Abstract:
:According to the recruitment model of transcriptional activation, an activator helps initiate transcription by bringing the RNA polymerase to a specific location on the DNA through interaction with components of the transcriptional machinery. However, it is difficult to isolate and define the activities of specific activator-target pairs experimentally through rearranging existing protein parts. Here we designed and constructed an RNA-based transcriptional activator to study specificity from both sides of the activator-target interface. Utilizing a well-characterized site-specific RNA aptamer for TFIIB, we were able to delineate some key features of this process. By rationally converting an inhibitory aptamer into the activation domain of the activator, we also introduced a new source of submolecular building blocks to synthetic biology.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Wang S,Shepard JR,Shi Hdoi
10.1093/nar/gkp1227subject
Has Abstractpub_date
2010-04-01 00:00:00pages
2378-86issue
7eissn
0305-1048issn
1362-4962pii
gkp1227journal_volume
38pub_type
杂志文章abstract::Toxin-antitoxin systems are widespread in bacteria and archaea. They perform diverse functional roles, including the generation of persistence, maintenance of genetic loci and resistance to bacteriophages through abortive infection. Toxin-antitoxin systems have been divided into three types, depending on the nature of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks231
更新日期:2012-07-01 00:00:00
abstract::The DNA sequence of a 354 basepair EcoRI-HindIII fragment of plasmid pMB9 which has originally been derived from plasmid pSC101 has been resolved. This fragment contains a promoter for transcription directed towards the EcoRI site. Escherichia coli RNA polymerase binds to a region within the EcoRI-HindIII fragment whi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.7.1535
更新日期:1980-04-11 00:00:00
abstract::Sequence-specific interactions between aminoacyl-tRNA synthetases and their cognate tRNAs ensure both accurate RNA recognition and the efficient catalysis of aminoacylation. The effects of tRNA(Trp)variants on the aminoacylation reaction catalyzed by wild-type Escherichia coli tryptophanyl-tRNA synthe-tase (TrpRS) hav...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.18.3631
更新日期:1999-09-15 00:00:00
abstract::We have examined the expression and structure of several genes belonging to two classes of vegetative specific genes of the simple eukaryote, Dictyostelium discoideum. In amebae grown on bacteria, deactivation of all vegetative specific genes occurred at the onset of development and very little mRNA exists by 8 to 10 ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.23.9679
更新日期:1989-12-11 00:00:00
abstract::DNase I and MPE.Fe (II) footprinting both employ partial cleavage of ligand-protected DNA restriction fragments and Maxam-Gilbert sequencing gel methods of analysis. One method utilizes the enzyme, DNase I, as the DNA cleaving agent while the other employs the synthetic molecule, methidium-propyl-EDTA (MPE). For actin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.16.5555
更新日期:1983-08-25 00:00:00
abstract::We have isolated from a single human liver cDNA library two clones which are highly homologous (78% over the coding region) to the major phenobarbital-inducible P450 from rat (P450IIB1). This is the first direct demonstration of the presence of the P450IIB gene subfamily in humans. This subfamily is much less extensiv...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.13.5783
更新日期:1988-07-11 00:00:00
abstract::MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation of metazoan genes. The mature approximately 22-nt long RNA molecules are processed from genome-encoded stem-loop structured precursor genes. Hundreds of such genes have been experimentally val...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn707
更新日期:2009-01-01 00:00:00
abstract::We report the isolation of a novel human POU domain encoding gene named RDC-1. The POU domain of the RDC-1 encoded protein is highly related to the POU domain potentially encoded by the rat brain-3 sequence and to that of the Drosophila I-POU protein; outside of the POU region, RDC-1 is unrelated to any previously cha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.18.4919
更新日期:1992-09-25 00:00:00
abstract::NikR is a transcriptional metalloregulator central in the mandatory response to acidity of Helicobacter pylori that controls the expression of numerous genes by binding to specific promoter regions. NikR/DNA interactions were proposed to rely on protein activation by Ni(II) binding to high-affinity (HA) and possibly s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1216
更新日期:2010-05-01 00:00:00
abstract::It has been proposed that DNA multiply damaged sites (MDS), where more than one moiety in a local region ( approximately 1 helical turn, 10 bp) of the DNA is damaged, are lesions of enhanced biological significance. However, other than indirect measures, there are few analytical techniques that allow direct detection ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.20.e101
更新日期:2001-10-15 00:00:00
abstract::The cloned 18 S ribosomal RNA gene from Saccharomyces cerevisiae have been sequenced, using the Maxam-Gilbert procedure. From this data the complete sequence of 1789 nucleotides of the 18 S RNA was deduced. Extensive homology with many eucaryotic as well as E. coli ribosomal small subunit rRNA (S-rRNA) has been observ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.23.5779
更新日期:1980-12-11 00:00:00
abstract::Right-handed RNA duplexes of (CG)n sequence undergo salt-induced helicity reversal, forming left-handed RNA double helices (Z-RNA). In contrast to the thoroughly studied Z-DNA, no Z-RNA structure of natural origin is known. Here we report the NMR structure of a half-turn, left-handed RNA helix (CGCGCG)2 determined in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh736
更新日期:2004-08-03 00:00:00
abstract::We present a rapid and efficient method for the detection of related transcripts with different expression levels. This approach combines the rapid amplification of cDNA ends (RACE) method with a cDNA subtractive technique. The strategy is based on successive subtractions of prevalent isoforms resulting in enrichment ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.8.2031
