Abstract:
:Topoisomerases are ubiquitous proteins found in all three domains of life. They change the topology of DNA via transient breaks on either one or two of the DNA strands to allow passage of another single or double DNA strand through the break. Topoisomerases are classified into two types: type I enzymes cleave one DNA strand and pass either one or two DNA strands through the break before resealing it, while type II molecules cleave both DNA strands in concert and pass another double strand through the break followed by religation of the double strand break. Here we review recent work on the structure of type I enzymes. These structural studies are providing atomic details that, together with the existing wealth of biochemical and biophysical data, are bringing our understanding of the mechanism of action of these enzymes to the atomic level.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Baker NM,Rajan R,Mondragón Adoi
10.1093/nar/gkn1009subject
Has Abstractpub_date
2009-02-01 00:00:00pages
693-701issue
3eissn
0305-1048issn
1362-4962pii
gkn1009journal_volume
37pub_type
杂志文章,评审abstract::Planarian flatworms are in the midst of a renaissance as a model system for regeneration and stem cells. Besides two well-studied model species, hundreds of species exist worldwide that present a fascinating diversity of regenerative abilities, tissue turnover rates, reproductive strategies and other life history trai...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1148
更新日期:2016-01-04 00:00:00
abstract::Motif3D is a web-based protein structure viewer designed to allow sequence motifs, and in particular those contained in the fingerprints of the PRINTS database, to be visualised on three-dimensional (3D) structures. Additional functionality is provided for the rhodopsin-like G protein-coupled receptors, enabling finge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg534
更新日期:2003-07-01 00:00:00
abstract::PPARγ2 is a critical lineage-determining transcription factor that is essential for adipogenic differentiation. Here we report characterization of the three-dimensional structure of the PPARγ2 locus after the onset of adipogenic differentiation and the mechanisms by which it forms. We identified a differentiation-depe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw129
更新日期:2016-06-20 00:00:00
abstract::The molecular organization of the dunce gene of Drosophila melanogaster has proved to be particularly complex, with two divergently transcribed genes, Sgs-4 and Pig-1, nested within its 79 kb intron (1). Here we report the identification and the molecular characterization of a third gene nested within the transcriptio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.19.5837
更新日期:1990-10-11 00:00:00
abstract::Accurate T-cell epitope prediction is a principal objective of computational vaccinology. As a service to the immunology and vaccinology communities at large, we have implemented, as a server on the World Wide Web, a partial least squares-based multivariate statistical approach to the quantitative prediction of peptid...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg510
更新日期:2003-07-01 00:00:00
abstract::DNA synthesized by in vitro transcription on rat interferon (IFN) mRNA has been cloned and amplified as recombinant DNA. The nucleotide sequence of these rat IFN cDNA clones revealed i. the partial presence of the coding region of the gene and ii all cDNA clones were derived from the same subtype of rat IFN-alpha mRNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.2.1227
更新日期:1984-01-25 00:00:00
abstract::Sequencing of the 3'-untranslated region of the CCT8 gene of the fungal pathogen Candida albicans revealed that the CCT8 coding region overlaps 13 bp with the coding region of the convergently orientated TRP1 gene. The same overlap was found in three strains with different genetic backgrounds. 3'-RACE was used to dete...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.22.5061
更新日期:1998-11-15 00:00:00
abstract::Full-length cDNA of the 6.3 kb turnip yellow mosaic virus (TYMV) genome was placed between a T7 promoter and a unique Hind III site. In vitro transcription of Hind III-linearized DNA of clone pTYMC yielded full-length RNA transcripts. In inoculations of Chinese cabbage protoplasts and plants, capped transcripts and vi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.12.4675
更新日期:1989-06-26 00:00:00
abstract::We have developed a PCR-based short interfering RNA (siRNA) quantification method based on competition between siRNA and a homologous DNA primer for annealing to template DNA, avoiding the requirement for prior conversion of RNA to cDNA. Primers and probe were designed to amplify regions of the human papillomavirus E6...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn903
更新日期:2009-01-01 00:00:00
abstract::Model single base extension (SBE) genotyping reactions with individual deoxy-, dideoxy- and acyclonucleoside triphosphates are monitored by MALDI-TOF mass spectrometry. Three non-proofreading DNA polymerases display remarkably high misincorporation (up to 64% of correct incorporation) when extending primers with singl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng007
更新日期:2003-02-01 00:00:00
abstract::Mitochondrial proteins remain the subject of intense research interest due to their implication in an increasing number of different conditions including mitochondrial and metabolic disease, cancer, and neuromuscular degenerative and age-related disorders. However, the mitochondrial proteome has yet to be accurately a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1001
更新日期:2016-01-04 00:00:00
abstract::Using a powerful computer-assisted analysis strategy, a large-scale search of small nucleolar RNA (snoRNA) genes in the recently released draft sequence of the rice genome was carried out. This analysis identified 120 different box C/D snoRNA genes with a total of 346 gene variants, which were predicted to guide 135 2...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg373
更新日期:2003-05-15 00:00:00
abstract::Abasic substitutions in the non-template strand and promoter sequence changes were made to assess the roles of various promoter features in sigma70 holoenzyme interactions with fork junction probes. Removal of -10 element non-template single strand bases, leaving the phosphodiester backbone intact, did not interfere w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg400
更新日期:2003-06-01 00:00:00
