Abstract：
:Binding of the DnaA protein to oriC leads to DNA melting within the DNA unwinding element (DUE) and initiates replication of the bacterial chromosome. Helicobacter pylori oriC was previously identified as a region localized upstream of dnaA and containing a cluster of DnaA boxes bound by DnaA protein with a high affinity. However, no unwinding within the oriC sequence has been detected. Comprehensive in silico analysis presented in this work allowed us to identify an additional region (oriC2), separated from the original one (oriC1) by the dnaA gene. DnaA specifically binds both regions, but DnaA-dependent DNA unwinding occurs only within oriC2. Surprisingly, oriC2 is bound exclusively as supercoiled DNA, which directly shows the importance of the DNA topology in DnaA-oriC interactions, similarly as previously presented only for initiator-origin interactions in Archaea and some Eukaryota. We conclude that H. pylori oriC exhibits bipartite structure, being the first such origin discovered in a Gram-negative bacterium. The H. pylori mode of initiator-oriC interactions, with the loop formation between the subcomplexes of the discontinuous origin, resembles those discovered in Bacillus subtilis chromosome and in many plasmids, which might suggest a similar way of controlling initiation of replication.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Donczew R,Weigel C,Lurz R,Zakrzewska-Czerwinska J,Zawilak-Pawlik Adoi
10.1093/nar/gks742subject
Has Abstractpub_date
2012-10-01 00:00:00pages
9647-60issue
19eissn
0305-1048issn
1362-4962pii
gks742journal_volume
40pub_type
杂志文章abstract：:Explicit solvent molecular dynamics (MD) simulations were carried out for sarcin-ricin domain (SRD) motifs from 23S (Escherichia coli) and 28S (rat) rRNAs. The SRD motif consists of GAGA tetraloop, G-bulged cross-strand A-stack, flexible region and duplex part. Detailed analysis of the overall dynamics, base pairing, ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkj470
更新日期：2006-02-02 00:00:00
abstract：:To address how eukaryotic replication forks respond to fork stalling caused by strong non-covalent protein-DNA barriers, we engineered the controllable Fob-block system in Saccharomyces cerevisiae. This system allows us to strongly induce and control replication fork barriers (RFB) at their natural location within the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt051
更新日期：2013-03-01 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：:Long terminal repeat (LTR)-retrotransposons comprise a significant portion of the rice genome. Their complete characterization is thus necessary if the sequenced genome is to be annotated correctly. In addition, because LTR-retrotransposons can influence the expression of neighboring genes, the complete identification...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl780
更新日期：2007-01-01 00:00:00
abstract：:Numerous examples exist of how disrupting the actions of physiological regulators of blood cell development yields hematologic malignancies. The master regulator of hematopoietic stem/progenitor cells GATA-2 was cloned almost 20 years ago, and elegant genetic analyses demonstrated its essential function to promote hem...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gks281
更新日期：2012-07-01 00:00:00
abstract：:Successful development of biological databases requires accommodation of the burgeoning amounts of data from high-throughput genomics pipelines. As the volume of curated data in Animal QTLdb (https://www.animalgenome.org/QTLdb) increases exponentially, the resulting challenges must be met with rapid infrastructure dev...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1084
更新日期：2019-01-08 00:00:00
abstract：:The Pathway Tools cellular overview diagram is a visual representation of the biochemical network of an organism. The overview is automatically created from a Pathway/Genome Database describing that organism. The cellular overview includes metabolic, transport and signaling pathways, and other membrane and periplasmic...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl334
更新日期：2006-08-07 00:00:00
abstract：:CAG repeats occur predominantly in the coding regions of human genes, which suggests their functional importance. In some genes, these sequences can undergo pathogenic expansions leading to neurodegenerative polyglutamine (poly-Q) diseases. The mutant transcripts containing expanded CAG repeats possibly contribute to ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq700
更新日期：2010-12-01 00:00:00
abstract：:We took advantage of the unusual genomic organization of the ciliate Oxytricha trifallax to screen for eukaryotic non-coding RNA (ncRNA) genes. Ciliates have two types of nuclei: a germ line micronucleus that is usually transcriptionally inactive, and a somatic macronucleus that contains a reduced, fragmented and rear...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr501
更新日期：2011-09-01 00:00:00
abstract：:We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 μs) with the aim to study folding landscapes of the rGGGUUAGGG and rGGGAGGG parallel G-hairpins (PH) with propeller loop. We identify folding and unfolding pathways of the PH, which is bridged ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky712