更新日期:1998-04-15 00:00:00
abstract::The genome of Kirsten murine sarcoma virus was formed by recombination between Kirsten murine leukaemia virus sequences, and rat sequences derived from a retrovirus-like '30S' (VL30) genetic element encompassing the Kras oncogene. Using cloned DNAs we have determined the nucleotide sequences of the long terminal repea...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.17.6839
更新日期:1984-09-11 00:00:00
abstract::The yeast protein Rrf1p encoded by the FIL1 nuclear gene bears significant sequence similarity to Escherichia coli ribosome recycling factor (RRF). Here, we call FIL1 Ribosome Recycling Factor of yeast, RRF1. Its gene product, Rrf1p, was localized in mitochondria. Deletion of RRF1 leads to a respiratory incompetent ph...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg449
更新日期:2003-07-15 00:00:00
abstract::The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing infor...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl793
更新日期:2007-01-01 00:00:00
abstract::To examine the influence of thyrotropin (TSH) on the thyroglobulin (Tgb) mRNA content, the latter was evaluated in the cytoplasm of hog thyroid cells cultured in the absence (control cells) or presence of TSH. The Tgb mRNA levels were determined by, (i) kinetics of hybridization to sheep Tgb cDNA, (ii) capacity of cod...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.10.3353
更新日期:1979-07-25 00:00:00
abstract::Extreme overloading of HPLC columns with sample can create a condition of binding site saturation causing competition and displacement among solutes during column elution. This has been termed solute-displacement chromatography (SD-HPLC). We present an example of this phenomenon for the preparative fractionation and p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.12.2913
更新日期:1993-06-25 00:00:00
abstract::Many proteins of the SNF2 family, which share a similar DNA-dependent ATPase/putative helicase domain, are involved in global transcriptional control and processing of DNA damage. We report here the partial cloning and characterization of 89B helicase, a gene encoding a new Drosophila melanogaster member of the SNF2 f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.16.3121
更新日期:1996-08-15 00:00:00
abstract::Transcription factor IIIA (TFIIIA) is specifically required for transcription of 5S rRNA genes and is the archetypal C2H2 zinc finger protein. All known vertebrate TFIIIAs have a similar organization: nine zinc fingers, followed by a C-terminal domain of unknown structure. The zinc fingers of Saccharomyces cerevisiae ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf385
更新日期:2002-07-01 00:00:00
abstract::Labeling of a covalently closed circular double-stranded DNA was achieved using a so-called 'padlock oligonucleotide'. The oligonucleotide was targeted to a sequence which is present in the replication origin of phage f1 and thus in numerous commonly used plasmids. After winding around the double-stranded target DNA s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.3.e12
更新日期:2002-02-01 00:00:00
abstract::Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The CORUM (http://mips.gsf.de/genre/proj/corum/index.html) database is a collection of experimentally verified mammalian protein complexes. Information is manually derived by critical reading of the scient...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm936
更新日期:2008-01-01 00:00:00
abstract::MicroRNAs (miRNAs) are small RNAs ∼22 nt in length that are involved in the regulation of a variety of physiological and pathological processes. Advances in high-throughput small RNA sequencing (smRNA-seq), one of the next-generation sequencing applications, have reshaped the miRNA research landscape. In this study, w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1238
更新日期:2013-01-01 00:00:00
abstract::Mung bean nuclease hydrolyzes synthetic esters of 3'-nucleotides to nucleosides and phosphate esters; esters of 2'-nucleotides, and 2'--> 5' internucleotide linkages, are resistant. Esters of ribonucleotides are cleaved at 100-fold the rate for deoxyribonucleotides, the increased rate being due to presence of the 2'-h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.5.699
更新日期:1974-05-01 00:00:00
abstract::While RNA structures have been extensively characterized in vitro, very few techniques exist to probe RNA structures inside cells. Here, we have exploited mechanisms of post-transcriptional regulation to synthesize fluorescence-based probes that assay RNA structures in vivo. Our probing system involves the co-expressi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1191
更新日期:2015-01-01 00:00:00
abstract::Numerous eukaryotic genes are alternatively spliced. Recently, deep transcriptome sequencing has skyrocketed proportion of alternatively spliced genes; over 95% human multi-exon genes are alternatively spliced. One fundamental question is: are all these alternative splicing (AS) events functional? To look into this is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1253
更新日期:2014-12-16 00:00:00
abstract::In Euplotes crassus millions of telomeres are synthesized during the sexual phase of the life cycle. Since these newly synthesized telomeres are longer than normal macronuclear telomeres, they must be trimmed to the mature size. We have examined the timing and mechanism of this trimming step. We have shown that a sudd...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.23.5366
更新日期:1993-11-25 00:00:00
abstract::Much effort has long been devoted to unraveling the coordinated cellular response to genotoxic insults. In view of the difficulty of obtaining human biological samples of homogeneous origin, I have established a set of stable human clones where one DNA repair gene has been stably silenced by means of RNA interference....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm195
更新日期:2007-01-01 00:00:00
abstract::Plasmid DNA incubated in interphase Xenopus egg extracts is normally assembled into chromatin and then into synthetic nuclei which undergo one round of regulated replication. During a study of restriction endonuclease cut plasmid replication intermediates (RIs) by the Brewer-Fangman 2D gel electrophoresis technique, w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.10.2187
更新日期:2000-05-15 00:00:00
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