Abstract:
:A series of plasmids were constructed in which a promoter was introduced into a lac-based operon fusion vector. A perfectly symmetrical oligonucleotide of 22-bp corresponding to an idealized binding site for cAMP receptor protein (CRP) of E. coli was chemically synthesized. The synthetic CRP site was placed between the promoter and the lacZ structural gene with varying distances from the promoter. Specific binding of cAMP-CRP complex to the synthetic CRP site was shown by a gel retardation and a DNase I footprinting assays. Plasmid constructs were transformed into crp+ and crp- cells carrying a chromosomal deletion of the lac genes. The regulatory effect of the inserted CRP site was examined by comparing the beta-galactosidase activity and the levels of RNA transcript in two cells harboring the plasmids. We found a strong inhibitory effect of the CRP site in the presence of cAMP and CRP when it was placed close to the promoter. When the CRP site was placed far downstream of the promoter, a moderate repression of transcription was observed.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Morita T,Shigesada K,Kimizuka F,Aiba Hdoi
10.1093/nar/16.15.7315subject
Has Abstractpub_date
1988-08-11 00:00:00pages
7315-32issue
15eissn
0305-1048issn
1362-4962journal_volume
16pub_type
杂志文章abstract::By transporting one DNA double helix (T-segment) through a double-strand break in another (G-segment), topoisomerase II reduces fractions of DNA catenanes, knots and supercoils to below equilibrium values. How DNA segments are selected to simplify the equilibrium DNA topology is enigmatic, and the biological relevance...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1037
更新日期:2014-02-01 00:00:00
abstract::Three-dimensional protein structures provide invaluable information for understanding and regulating biological functions of proteins. The GalaxyWEB server predicts protein structure from sequence by template-based modeling and refines loop or terminus regions by ab initio modeling. This web server is based on the met...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks493
更新日期:2012-07-01 00:00:00
abstract::Mixed-lineage leukemia (MLL) maintains the expression of cellular memory genes during development, while leukemic MLL fusion proteins aberrantly maintain expression of hematopoietic stem cell program genes such as HOXA9 to cause leukemia. However, the molecular mechanism of gene activation is unclear. Here we show tha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1394
更新日期:2014-04-01 00:00:00
abstract::This paper presents TurboFold II, an extension of the TurboFold algorithm for predicting secondary structures for multiple RNA homologs. TurboFold II augments the structure prediction capabilities of TurboFold by additionally providing multiple sequence alignments. Probabilities for alignment of nucleotide positions b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx815
更新日期:2017-11-16 00:00:00
abstract::The human gene for plasminogen activator inhibitor type-1 (PAI-1) has been isolated and its promoter region characterized. PAI-1 regulation by glucocorticoids, transforming growth factor-beta (TGF-beta) and the phorbol ester PMA is shown to be exerted at the promoter level. A fragment spanning 805 nucleotides of the 5...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.7.2805
更新日期:1988-04-11 00:00:00
abstract::We describe a dedicated RNA motif search program and web server to identify RNA riboswitches. The Riboswitch finder analyses a given sequence using the web interface, checks specific sequence elements and secondary structure, calculates and displays the energy folding of the RNA structure and runs a number of tests in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh352
更新日期:2004-07-01 00:00:00
abstract::Pds5 is required for sister chromatid cohesion, and somewhat paradoxically, to remove cohesin from chromosomes. We found that Pds5 plays a critical role during DNA replication that is distinct from its previously known functions. Loss of Pds5 hinders replication fork progression in unperturbed human and mouse cells. I...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky519
更新日期:2019-02-20 00:00:00
abstract::Single-walled carbon nanotubes (SWNTs) have been considered as the leading candidate for nanodevice applications ranging from gene therapy and novel drug delivery to membrane separations. The miniaturization of DNA-nanotube devices for biological applications requires fully understanding DNA-nanotube interaction mecha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl513
