Abstract：
:Transcription factor IIIA (TFIIIA) and p43 zinc finger protein form distinct complexes with 5S ribosomal RNA in Xenopus oocytes. Additionally, TFIIIA binds the internal promoter of the 5S RNA gene and supports assembly of a transcription initiation complex. Both proteins have nine tandemly repeated zinc fingers with almost identical linker lengths between corresponding fingers, yet p43 has no detectable affinity for the 5S RNA gene. TFIIIA zinc fingers 1-3 are connected by highly conserved linkers, first identified in the Drosophila protein Krüppel, that are found in many DNA binding zinc finger proteins. To understand the role of these linkers in RNA and DNA binding we exchanged three TFIIIA linker amino acids with the equivalent amino acids from p43. The major effect of linker substitution is a 50-fold reduction in DNA specificity, concomitant with an 8-fold reduction in affinity. N-Terminal zinc fingers from either TFIIIA or p43 bind to multiple specific sites on 5S RNA that are resistant to competition by tRNA or poly(rA). This mode of RNA binding is unaffected by linker substitution. These data suggest that zinc finger linkers significantly facilitate the specificity of DNA binding.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Ryan RF,Darby MKdoi
10.1093/nar/26.3.703subject
Has Abstractpub_date
1998-02-01 00:00:00pages
703-9issue
3eissn
0305-1048issn
1362-4962pii
gkb160journal_volume
26pub_type
杂志文章abstract：:A total of 10 B-lymphocyte-specific DNase I hypersensitive sites located in the chicken Ig-beta locus were divided into four regions and combinations of deletions of these regions were carried out. A decrease in transcription of the Ig-beta gene to <3% was demonstrated in cells with deletions in all four regions. The ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl469
更新日期：2006-08-11 00:00:00
abstract：:The Mouse Genome Database (MGD) (http://www.informatics.jax.org) one component of a community database resource for the laboratory mouse, a key model organism for interpreting the human genome and for understanding human biology. MGD strives to provide an extensively integrated information resource with experimental d...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg047
更新日期：2003-01-01 00:00:00
abstract：:We have previously mapped a repression domain from the active transcriptional repressor E4BP4 to a 65 amino acid segment near the C-terminus of the polypeptide. Here we show that the E4BP4 repression domain interacts specifically with the TBP binding repressor protein Dr1. Mutants that affect the ability of E4BP4 to b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.18.3607
更新日期：1996-09-15 00:00:00
abstract：:PSF (a.k.a. SFPQ) is a ubiquitously expressed, essential nuclear protein with important roles in DNA damage repair and RNA biogenesis. In stimulated T cells, PSF binds to and suppresses the inclusion of CD45 exon 4 in the final mRNA; however, in resting cells, TRAP150 binds PSF and prevents access to the CD45 RNA, tho...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv816
更新日期：2015-10-15 00:00:00
abstract：:Pseudogenes are copies of genes that cannot produce a protein. They can be detected from disruptions to their apparent coding sequence, caused by frameshifts and premature stop codons. They are classed as either processed pseudogenes (made by reverse transcription from an mRNA) or duplicated pseudogenes, arising from ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg169
更新日期：2003-02-01 00:00:00
abstract：:The cytosine base in DNA undergoes hydrolytic deamination at a considerable rate when UV radiation induces formation of a cyclobutane pyrimidine dimer (CPD) with an adjacent pyrimidine base. We have synthesized a phosphoramidite building block of a cis-syn cyclobutane thymine-uracil dimer (T[]U), which is the deaminat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh342
更新日期：2004-03-12 00:00:00
abstract：:Restriction endonuclease Bse634I recognizes and cleaves the degenerate DNA sequence 5'-R/CCGGY-3' (R stands for A or G; Y for T or C, '/' indicates a cleavage position). Here, we report the crystal structures of the Bse634I R226A mutant complexed with cognate oligoduplexes containing ACCGGT and GCCGGC sites, respectiv...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks300
更新日期：2012-08-01 00:00:00
abstract：:The ciliate Tetrahymena thermophila is an important eukaryotic model organism that has been used in pioneering studies of general phenomena, such as ribozymes, telomeres, chromatin structure and genome reorganization. Recent work has shown that Tetrahymena has many classes of small RNA molecules expressed during veget...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr792
更新日期：2012-02-01 00:00:00
abstract：:DNA tandem repeats (TRs) are ubiquitous genomic features which consist of two or more adjacent copies of an underlying pattern sequence. The copies may be identical or approximate. Variable number of tandem repeats or VNTRs are polymorphic TR loci in which the number of pattern copies is variable. In this paper we des...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku642
更新日期：2014-08-01 00:00:00
abstract：:A number of novel phosphate triester derivatives of the anti-cancer nucleoside analogue araC have been prepared by a rapid 2-step procedure, not necessitating prior sugar protection. Spectroscopic and lipophilicity data have been collected on these compounds. An in vitro assay indicated inhibition of thymidine incorpo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.18.7195
更新日期：1989-09-25 00:00:00
abstract：:Gene transfer and expression in eukaryotes is often limited by a number of stably maintained gene copies and by epigenetic silencing effects. Silencing may be limited by the use of epigenetic regulatory sequences such as matrix attachment regions (MAR). Here, we show that successive transfections of MAR-containing vec...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr436
更新日期：2011-08-01 00:00:00
abstract：:Protein classification by machine learning algorithms is now widely used in structural and functional annotation of proteins. The Protein Classification Benchmark collection (http://hydra.icgeb.trieste.it/benchmark) was created in order to provide standard datasets on which the performance of machine learning methods ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl812
更新日期：2007-01-01 00:00:00
abstract：:Transactivation by the ETS family of transcription factors, whose members share structurally conserved DNA-binding domains, is variably sensitive to methylation of their target genes. The mechanism by which DNA methylation controls ETS proteins remains poorly understood. Uncertainly also pervades the effects of hemi-m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw528
