Abstract:
:Using a partially purified replication complex from tobacco chloroplasts, replication origins have been localized to minimal sequences of 82 (pKN8, positions 137 683-137 764) and 243 bp (pKN3, positions 130 513-130 755) for ori A and ori B respectively. Analysis of in vitro replication products by two-dimensional agarose gel electrophoresis showed simple Y patterns for single ori sequence-containing clones, indicative of rolling circle replication. Double Y patterns were observed when a chloroplast DNA template containing both ori s (pKN9) was tested. Dpn I analysis and control assays with Escherichia coli DNA polymerase provide a clear method to distinguish between true replication and DNA repair synthesis. These controls also support the reliability of this in vitro chloroplast DNA replication system. EM analysis of in vitro replicated products showed rolling circle replication intermediates for single ori clones (ori A or ori B), whereas D loops were observed for a clone (pKN9) containing both ori s. The minimal ori regions contain sequences which are capable of forming stem-loop structures with relatively high free energy and other sequences which interact with specific protein(s) from the chloroplast replication fraction. Apparently the minimal ori sequences reported here contain all the necessary elements for support of chloroplast DNA replication in vitro.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Kunnimalaiyaan M,Nielsen BLdoi
10.1093/nar/25.18.3681subject
Has Abstractpub_date
1997-09-15 00:00:00pages
3681-6issue
18eissn
0305-1048issn
1362-4962pii
gka585journal_volume
25pub_type
杂志文章abstract::We have constructed a complete, five-enzyme restriction map of the genome of the archaeon Halobacterium sp. GRB, based on a set of 84 overlapping cosmid clones. Fewer than 30 kbp, in three gaps, remain uncloned. The genome consists of five replicons: a chromosome (2038 kbp) and four plasmids (305, 90, 37, and 1.8 kbp)...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.8.1476
更新日期:1994-04-25 00:00:00
abstract::The P. falciparum pPFrep20 repetitive element from the Palo Alto Uganda strain has been isolated and sequenced. The Palo Alto pPFrep20 repeat (pPFPArep20) has a clustered subtelomeric location and on chromosome 1 has been deleted from one end. Analysis of chromosome 1 from 5 other strains has revealed that pPFrep20 se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.10.4331
更新日期:1988-05-25 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.6.1977
更新日期:1985-03-25 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.4.913
更新日期:1993-02-25 00:00:00
abstract::Many interacting proteins regulate and/or assist the activities of RAD51, a recombinase which plays a critical role in both DNA repair and meiotic recombination. Yeast two-hybrid screening of a human testis cDNA library revealed a new protein, RAD51AP2 (RAD51 Associated Protein 2), that interacts strongly with RAD51. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl665
更新日期:2006-01-01 00:00:00
abstract::In Saccharomyces cerevisiae, RNA polymerase II assembly is probably initiated by the formation of the RPB3-RPB11 heterodimer. RPB3 is encoded by a single copy gene in the yeast, mouse and human genomes. The RPB11 gene is also unique in yeast and mouse, but in humans a gene family has been identified that potentially e...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki672
更新日期:2005-06-24 00:00:00
abstract::In the filamentous cyanobacterium Anabaena sp. PCC 7120, the ferric uptake regulator FurA functions as a global transcriptional regulator. Despite several analyses have focused on elucidating the FurA-regulatory network, the number of target genes described for this essential transcription factor is limited to a handf...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku123
更新日期:2014-04-01 00:00:00
abstract::A comprehensive listing is made of posttranscriptionally modified nucleosides from RNA reported in the literature through mid-1994. Included are chemical structures, common names, symbols, Chemical Abstracts registry numbers (for ribonucleoside and corresponding base), Chemical Abstracts Index Name, phylogenetic sourc...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/22.12.2183
更新日期:1994-06-25 00:00:00
abstract::We have sequenced 14 introns from the ciliate Tetrahymena thermophila and include these in an analysis of the 27 intron sequences available from seven T. thermophila protein-encoding genes. Consensus 5' and 3' splice junctions were determined and found to resemble the junctions of other nuclear pre-mRNA introns. Uniqu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.17.5133
更新日期:1990-09-11 00:00:00
abstract::The cDNA of human DNA polymerase delta was cloned. The cDNA had a length of 3.5 kb and encoded a protein of 1107 amino acid residues with a calculated molecular mass of 124 kDa. Northern blot analysis showed that the cDNA hybridized to a mRNA of 3.4 kb. Monoclonal and polyclonal antibodies to the C-terminal 20 residue...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.4.735
更新日期:1992-02-25 00:00:00
abstract::Riboswitches are RNA-based regulatory devices that mediate ligand-dependent control of gene expression. However, there has been limited success in rationally designing riboswitches. Moreover, most previous riboswitches are confined to a particular gene and only perform one-way regulation. Here, we used a library scree...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr609
更新日期:2011-10-01 00:00:00
abstract::Cell surface mannose 6-phosphate/insulin-like growth factor II receptors (M6P/IGF2R) bind and target exogenous insulin-like growth factor II (IGF2) to the prelysosomes where it is degraded. Loss of heterozygosity (LOH) for M6P/IGF2R is found in cancers, with mutational inactivation of the remaining allele. We exploite...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj468
更新日期:2006-01-23 00:00:00
abstract::Escherichia coli Exonuclease I (ExoI) digests single-stranded DNA (ssDNA) in the 3'-5' direction in a highly processive manner. The crystal structure of ExoI, determined previously in the absence of DNA, revealed a C-shaped molecule with three domains that form a central positively charged groove. The active site is a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt278
更新日期:2013-06-01 00:00:00
abstract::In many organisms (e.g., gram-positive eubacteria) Gin-tRNA is not formed by direct glutaminylation of tRNAGln but by a specific transamidation of Glu-tRNAGln. We wondered whether a similar transamidation pathway also operates in the formation of Asn-tRNA in these organisms. Therefore we tested in S-100 preparations o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.14.2648
