Abstract：
:Two similar, but not identical, models have been proposed for the amino acid-base pair contacts in the CAP-DNA complex ('Model I,' Weber, I. and Steitz, T., Proc. Natl. Acad. Sci. USA, 81, 3973-3977, 1984; 'Model II,' Ebright, et al., Proc. Natl. Acad. Sci. USA, 81, 7274-7278, 1984). One difference between the two models involves Glu181 of CAP. Model I predicts that Glu181 of CAP makes two specificity determining contacts: one H-bond with the cytosine N4 atom of G:C at base pair 7 of the DNA half site, and one H-bond with the adenine N6 atom of T:A at base pair 6 of the DNA half site. In contrast, Model II predicts that Glu181 makes only one specificity determining contact: one H-bond with the cytosine N4 atom of G:C at base pair 7 of the DNA half site. In the present work, we show that replacement of T:A at base pair 6 of the DNA half site by T:N6-methyl-adenine has no, or almost no, effect on the binding of CAP. We conclude, contrary to Model I, that Glu181 of CAP makes no contact with the adenine N6 atom of base pair 6 of the DNA half site.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Gunasekera A,Ebright YW,Ebright RHdoi
10.1093/nar/18.23.6853subject
Has Abstractpub_date
1990-12-11 00:00:00pages
6853-6issue
23eissn
0305-1048issn
1362-4962journal_volume
18pub_type
杂志文章abstract：:RegulonDB, first published 20 years ago, is a comprehensive electronic resource about regulation of transcription initiation of Escherichia coli K-12 with decades of knowledge from classic molecular biology experiments, and recently also from high-throughput genomic methodologies. We curated the literature to keep Reg...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1077
更新日期：2019-01-08 00:00:00
abstract：:The current version of PLMItRNA has been realized to constitute a database for tRNA molecules and genes identified in the mitochondria of all green plants ( Viridiplantae ). It is the enlargement of a previous database originally restricted to seed plants [Ceci,L.R., Volpicella,M., Liuni,S., Volpetti,V., Licciulli,F. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.1.159
更新日期：2000-01-01 00:00:00
abstract：:To enhance our knowledge regarding biological pathway regulation, we took an integrated approach, using the biomedical literature, ontologies, network analyses and experimental investigation to infer novel genes that could modulate biological pathways. We first constructed a novel gene network via a pairwise compariso...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku678
更新日期：2014-10-01 00:00:00
abstract：:We attempted to use the polymerase chain reaction (PCR) to monitor in vitro recombination in a plasmid containing directly repeated sequences. Some of the plasmid preparations which had not been exposed to recombination conditions were however found to behave in the PCR test as if they had undergone homologous recombi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.9.2423
更新日期：1991-05-11 00:00:00
abstract：:Ovarian poly (A) + RNA from Xenopus laevis and Xenopus borealis was used to construct two cDNA libraries which were screened for histone sequences. cDNA clones to H4 mRNA were obtained from both species and an H3 cDNA clone from Xenopus laevis. The complete DNA sequences of these clones have been determined and are pr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.12.3769
更新日期：1982-06-25 00:00:00
abstract：:Several proteins that have substantially diverged during evolution retain similar three-dimensional structures and biological function inspite of poor sequence identity. The database on Genomic Distribution of protein structural domain Superfamilies (GenDiS) provides record for the distribution of 4001 protein domains...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki087
更新日期：2005-01-01 00:00:00
abstract：:RNA sequencing (RNA-Seq) is a powerful tool for analyzing the identity of cellular RNAs but is often limited by the amount of material available for analysis. In spite of extensive efforts employing existing protocols, we observed that it was not possible to obtain useful sequencing libraries from nuclear RNA derived ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv213
更新日期：2015-06-23 00:00:00
abstract：:How DNA sequence variation influences gene expression remains poorly understood. Diploid organisms have two homologous copies of their DNA sequence in the same nucleus, providing a rich source of information about how genetic variation affects a wealth of biochemical processes. However, few computational methods have ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz176
