Abstract：
:In HIV-1 infection, Tat acts at least in part to control transcriptional elongation by overcoming premature transcriptional termination. In some other genes this process is governed by DNA elements called attenuators in concert with cellular transcription factors. To understand the action of Tat more fully and explore its role as an anti-attenuator, we examined the ability of several natural and synthetic attenuation sequences to modulate transcription initiated at the HIV LTR. Fragments containing these signals were inserted downstream of the TAR element in an HIV-CAT chimera and their effects on transcription were assessed both in vitro and in vivo. Runoff transcription assays in HeLa cell extracts demonstrated that the attenuators give rise to premature termination of transcripts initiated from the heterologous HIV-LTR promoter in vitro. When transiently expressed following transfection into Cos cells, however, premature transcript termination at the attenuation site was not observed. Nevertheless, many of the inserted sequences exerted marked effects on CAT gene expression and on transactivation by Tat at both the RNA and protein levels. The nature and magnitude of the effects depended upon the identity of the attenuator and its orientation but only one of 16 sequences tested met the criteria for a Tat-suppressible attenuator in vivo. One other sequence, in contrast, severely reduced Tat-activated transcription without inhibiting basal transcription These results indicate that sequences downstream of the HIV LTR can influence its function as a promoter and its response to Tat transactivation, but lend little support to their role as attenuators in vivo.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Greenberg ME,Mathews MBdoi
10.1093/nar/25.24.5017subject
Has Abstractpub_date
1997-12-15 00:00:00pages
5017-24issue
24eissn
0305-1048issn
1362-4962pii
gka789journal_volume
25pub_type
杂志文章abstract：:The gene, rpb1, encoding the largest subunit of RNA polymerase II has been cloned from Schizosaccharomyces pombe using the corresponding gene, RPB1, of Saccharomyces cerevisiae as a cross-hybridization probe. We have determined the complete sequence of this gene, and parts of PCR-amplified rpb1 cDNA. The predicted cod...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.3.461
更新日期：1991-02-11 00:00:00
abstract：:Cre recombinase catalyzes the cleavage and religation of DNA at loxP sites. The enzyme is a homotetramer in its functional state, and the symmetry of the protein complex enforces a pseudo-palindromic symmetry upon the loxP sequence. The Cre-lox system is a powerful tool for many researchers. However, broader applicati...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv901
更新日期：2015-10-15 00:00:00
abstract：:Thermal elution poly(U)-Sepharose chromatography was utilized to fractionate yeast mRNA based on poly(A) size. Analysis of the in vitro translation products of the fractionated RNAs in a wheat-embryo cell-free protein synthesis system shows a heterogeneous but equal distribution of these abundant translatable mRNAs in...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.17.3841
更新日期：1980-09-11 00:00:00
abstract：:Insertion of the insertion sequence Is2(I) directly before the galE gene of the galactose operon results in a Gal minus phenotype (1, 2). The Gal-constitutive allele galc200 (and its deletion derivative galc200 delta 31) arise from such a Gal minus mutant by the insertion of LS2(II) DNA within the LS2(I) sequence (3)....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.16.5015
更新日期：1982-08-25 00:00:00
abstract：:In Eukaryotes, DNA is wound around the histone octamer forming the basic chromatin unit, the nucleosome. Atomic structures have been obtained from crystallography and single particle cryo-electron microscopy (cryoEM) of identical engineered particles. But native nucleosomes are dynamical entities with diverse DNA sequ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky670
更新日期：2018-09-28 00:00:00
abstract：:Two triple helix structures (15-mers containing only T.A-T triplets or containing mixed T.A-T and C.G-C triplets) have been studied by uranyl mediated DNA photocleavage to probe the accessibility of the phosphates of the DNA backbone. Whereas the phosphates of the pyrimidine strand are at least as accessible as in dou...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.11.2735
更新日期：1992-06-11 00:00:00
abstract：:During DNA replication, the presence of 8-oxoguanine (8-oxoG) lesions in the template strand cause the high-fidelity (HiFi) DNA polymerase (Pol) to stall. An early response to 8-oxoG lesions involves 'on-the-fly' translesion synthesis (TLS), in which a specialized TLS Pol is recruited and replaces the stalled HiFi Pol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa803
更新日期：2020-11-04 00:00:00
abstract：:Complementary DNA clones encoding the human kidney epidermal growth factor (EGF) precursor have been isolated and sequenced. They predict the sequence of a 1,207 amino acid protein which contains EGF flanked by polypeptide segments of 970 and 184 residues at its NH2- and COOH-termini, respectively. The structural orga...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.21.8427
更新日期：1986-11-11 00:00:00
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 a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.3.703
更新日期：1998-02-01 00:00:00
abstract：:DNA predominantly contains Watson-Crick (WC) base pairs, but a non-negligible fraction of base pairs are in the Hoogsteen (HG) hydrogen bonding motif at any time. In HG, the purine is rotated ∼180° relative to the WC motif. The transitions between WC and HG may play a role in recognition and replication, but are diffi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz837
更新日期：2019-12-02 00:00:00
abstract：:The majority of genome-wide association study (GWAS) risk variants reside in non-coding DNA sequences. Understanding how these sequence modifications lead to transcriptional alterations and cell-to-cell variability can help unraveling genotype-phenotype relationships. Here, we describe a computational method, dubbed C...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1263
更新日期：2017-03-17 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：:The three chromosomal DNAs of S. pombe have been fractionated by pulsed field gel electrophoresis. The resulting molecular karyotype will greatly speed gene mapping in this organism, and it indicates that the separation range of the technique extends to DNA molecules as large as 9,000,000 base pairs. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.11.4481
更新日期：1987-06-11 00:00:00
