Abstract:
:Several modified nucleosides were introduced during in vitro RNA synthesis into a pre-tRNA(Ser). The pre-tRNAs were used as substrates for RNase P enzymes. No effects were observed with biotin-8-ATP or [alpha-S]-GPT, whereas with m7GTP, the cleavage reaction was completely inhibited. Analysis of pre-tRNAs which contained m7G at various positions has revealed a single base at the 5'-end of the acceptor stem where this modification absolutely prevents cleavage by catalytic M1 RNA, eukaryotic and prokaryotic RNase P holoenzymes. These results suggest that a critical contact must be made between pre-tRNA substrate and enzyme/ribozyme or that the approach of the potential cleaving agent (a positive magnesium ion) is made impossible by the positive charge at N-7 of the guanosine. In addition, we have shown that a pre-tRNA containing only m7G's can still form a complex with M1 RNA in a gel retardation assay.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Kahle D,Wehmeyer U,Char S,Krupp Gdoi
10.1093/nar/18.4.837subject
Has Abstractpub_date
1990-02-25 00:00:00pages
837-44issue
4eissn
0305-1048issn
1362-4962journal_volume
18pub_type
杂志文章abstract::The genome-wide identification of microRNA transcription start sites (miRNA TSSs) is essential for understanding how miRNAs are regulated in development and disease. In this study, we developed mirSTP (mirna transcription Start sites Tracking Program), a probabilistic model for identifying active miRNA TSSs from nasce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx318
更新日期:2017-07-27 00:00:00
abstract::Nuclear factor I (NFI) is a site-specific DNA binding protein required for the replication of adenovirus type 2 DNA in vitro and in vivo. To study sequence requirements for the interaction of NFI with DNA, we have measured the binding of the protein to a variety of synthetic sites. Binding sites for NFI (FIB sites) we...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.14.5545
更新日期:1987-07-24 00:00:00
abstract::The proteins in a cell often assemble into complexes to carry out their functions and play an essential role of biological processes. The PCFamily server identifies template-based homologous protein complexes [called protein complex family (PCF)] and infers functional modules of the query proteins. This server first f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq464
更新日期:2010-07-01 00:00:00
abstract::Assessment of the fidelity of gene expression is crucial to understand cell homeostasis. Here we present a highly sensitive method for the systematic Quantification of Rare Amino acid Substitutions (QRAS) using absolute quantification by targeted mass spectrometry after chromatographic enrichment of peptides with miss...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1319
更新日期:2019-04-08 00:00:00
abstract::The Blocks Database contains multiple alignments of conserved regions in protein families which can be searched by e-mail (blocks@blocks.fhcrc.org) and World Wide Web (http://blocks.fhcrc.org/ ) servers to classify protein and nucleotide sequences. Recent enhancements to the servers include: (i) improved calculation o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.1.222
更新日期:1997-01-01 00:00:00
abstract::Infection of cultured cells with herpes simplex virus (HSV) results in the transcriptional induction of a small number of cellular genes. Although the majority of such genes are dependent upon viral protein synthesis for their induction, a small minority are not. These genes are induced by events occurring prior to th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.23.9261
更新日期:1986-12-09 00:00:00
abstract::Nuclei from frozen calf thymus suspended in buffer were analyzed for metal content prior to and after repeated washing. After three such extractions about 0.1 micrograms Zn/mg DNA and 0.025 micrograms Cu/mg DNA remained tightly associated with chromatin. This level of metal was essentially unchanged with subsequent wa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.21.5811
更新日期:1981-11-11 00:00:00
abstract::The RosettaDesign server identifies low energy amino acid sequences for target protein structures (http://rosettadesign.med.unc.edu). The client provides the backbone coordinates of the target structure and specifies which residues to design. The server returns to the client the sequences, coordinates and energies of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl163
更新日期:2006-07-01 00:00:00
abstract::Enzymatic hydrolysis and base analysis by high performance liquid chromatography showed that mouse satellite DNA had 30-50% less 5-methylcytosine in sperm than in somatic tissue (1.59 mols % vs 2.40-3.11 mols %). Maxam-Gilbert sequencing and analysis of the intensity of the cytosine bands indicated that the level of m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.11.3969
更新日期:1985-06-11 00:00:00
abstract::The complete sequences of three kinetoplast DNA minicircles (B4, D3 and D12) from Leishmania tarentolae are reported. All L. tarentolae minicircles encode single gRNAs localized within the variable region approximately 150 bp from the conserved region. The 5' termini and tentative 3' termini of the new gRNAs were dete...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.22.6277
更新日期:1991-11-25 00:00:00
abstract::The response to amino acid (AA) limitation of the entire aminoacyl-tRNA synthetase (ARS) gene family revealed that 16/20 of the genes encoding cytoplasmic-localized enzymes are transcriptionally induced by activating transcription factor 4 (Atf4) via C/ebp-Atf-Response-Element (CARE) enhancers. In contrast, only 4/19 ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw667
更新日期:2016-11-16 00:00:00
abstract::Effective transcript profiling in animal systems requires isolation of homogenous tissue or cells followed by faithful mRNA amplification. Linear amplification based on cDNA synthesis and in vitro transcription is reported to maintain representation of mRNA levels, however, quantitative data demonstrating this as well...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.5.e29
更新日期:2001-03-01 00:00:00
