Abstract:
:The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and replication. In this work, we report the structure of a biologically relevant G-quadruplex within the LTR promoter region of HIV-1. The guanine-rich sequence designated LTR-IV forms a well-defined structure in physiological cationic solution. The nuclear magnetic resonance (NMR) structure of this sequence reveals a parallel-stranded G-quadruplex containing a single-nucleotide thymine bulge, which participates in a conserved stacking interaction with a neighboring single-nucleotide adenine loop. Transcription analysis in a HIV-1 replication competent cell indicates that the LTR-IV region may act as a modulator of G-quadruplex formation in the LTR promoter. Consequently, the LTR-IV G-quadruplex structure presented within this work could represent a valuable target for the design of HIV therapeutics.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
De Nicola B,Lech CJ,Heddi B,Regmi S,Frasson I,Perrone R,Richter SN,Phan ATdoi
10.1093/nar/gkw432subject
Has Abstractpub_date
2016-07-27 00:00:00pages
6442-51issue
13eissn
0305-1048issn
1362-4962pii
gkw432journal_volume
44pub_type
杂志文章abstract::MicroArray Gene expression and Network Evaluation Toolkit (MAGNET) is a web-based application that provides tools to generate and score both protein-protein interaction networks and coexpression networks. MAGNET integrates user-provided experimental measurements with high-throughput proteomic datasets, generating weig...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks526
更新日期:2012-07-01 00:00:00
abstract::Biological pathways can provide key information on the organization of biological systems. ArrayXPath (http://www.snubi.org/software/ArrayXPath/) is a web-based service for mapping and visualizing microarray gene-expression data for integrated biological pathway resources using Scalable Vector Graphics (SVG). By integ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh476
更新日期:2004-07-01 00:00:00
abstract::Homing endonuclease genes (HEGs) are mobile DNA elements that are thought to confer no benefit to their host. They encode site-specific DNA endonucleases that perpetuate the element within a species population by homing and disseminate it between species by horizontal transfer. Several yeast species contain the VMA1 H...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh734
更新日期:2004-07-27 00:00:00
abstract::The inherent properties of DNA as a stable polymer with unique affinity for partner molecules determined by the specific Watson-Crick base pairing makes it an ideal component in self-assembling structures. This has been exploited for decades in the design of a variety of artificial substrates for investigations of DNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1124
更新日期:2008-03-01 00:00:00
abstract::The E. coli protein StpA has RNA annealing and strand displacement activities and it promotes folding of RNAs by loosening their structures. To understand the mode of action of StpA, we analysed the relationship of its RNA chaperone activity to its RNA-binding properties. For acceleration of annealing of two short RNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1143
更新日期:2007-01-01 00:00:00
abstract::We have analysed DNA modification in a HapII site (CCGG) present in the major intron of the discontinuous rabbit beta-globin gene. In most somatic tissues, including erythroid and non-erythroid tissues, about 50% of the DNA is resistant to cleavage at this site by HapII, though 100% cleavage is found with the isoschiz...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.12.4631
更新日期:1978-12-01 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::The RSC complex of Saccharomyces cerevisiae is closely related to the SWI/SNF complex. Both complexes are involved in remodeling chromatin structure and they share conserved components. The RSC proteins Sth1, Rsc8/Swh3, Sfh1 and Rsc6 are homologs of the SWI/SNF proteins Swi2/Snf2, Swi3, Snf5 and Swp73 respectively. To...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.16.3739
更新日期:1998-08-15 00:00:00
abstract::The 'druggable genome' encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly available. The Illuminating the Druggable Genome (IDG) program was initiated in 2014, has the goal of developing experimental...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1072
更新日期:2017-01-04 00:00:00
abstract::Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading bacterial organism with respect to global protein-protein networks. Yet, there has been no global census of RNA/protein complexes in this model species of microbiology. Here,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa676
更新日期:2020-09-18 00:00:00
abstract::TORQUE is a tool for cross-species querying of protein-protein interaction networks. It aims to answer the following question: given a set of proteins constituting a known complex or a pathway in one species, can a similar complex or pathway be found in the protein network of another species? To this end, Torque seeks...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp474
更新日期:2009-07-01 00:00:00
abstract::SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) responsive genes during oxidative stress. However, while the mechanism of SIRT6-mediated silencing is well understood, the mechanism of SIRT6-mediated transcriptional activation is unknown. Here, we employed SIRT6 sepa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz528
更新日期:2019-09-05 00:00:00
abstract::Over 50 introns have been reported in archaeal rRNA genes (rDNAs), a subset of which nests putative homing endonuclease (HEase) genes. Here, we report the identification and characterization of a novel archaeal LAGLIDADG-type HEase, I-ApeKI [corrected], encoded by the ApeK1.S908 intron within the 16S rDNA of Aeropyrum...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni118
更新日期:2005-07-26 00:00:00
abstract::The prime mechanism by which p53 acts as a tumor suppressor is as a transcription factor regulating the expression of diverse downstream genes. The DNA-binding domain of p53 (p53DBD) interacts with defined DNA sites and is the main target for mutations in human primary tumors. Here, we show that the CWWG motif, found ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1044
更新日期:2011-03-01 00:00:00
