Abstract:
:The proposition that the 2-amino group of guanine plays a critical role in determining how antibiotics recognise their binding sites in DNA has been tested by relocating it, using tyrT DNA derivative molecules substituted with inosine plus 2,6-diaminopurine (DAP). Irrespective of their mode of interaction with DNA, such GC-specific antibiotics as actinomycin, echinomycin, mithramycin and chromomycin find new binding sites associated with DAP-containing sequences and are excluded from former canonical sites containing I.C base pairs. The converse is found to be the case for a group of normally AT-selective ligands which bind in the minor groove of the helix, such as netropsin: their preferred sites become shifted to IC-rich clusters. Thus the binding sites of all these antibiotics strictly follow the placement of the purine 2-amino group, which accordingly must serve as both a positive and negative effector. The footprinting profile of the 'threading' intercalator nogalamycin is potentiated in DAP plus inosine-substituted DNA but otherwise remains much the same as seen with natural DNA. The interaction of echinomycin with sites containing the TpDAP step in doubly substituted DNA appears much stronger than its interaction with CpG-containing sites in natural DNA.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Bailly C,Waring MJdoi
10.1093/nar/23.6.885subject
Has Abstractpub_date
1995-03-25 00:00:00pages
885-92issue
6eissn
0305-1048issn
1362-4962pii
5b0002journal_volume
23pub_type
杂志文章abstract::The mRNAs for different variant surface antigens of Trypanosoma brucei start with the same 35 nucleotides. This sequence is encoded by a separate mini-exon, located in a 1.35-kb repetitive element. We have reported that trypanosomes contain many transcripts that hybridize to mini-exon probes, even if they do not make ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.9.3777
更新日期:1984-05-11 00:00:00
abstract::A simplified and economical method for the attachment of 2'-deoxyribo, ribo and arabinonucleosides onto long-chain alkylamidopropanoic acid controlled-pore glass (LCAAP-CPG, P-3) is described. In this procedure, 5'-O-tritylated nucleosides are coupled directly to LCAAP-CPG in excellent yields using 1-(3-dimethylaminop...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.13.3813
更新日期:1990-07-11 00:00:00
abstract::Gene set enrichment testing can enhance the biological interpretation of ChIP-seq data. Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene locus length (the length of the gene body and its surrounding non-coding sequence). Adjustment for gene locus length is necessary because ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku463
更新日期:2014-07-01 00:00:00
abstract::The nucleotide sequence of 5.8S rRNA from the Chinese silkworm Philosamia cynthia ricini has been determined by gel sequencing and mobility shift methods. The complete primary structure is (sequence in text). This is one of the largest known 5.8S rRNAs. As compared to Bombyx 5.8S rRNA, it is two nucleotides longer; t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.20.6383
更新日期:1982-10-25 00:00:00
abstract::The bacteriophage ø29 DNA packaging motor that assembles on the precursor capsid (prohead) contains an essential 174-nt structural RNA (pRNA) that forms multimers. To determine the structural features of the CE- and D-loops believed to be involved in multimerization of pRNA, 35- and 19-nt RNA molecules containing the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm874
更新日期:2008-02-01 00:00:00
abstract::TOP mRNAs are vertebrate transcripts which contain a 5'terminal oligopyrimidine tract (5'TOP), encode for ribosomal proteins and elongation factors 1alpha and 2, and are candidates for growth-dependent translational control mediated through their 5'TOP. In the present study we show that elongation factor 2 (EF2) mRNA ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.5.995
更新日期:1997-03-01 00:00:00
abstract::The advances of next-generation sequencing technology have facilitated metagenomics research that attempts to determine directly the whole collection of genetic material within an environmental sample (i.e. the metagenome). Identification of genes directly from short reads has become an important yet challenging probl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq747
更新日期:2010-11-01 00:00:00
