Abstract：
:The pol gene of all retroviruses is expressed as a gag-pol fusion protein which is proteolytically processed to produce all viral enzymes. In the human immunodeficiency virus (HIV), the gag and pol genes overlap by 241 nucleotides with pol in the -1 phase with respect to gag. The gag-pol fusion is produced via a -1 ribosomal frameshifting event that brings the overlapping, out-of-phase gag and pol genes into translational phase. Frameshifting occurs at a so called 'shift site' 8-10 nucleotides upstream of a hairpin loop which may play a role in the regulation of frameshifting. We have fused this region of HIV-1 to the 5' end of the firefly luciferase reporter gene in order to quantitatively measure ribosomal frameshifting both in cells and by in vitro translation. A series of 2'-O-methyl oligonucleotides was designed to specifically bind the sequences which flank the gag-pol hairpin. Ribosomal frameshifting is enhanced up to 6 fold by those oligonucleotides which bind the area just 3 to the stem. Oligonucleotides which bind 5' to the stem have no effect on frameshift efficiency. In addition, we have constructed a series of fusion genes which mimic the effect of the bound oligonucleotides with intramolecular hairpins. The results suggest that increasing RNA secondary structure downstream of the shift site increases the frequency of ribosomal frameshifting, and that this effect can be mimicked by antisense oligonucleotides.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Vickers TA,Ecker DJdoi
10.1093/nar/20.15.3945keywords:
subject
Has Abstractpub_date
1992-08-11 00:00:00pages
3945-53issue
15eissn
0305-1048issn
1362-4962journal_volume
20pub_type
杂志文章abstract：:The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). Access to promoter sequences is provided by pointers to positions in the corresponding genomes. Promoter evidence comes from conventional TSS mappi...
journal_title：Nucleic acids research
pub_type： 历史文章,杂志文章
doi：10.1093/nar/gkj146
更新日期：2006-01-01 00:00:00
abstract：:The newest genomic advances have uncovered an unprecedented degree of structural variation throughout genomes, with great amounts of data accumulating rapidly. Here we introduce InvFEST (http://invfestdb.uab.cat), a database combining multiple sources of information to generate a complete catalogue of non-redundant hu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1122
更新日期：2014-01-01 00:00:00
abstract：:We created a single cell sorting system to screen for enzyme activity in Escherichia coli producing 3,4 dihydroxy benzoate (34DHB). To do so, we engineered a transcription factor regulon controlling the expression of green fluorescent protein (GFP) for induction by 34DHB. An autoregulated transcription factor, pcaU, w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku444
更新日期：2014-07-01 00:00:00
abstract：:Expression from the K. pneumoniae nifLA promoter is oxygen sensitive and is also inhibited by the DNA gyrase inhibitor coumermycin A1 under anaerobic growth conditions. The activity of this promoter was found to be highly sensitive to changes in DNA topology in vitro. Transcription was completely dependent on negative...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.21.9933
更新日期：1988-11-11 00:00:00
abstract：:Clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated Cas proteins comprise a prokaryotic RNA-guided adaptive immune system that interferes with mobile genetic elements, such as plasmids and phages. The type I-E CRISPR interference complex Cascade from Escherichia coli is composed of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1285
更新日期：2015-01-01 00:00:00
abstract：:The Chemical Effects in Biological Systems database (CEBS) is a comprehensive and unique toxicology resource that compiles individual and summary animal data from the National Toxicology Program (NTP) testing program and other depositors into a single electronic repository. CEBS has undergone significant updates in re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1077
更新日期：2017-01-04 00:00:00
abstract：:The biogenesis of ribosomes in vivo is an essential process for cellular functions. Transcription of ribosomal RNA (rRNA) genes is the rate-limiting step in ribosome biogenesis controlled by environmental conditions. Here, we investigated the role of folate antagonist on changes of DNA double-strand breaks (DSBs) land...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1208
更新日期：2017-03-17 00:00:00