更新日期:2006-08-02 00:00:00
abstract::The mouse c-Ki-ras protooncogene promoter contains an unusual DNA element consisting of a 27 bp-long homopurine-homopyrimidine mirror repeat (H-motif) adjacent to a d(C-G)5 repeat. We have previously shown that in vitro these repeats may adopt H and Z conformations, respectively, causing nuclease and chemical hypersen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.16.3271
更新日期:1994-08-25 00:00:00
abstract::ADAR enzymes, adenosine deaminases that act on RNA, form a family of RNA editing enzymes that convert adenosine to inosine within RNA that is completely or largely double-stranded. Site-selective A-->I editing has been detected at specific sites within a few structured pre-mRNAs of metazoans. We have analyzed the edit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg681
更新日期:2003-08-15 00:00:00
abstract::Lens epithelium-derived growth factor/p75 (LEDGF/p75) is a transcriptional coactivator involved in stress response, autoimmune disease, cancer and HIV replication. A fusion between the nuclear pore protein NUP98 and LEDGF/p75 has been found in human acute and chronic myeloid leukemia and association of LEDGF/p75 with ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq410
更新日期:2010-10-01 00:00:00
abstract::Alternative splicing of a single pre-mRNA transcript can produce protein isoforms that promote either cell growth or death. Here we show that Ro-31-8220 (Ro), an apoptotic agent that inhibits protein kinase C and activates the c-Jun N terminal kinase, decreased the proportion of the cell growth-promoting Bcl-xL splice...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn207
更新日期:2008-06-01 00:00:00
abstract::A new way of studying RNA-protein complexes, using neutron small angle scattering in solution, is described and was applied in the case of the system, yeast valyl-tRNA synthetase, interacting with its cognate and non cognate yeast tRNAs. It was shown that, when limited amounts of tRNA (either cognate or non cognate) a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.7.2421
更新日期:1977-07-01 00:00:00
abstract::Transcription factors (TFs) are sequence-specific DNA-binding proteins acting as critical regulators of gene expression. The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN2.itps.ncku.edu.tw) provides an informative resource for detecting transcription factor binding sites (TFBSs), corresponding TFs, and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1035
更新日期:2016-01-04 00:00:00
abstract::RNA polymerase (RNAP) is a major target of gene regulation. Thermus thermophilus bacteriophage P23-45 encodes two RNAP binding proteins, gp39 and gp76, which shut off host gene transcription while allowing orderly transcription of phage genes. We previously reported the structure of the T. thermophilus RNAP•σA holoenz...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1162
更新日期:2018-01-09 00:00:00
abstract::T7 RNA polymerase promoters consist of a highly conserved 23 base-pair sequence that spans the site of the initiation of transcription (+1) and extends from -17 to +6. To determine the bases within the T7 consensus promoter that are essential for promoter function a library of mutant T7 promoters was constructed, and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.10.2517
更新日期:1992-05-25 00:00:00
abstract::Nucleosomes are the most abundant protein-DNA complexes in eukaryotes that provide compaction of genomic DNA and are implicated in regulation of transcription, DNA replication and repair. The details of DNA positioning on the nucleosome and the DNA conformation can provide key regulatory signals. Hydroxyl-radical foot...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx616
更新日期:2017-09-19 00:00:00
abstract::Structural information on interacting proteins is important for understanding life processes at the molecular level. Genome-wide docking database is an integrated resource for structural studies of protein-protein interactions on the genome scale, which combines the available experimental data with models obtained by ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp944
更新日期:2010-01-01 00:00:00
abstract::A novel method of determining the number of superhelical turns of a covalently-closed plasmid DNA is described. It relies on the determination of the hyperchromicity, and hence the proportion of unstacked basepairs, of a partially heat-denatured sample which co-migrates during electrophoresis with nicked circular dupl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.2.525
