Abstract:
:Major efforts are underway to elucidate the spatial distribution of ribosomal RNAs (rRNAs) in the ribosome. An especially informative approach is the identification of likely base-base tertiary interactions within the RNA by phylogenetic comparison. Herein evidence is presented for three heretofore unrecognized candidate tertiary interactions, G506/C525, C779/G803 and A994/U1380 (1) in 16S-like rRNAs. This brings to eight the number of such interactions that are strongly supported by phylogenetic evidence. The three newly identified interactions further define the folding within domains II and III of 16S-like rRNA. No interactions have yet been found that would serve to orient the domains relative to one another.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Haselman T,Camp DG,Fox GEdoi
10.1093/nar/17.6.2215subject
Has Abstractpub_date
1989-03-25 00:00:00pages
2215-21issue
6eissn
0305-1048issn
1362-4962journal_volume
17pub_type
杂志文章abstract::Recently, we described a method for multiplex genome editing by natural transformation (MuGENT). Mutant constructs for MuGENT require large arms of homology (>2000 bp) surrounding each genome edit, which necessitates laborious in vitro DNA splicing. In Vibrio cholerae, we uncover that this requirement is due to cytopl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx496
更新日期:2017-07-07 00:00:00
abstract::UMSBP is a CCHC-type zinc finger protein, which functions during replication initiation of kinetoplast DNA minicircles and the segregation of kinetoplast DNA networks. Interactions of UMSBP with origin sequences, as well as the protein oligomerization, are affected by its redox state. Reduction yields UMSBP monomers a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn927
更新日期:2009-01-01 00:00:00
abstract::Perturbation and time-course data sets, in combination with computational approaches, can be used to infer transcriptional regulatory networks which ultimately govern the developmental pathways and responses of cells. Here, we individually knocked down the four transcription factors PU.1, IRF8, MYB and SP1 in the huma...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq729
更新日期:2010-12-01 00:00:00
abstract::The four Hu [embryonic lethal abnormal vision-like (ELAVL)] protein family members regulate alternative splicing by binding to U-rich sequences surrounding target exons and affecting the interaction of the splicing machinery and/or local chromatin modifications. Each of the Hu proteins contains a divergent N-terminus,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt166
更新日期:2013-05-01 00:00:00
abstract::Nucleobase analogs 5-methylisocytosine ((Me)isoC) and isoguanine (isoG) form a non-natural base pair in duplex nucleic acids with base pairing specificity orthogonal to the natural nucleobase pairs. Sequencing reactions were conducted with oligodeoxyribonucleotides (ODNs) containing d(Me)isoC and disoG using modified ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki628
更新日期:2005-06-02 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::Riboswitches are RNA-based regulatory devices that mediate ligand-dependent control of gene expression. However, there has been limited success in rationally designing riboswitches. Moreover, most previous riboswitches are confined to a particular gene and only perform one-way regulation. Here, we used a library scree...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr609
更新日期:2011-10-01 00:00:00
abstract::The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz943
更新日期:2020-01-08 00:00:00
abstract::The structure-specific Mus81-Eme1/Mms4 endonuclease contributes importantly to DNA repair and genome integrity maintenance. Here, using budding yeast, we have studied its function and regulation during the cellular response to DNA damage and show that this endonuclease is necessary for successful chromosome replicatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt645
更新日期:2013-10-01 00:00:00
abstract::Using circular dichroism spectroscopy, UV absorption spectroscopy and polyacrylamide gel electrophoresis, we studied conformational properties of guanine-rich DNA strands of the fragile X chromosome repeats d(GGC)n, d(GCG)n and d(CGG)n, with n = 2, 4, 8 and 16. These strands are generally considered in the literature ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh179
更新日期:2004-01-12 00:00:00
abstract::Accurate T-cell epitope prediction is a principal objective of computational vaccinology. As a service to the immunology and vaccinology communities at large, we have implemented, as a server on the World Wide Web, a partial least squares-based multivariate statistical approach to the quantitative prediction of peptid...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg510
更新日期:2003-07-01 00:00:00
abstract::We took advantage of the unusual genomic organization of the ciliate Oxytricha trifallax to screen for eukaryotic non-coding RNA (ncRNA) genes. Ciliates have two types of nuclei: a germ line micronucleus that is usually transcriptionally inactive, and a somatic macronucleus that contains a reduced, fragmented and rear...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr501
更新日期:2011-09-01 00:00:00
abstract::The nucleobase modification 5-methylcytosine (m(5)C) is widespread both in DNA and different cellular RNAs. The functions and enzymatic mechanisms of DNA m(5)C-methylation were extensively studied during the last decades. However, the location, the mechanism of formation and the cellular function(s) of the same modifi...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
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更新日期:2010-03-01 00:00:00
abstract::SSCP and heteroduplex analysis (HA) continue to be the most popular methods of mutation detection due to their simplicity, high sensitivity and low cost. The advantages of these methods are most clearly visible when large genes, such as BRCA1 and BRCA2, are scanned for scattered unknown mutations and/or when a large n...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.14.e71
更新日期:2001-07-15 00:00:00
abstract::In plant organelles, RNA editing alters specific cytidine residues to uridine in transcripts. All of the site-specificity factors of RNA editing identified so far are pentatricopeptide repeat (PPR) proteins. A defect in a specific PPR protein often impairs RNA editing at multiple sites, at which the cis-acting element...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks164