abstract：:Eight base analogs were tested as third strand residues in otherwise homopyrimidine strands opposite each of the 'direct' (A.T and G.C) and 'inverted' (T.A and C.G) Watson-Crick base pairs, using UV melting profiles to assess triplex stability. The target duplexes contained 20 A.T base pairs and a central test base pa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.23.4632
更新日期：1999-12-01 00:00:00
abstract：:Naturally occurring RNAs are known to exhibit a high degree of modularity, whereby specific structural modules (or motifs) can be mixed and matched to create new molecular architectures. The modular nature of RNA also affords researchers the ability to characterize individual structural elements in controlled syntheti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz304
更新日期：2019-07-09 00:00:00
abstract：:Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure-based approach. Prediction of protein-protein interactions (PPIs) is a central area of interest and successful prediction would provide leads for experiments and drug design; however, the experimental coverage of t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq481
更新日期：2010-07-01 00:00:00
abstract：:A newly discovered group of spherical plant viruses contains a bipartite genome consisting of a single-strand linear RNA molecule (RNA 1, Mr 1.5 x 10(6) ), and a single-strand, covalently closed circular viroid-like RNA molecule (RNA 2, Mr approximately 125,000). The nucleotide sequences of the RNA 2 of two of these, ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.12.3681
更新日期：1982-06-25 00:00:00
abstract：:Partial acid cleavage, comparative HPLC tryptic peptide mapping and amino acid sequencing of the C1 and C2 proteins of HeLa heterogeneous nuclear ribonucleoprotein (hnRNP) particles demonstrate that proteins C1 and C2 differ in primary structure by the presence of a 13 amino acid insert sequence in C2. This C2 insert ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.21.8441
更新日期：1989-11-11 00:00:00
abstract：:The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is a repository for the submission, maintenance and presentation of nucleotide sequence data and related sample and experimental information. In this article we report on ENA in 2015 regarding general activity, notable published data sets and major achiev...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1311
更新日期：2016-01-04 00:00:00
abstract：:We have studied a novel class of DNA sequences that cause DNA polymerases to pause. These sequences have the central consensus Py-G-C and are not necessarily adjacent to hairpins in the DNA template. Since most consensus sequences do not cause pauses under standard conditions, additional template features must exist t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.14.2774
更新日期：1996-07-15 00:00:00
abstract：:Oligonucleotide-mediated multiplex genome engineering is an important tool for bacterial genome editing. The efficient application of this technique requires the inactivation of the endogenous methyl-directed mismatch repair system that in turn leads to a drastically elevated genomic mutation rate and the consequent a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku105
更新日期：2014-04-01 00:00:00
abstract：:The cells of the bronchial epithelium of man are targets for benzo(a)pyrene carcinogenesis. When cultures of these cells, and of non-target fibroblasts, are exposed to [3H]-benzo(a)pyrene, we find that the epithelial cells metabolise and bind to DNA far greater amounts of benzpyrene than do fibroblasts. By analysis of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.5.1547
更新日期：1982-03-11 00:00:00
abstract：:The MalaCards human disease database (http://www.malacards.org/) is an integrated compendium of annotated diseases mined from 68 data sources. MalaCards has a web card for each of ∼20 000 disease entries, in six global categories. It portrays a broad array of annotation topics in 15 sections, including Summaries, Symp...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkw1012
更新日期：2017-01-04 00:00:00
abstract：:SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. Protein domain assignments for over 900 genomes are included in the database, which can be accessed at http://supfam.org/. Hidden Markov models ba...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn762
更新日期：2009-01-01 00:00:00
abstract：:Proteins perform biological functions through cascading interactions with each other by forming protein complexes. As a result, interactions among proteins, called protein-protein interactions (PPIs) are not completely free from selection constraint during evolution. Therefore, the identification and analysis of PPI c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky378