abstract::Effective transcript profiling in animal systems requires isolation of homogenous tissue or cells followed by faithful mRNA amplification. Linear amplification based on cDNA synthesis and in vitro transcription is reported to maintain representation of mRNA levels, however, quantitative data demonstrating this as well...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.5.e29
更新日期:2001-03-01 00:00:00
abstract::During protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5A (a/eIF-5A) and in bacteria by the homologous protein EF-P. While a structure of EF-P bound to the 70S ribosome exists, structural insight into eIF-5A on ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1517
更新日期:2016-02-29 00:00:00
abstract::As an approach to gene therapy for the respiratory manifestations of cystic fibrosis (CF), in vivo plasmid-mediated direct transfer of the normal CF transmembrane conductance regulator (CFTR) gene to the airway epithelium was investigated in mice. To evaluate the feasibility of this strategy, pRSVL, a plasmid composed...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.12.3233
更新日期:1992-06-25 00:00:00
abstract::Primer design is a fundamental technique that is widely used for polymerase chain reaction (PCR). Although many methods have been proposed for primer design, they require a great deal of manual effort to generate feasible and valid primers, including homology tests on off-target sequences using BLAST-like tools. That ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv632
更新日期:2015-11-16 00:00:00
abstract::Nucleotide incorporation opposite an oxidative form of adenine, 2-hydroxyadenine (2-OH-Ade) was investigated. When a primed template with 2-OH-Ade was treated with an exonuclease-deficient Klenow fragment of Escherichia coli DNA polymerase I (KFexo-), recombinant rat DNA polymerase beta (pol beta) or calf thymus DNA p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.5.761
更新日期:1995-03-11 00:00:00
abstract::The database of molecular motions, MolMovDB (http://molmovdb.org), has been in existence for the past decade. It classifies macromolecular motions and provides tools to interpolate between two conformations (the Morph Server) and predict possible motions in a single structure. In 2005, we expanded the services offered...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj046
更新日期:2006-01-01 00:00:00
abstract::Foldback DNA, prepared from mouse and Scilla sibirica main band DNA, and from rye (Secale cereale) total DNA, was characterised by denaturation, renaturation, and electron microscopy. 3H-cRNA of this DNA was hybridised in situ to nuclei and chromosomes of the respective species. There is no universal labelling pattern...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.10.3589
更新日期:1978-10-01 00:00:00
abstract::Sequential chromatin immunoprecipitation (SeqChIP) is a procedure in which formaldehyde-crosslinked, protein-DNA complexes from living cells are subjected to two sequential immunoprecipitations with antibodies of different specificity. SeqChIP has been used to address, in a qualitative manner, whether two proteins can...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh148
更新日期:2004-11-01 00:00:00
abstract::The splicing factor Sam68 is upregulated in many human cancers, including prostate cancer (PCa) where it promotes cell proliferation and survival. Nevertheless, in spite of its frequent upregulation in cancer, the mechanism(s) underlying its expression are largely unknown. Herein, bioinformatics analyses identified th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz344
更新日期:2019-07-09 00:00:00
abstract::Transcriptional regulation of the delta-aminolevulinic acid synthetase gene of Rhizobium meliloti was investigated under conditions of normal vegetative growth and during symbiosis with the legume host alfalfa. S1 nuclease mapping and DNA sequence analysis indicated that transcription originates from two sites separat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.16.5965
更新日期:1985-08-26 00:00:00
abstract::Intragenomic and intergenomic comparisons of upstream nucleotide sequences of archaeal genes were performed with the goal of predicting transcription regulatory sites (operators) and identifying likely regulons. Learning sets for the detection of regulatory sites were constructed using the available experimental data ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.3.695
更新日期:2000-02-01 00:00:00
abstract::PRMT5 is an arginine methyltransferase that accounts for the vast majority of the symmetric methylation in cells. PRMT5 exerts its function when complexed with MEP50/WDR77. This activity is often elevated in cancer cells and correlates with poor prognosis, making PRMT5 a therapeutic target. To investigate the PRMT5 si...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz200