更新日期:1982-01-22 00:00:00
abstract::Chicken erythrocyte inner histones (H2A, H2B, H3 and H4) were associated with the two complementary homopolymeric polydeoxyribonucleotides and the two alternating copolymeric polydeoxyribonucleotides. No evidence for formation of chromatin-like structures was obtained for the complexes with poly(dG) . poly(dC) or poly...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.4.1387
更新日期:1979-04-01 00:00:00
abstract::The model mRNA (MR), 11-mer RNA containing two nitroxide spin labels at the 5'- and 3'-terminal nucleotides and prone to form a stable homodimer (MR)2, was used for Electron Paramagnetic Resonance study of structural rearrangements in mRNA occurring upon its binding to human 80S ribosomes. The formation of two differe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1136
更新日期:2018-01-25 00:00:00
abstract::Kinetically monitored, reverse transcriptase-initiated PCR (kinetic RT-PCR, kRT-PCR) is a novel application of kinetic PCR for high throughput transcript quantitation in total cellular RNA. The assay offers the simplicity and flexibility of an enzyme assay with distinct advantages over DNA microarray hybridization and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.2.e2
更新日期:2000-01-15 00:00:00
abstract::The synthesis of stable RNA in Mycoplasma capricolum was studied by [32P] labeling of cellular RNA of cells grown in a partially-defined medium in the presence or absence of an amino acid mixture supplement. The results indicate that M. capricolum employs the same stringent control mechanism used by E. coli cells, as ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.15.3641
更新日期:1981-08-11 00:00:00
abstract::Genome length complementary DNA (cDNA) transcripts were synthesized in vitro by using purified virions of a cloned isolate of mouse sarcoma virus (MSV Clone 124). The cDNA transcripts were converted to double-stranded form by utilizing DNase-digested calf thymus DNA primers and E. coli DNA polymerase I. Restriction en...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.5.1863
更新日期:1979-01-01 00:00:00
abstract::Previously, we developed jumping profile hidden Markov model (jpHMM), a new method to detect recombinations in HIV-1 genomes. The jpHMM predicts recombination breakpoints in a query sequence and assigns to each position of the sequence one of the major HIV-1 subtypes. Since incorrect subtype assignment or recombinatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp371
更新日期:2009-07-01 00:00:00
abstract::Gut-enriched Krüppel-like factor (GKLF or KLF4) is a pleiotropic (activating and repressive) transcription factor. This study characterizes the mechanisms of transactivation by GKLF. Using a GAL4 fusion assay, the activating domain of murine GKLF was localized to the 109 amino acid residues in the N-terminus. Site-dir...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.5.1106
更新日期:2000-03-01 00:00:00
abstract::Several different computational problems have been solved using DNA as a medium. However, the DNA computations that have so far been carried out have examined a relatively small number of possible sequence solutions in order to find correct sequence solutions. We have encoded a search algorithm in DNA that required th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.22.5203
更新日期:1998-11-15 00:00:00
abstract::MicroRNAs are small (approximately 22 nt) RNAs that regulate gene expression and play important roles in both normal and disease physiology. The use of microarrays for global characterization of microRNA expression is becoming increasingly popular and has the potential to be a widely used and valuable research tool. H...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn932
更新日期:2009-02-01 00:00:00
abstract::The 5'- and 3'-untranslated regions (5'- and 3'-UTRs) of eukaryotic mRNAs are known to play a crucial role in post-transcriptional regulation of gene expression modulating nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and stability. UTRdb is a specialized database of 5' and 3' unt...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.1.335
更新日期:2002-01-01 00:00:00
abstract::RNase J is a conserved ribonuclease that belongs to the β-CASP family of nucleases. It possesses both endo- and exo-ribonuclease activities, which play a key role in pre-rRNA maturation and mRNA decay. Here we report high-resolution crystal structures of Deinococcus radiodurans RNase J complexed with RNA or uridine 5'...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv444
更新日期:2015-06-23 00:00:00