abstract：:Light is a major external factor in regulating seed germination. Photoreceptor phytochrome B (PHYB) plays a predominant role in promoting seed germination in the initial phase after imbibition, partially by repressing phytochrome-interacting factor1 (PIF1). However, the mechanism underlying the PHYB-PIF1-mediated tran...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx283
更新日期：2017-07-07 00:00:00
abstract：:A novel, site-specific, DNA backbone S-modification (phosphorothioation) has been discovered, but its in vivo function(s) have remained obscure. Here, we report that the enteropathogenic Salmonella enterica serovar Cerro 87, which possesses S-modified DNA, restricts DNA isolated from Escherichia coli, while protecting...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq610
更新日期：2010-11-01 00:00:00
abstract：:Polyploidy, the presence of multiple sets of chromosomes that are similar but not identical, complicates both chromosome walking and assembly of sequence-ready contigs for many plant taxa including a large number of economically-significant crops. Traditional 'dot-blot hybridization' or PCR-based assays for identifyin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.7.e23
更新日期：2000-04-01 00:00:00
abstract：:Molecular replacement (MR) is the method of choice for X-ray crystallography structure determination when structural homologues are available in the Protein Data Bank (PDB). Although the success rate of MR decreases sharply when the sequence similarity between template and target proteins drops below 35% identical res...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh400
更新日期：2004-07-01 00:00:00
abstract：:Vaccinia virus DNA topoisomerase catalyzes resolution of synthetic Holliday junctions in vitro. The mechanism entails concerted transesterifications at two recognition sites, 5'-CCCTT/, that are opposed within a partially mobile four-way junction. Efficient resolution occurs on a junction with a 10 bp segment of branc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.14.2658
更新日期：2000-07-15 00:00:00
abstract：:Upon endocytosis, most oligodeoxynucleotides (ODNs) accumulate in vesicular compartments; a tiny number of them cross the vesicle membrane, reach the cytosol and by passive diffusion enter the nucleus where they are entrapped. So far, the compartment in which an antisense ODN interacts with its mRNA target has not bee...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.13.2730
更新日期：1999-07-01 00:00:00
abstract：:We describe a database of macromolecular motions meant to be of general use to the structural community. The database, which is accessible on the World Wide Web with an entry point at http://bioinfo.mbb.yale.edu/MolMovDB , attempts to systematize all instances of protein and nucleic acid movement for which there is at...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.18.4280
更新日期：1998-09-15 00:00:00
abstract：:A gene bank of Staphylococcus aureus strain Cowan I was established using an E. coli HB101/pBR327 host-vector system. Recombinants expressing staphylococcal protein A (SPA) were detected using an IgG-binding assay. A 3.2 Kb DNA fragment directing the synthesis of SPA in E. coli was identified. SPA produced by E. coli ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.10.3065
更新日期：1983-05-25 00:00:00
abstract：:Six 1',5'-anhydrohexitol uridine triphosphates were synthesized with aromatic substitutions appended via a carboxamide linker to the 5-position of their bases. An improved method for obtaining such 5-substituted hexitol nucleosides and nucleotides is described. The incorporation profile of the nucleotide analogues int...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz008
更新日期：2019-03-18 00:00:00
abstract：:ATP-dependent type I topoisomerases from extremely thermophilic archaebacteria--reverse gyrases--drive positive supercoiling of DNA. We showed that reverse gyrase from Desulfurococcus amylolyticus breaks the DNA at specific sites and covalently binds to the 5' end. In 30 out of 31 sites located in pBR322 DNA fragments...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.9.2801
更新日期：1990-05-11 00:00:00
abstract：:The integrity and stability of nucleosomes under transcription assay conditions has been found to depend on concentration and ionic environment. Rifamycin AF/013, a commonly used inhibitor of initiation, is particularly effective in destabilisation of nucleosomes. Intact nucleosomes are refractory to transcription by ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/7.2.377
更新日期：1979-09-25 00:00:00
abstract：:Specific guanine-rich regions in human genome can form higher-order DNA structures called G-quadruplexes, which regulate many relevant biological processes. For instance, the formation of G-quadruplex at telomeres can alter cellular functions, inducing apoptosis. Thus, developing small molecules that are able to bind ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku247
更新日期：2014-05-01 00:00:00
abstract：:Current literature describes several methods for the design of efficient siRNAs with 19 perfectly matched base pairs and 2 nt overhangs. Using four independent databases totaling 3336 experimentally verified siRNAs, we compared how well several of these methods predict siRNA cleavage efficiency. According to receiver ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm088
更新日期：2007-01-01 00:00:00
abstract：:Hippo pathway is involved in tumorigenesis, and its regulation in cytosol has been extensively studied, but its regulatory mechanisms in the nuclear are not clear. In the current study, using a FBS-inducing model following serum starvation, we identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1317
更新日期：2019-03-18 00:00:00
abstract：:Multivalent cations are known to condense DNA into higher ordered structures, including toroids and rods. Here we report that solid supports treated with monovalent or multivalent cationic silanes, followed by removal of soluble molecules, can condense DNA. The mechanism of this surface-directed condensation depends o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.2.588
更新日期：1998-01-15 00:00:00
abstract：:Single-stranded mRNA molecules form secondary structures through complementary self-interactions. Several hypotheses have been proposed on the relationship between the nucleotide sequence, encoded amino acid sequence and mRNA secondary structure. We performed the first transcriptome-wide in silico analysis of the huma...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl287
更新日期：2006-05-08 00:00:00
abstract：:A simple and efficient method is described to introduce structurally pre-determined mutations into recombinant genomes of filamentous phage M13. The method rests on gapped duplex DNA (gdDNA) molecules of the phage M13 genome as the key intermediate. In this gdDNA, the (+) and the (shorter) (-) strand carry different g...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.24.9441
更新日期：1984-12-21 00:00:00