更新日期：2019-06-20 00:00:00
abstract：:In the virion core of retroviruses, the genomic RNA is tightly associated with nucleocapsid (NC) protein molecules, forming the nucleocapsid structure. NC protein, a highly basic protein with two zinc fingers, is indispensable for RNA dimerization, encapsidation and the initiation of reverse transcription in avian, mu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.4.831
更新日期：1993-02-25 00:00:00
abstract：:Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid-liquid phase separation (LLPS), a process that relies on multivalent weak interactions of the constituent proteins and other macromole...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz848
更新日期：2020-01-08 00:00:00
abstract：:Synthesis and antisense activity of oligonucleotides modified with 2'-O-[2-[(N,N-dimethylamino)oxy] ethyl] (2'-O-DMAOE) are described. The 2'-O-DMAOE-modified oligonucleotides showed superior metabolic stability in mice. The phosphorothioate oligonucleotide 'gapmers', with 2'-O-DMAOE- modified nucleoside residues at t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh220
更新日期：2004-02-03 00:00:00
abstract：:We have recently developed a novel method for the affinity purification of the complete suite of translating mRNA from genetically labeled cell populations. This method permits comprehensive quantitative comparisons of the genes employed by each specific cell type. We provide a detailed description of tools for analys...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq130
更新日期：2010-07-01 00:00:00
abstract：:Splicing of mammalian introns requires that the intron possess at least 80 nucleotides. This length requirement presumably reflects the constraints of accommodating multiple snRNPs simultaneously in the same intron. In the free-living nematode, C. elegans, introns typically are 45 to 55 nucleotides in length. In this ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.1.143
更新日期：1990-01-11 00:00:00
abstract：:The RNA sequences boxA, boxB and boxC constitute the nut regions of phage lambda. They nucleate the formation of a termination-resistant RNA polymerase complex on the lambda chromosome. The complex includes E. coli proteins NusA, NusB, NusG and NusE, and the lambda N protein. A complex that includes the Nus proteins a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp452
更新日期：2009-08-01 00:00:00
abstract：:Infrared Spectroscopy was used to determine the numbers of base pairs for yeast 5S RNA and 5.8S RNA. The spectra were recorded at 20 degrees C and 50 degrees C, where tertiary interactions are assumed to be of less importance. It may be concluded that the structure of both RNAs is highly ordered and that there are lar...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.15.3851
更新日期：1981-08-11 00:00:00
abstract：:Software has been developed to assist RNA fingerprinting analysis. One program generates, from a DNA sequence data file, the oligonucleotides resulting from digestion of an RNA transcript labeled with any specified nucleotide(s). Oligonucleotides are sorted according to their position on the fingerprint. Expected mola...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.5.1799
更新日期：1988-03-11 00:00:00
abstract：:We previously showed that histone H4 serine-1 phosphorylation (H4S1ph) is evolutionarily conserved during gametogenesis, and contributes to post-meiotic nuclear compaction and to full completion of sporulation in the yeast Saccharomyces cerevisiae. Previous studies showed that H4S1ph and another modification of the sa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq218
更新日期：2010-08-01 00:00:00
abstract：:The Agrobacterium tumefaciens Ti plasmid contains at least six transcriptional units (designated vir loci) which are essential for efficient crown gall tumorigenesis. Mutations in one of these loci, virE, result in a sharply attenuated virulence phenotype. In the present communication, we have analyzed the virE operon...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.2.825
更新日期：1987-01-26 00:00:00
abstract：:Transcription and mRNA export are linked processes. However, the molecular mechanisms of this coordination are not clear. Sus1 (hENY2) participates in this coordination as part of two protein complexes: SAGA, a transcriptional co-activator; TREX-2, which functions in mRNA biogenesis and export. Here, we investigate th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt272
更新日期：2013-06-01 00:00:00