更新日期:2012-06-01 00:00:00
abstract::The HIRA histone chaperone complex deposits histone H3.3 into nucleosomes in a DNA replication- and sequence-independent manner. As herpesvirus genomes enter the nucleus as naked DNA, we asked whether the HIRA chaperone complex affects herpesvirus infection. After infection of primary cells with HSV or CMV, or transie...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx771
更新日期:2017-11-16 00:00:00
abstract::To understand the epigenetic regulation of transcriptional response of macrophages during early-stage M. tuberculosis (Mtb) infection, we performed ChIPseq analysis of H3K4 monomethylation (H3K4me1), a marker of poised or active enhancers. De novo H3K4me1 peaks in infected cells were associated with genes implicated i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw782
更新日期:2016-12-15 00:00:00
abstract::To efficiently utilize the growing body of available protein localization data, we have developed Organelle DB, a web-accessible database cataloging more than 25,000 proteins from nearly 60 organelles, subcellular structures and protein complexes in 154 organisms spanning the eukaryotic kingdom. Organelle DB is the fi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki071
更新日期:2005-01-01 00:00:00
abstract::Post-translational modifications (PTMs) play a key role in numerous cellular processes by directly affecting structure, dynamics and interaction networks of target proteins. Despite their importance, our understanding of protein PTMs at the atomistic level is still largely incomplete. Molecular dynamics (MD) simulatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt416
更新日期:2013-07-01 00:00:00
abstract::Current knowledge of parameters affecting RNA stability is very restricted in plants. Here we investigated factors which might contribute to the stability of a particular plant messenger RNA. To this end, insertion and deletion mutants were made in two different exons and an intron of the transcribed region of a well ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.10.2917
更新日期:1990-05-25 00:00:00
abstract::Brome mosaic virus (BMV) is a tripartite genome, positive-sense RNA virus of plants. Previously it was demonstrated that local hybridization between BMV RNAs (RNA-RNA heteroduplex formation) efficiently promotes non-homologous RNA recombination. In addition, studies on the role of the BMV polymerase in RNA recombinati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.8.1714
更新日期:2000-04-15 00:00:00
abstract::We have compiled the DNA sequence data for E. coli available from the GENBANK and EMBL data libraries and over a period of several years independently from the literature. This is the fifth listing replacing and increasing the former listings substantially. However, in order to save space this printed version contains...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.13.2973
更新日期:1993-07-01 00:00:00
abstract::A typical G-rich telomeric DNA strand, which runs 5'-->3' toward the chromosome ends, protrudes by several nucleotides in lower eukaryotes. In human chromosomes long G-rich 3'-overhangs have been found. Apart from the standard G-rich tail, several non-canonical terminal structures have been proposed. However, the mech...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.7.e35
更新日期:2001-04-01 00:00:00
abstract::This paper describes a computer program designed to look for similarities between pairs of nucleic or amino acid sequences. The program looks both for segments of perfect identity or for regions where, using a scoring matrix, a minimum value is exceeded. The results of comparisons are presented as a matrix which is di...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.9.2951
更新日期:1982-05-11 00:00:00
abstract::The smallest catalytic RNA identified to date is a manganese-dependent ribozyme that requires only a complex between GAAA and UUU to effect site-specific cleavage. We show here that this ribozyme occurs naturally in the 3'-UTR of Vg1 and beta-actin mRNAs. In accord with earlier studies with model RNAs, cleavage occurs...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn530
更新日期:2008-10-01 00:00:00
abstract::The viral RNA (vRNA) genome of influenza viruses is replicated by the RNA-dependent RNA polymerase (RNAP) via a complementary RNA (cRNA) intermediate. The vRNA promoter can adopt multiple conformations when bound by the RNAP. However, the dynamics, determinants, and biological role of these conformations are unknown; ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz313
更新日期:2019-07-09 00:00:00
abstract::The CABS-fold web server provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS modeling procedures ranked in previous Critical Assessment of techniques for protein Structure Prediction competi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt462
更新日期:2013-07-01 00:00:00
abstract::Ionizing radiation induces clustered DNA damage, which presents a challenge to the cellular repair machinery. The repair efficiency of a single-strand break (SSB) is approximately 4x less than that for repair of an abasic (AP) site when in a bistranded cluster containing 8-oxoG. To explore whether this difference in r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm947
更新日期:2007-01-01 00:00:00
abstract::Resistance to androgen receptor (AR)-targeted therapies in prostate cancer (PC) is a major clinical problem. A key mechanism of treatment resistance in advanced PC is the generation of alternatively spliced forms of the AR termed AR variants (AR-Vs) that are refractory to targeted agents and drive tumour progression. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz286
更新日期:2019-06-20 00:00:00
abstract::As more and more high-throughput data has been produced by next-generation sequencing, it is still a challenge to classify RNA transcripts into protein-coding or non-coding, especially for poorly annotated species. We upgraded our original coding potential calculator, CNCI (Coding-Non-Coding Index), to CNIT (Coding-No...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz400
更新日期:2019-07-02 00:00:00