更新日期:2019-06-04 00:00:00
abstract::The binding of anti poly(I). poly (C) Fab fragments to double or triple stranded polynucletides has been studied by fluorescence. Association constants were deduced from competition experiments. The comparison of the association constants leads to the conclusion that several atoms of the base residues do not interact ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.12.3337
更新日期:1976-12-01 00:00:00
abstract::TERC is an RNA component of telomerase. However, TERC is also ubiquitously expressed in most human terminally differentiated cells, which don't have telomerase activity. The function of TERC in these cells is largely unknown. Here, we report that TERC enhances the expression and secretion of inflammatory cytokines by ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz584
更新日期:2019-09-05 00:00:00
abstract::Transfer RNAGlu4 was isolated from Drosophila melanogaster by affinity chromatography. The tRNA was iodinated "in vitro" with Na[25I] and hybridized "in situ" to salivary gland chromosomes from Drosophila. Subsequent autoradiography allowed the localization of the genes for tRNAGlu4 to the right arm of the second chro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.5.1465
更新日期:1978-05-01 00:00:00
abstract::Adenosine to inosine editing of mRNA from the human 5-HT2C receptor gene (HTR2C) occurs at five exonic positions (A-E) in a stable stem-loop that includes the normal 5' splice site of intron 5 and is flanked by two alternative splice sites. Using in vitro editing, we identified a novel editing site (F) located in the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh536
更新日期:2004-04-15 00:00:00
abstract::The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Stud...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw992
更新日期:2017-01-04 00:00:00
abstract::In an RNase III-deficient strain of E. coli 23S pre-rRNA accumulates unprocessed in 50S ribosomes and in polysomes. These ribosomes provide a substrate for the analysis of rRNA maturation in vitro. S1 nuclease protection analysis of the products obtained in in vitro processing reactions demonstrates that 23S rRNA proc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.14.5041
更新日期:1985-07-25 00:00:00
abstract::Recent advances in DNA-sequencing technology have made it possible to obtain large datasets of small RNA sequences. Here we demonstrate that not all non-perfectly matched small RNA sequences are simple technological sequencing errors, but many hold valuable biological information. Analysis of three small RNA datasets ...
journal_title:Nucleic acids research
pub_type: 杂志文章,meta分析
doi:10.1093/nar/gkp093
更新日期:2009-05-01 00:00:00
abstract::Isolated yeast mitochondria incorporate added UTP into RNA. Amongst the products formed are the two rRNAs, 4S RNA and several components presumed to be mRNAs. In omega+ strains (containing an intervening sequence in the 21S rRNA gene) besides mature 21S rRNA a transcript could be detected still containing nucleotide s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.23.6369
更新日期:1981-12-11 00:00:00
abstract::Infrared and UV spectroscopies have been used to study the assembly of a hairpin nucleotide sequence (nucleotides 3-30) of the 5' non-coding region of the hepatitis C virus RNA (5'-GGCGGGGAUUAUCCCCGCUGUGAGGCGG-3') with a RNA 20mer ligand (5'-CCGCCUCACAAAGGUGGGGU-3') in the presence of magnesium ion and spermidine. The...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.6.1333
更新日期:2002-03-15 00:00:00
abstract::Mariner transposition is a complex reaction that involves three recombination sites and six strand breaking and joining reactions. This requires precise spatial and temporal coordination between the different components to ensure a productive outcome and minimize genomic instability. We have investigated how the cleav...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku172
更新日期:2014-05-01 00:00:00
abstract::Use of antisense oligonucleotides is a versatile strategy for achieving control of gene expression. Unfortunately, the interpretation of antisense-induced phenotypes is sometimes difficult, and chemical modifications that improve the potency and specificity of antisense action would be useful. The introduction of lock...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf651
更新日期:2002-12-01 00:00:00