Abstract:
:The inducibility of the vir genes (virA, -B, -C, -D, -E, and -G) on pRiA4 was examined at the transcriptional level, and the RNA-starting sites were determined by S1-nuclease mapping and primer-extension experiments. All of these genes were inducible, while virA, -E, and -G were transcribed even under noninducing conditions. Each transcription of virB, -C, -D, and -E was initiated at one particular site, but that of virA and -G occurred at two and three sites, respectively, depending on the conditions used. In the DNA region upstream from each inducible transcript, one or more blocks of six base-pairs, 5'TGATAACT3' (vir box), were found to be placed characteristically. These blocks were phasing with an interval of 11 base-pairs, and the most upstream one in each upstream region was preceded by an additional block in the inverted orientation. Although the distance between the block(s) and the promoter varied with the vir gene, every block was placed in a phase nearly opposite to the -35 and -10 regions of the promoter.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Aoyama T,Takanami M,Oka Adoi
10.1093/nar/17.21.8711subject
Has Abstractpub_date
1989-11-11 00:00:00pages
8711-25issue
21eissn
0305-1048issn
1362-4962journal_volume
17pub_type
杂志文章abstract::The effect of mutations in the highly conserved Y-GG/A motif of B-type DNA polymerases was studied in the DNA polymerase from the hyperthermophilic euryarchaeon Thermococcus aggregans. This motif plays a critical role in the balance between the synthesis and degradation of the DNA chain. Five different mutations of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.20.3910
更新日期:2000-10-15 00:00:00
abstract::During culture, a chicken B cell line DT40 spontaneously mutates immunoglobulin (Ig) genes by gene conversion, which involves activation-induced cytidine deaminase (AID)-dependent homologous recombination of the variable (V) region gene with upstream pseudo-V genes. To explore whether this mutation mechanism can targe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnj013
更新日期:2006-01-18 00:00:00
abstract::OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from a single gene in their last common ancestor. In 2016 OrthoDB reached its 9th release, growing to over 22 million genes from over 5000 species, now adding plants, archaea and viruses. In this update we focused on usability of this f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1119
更新日期:2017-01-04 00:00:00
abstract::The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1013
更新日期:2020-12-16 00:00:00
abstract::DNA3'pp5'G caps synthesized by the 3'-PO4/5'-OH ligase RtcB have a strong impact on enzymatic reactions at DNA 3'-OH ends. Aprataxin, an enzyme that repairs A5'pp5'DNA ends formed during abortive ligation by classic 3'-OH/5'-PO4 ligases, is also a DNA 3' de-capping enzyme, converting DNAppG to DNA3'p and GMP. By takin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv501
更新日期:2015-07-13 00:00:00
abstract::Magnetic tweezers are a powerful single-molecule technique that allows real-time quantitative investigation of biomolecular processes under applied force. High pulling forces exceeding tens of picoNewtons may be required, e.g. to probe the force range of proteins that actively transcribe or package the genome. Frequen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku677
更新日期:2014-10-01 00:00:00
abstract::LTR-IS elements are middle repetitive sequences in the mouse genome with structural features of solitary retroviral LTRs. In order to get some insight in the possible functional role of these sequences the promotor activity of two LTR-IS representatives differing by 105 bp in their U3 region was investigated. Gene fus...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.7.2631
更新日期:1985-04-11 00:00:00
abstract::Reconstructing full-length transcript isoforms from sequence fragments (such as ESTs) is a major interest and challenge for bioinformatic analysis of pre-mRNA alternative splicing. This problem has been formulated as finding traversals across the splice graph, which is a directed acyclic graph (DAG) representation of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl396
更新日期:2006-06-06 00:00:00
abstract::An examination, using reversed-phase chromatography and cyanogen bromide treatment, of tRNATyr, tRNAHis, tRNAAsn, and tRNAAsp from SV40-transformed mouse fibroblasts grown to different cell densities, untransformed cells grown to confluence, and mouse liver indicates that: (1) The tissue cultured mouse fibroblasts exa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.7.2513
更新日期:1978-07-01 00:00:00
abstract::Treatment of responsive cells by interferons (IFNs) induces within a few hours a rise in the concentration of several proteins and mRNAs. In order to characterize these IFN-induced mRNA species, we have cloned in E. coli the cDNA made from a 17-18S poly(A)+ RNA of human fibroblastoid cells (SV80) treated with IFN-beta...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.5.1213
更新日期:1983-03-11 00:00:00
abstract::Dnmt3a and Dnmt3b are paralogous enzymes responsible for de novo DNA methylation but with distinguished biological functions. In mice, disruption of Dnmt3b but not Dnmt3a causes global DNA hypomethylation, especially in repetitive sequences, which comprise the large majority of methylated DNA in the genome. By measuri...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq456
更新日期:2010-10-01 00:00:00
abstract::In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utili...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj158
更新日期:2006-01-01 00:00:00
abstract::VIDA is a new virus database that organizes open reading frames (ORFs) from partial and complete genomic sequences from animal viruses. Currently VIDA includes all sequences from GenBank for Herpesviridae, Coronaviridae and Arteriviridae. The ORFs are organized into homologous protein families, which are identified on...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.1.133
更新日期:2001-01-01 00:00:00
abstract::Uracil-Specific Exision Reagent (USER) fusion is a recently developed technique that allows for assembly of multiple DNA fragments in a few simple steps. However, designing primers for USER fusion is both tedious and time consuming. Here, we present the Primer Help for USER (PHUSER) software, a novel tool for designin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr394
