-10-25 00:00:00
abstract::For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein-ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23,269 complexes ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1088
更新日期:2015-01-01 00:00:00
abstract::PRMT5 is an arginine methyltransferase that accounts for the vast majority of the symmetric methylation in cells. PRMT5 exerts its function when complexed with MEP50/WDR77. This activity is often elevated in cancer cells and correlates with poor prognosis, making PRMT5 a therapeutic target. To investigate the PRMT5 si...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz200
更新日期:2019-06-04 00:00:00
abstract::Mammalian mitochondrial ribosomes evolved from bacterial ribosomes by reduction of ribosomal RNAs, increase of ribosomal protein content, and loss of guanine nucleotides. Guanine is the base most sensitive to oxidative damage. By systematically comparing high-quality, small ribosomal subunit RNA sequence alignments an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky762
更新日期:2018-11-16 00:00:00
abstract::As an approach to gene therapy for the respiratory manifestations of cystic fibrosis (CF), in vivo plasmid-mediated direct transfer of the normal CF transmembrane conductance regulator (CFTR) gene to the airway epithelium was investigated in mice. To evaluate the feasibility of this strategy, pRSVL, a plasmid composed...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.12.3233
更新日期:1992-06-25 00:00:00
abstract::Long non-coding RNAs (lncRNAs) that have no protein-coding capacity make up a large proportion of the transcriptome of various species. Many lncRNAs are expressed within the animal central nervous system in spatial- and temporal-specific patterns, indicating that lncRNAs play important roles in cellular processes, neu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks943
更新日期:2012-12-01 00:00:00
abstract::High performance liquid chromatography analysis of imidazole open ring 7-methylguanine, 2-6 diamino-4-hydroxy-5N-methyl-formamidopyrimidine (rom7G), showed two well-separated peaks (fI and fII) of the same magnitude. Rechromatography of each isolated component indicated that they are slowly interconverted to give a 1:...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.13.5429
更新日期:1984-07-11 00:00:00
abstract::Tight cell-cycle regulation of the histone H4-K20 methyltransferase PR-Set7 is essential for the maintenance of genome integrity. In mammals, this mainly involves the interaction of PR-Set7 with the replication factor PCNA, which triggers the degradation of the enzyme by the CRL4CDT2 E3 ubiquitin ligase. PR-Set7 is al...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky034
更新日期:2018-04-06 00:00:00
abstract::The nucleotide sequence of Neurospora crassa 5.8 S rDNA and adjacent regions has been determined. The deduced 5.8 S rRNA sequence of Neurospora differs from the 5.8 S rRNA sequence of Saccharomyces cerevisiae at 13 of 158 residues. Nine of these differences are clustered in a segment capable of forming a short hairpin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.7.2561
更新日期:1979-06-11 00:00:00
abstract::Analysis of the human VK (ref. 2) gene locus led to the detection of a new sequence family (L sequences). Its copy number is in the range of 10(2). The L sequences, which are about 500 bp long, are found as part of the 3' flanking regions of a clustered set of human VKI genes but they occur also separate from the gene...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.13.5265
更新日期:1984-07-11 00:00:00
abstract::Most mutations in cancer genomes occur in the non-coding regions with unknown impact on tumor development. Although the increase in the number of cancer whole-genome sequences has revealed numerous putative non-coding cancer drivers, their information is dispersed across multiple studies making it difficult to underst...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa915
更新日期:2021-01-08 00:00:00
abstract::Expression of the rpoBC genes encoding the beta and beta' RNA polymerase subunits of Escherichia coli is autogenously regulated. Although previous studies have demonstrated a post-transcriptional feedback mechanism, complex transcriptional controls of rpoBC expression may also contribute. We show that an attenuator (r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.18.4773
更新日期:1992-09-25 00:00:00
abstract::DNA-binding and RNA-binding proteins are usually considered 'undruggable' partly due to the lack of an efficient method to identify inhibitors from existing small molecule repositories. Here we report a rapid and sensitive high-throughput screening approach to identify compounds targeting protein-nucleic acids interac...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv069
更新日期:2015-04-30 00:00:00
abstract::The Aspergillus nidulans sequence ans1, previously known to enhance transformation frequencies of pyr4-based vectors, was shown to enhance the efficiency of argB and trpC-based vectors. Increased efficiencies could be obtained by constructing vectors containing argB and ans1 or by cotransforming selectable plasmids (c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.22.9163
更新日期:1987-11-25 00:00:00
abstract::We have demonstrated that the DNA sequence between two triplex-forming polypurine.polypyrimidine (Pu.Py) tracts was protected from DNA modifying enzymes upon formation of triplex DNA structures with an oligodeoxyribonucleotide in which two triplex-forming Pu or Py tracts were placed at the termini (triplex-bridge form...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.3.452
更新日期:1995-02-11 00:00:00
abstract::Spermine-DNA complexes have been examined by small-angle and wide-angle X-ray scattering as well as by circular dichroism studies. Condensed complexes are building up below a critical ionic strength. We have found that at one and the same ionic strength condensed complexes having two different supramolecular structure...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.5.1297
更新日期:1979-11-10 00:00:00
abstract::The molecular structure of the DNA double helix has been known for 60 years, but we remain surprisingly ignorant of the balance of forces that determine its mechanical properties. The DNA double helix is among the stiffest of all biopolymers, but neither theory nor experiment has provided a coherent understanding of t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt808
更新日期:2013-12-01 00:00:00
abstract::Using a combination of bioinformatic and molecular biology approaches a Drosophila melanogaster protein, DmTTF, has been identified, which exhibits sequence and structural similarity with two mitochondrial transcription termination factors, mTERF (human) and mtDBP (sea urchin). Import/processing assays indicate that D...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg272
更新日期:2003-03-15 00:00:00
abstract::Members of several classes of proto-oncogenes replicate during the first third of S-phase in two human (K562 erythroleukemia and HeLa), one Chinese hamster (CHO) and eight mouse cell lines. These cell lines exhibit a variety of specialized functions characteristic of pre-B and B cells, T cells and erythroid cells. The...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.1.87
更新日期:1987-01-12 00:00:00
abstract::DDBJ (http://www.ddbj.nig.ac.jp) collected and released 1 880 115 entries or 1 134 086 245 bases in the period from July 2006 to June 2007. The released data contains the high-throughput cDNAs of cricket and high-quality draft genome of medaka among others. Our computer system has been upgraded since March 2007. Anoth...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm889
更新日期:2008-01-01 00:00:00
abstract::Evidence will be presented to show that the reagents 3a-c (X = O) obtained by the reaction of 2-chlorophenylphosphorodichloridate with 1-hydroxybenzotriazole or 1-hydroxy-6-trifluoromethyl (6-nitro) benzotriazoles, respectively, do not give, under normal coupling conditions, phosphorylation of the lactam functions in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.14.5885
更新日期:1986-07-25 00:00:00