更新日期：2016-10-14 00:00:00
abstract：:The mitochondrial DNA (mtDNA) control regions for common chimpanzee, pygmy chimpanzee and gorilla were sequenced and the lengths and termini of their D-loop DNA's characterized. In these and all other species for which there are data, 5' termini map to sequences that contain the trinucleotide YAY. 3' termini are 25-51...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.13.5841
更新日期：1988-07-11 00:00:00
abstract：:We described here an approach for mapping proteins on any sequence of genomic DNA. UV-induced DNA-protein crosslinking within whole cells and the 'protein image' hybridization technique (1) were applied to test the proteins bound to different regions of the D. melanogaster hsp-70 gene. The histone H1-DNA association w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.4.1031
更新日期：1993-02-25 00:00:00
abstract：:Genome browsers are widely used for individually exploring various types of genomic data. A handful of genome browsers offer limited tools for collaboration among multiple users. Here, we describe PBrowse, an integrated real-time collaborative genome browser that enables multiple users to simultaneously view and acces...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1358
更新日期：2017-05-19 00:00:00
abstract：:Chromatin core particles near physiological ionic strength undergo a reversible transition induced by changes in pH near neutrality. While sedimentation studies indicate no significant effect on size or shape, changes in tyrosine fluorescence anisotropy and in circular dichroism suggest a somewhat looser structure at ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.10.4351
更新日期：1984-05-25 00:00:00
abstract：:Hexokinase 2 is an essential factor for signalling repression through the Saccharomyces cerevisiae high-glucose sensing pathway. The main regulatory mechanism that controls the HXK2 gene expression in yeast is mediated by the Rgt1 and Med8 transcription factors, which repress HXK2 expression in low-glucose containing ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl028
更新日期：2006-03-09 00:00:00
abstract：:Although secondary structure predictions of an individual RNA sequence have been widely used in a number of sequence analyses of RNAs, accuracy is still limited. Recently, we proposed a method (called 'CentroidHomfold'), which includes information about homologous sequences into the prediction of the secondary structu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr290
更新日期：2011-07-01 00:00:00
abstract：:Radioactive iodine has been used to probe the relative reactivities of nucleosomal H4 tyrosine residues under various conditions of subphysiological ionic strength. We observe that tyrosine 72 of H4, which is not reactive over the range 20-150 mM NaCl, becomes the predominant site of iodination within H4 when nucleoso...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.17.4367
更新日期：1981-09-11 00:00:00
abstract：:Besides the nicking-closing (topoisomerase I) activity, an ATP-dependent DNA topoisomerase is present in rat liver nuclei. The enzyme, partially purified, is able to catenate in vitro closed DNA circles in a magnesium-dependent, ATP-dependent, histone H1-dependent reaction, and to decatenate in vitro kinetoplast DNA n...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.4.1059
更新日期：1983-02-25 00:00:00
abstract：:I-motif DNAs have been widely employed as robust modulating components to construct reconfigurable DNA nanodevices that function well in acidic cellular environments. However, they generally display poor interactivity with fluorescent ligands under these complex conditions, illustrating a major difficulty in utilizing...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa020
更新日期：2020-02-28 00:00:00
abstract：:ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky420
更新日期：2018-07-02 00:00:00
abstract：:Homologous recombination provides a means for the in vivo construction of recombinant DNA molecules that may be problematic to assemble in vitro. We have investigated the efficiency of recombination within the Caenorhabditis elegans germ line as a function of the length of homology between recombining molecules. Our f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm857
更新日期：2007-01-01 00:00:00
abstract：:Insertion of DNA containing PR, the early rightward promoter of bacteriophage lambda, is lethal to M13-derived vectors when the promoter directs transcription (using the '+' strand as template) toward the M13 origin of replication (ori). Lethality can be relieved by mutation of PR, repression of the promoter by the la...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.20.5961
更新日期：1990-10-25 00:00:00
abstract：:Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1195
更新日期：2021-01-11 00:00:00
abstract：:Upstream open reading frame (uORF)-mediated translational inhibition is important in controlling key regulatory genes expression. However, understanding the underlying molecular mechanism of such uORF-mediated control system in vivo is challenging in the absence of an animal model. Therefore, we generated a zebrafish ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr645
更新日期：2011-11-01 00:00:00
abstract：:The influence of an upstream small open reading frame (URF) on the translation of two consecutive coding regions on an eukaryotic mRNA was studied. The cis effects of leader length, URF length, the sequences of the URF and neighboring regions, and the trans effects of the Cauliflower mosaic virus transactivator (TAV) ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.15.3851
更新日期：1992-08-11 00:00:00
abstract：:IStrons are chimeric genetic elements composed of a group I intron associated with an insertion sequence (IS). The group I intron is a catalytic RNA providing the IStron with self-splicing ability, which renders IStron insertions harmless to the host genome. The IS element is a DNA transposon conferring mobility, and ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku939
更新日期：2014-11-10 00:00:00
abstract：:Intramolecular RNA cross-links were induced within the large ribosomal subunit of E. coli by mild ultraviolet irradiation. Regions of the 23S RNA previously implicated in interactions with ribosomal-bound tRNA were then specifically excised by addressed cleavage using ribonuclease H, in conjunction with synthetic comp...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.15.4325
更新日期：1990-08-11 00:00:00