更新日期：2018-07-02 00:00:00
abstract：:Various oligonucleotides containing 8-methylguanine (m8G) have been synthesized and their structures and thermodynamic properties investigated. Introduction Of M8G into DNA sequences markedly stabilizes the Z conformation under low salt conditions. The hexamer d(CGC[M8G]CG)2 exhibits a CD spectrum characteristic of th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.7.1272
更新日期：1996-04-01 00:00:00
abstract：:Heterotrimeric eukaryotic/archaeal translation initiation factor 2 (e/aIF2) binds initiator methionyl-tRNA and plays a key role in the selection of the start codon on messenger RNA. tRNA binding was extensively studied in the archaeal system. The γ subunit is able to bind tRNA, but the α subunit is required to reach h...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1180
更新日期：2013-01-01 00:00:00
abstract：:Eukaryotic cells use numerous pathways to regulate RNA production, localization and stability. Several of these pathways are controlled by ribonucleases. The essential ribonuclease, Dis3, plays important roles in distinct RNA metabolic pathways. Despite much progress in understanding general characteristics of the Dis...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq295
更新日期：2010-09-01 00:00:00
abstract：:We present FIGfams, a new collection of over 100,000 protein families that are the product of manual curation and close strain comparison. Using the Subsystem approach the manual curation is carried out, ensuring a previously unattained degree of throughput and consistency. FIGfams are based on over 950,000 manually a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp698
更新日期：2009-11-01 00:00:00
abstract：:The GeneNet system is designed for collection and analysis of the data on gene and metabolic networks, signal transduction pathways and kinetic characteristics of elementary processes. In the past 2 years, the GeneNet structure was considerably improved: (i) the current version of the database is now implemented using...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki077
更新日期：2005-01-01 00:00:00
abstract：:The thermal denaturation spectra of E. coli 50s and 30s ribosomal sub units and of their isolated RNA's were studied over the wavelength range of 2300-3000 Angstrom. It was possible to fit the experimental denaturation spectra with super positions of the reference spectra for denaturation of A - U and G - C base pairs...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.3.373
更新日期：1975-03-01 00:00:00
abstract：:Ribosomal recruitment of cellular mRNAs depends on binding of eIF4F to the mRNA's 5'-terminal 'cap'. The minimal 'cap0' consists of N7-methylguanosine linked to the first nucleotide via a 5'-5' triphosphate (ppp) bridge. Cap0 is further modified by 2'-O-methylation of the next two riboses, yielding 'cap1' (m7GpppNmN) ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1321
更新日期：2014-03-01 00:00:00
abstract：:The cold shock domain is one of the most highly conserved motifs between bacteria and higher eukaryotes. Y-box-binding proteins represent a subfamily of cold shock domain proteins with pleiotropic functions, ranging from transcription in the nucleus to translation in the cytoplasm. These proteins have been investigate...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1077
更新日期：2014-12-01 00:00:00
abstract：:Insertion/deletion (indel) is one of the most common methods of protein sequence variation. Recent studies showed that indels could affect their flanking regions and they are important for protein function and evolution. Here, we describe the Indel Flanking Region Database (IndelFR, http://indel.bioinfo.sdu.edu.cn), w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1107
更新日期：2012-01-01 00:00:00
abstract：:Isogenic pluripotent stem cells are critical tools for studying human neurological diseases by allowing one to study the effects of a mutation in a fixed genetic background. Of particular interest are the spectrum of autism disorders, some of which are monogenic such as Timothy syndrome (TS); others are multigenic suc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv164
更新日期：2015-05-26 00:00:00
abstract：:To explain biochemical and genetic data on spontaneous nucleotide replacements in nucleic acid biosynthesis all the 8 mispairs in normal tautomeric forms have been considered. Possible B-conformations of DNA fragments containing each of such mispairs incorporated between Watson-Crick pairs have been found using comput...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.1.141
更新日期：1985-01-11 00:00:00
