Abstract:
:We have created a database of comparatively derived group I intron secondary structure diagrams. This collection currently contains a broad sampling of phylogenetically and structurally similar and diverse structures from over 200 publicly available intron sequences. As more group I introns are sequenced and added to the database, we anticipate minor refinements in these secondary structure diagrams. These diagrams are directly accessible by computer as well as from the authors.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Damberger SH,Gutell RRdoi
10.1093/nar/22.17.3508subject
Has Abstractpub_date
1994-09-01 00:00:00pages
3508-10issue
17eissn
0305-1048issn
1362-4962journal_volume
22pub_type
杂志文章abstract::The human 7SL RNA component of the signal recognition particle can be separated into four major conformers by nondenaturing polyacrylamide gel electrophoresis. We have investigated what sequences give 7SL RNA the property to exist in different conformations. The human 7SL gene 7L30.1 was mutagenized using the random l...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.11.4639
更新日期:1986-06-11 00:00:00
abstract::Sequencing of RNAs (RNA-Seq) has revolutionized the field of transcriptomics, but the reads obtained often contain errors. Read error correction can have a large impact on our ability to accurately assemble transcripts. This is especially true for de novo transcriptome analysis, where a reference genome is not availab...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt215
更新日期:2013-05-01 00:00:00
abstract::Two novel fluorescent cyanine-AMP conjugates, F550/570 and F650/670, have been synthesized to serve as transcription initiators under the T7 phi2.5 promoter. Efficient fluorophore labeling of 5' RNA is achieved in a single transcription step by including F550/570 and F650/670 in the transcription solution. The current...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni036
更新日期:2005-02-24 00:00:00
abstract::The accurate calculation of protein/nucleic acid-ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx312
更新日期:2017-07-03 00:00:00
abstract::Numerous examples exist of how disrupting the actions of physiological regulators of blood cell development yields hematologic malignancies. The master regulator of hematopoietic stem/progenitor cells GATA-2 was cloned almost 20 years ago, and elegant genetic analyses demonstrated its essential function to promote hem...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gks281
更新日期:2012-07-01 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::TGGCA-binding proteins are nuclear proteins with high affinity for double-stranded DNA homologous to the prototype recognition sequence 5'YTGGCANNNTGCCAR 3'. Their ubiquitous tissue distribution in higher vertebrates characterizes them as a class of highly conserved proteins which may exert a basic function. To obtain...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.6.2045
更新日期:1985-03-25 00:00:00
abstract::TFIIIC is a RNA polymerase (pol) III-specific DNA-binding factor that is required for transcription of tRNA and 5S rRNA genes. Active human TFIIIC consists of five subunits. However, an inactive form has also been isolated that lacks one of the five subunits, called TFIIIC110. A model was proposed in which pol III tra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl432
更新日期:2006-07-05 00:00:00
abstract::DnaD and DnaB are essential DNA-replication-initiation proteins in low-G+C content Gram-positive bacteria. Here we use sensitive Hidden Markov Model-based techniques to show that the DnaB and DnaD proteins share a common structure that is evident across all their structural domains, termed DDBH1 and DDBH2 (DnaD DnaB H...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq465
更新日期:2010-11-01 00:00:00
abstract::Most microbes have not been cultured, and many of those that are cultivatable are difficult, dangerous or expensive to propagate or are genetically intractable. Routine cloning of large genome fractions or whole genomes from these organisms would significantly enhance their discovery and genetic and functional charact...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq119
更新日期:2010-05-01 00:00:00
abstract::Distamycin binds the minor groove of duplex DNA at AT-rich regions and has been a valuable probe of protein interactions with double-stranded DNA. We find that distamycin can also inhibit protein interactions with G-quadruplex (G4) DNA, a stable four-stranded structure in which the repeating unit is a G-quartet. Using...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg392
更新日期:2003-06-01 00:00:00
abstract::A suppressor tRNA(Tyr) and mutant tyrosyl-tRNA synthetase (TyrRS) pair was developed to incorporate 3-iodo-L-tyrosine into proteins in mammalian cells. First, the Escherichia coli suppressor tRNA(Tyr) gene was mutated, at three positions in the D arm, to generate the internal promoter for expression. However, this tRN...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf589
更新日期:2002-11-01 00:00:00
abstract::alpha2-Macroglobulin covalently linked to poly(L)-lysine can be used as a vehicle for receptor-mediated gene transfer. This modified alpha2-macroglobulin maintains its ability to bind to the alpha2-macroglobulin receptor, and was shown to introduce a luciferase reporter gene plasmid into HepG2 human hepatoma cells in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.19.3873
更新日期:1996-10-01 00:00:00
abstract::Bacteria belonging to the class Mollicutes were among the first ones to be selected for complete genome sequencing because of the minimal size of their genomes and their pathogenicity for humans and a broad range of animals and plants. At this time six genome sequences have been publicly released (Mycoplasma genitaliu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh114
更新日期:2004-01-01 00:00:00