更新日期:1996-07-15 00:00:00
abstract::Multiple myeloma, the second most frequent hematologic tumor after lymphomas, is an incurable cancer. Recent sequencing efforts have identified the ribonuclease DIS3 as one of the most frequently mutated genes in this disease. DIS3 represents the catalytic subunit of the exosome, a macromolecular complex central to th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv387
更新日期:2015-05-26 00:00:00
abstract::Increasing evidence indicates that active DNA demethylation is involved in several processes in mammals, resulting in developmental stage-specificity and cell lineage-specificity. The recently discovered Ten-Eleven Translocation (TET) dioxygenases are accepted to be involved in DNA demethylation by initiating 5-mC oxi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1019
更新日期:2014-02-01 00:00:00
abstract::The delivery of site-specific post-translational modifications to histones generates an epigenetic regulatory network that directs fundamental DNA-mediated processes and governs key stages in development. Methylation of histone H4 lysine-20 has been implicated in DNA repair, transcriptional silencing, genomic stabilit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt776
更新日期:2014-01-01 00:00:00
abstract::Large-scale automatic annotation of protein sequences remains challenging in postgenomics era. E1DS is designed for annotating enzyme sequences based on a repository of 1D signatures. The employed sequence signatures are derived using a novel pattern mining approach that discovers long motifs consisted of several sequ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn324
更新日期:2008-07-01 00:00:00
abstract::The bacterial transcription terminator, Rho, terminates transcription at half of the operons. According to the classical model derived from in vitro assays on a few terminators, Rho is recruited to the transcription elongation complex (EC) by recognizing specific sites (rut) on the nascent RNA. Here, we explored the m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku690
更新日期:2014-09-01 00:00:00
abstract::The nucleotide sequence of a 2.14 kb fragment of Bacillus subtilis DNA containing the citG gene encoding fumarase was determined using the dideoxy chain termination method. The citG coding region of 1392 base pairs (464 codons) was identified, and the deduced Mr (50425) is in good agreement with that of the protein id...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.1.131
更新日期:1985-01-11 00:00:00
abstract::The human lymphoid cell lines Walker and Daudi constitute a particularly suitable system for studies on the chromatin structure of K light chain genes (see preceding paper). The rearranged and non-rearranged alleles of Walker cells were found to be about equally sensitive towards digestion with DNAase I. A DNAase I hy...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.18.7007
更新日期:1984-09-25 00:00:00
abstract::We describe a versatile genetic system for rapid analysis of mammalian gene function. In this, loss of reporter activity in a novel embryonic stem (ES) cell line enables rapid identification of targeting to the ubiquitously expressed Rosa26 locus. Subsequent regulation of gene activity is governed by a dual regulatory...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni146
更新日期:2005-10-12 00:00:00
abstract::We show that nucleic acid structures may be conveniently and inexpensively characterized by their UV thermal difference spectra. A thermal difference spectrum (TDS) is obtained for a nucleic acid by simply recording the ultraviolet absorbance spectra of the unfolded and folded states at temperatures above and below it...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni134
更新日期:2005-09-12 00:00:00
abstract::HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G downward arrowCGC in DNA. We report three structures of HinP1I-DNA complexes: in the presence of Ca(2+) (pre-reactive complex), in the absence of metal ion (binary complex) and in the presence of Mg(2+) (post-reactive complex). HinP1I forms a bac...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj484
更新日期:2006-02-09 00:00:00
abstract::We have sequenced mouse tRNA genes from two recombinant lambda phage. An 1800 bp sequence from one phage contains 3 tRNA genes, potentially encoding tRNAAsp, tRNAGly, and tRNAGlu, separated by spacer sequences of 587 bp and 436 bp, respectively. The mouse tRNA gene cluster is homologous to a rat sequence (Sekiya et al...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.24.8761
更新日期:1983-12-20 00:00:00
abstract::A cDNA clone named 1A11 was isolated in a screen for genes that are activated by both mesoderm inducing factors FGF and activin in animal explants of Xenopus laevis embryos. In undisturbed embryos, 1A11 is expressed during the gastrula stage in the entire marginal zone where mesoderm originates, and later in the somit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.10.2375
更新日期:1993-05-25 00:00:00
abstract::p16 is a key regulator of cellular senescence, yet the drivers of this stable state of proliferative arrest are not well understood. Here, we identify 22 senescence-associated microRNAs (SA-miRNAs) in normal human mammary epithelial cells. We show that SA-miRNAs-26b, 181a, 210 and 424 function in concert to directly r...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2014-02-01 00:00:00
abstract::The growing application of gene expression profiling demands powerful yet user-friendly bioinformatics tools to support systems-level data understanding. NetworkAnalyst was first released in 2014 to address the key need for interpreting gene expression data within the context of protein-protein interaction (PPI) netwo...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2019-07-02 00:00:00
abstract::MicA is a trans-encoded small non-coding RNA, which downregulates porin-expression in stationary-phase. In this work, we focus on the role of endoribonucleases III and E on Salmonella typhimurium sRNA MicA regulation. RNase III is shown to regulate MicA in a target-coupled way, while RNase E is responsible for the con...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1239
更新日期:2011-04-01 00:00:00
abstract::The Class 3 aldehyde dehydrogenase gene (ALDH-3) is differentially expressed. Expression is either constitutive or xenobiotic inducible via an aromatic hydrocarbon (Ah) receptor-mediated pathway, depending upon the tissue. A series of studies were performed to examine the regulation of rat ALDH-3 basal expression. DNa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.21.4185
更新日期:1996-11-01 00:00:00