Abstract:
:We have characterized triple-helix-mediated inhibition of an artificial bacteriophage promoter with respect to relief of inhibition by incoming RNA polymerases that initiate upstream or downstream from the operator sequence. Whereas oligonucleotide-directed triple-helix formation inhibits the test promoter, promoter activity is restored when the triple-helical complexes are disrupted by transcription of either strand of the homopurine operator sequence. The degree of relief from inhibition is related to the frequency of operator transcription. These observations demonstrate that this artificial repressor-operator complex is subject to antagonism by cis elements (other promoters) acting at a distance. Such antagonism might also arise between certain natural transcriptional control regions. Our results suggest that the efficiency of artificial repressors based on triple-helix formation may be limited by transcriptional activity in the gene control region.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Skoog JU,Maher LJ 3rddoi
10.1093/nar/21.17.4055subject
Has Abstractpub_date
1993-08-25 00:00:00pages
4055-8issue
17eissn
0305-1048issn
1362-4962journal_volume
21pub_type
杂志文章abstract::Overlap-directed DNA assembly methods allow multiple DNA parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of DNA parts, have become widely adopted in synthetic biology, despite being incompatible with a key principle of engineering: modularity. To answer t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt915
更新日期:2014-01-01 00:00:00
abstract::With the recent increase in the number of mammalian genomes being sequenced, large-scale genome scans for human-specific positive selection are now possible. Selection can be inferred through phylogenetic analysis by comparing the rates of silent and replacement substitution between related species. Maximum-likelihood...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm764
更新日期:2008-01-01 00:00:00
abstract::As the largest group of MYB family transcription factors, R2R3-MYB proteins play essential roles during plant growth and development. However, the structural basis underlying how R2R3-MYBs recognize the target DNA remains elusive. Here, we report the crystal structure of Arabidopsis WEREWOLF (WER), an R2R3-MYB protein...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1081
更新日期:2020-01-10 00:00:00
abstract::The base excision repair DNA glycosylase MutY homolog (MYH) is responsible for removing adenines misincorporated into DNA opposite guanine or 7,8-dihydro-8-oxo-guanine (8-oxoG), thereby preventing G:C to T:A mutations. Biallelic germline mutations in the human MYH gene predispose individuals to multiple colorectal ade...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki209
更新日期:2005-01-26 00:00:00
abstract::X chromosome inactivation results in the cis-limited inactivation of most, but not all, genes on one of the two X chromosomes in mammalian females. The molecular basis for inactivation is unknown. In order to examine the transcriptional activity of human X-linked genes, a series of mouse-human somatic cell hybrids und...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.14.4191
更新日期:1990-07-25 00:00:00
abstract::Most small nucleolar RNAs (snoRNAs) guide rRNA nucleotide modifications, some participate in pre-rRNA cleavages, and a few have both functions. These activities involve direct base-pairing of the snoRNA with pre-rRNA using different domains. It is not known if the modification and processing functions occur independen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq043
更新日期:2010-06-01 00:00:00
abstract::IMP (Integrative Multi-species Prediction), originally released in 2012, is an interactive web server that enables molecular biologists to interpret experimental results and to generate hypotheses in the context of a large cross-organism compendium of functional predictions and networks. The system provides biologists...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv486
更新日期:2015-07-01 00:00:00
abstract::The mini-exon, a short segment found at the 5' end of trypanosome mRNAs, is contributed by a small RNA, the mini-exon donor (medRNA). In vivo 32P-labeled medRNA, a set of smaller RNAs related to it, and mRNA, were purified from Trypanosoma brucei by hybrid selection and gel electrophoresis. Using RNA fingerprinting an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.23.9861
更新日期:1987-12-10 00:00:00
abstract::The c-myc proto-oncogene encodes a highly unstable mRNA. Stabilized, truncated myc transcripts have been found in several human and murine tumors of hematopoietic origin. Recently, two tumors expressing 3' truncated c-myc mRNAs that were five times more stable than normal myc transcripts, were described. We have tried...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.9.2387
更新日期:1991-05-11 00:00:00
abstract::Adaptation of eucaryotic cDNA to heterologous expression was studied by mutating the translation initiation (TI) region upstream (mTI) and downstream (MTI) of the start codon. In the mTI subregion the 8 bases flanking the invariant Shine-Dalgarno motif GG-AG were mutagenized exhaustively, while the MTI subregion was s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.12.3127
更新日期:1992-06-25 00:00:00
abstract::The hypoxia-inducible factor-1 (HIF-1) was first described as a DNA binding activity that specifically recognizes an 8 bp motif known to be essential for hypoxia-inducible erythropoietin gene transcription. Subsequently HIF-1 activity has also been found in cell lines which do not express erythropoietin, suggesting th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.22.4542
更新日期:1995-11-25 00:00:00
abstract::Terminal deoxynucleotidyl transferase, which requires a single-stranded DNA primer under the usual assay conditions, can be made to accept double-stranded DNA as primer for the addition of either rNMP or dNMP, if Mg+2 ion is replaced by Co+2 ion. The priming efficiency in the presence of (C leads to) CO+2 ion with res...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.1.101
更新日期:1976-01-01 00:00:00
abstract::Mammalian mitochondrial ribosomes evolved from bacterial ribosomes by reduction of ribosomal RNAs, increase of ribosomal protein content, and loss of guanine nucleotides. Guanine is the base most sensitive to oxidative damage. By systematically comparing high-quality, small ribosomal subunit RNA sequence alignments an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky762