abstract::The cartilage matrix is composed of characteristic components including type II collagen, aggrecan and link protein. In this paper, we report two DNA elements that regulate the link protein gene. Using transient transfection assays with link protein gene constructs in chondrocytes, chloramphenicol acetyl transferase (...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.12.2305
更新日期:1995-06-25 00:00:00
abstract::The 80S ribosome from Saccharomyces cerevisiae has been reconstructed from cryo electron micrographs to a resolution of 35 A. It is strikingly similar to the 70S ribosome from Escherichia coli, while displaying the characteristic eukaryotic features familiar from reconstructions of ribosomes from higher eukaryotes. As...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.2.655
更新日期:1998-01-15 00:00:00
abstract::Ethidium causes the cleavage of DNA via a light and oxygen dependent process. Using covalently closed circular DNA as a substrate, the saturation kinetics and the dependence on superhelical density of the cleavage indicate that intercalated ethidium is mainly responsible for nicking DNA. Superoxide dismutase has littl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.2.315
更新日期:1976-02-01 00:00:00
abstract::The Escherichia coli cyclic AMP receptor protein (CRP) is a global regulator that controls transcription initiation from more than 100 promoters by binding to a specific DNA sequence within cognate promoters. Many genes in the CRP regulon have been predicted simply based on the presence of DNA-binding sites within gen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh908
更新日期:2004-11-01 00:00:00
abstract::Cytokines are cell-to-cell signaling proteins that play a central role in immune development, pathogen responses, and diseases. Cytokines are highly regulated at the transcriptional level by combinations of transcription factors (TFs) that recruit cofactors and the transcriptional machinery. Here, we mined through thr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky787
更新日期:2018-10-12 00:00:00
abstract::Aberration within the p53 tumor suppressor gene is the most frequently identified genetic damage in human cancer. Regulatory functions proposed for the p53 protein include modulation of the cell cycle, cellular differentiation, signal transduction, and gene expression. Additionally, the p53 gene product may guard the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.3.713
更新日期:1993-02-11 00:00:00
abstract::By putting heterologous genomic regulatory systems into contact, chromosome addition lines derived from interspecific or intergeneric crosses allow the investigation of transcriptional regulation in new genomic environments. Here, we report the transcriptional and epigenetic adaptation of stably inherited alien maize ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky209
更新日期:2018-06-01 00:00:00
abstract::Five peaks of DNA glycosylase activity showing a preference for MNNG alkylated DNA have been identified from extracts of adapted M. luteus. They are numerically designated as GI to GV in order of their decreasing molecular weights. The first two of these peaks have been highly purified. GI, is a constitutive heat labi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.16.6607
更新日期:1987-08-25 00:00:00
abstract::The aminoacylation kinetics of T7 transcripts representing defined regions of Escherichia coli serine tRNAs were determined using purified E.coli seryl-tRNA synthetase (SerRS) and the kinetic values were used to estimate the relative contribution of various tRNA(Ser) domains to recognition by SerRS. The analysis revea...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.19.4467
更新日期:1993-09-25 00:00:00
abstract::In Saccharomyces cerevisiae, DNA double-strand breaks (DSBs) initiate meiotic recombination at open sites in chromatin, which display a meiosis-specific increase in micrococcal nuclease (MNase) sensitivity. The arg4 promoter contains such a DSB site. When arg4 sequences are placed in a pBR322-derived insert at HIS4 (h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.10.2175
更新日期:1999-05-15 00:00:00
abstract::The eukaryotic ribosomal protein S26e (rpS26e) lacking eubacterial counterparts is a key component of the ribosomal binding site of mRNA region 5' of the codon positioned at the exit site. Here, we determined the rpS26e oligopeptide neighboring mRNA on the human 80S ribosome using mRNA analogues bearing perfluoropheny...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1212
更新日期:2012-04-01 00:00:00
abstract::The glycoprotein C (gC) gene of herpes simplex virus type 1 is a true late gene, in that its expression occurs late in infection with a strict requirement for viral DNA replication. Recently, we reported on gC expression during infection with mutant viruses carrying deletions in the gC gene promoter. Analysis of RNA e...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.7.3097
更新日期:1987-04-10 00:00:00
abstract::Deciphering gene regulatory network architecture amounts to the identification of the regulators, conditions in which they act, genes they regulate, cis-acting motifs they bind, expression profiles they dictate and more complex relationships between alternative regulatory partnerships and alternative regulatory motifs...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki166
更新日期:2005-01-31 00:00:00
abstract::The X chromosome-linked inhibitor of apoptosis protein (XIAP) is the most potent intrinsic caspase inhibitor and plays an important role in the maintenance of intestinal epithelial integrity. The RNA binding protein, HuR, regulates the stability and translation of many target transcripts. Here, we report that HuR asso...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp755
更新日期:2009-12-01 00:00:00
abstract::The reported binding preference of human hnRNP protein A1 for the 3'-splice site of some introns (Swanson and Dreyfuss (1988) EMBO J. 7, 3519-3529; Mayrand and Pederson (1990) Nucleic Acids Res. 18, 3307-3318) was tested by assaying in vitro the binding of purified recombinant A1 protein (expressed in bacteria) to syn...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.22.6595
更新日期:1990-11-25 00:00:00
abstract::As shown in the accompanying paper (5), the oligonucleotide composition of the E. coli genome is highly asymmetric for sequences up to 6 bp in length when ranked from highest to lowest abundance. We show here that this largely reflects codon usage because heavily used codons were found in the highly abundant oligomers...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.6.2627
更新日期:1987-03-25 00:00:00