更新日期:2011-07-01 00:00:00
abstract::From a sarkosyl-insoluble outer membrane fraction prepared from the Helicobacter pylori strain ATCC 43504, 19 proteins could be sequenced N-terminally by Edman degradation. Oligonucleotides were deduced and used for screening of a genomic library. From the isolated genes, five code for different members of a H.pylori ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.16.3325
更新日期:1999-08-15 00:00:00
abstract::The rapidly growing amount of genomic sequence data being generated and made publicly available necessitate the development of new data storage and archiving methods. The vast amount of data being shared and manipulated also create new challenges for network resources. Thus, developing advanced data compression techni...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks709
更新日期:2012-11-01 00:00:00
abstract::CAG repeats occur predominantly in the coding regions of human genes, which suggests their functional importance. In some genes, these sequences can undergo pathogenic expansions leading to neurodegenerative polyglutamine (poly-Q) diseases. The mutant transcripts containing expanded CAG repeats possibly contribute to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq700
更新日期:2010-12-01 00:00:00
abstract::A common goal in the discovery of rare functional DNA variants via medical resequencing is to incur a relatively lower proportion of false positive base-calls. We developed a novel statistical method for resequencing arrays (SRMA, sequence robust multi-array analysis) to increase the accuracy of detecting rare variant...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq750
更新日期:2011-01-01 00:00:00
abstract::Plasmodium falciparum origin recognition complex 1 (ORC1) protein has been implicated in DNA replication and silencing var gene family. However, the mechanism and the domain structure of ORC1 related to the regulation of var gene family are unknown. Here we show that the unique N-terminus of PfORC1 (PfORC1N(1-238)) is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks202
更新日期:2012-07-01 00:00:00
abstract::Furvina®, also denominated G1 (MW 297), is a synthetic nitrovinylfuran [2-bromo-5-(2-bromo-2-nitrovinyl)-furan] antibiotic with a broad antimicrobial spectrum. An ointment (Dermofural®) containing G1 as the only active principle is currently marketed in Cuba and successfully used to treat dermatological infections. He...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks822
更新日期:2012-11-01 00:00:00
abstract::Minigenes encoding the peptide Met-Arg-Arg have been used to study the mechanism of toxicity of AGA codons proximal to the start codon or prior to the termination codon in bacteria. The codon sequences of the 'mini-ORFs' employed were initiator, combinations of AGA and CGA, and terminator. Both, AGA and CGA are low-us...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh784
更新日期:2004-08-18 00:00:00
abstract::Frequencies for each of the 61 amino acid codons have been determined in every published mRNA sequence of 50 or more codons. The frequencies are shown for each kind of genome and for each individual gene. A surprising consistency of choices exists among genes of the same or similar genomes. Thus each genome, or kind o...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/8.1.197-c
更新日期:1980-01-11 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::We present the complete nucleotide sequence of the larval beta I-globin gene of Xenopus laevis including 240 nucleotides of the 5' flanking region and 594 nucleotides beyond the polyadenylation site. The site of transcription initiation was mapped by S1 nuclease, and the site of polyadenylation was determined by compa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.20.7705
更新日期:1984-10-25 00:00:00
abstract::We have analyzed the DNaseI sensitivity of chromatin from the rat albumin and alpha-fetoprotein genes in the fetal liver (which synthesizes albumin and alpha-fetoprotein), adult liver (which synthesizes albumin), fetal yolk sac (which synthesizes alpha-fetoprotein), and adult kidney (which synthesizes neither). Active...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.1.115
更新日期:1985-01-11 00:00:00
abstract::The heterodimeric subunit, SRP9/14, of the signal recognition particle (SRP) has previously been found to bind to scAlu and scB1 RNAs in vitro and to exist in large excess over SRP in anthropoid cells. Here we show that human and mouse SRP9/14 bind with high affinities to other Alu-like RNAs of different evolutionary ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.2.318
更新日期:1997-01-15 00:00:00
abstract::A non-redundant database of nuclear, protein-encoding, genomic DNA sequences highlighting nuclear pre-mRNA introns was constructed using information contained in the SWISS-PROT and GenBank sequence databases. This Intron DataBase (IDB) contains information about (i) introns (including nucleotide sequence, location, ph...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.1.181
更新日期:2000-01-01 00:00:00
abstract::Although the involvement of Ser/Arg-rich (SR) proteins in RNA metabolism is well documented, their role in vertebrate development remains elusive. We, therefore, elected to take advantage of the zebrafish model organism to study the SR genes' functions using the splicing morpholino (sMO) microinjection and the program...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx638
更新日期:2017-09-19 00:00:00
abstract::The NCBI has introduced two new web resources-LocusLink and RefSeq-that facilitate retrieval of gene-based information and provide reference sequence standards. These resources are designed to provide a non-redundant view of current knowledge about human genes, transcripts and proteins. Additional information about th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.1.126
更新日期:2000-01-01 00:00:00
abstract::When averaged over the full yeast protein-protein interaction and transcriptional regulatory networks, protein hubs with many interaction partners or regulators tend to evolve significantly more slowly due to increased negative selection. However, genome-wide analysis of protein evolution in the subnetworks of associa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq353
更新日期:2010-10-01 00:00:00