abstract：:The conserved bacterial anticodon nuclease (ACNase) RloC and its phage-excluding homolog PrrC comprise respective ABC-adenosine triphosphatase (ATPase) and ACNase N- and C-domains but differ in three key attributes. First, prrC is always linked to an ACNase silencing, DNA restriction-modification (R-M) locus while rlo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks593
更新日期：2012-09-01 00:00:00
abstract：:Gene promoters are enriched in guanine clusters that potentially fold into quadruplex structures. Such quadruplexes were implicated in the regulation of gene expression, plausibly by interacting with transcription factors. We showed previously that homodimers of the myogenic transcription factor MyoD bound in vitro mo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp1208
更新日期：2010-04-01 00:00:00
abstract：:Immature oocytes from Xenopus laevis contain a 42S ribonucleoprotein particle (RNP) containing 5S RNA, tRNA, a 43 kDa protein, and a 48 kDa protein. A particle containing 5S RNA and the 43 kDa protein (p43-5S) liberated from the 42S particle upon brief treatment with urea can be purified by anion exchange chromatograp...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.8.1797
更新日期：1991-04-25 00:00:00
abstract：:Structured RNA molecules form complex 3D architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. A significant percentage of the bases in structured RNA molecules in the Protein Data Bank (PDB) hydrogen-bond with phosphates of other nucleotides. By extracting and ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp468
更新日期：2009-08-01 00:00:00
abstract：:CDK12 (cyclin-dependent kinase 12) is a regulatory kinase with evolutionarily conserved roles in modulating transcription elongation. Recent tumor genome studies of breast and ovarian cancers highlighted recurrent CDK12 mutations, which have been shown to disrupt DNA repair in cell-based assays. In breast cancers, CDK...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx187
更新日期：2017-06-20 00:00:00
abstract：:Cell-free extracts employed as chromatin assembly systems contain a myriad of proteins, polyanions and nucleic acids. The roles of ATP, MgCl2 and other cofactors in the catalysis of nucleosome formation by the Xenopus laevis oocyte S-150 have yet to be established unequivocally. In this study we examine the influence ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.4.889
更新日期：1992-02-25 00:00:00
abstract：:The ability to sense and respond to environmental and physiological signals is critical for the survival of the soil-dwelling Gram-positive bacterium Streptomyces coelicolor. Nutrient deprivation triggers the onset of a complex morphological differentiation process that involves the raising of aerial hyphae and format...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1096
更新日期：2008-02-01 00:00:00
abstract：:Messenger RNA in eukaryotes is comprised of several abundance classes. Also, the decay of these unstable molecules shows at least two very different lifetimes. Two independent techniques are used here to examine the relation between message abundance and lifetime in cell lines from very different organisms. The method...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.8.3057
更新日期：1978-08-01 00:00:00
abstract：:BsoFI , ItaI and Fsp4HI are isoshizomers of Fnu4HI (5'-GC NGC-3'). Both Fnu4HI and BsoFI have previously been shown to be inhibited by cytosine-specific methylation within the recognition sequence. Fnu4HI is inhibited if either the internal cytosine at position 2 or the external cytosine at position 5 of the restricti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.16.3196
更新日期：1997-08-15 00:00:00
abstract：:Many types of DNA structures are generated in response to DNA damage, repair and recombination that require processing via specialized nucleases. DNA hairpins represent one such class of structures formed during V(D)J recombination, palindrome extrusion, DNA transposition and some types of double-strand breaks. Here w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1059
更新日期：2012-03-01 00:00:00
abstract：:Traditional Chinese medicine (TCM) is not only an effective solution for primary health care, but also a great resource for drug innovation and discovery. To meet the increasing needs for TCM-related data resources, we developed ETCM, an Encyclopedia of Traditional Chinese Medicine. ETCM includes comprehensive and sta...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky987
更新日期：2019-01-08 00:00:00