abstract::Unlike most yeast ribosomal protein genes studied so far the genes coding for S24 and L46 are adjacent on the genome. Sequence analysis showed that the two genes are transcribed divergently, their initiation codons being 630 bp apart. Taking the respective ATG translation start sites as reference points, the 5'- end o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.3.701
更新日期:1985-02-11 00:00:00
abstract::The photostability and narrow emission spectra of non-organic quantum dot fluorophores (QDs) make them desirable candidates for fluorescent in situ hybridization (FISH) to study the expression of specific mRNA transcripts. We developed a novel method for direct QD labeling of modified oligonucleotide probes through st...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni162
更新日期:2005-10-13 00:00:00
abstract::A vexing difficulty of the RNA world hypothesis is how RNA molecules of significant complexity could ever have evolved given their susceptibility to degradation. One way degradation might have been reduced is through low temperature. Here we report that truncated and fragmented derivatives of the hairpin ribozyme can ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh601
更新日期:2004-05-25 00:00:00
abstract::A repeated sequence element which is located about 200 nucleotides upstream from the protein-coding portion of the muscle actin gene (probably within a large 5' intron) in the genome of the sea urchin, Strongylocentrotus purpuratus has been characterized, and shown to contain the sequence features which indicate that ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.4.1431
更新日期:1988-02-25 00:00:00
abstract::COMPASS is a method for homology detection and local alignment construction based on the comparison of multiple sequence alignments (MSAs). The method derives numerical profiles from given MSAs, constructs local profile-profile alignments and analytically estimates E-values for the detected similarities. Until now, CO...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm293
更新日期:2007-07-01 00:00:00
abstract::We present a general method for isolating molecular markers specific to any region of a chromosome using existing mapping populations. Two pools of DNA from individuals homozygous for opposing alleles for a targeted chromosomal interval, defined by two or more linked RFLP markers, are constructed from members of an ex...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.23.6553
更新日期:1991-12-11 00:00:00
abstract::Chelation of divalent cations by 5 mM EDTA and subsequent removal by dialysis from a cytoplasmic HeLa cell extract leads to a complete loss of 5S rRNA transcription without affecting tRNA synthesis. Transcription complexes for 5S RNA can no longer be assembled in such a zinc-depleted extract and this ability can be fu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.23.8971
更新日期:1984-12-11 00:00:00
abstract::An adequate supply of nucleotides is essential for DNA replication and DNA repair. Moreover, inhibition of TTP synthesis can cause cell death by a poorly characterized mechanism called thymine-less death. In the yeast Saccharomyces cerevisiae, the genes encoding thymidylate synthetase (CDC21) and thymidylate kinase (C...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki219
更新日期:2005-01-28 00:00:00
abstract::cDNA cloning is a central technology in molecular biology. cDNA sequences are used to determine mRNA transcript structures, including splice junctions, open reading frames (ORFs) and 5'- and 3'-untranslated regions (UTRs). cDNA clones are valuable reagents for functional studies of genes and proteins. Expressed Sequen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni184
更新日期:2005-12-02 00:00:00
abstract::Proline-rich protein (PRP) gene MP6 was isolated from a mouse BALB/c genomic DNA library in lambda EMBL3, characterised by hybridisation and restriction mapping and the promoter region, from -162 to +72 around the PRP consensus cap-site, was sequenced. In gel shift assays this region formed complexes C1 and C2 with pa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.19.5205
更新日期:1991-10-11 00:00:00
abstract::The nucleotide sequence of the faeD gene of Escherichia coli and the amino acid sequence of its product is presented. The faeD product is an outer membrane protein required for transport of K88ab fimbrial subunits across the outer membrane. The protein is synthesized as a precursor containing a signal peptide, and the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.6.2443
更新日期:1986-03-25 00:00:00
abstract::Proper expression of the genes of the human beta-globin gene locus requires the associated locus control region (LCR). Structurally, the LCR is defined by the presence of four domains of erythroid-specific chromatin structure. These domains, which have been characterized as DNase I hypersensitive sites (HSs), comprise...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.24.5684
更新日期:1998-12-15 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::A sixty base pair DNA duplex containing the nucleotide sequence of the bacteriophage T5 early (T5P25) promoter has been constructed using a combination of chemical synthesis and enzymatic methods. Subsequent to cloning into pBR322, the promoter has been demonstrated to be biologically active being capable of directing...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.17.5921
更新日期:1983-09-10 00:00:00
abstract::Clones carrying sequences expressed at altered abundance levels in dunce mutants were isolated by differentially screening a genomic library with cDNA probes representing the RNA population from dunce+ flies and the RNA population from dunce mutant flies. These mutants have an elevated cAMP content, so some isolates p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.20.8313
更新日期:1989-10-25 00:00:00
abstract::Interactions between subunits in the Saccharomyces cerevisiae ribosome are mediated by universal and eukaryote-specific intersubunit bridges. Universal bridges are positioned close to the ribosomal functional centers, while eukaryote-specific bridges are mainly located on the periphery of the ribosome. Two bridges, eB...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1083
更新日期:2019-01-10 00:00:00
abstract::We developed a framework for quick and reliable construction of complex gene circuits for genetically engineering mammalian cells. Our hierarchical framework is based on a novel nucleotide addressing system for defining the position of each part in an overall circuit. With this framework, we demonstrate construction o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt605
更新日期:2013-09-01 00:00:00