abstract::A 9.2 kb segment of the maxi-circle of Trypanosoma brucei mitochondrial DNA contains the genes for cytochrome c oxidase subunits I and II (coxI and coxII) and seven Unassigned Reading Frames ("URFs"). The genes for coxI and coxII display considerable homology at the aminoacid level (38 and 25%, respectively) to the co...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.19.7327
更新日期:1984-10-11 00:00:00
abstract::U1-snRNA is an integral part of the U1 ribonucleoprotein pivotal for pre-mRNA splicing. Toll-like receptor (TLR) signaling has recently been associated with immunoregulatory capacities of U1-snRNA. Using lung A549 epithelial/carcinoma cells, we report for the first time on interferon regulatory factor (IRF)-3 activati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp525
更新日期:2009-08-01 00:00:00
abstract::A long-range physical map of the centromeric region of human chromosome 7 has been constructed in order to define the region containing sequences with potential involvement in centromere function. The map is centered around alpha satellite DNA, a family of tandemly repeated DNA forming arrays of hundreds to thousands ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.9.2295
更新日期:1991-05-11 00:00:00
abstract::Biophysical properties of DNA such as its longitudinal and torsional persistence length govern many processes and phenomena in biology, DNA nanotechnology and biotechnology. It has, for example, long been known that the circularization efficiency of short DNA fragments shows a periodic pattern where fragments with int...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1238
更新日期:2018-01-25 00:00:00
abstract::Activation of the transcription factor NF-kappaB is critical for the tumor necrosis factor-alpha (TNF-alpha)-induced inflammatory response. Here we report the complete gene expression profile from activated microvascular endothelial cells emphasizing the direct contribution of the NF-kappaB pathway. Human microvascula...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki836
更新日期:2005-09-21 00:00:00
abstract::In phytohemagglutinin stimulated human lymphocytes the time relationship was determined between induction of the parameters mentioned. The results indicate that the induction occurred in a specific sequence. Thus, a simultaneous increase in the activity of DNA polymerase and thymidinekinase occurred after 15 h of incu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.8.2713
更新日期:1977-08-01 00:00:00
abstract::The Human Disease Ontology (DO) (http://www.disease-ontology.org), database has undergone significant expansion in the past three years. The DO disease classification includes specific formal semantic rules to express meaningful disease models and has expanded from a single asserted classification to include multiple-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1032
更新日期:2019-01-08 00:00:00
abstract::A novel cytoplasmic gene expression system has been developed. This system differs from other expression systems in that it relies on the co-delivery of plasmid DNA and T7 RNA polymerase (RNAP) during transfection. The plasmid contains a T7 RNAP gene driven by the T7 promoter (T7 autogene) and a functional/reporter ge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.11.2114
更新日期:1994-06-11 00:00:00
abstract::The PROSITE pattern Zinc_Finger_C2H2 was extended to permit the detection of all C2H2 zinc fingers and their parent proteins in the recently completed sequence of the yeast genome. Additionally, a new computer program was written that extracts other zinc binding motifs (non C2H2 'fingers'), overlapping with the classi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.12.2464
更新日期:1997-06-15 00:00:00
abstract::Unfolding of the nucleosomes in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3 and permits the selective recovery of the unfolded nucleosomes by mercury-affinity chromatography. This new technique has been used to compare the nucleosomal proteins and their postsynthetic modifications i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.11.4375
更新日期:1987-06-11 00:00:00
abstract::The Eco57I restriction endonuclease and methylase were purified to homogeneity from the E.coli RR1 strain carrying the eco57IRM genes on a recombinant plasmid. The molecular weight of the denaturated methylase is 63 kDa. The restriction endonuclease exists in a monomeric form with an apparent molecular weight of 104-1...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.22.6043
更新日期:1992-11-25 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::The molecular mechanisms that underlie the neurological manifestations of patients with inherited diseases of vitamin B12 (cobalamin) metabolism remain to date obscure. We observed transcriptomic changes of genes involved in RNA metabolism and endoplasmic reticulum stress in a neuronal cell model with impaired cobalam...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky634
更新日期:2018-09-06 00:00:00
abstract::The gene for the thymidine kinase (TK) of Herpes simplex virus type 1 (HSV-1) is located in the KpnI m and BamHI p fragments of the genome (Wigler et al., Cell 11, 223-232 (1977)). These fragments have been inserted into the EcoRI and BamHI sites, respectively, of plasmid pBR322, and propagated in E.coli. The TK gene ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.4.859
更新日期:1979-10-25 00:00:00
abstract::Infection of Escherichia coli by a bacteriophage T4 regA, gene 44 double mutant leads to about a 7-fold increase in the amount of RNA ligase obtained after infection by wild-type phage. Using cells infected by the double mutant, RNA ligase was purified to homogeneity with a 20% yield. Unlike previous preparations of t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.9.3175
更新日期:1977-09-01 00:00:00
abstract::We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn524
更新日期:2008-10-01 00:00:00