abstract::One of the major issues in expression profiling analysis still is to outline proper thresholds to determine differential expression, while avoiding false positives. The problem being that the variance is inversely proportional to the log of signal intensities. Aiming to solve this issue, we describe a model, expressio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm093
更新日期:2007-01-01 00:00:00
abstract::Earlier studies in DNA self-assembly have foretold the feasibility of building addressable nanostructures with multi-stranded motifs, which is fully validated in this study. In realizing this feasibility in DNA nanotechnology, a diversified set of motifs of modified domain lengths is extended from a classic type. The ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx121
更新日期:2017-04-07 00:00:00
abstract::The PriA protein was identified in Escherichia coli as a factor involved in the replication of extrachromosomal elements such as bacteriophage phiX174 and plasmid pBR322. Recent data show that PriA plays an important role in chromosomal replication, by promoting reassembly of the replication machinery during reinitiat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.7.1593
更新日期:2002-04-01 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::Codon usage data has been compiled for 110 yeast genes. Cluster analysis on relative synonymous codon usage revealed two distinct groups of genes. One group corresponds to highly expressed genes, and has much more extreme synonymous codon preference. The pattern of codon usage observed is consistent with that expected...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.13.5125
更新日期:1986-07-11 00:00:00
abstract::The HUGO Gene Nomenclature Committee (HGNC) based at EMBL's European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 42,000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. While we still update placeholder and problema...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa980
更新日期:2021-01-08 00:00:00
abstract::We have developed a simple but powerful method and web server to quickly locate charged and hydrophobic clusters in proteins (http://www.netasa.org/qgrid/index.html). For the charged clusters, each atom in the protein is first assigned a charge according to a standard force field. Then a box is created with dimensions...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh363
更新日期:2004-07-01 00:00:00
abstract::The Escherichia coli AlkB protein catalyzes the direct reversal of alkylation damage to DNA; primarily 1-methyladenine (1mA) and 3-methylcytosine (3mC) lesions created by endogenous or environmental alkylating agents. AlkB is a member of the non-heme iron (II) alpha-ketoglutarate-dependent dioxygenase superfamily, whi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1031
更新日期:2007-01-01 00:00:00
abstract::Aspects of the metabolism of RNA have been studied in enzymatically isolated protoplasts from cotyledon and first leaf mesophyll tissue of two cultivars of cucumber. The first leaf mesophyll protoplasts incorporated (3H)-uridine into ribosomal RNA at a constant rate for up to 25 hr in a simple salts medium and for up ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.7.1111
更新日期:1975-07-01 00:00:00
abstract::A previously elaborated technique for fixing a chosen partially melted state of DNA with glyoxal was used in a study of the melting process of the replicative form (RF III) of phi X174 DNA. Electron-microscopic maps corresponding to five points of the melting curve of RF III were obtained and compared with the theoret...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.6.1867
更新日期:1982-03-25 00:00:00
abstract::The HIV-1 viral infectivity factor (Vif) allows productive infection of non-permissive cells (including most natural HIV-1 targets) by counteracting the cellular cytosine deaminases APOBEC-3G (hA3G) and hA3F. The Vif-induced degradation of these restriction factors by the proteasome has been extensively studied, but l...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1009
更新日期:2010-01-01 00:00:00
abstract::Ribosomal protein (RP) genes must be coordinately expressed for proper assembly of the ribosome yet the mechanisms that control expression of RP genes in metazoans are poorly understood. Recently, TATA-binding protein-related factor 2 (TRF2) rather than the TATA-binding protein (TBP) was found to function in transcrip...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx676
更新日期:2017-10-13 00:00:00
abstract::The Epstein-Barr virus gene BRLF1 encodes the transcription factor R, which is a sequence-specific DNA-binding protein important for the switch from latency to a productive cycle. We have defined a repertoire of specific R-binding sites using a GST-R fusion protein and a pool of 23 bp random DNA sequences. The R-bound...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.7.1172
更新日期:1994-04-11 00:00:00
abstract::We have used in vitro site-directed mutagenesis with synthetic DNA oligonucleotides to introduce single nucleotide mutations in yeast mtDNA. In addition to the expected DNA alterations we also recovered with high frequency mutants with large deletions and insertions which arose through interaction with the synthetic D...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.24.8595
更新日期:1983-12-20 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 mammalian transcription factor SRF and the yeast regulatory protein MCM1 contain DNA binding domains that are 70% identical; moreover, both proteins can bind the serum response element in the human c-fos promoter. Here we present an analysis of MCM1 sequence specificity by selection of sites from random sequence o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.13.3297
更新日期:1992-07-11 00:00:00
abstract::GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or st...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm929
更新日期:2008-01-01 00:00:00
abstract::Polyketide synthases (PKSs) catalyze biosynthesis of a diverse family of pharmaceutically important secondary metabolites. Bioinformatics analysis of sequence and structural features of PKS proteins plays a crucial role in discovery of new natural products by genome mining, as well as in design of novel secondary meta...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq340
更新日期:2010-07-01 00:00:00