更新日期:2018-11-16 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::Genomic DNA of African trypanosomes contains a hypermodified thymidine residue termed base J (beta-d-glucosyl-HOMedU). This modified base is localized primarily to repetitive DNA, namely the telomeres, and is implicated in the regulation of antigenic variation. The base is synthesized in a two-step pathway. Initially,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn1067
更新日期:2009-04-01 00:00:00
abstract::Previously, we have shown that all class-1 polypeptide release factors (RFs) share a common glycine-glycine-glutamine (GGQ) motif, which is critical for RF activity. Here, we subjected to site-directed mutagenesis two invariant amino acids, Gln185 and Arg189, situated in the GGQ minidomain of human eRF1, followed by d...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.19.3982
更新日期:2001-10-01 00:00:00
abstract::Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the identification and classification of new members of known sequence families, and distributes annotation of ncRNAs in over 200 comp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki081
更新日期:2005-01-01 00:00:00
abstract::Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translato...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1034
更新日期:2018-01-04 00:00:00
abstract::We have isolated the 5'-end of the gene for the rat and human link protein by screening genomic libraries with oligonucleotides corresponding to the 5'-cDNA sequence. Several overlapping clones were isolated for the human link protein gene, while only one clone was obtained for the rat. All the clones contained a sing...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.8.1933
更新日期:1991-04-25 00:00:00
abstract::The nucleoplasm is not homogenous; it consists of many types of nuclear bodies, also known as nuclear domains or nuclear subcompartments. These self-organizing structures gather machinery involved in various nuclear activities. Nuclear speckles (NSs) or splicing speckles, also called interchromatin granule clusters, w...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkx759
更新日期:2017-10-13 00:00:00
abstract::An improved algorithm was elaborated to analyse tRNA interaction with aminoacyl-tRNA synthetase based on analysis of tRNA sequences. The fundamental element defining the interaction between the tRNA and the synthetase is not a single nucleotide but a nucleotide combination named a tile which comprises of a given nucle...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.8.1941
更新日期:1993-04-25 00:00:00
abstract::Double-stranded soybean leghemoglobin DNA was synthesized from leghemoglobin mRNA isolated from soybean nodules. The dsDNA was inserted into the Bam H1 site of plasmid pBR322 using the poly-dAT-joiner method. A cloned DNA fragment of one recombinant plasmid was isolated and characterized by restriction endonuclease di...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.9.3061
更新日期:1979-07-11 00:00:00
abstract::Nucleosomes released from oviduct nuclei during brief micrococcal nuclease digestions are enriched in transcribed sequences (bloom K.S. and Anderson, J.N. (1978) Cell, 15, 141-150). Such nucleosomes released into this 1Sf supernatant fraction are enriched in proteins HMG14, 17 and a third lower molecular weight protei...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.12.2761
更新日期:1981-06-25 00:00:00
abstract::The RecQ family of helicases is highly conserved both structurally and functionally from bacteria to humans. Defects in human RecQ helicases are associated with genetic diseases that are characterized by cancer predisposition and/or premature aging. RecQ proteins exhibit 3'-5' helicase activity and play critical roles...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz708
更新日期:2019-10-10 00:00:00
abstract::A new approach has been developed for the rapid fragmentation and fractionation of DNA into a size suitable for shotgun cloning and sequencing. The restriction endonuclease CviJI normally cleaves the recognition sequence PuGCPy between the G and C to leave blunt ends. Atypical reaction conditions which alter the speci...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.14.3753
更新日期:1992-07-25 00:00:00
abstract::RNA processing is critical for proper spatial and temporal control of gene expression. The ubiquitous nuclear polyadenosine RNA binding protein, PABPN1, post-transcriptionally regulates multiple steps of gene expression. Mutations in the PABPN1 gene expanding an N-terminal alanine tract in the PABPN1 protein from 10 a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky535
更新日期:2018-09-06 00:00:00
abstract::Minimized trans-acting HDV ribozyme systems consisting of three (Rz-3) and two (Rz-2) RNA strands were prepared and their folding conformations were analyzed by NMR spectroscopy. The guanosine residues in one of the enzyme components of Rz-3 were labeled with 13C and 15N. Imino proton signals were assigned by analysis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.3.766
更新日期:2002-02-01 00:00:00
abstract::The presence of a homing endonuclease gene (HEG) within a microbial intron or intein empowers the entire element with the ability to invade genomic targets. The persistence of a homing endonuclease lineage depends in part on conservation of its DNA target site. One such rDNA sequence has been invaded both in archaea a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn846
更新日期:2008-12-01 00:00:00
abstract::We have recently shown that phosphorothioate (PS) oligodeoxynucleotide (ODN) analogs, unlike their normal congeners, exhibit significant anti-HIV activity (Matsukura et al., (1987) Proc. Natl. Acad. Sci. USA 84, 7706-7710). We now report the syntheses, melting temperatures (Tm), and nuclease susceptibilities of a seri...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.8.3209
更新日期:1988-04-25 00:00:00
abstract::NONO, SFPQ and PSPC1 make up a family of proteins with diverse roles in transcription, RNA processing and DNA double-strand break (DSB) repair. To understand long-term effects of loss of NONO, we characterized murine embryonic fibroblasts (MEFs) from knockout mice. In the absence of genotoxic stress, wild-type and mut...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku650
更新日期:2014-09-01 00:00:00