更新日期：2018-09-28 00:00:00
abstract：:Two of the tRNA's found in rabbit reticulocytes are substrates for a post-transcriptional modification leading to the incorporation of guanine into the polynucleotide chain. The major guanylated tRNA was previously identified as tRNA (His). In the present report we show that the minor guanylated tRNA is tRNA (Asn), an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.10.2521
更新日期：1976-10-01 00:00:00
abstract：:The transcription factor HIV-TF1, which binds to a region about 60 bp upstream from the enhancer of the human immunodeficiency virus-1 (HIV-1), was purified from human B cells. HIV-TF1 had a molecular weight of 39,000. Binding of HIV-TF1 to the HIV long terminal repeat (LTR) activated transcription from the HIV promot...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.17.4689
更新日期：1991-09-11 00:00:00
abstract：:We have studied the effect of temperature on transcription initiation in vitro at two related promoters ga/Pcon and ga/P1, which have the same nucleotide sequence around the -10 region and transcription start site, but differ in upstream sequences. One of the promoters, ga/Pcon, carries the consensus -35 hexamer, 5'TT...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.22.6113
更新日期：1991-11-25 00:00:00
abstract：:The anticancer drug cisplatin reacts with DNA leading to the formation of interstrand and intrastrand cross-links that are the critical cytotoxic lesions. In contrast to cells bearing mutations in other components of the nucleotide excision repair apparatus (XPB, XPD, XPG and CSB), cells defective for the ERCC1-XPF st...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf479
更新日期：2002-09-01 00:00:00
abstract：:Despite the increasing wealth of available data, the structure of cancer transcriptional space remains largely unknown. Analysis of this space would provide novel insights into the complexity of cancer, assess relative implications in complex biological processes and responses, evaluate the effectiveness of cancer mod...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr533
更新日期：2011-10-01 00:00:00
abstract：:We report here spectroscopic and biochemical data of a novel series of sugar-modified oligodeoxy-nucleotides, the carbocyclic oligothymidylates, c(dT)3-20. In c(dT)n a methylene group has been substituted for the oxygen atom of the deoxyribose ring of the natural thymidylate unit. c(dT)10-20 form helical structures, i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.8.2133
更新日期：1990-04-25 00:00:00
abstract：:Tetramers of the arginine-rich histones H3 and H4 associate with supercoiled SV40 DNA either singly, giving tetrameric nucleoprotein complexes or in pairs giving octameric complexes, both of which are visualized as beads in the electron microscope. The relative amounts of the two complexes may be revealed by complete ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/7.3.611
更新日期：1979-10-10 00:00:00
abstract：:Stability of aromatic phosphoramidates was studied using 2',3'-O-dibenzoyluridine 5'-phosphoramidates and N,2',3'-O-tribenzoylcytidine 5'-phosphate. The effect of dicyclohexylcarbodiimide in this mixture was investigated. Decomposition of the anilidate was slower in the presence of DCC. Substituted anilidates of uridi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/1.2.223
更新日期：1974-02-01 00:00:00
abstract：:In this paper, we present evidence that an efficient Rho-dependent terminator can be created by introducing a simple (AG/TC) n DNA repeat into a transcription unit. The Rho termination activity in vivo and in vitro is dependent on the length and the orientation of the insert. The transcription of at least 30 bp of the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.21.4895
更新日期：1998-11-01 00:00:00
abstract：:Single-molecule force spectroscopy provides insight into how proteins bind to and move along DNA. Such studies often embed a single-stranded (ss) DNA region within a longer double-stranded (ds) DNA molecule. Yet, producing these substrates remains laborious and inefficient, particularly when using the traditional thre...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx761
更新日期：2017-10-13 00:00:00
abstract：:G-quadruplex (G4) DNA structures can form physical barriers within the genome that must be unwound to ensure cellular genomic integrity. Here, we report unanticipated roles for the Escherichia coli Rep helicase and RecA recombinase in tolerating toxicity induced by G4-stabilizing ligands in vivo. We demonstrate that R...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa442
更新日期：2020-07-09 00:00:00
abstract：:The small proline-rich protein genes ( SPRRs ) code for precursors of the cornified cell envelope, and are specifically expressed during keratinocyte terminal differentiation. The single intron of SPRR2A enhanced the activity of the SPRR2A promoter in transient transfection assays. This enhancement was position depend...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.23.5288
更新日期：1998-12-01 00:00:00
abstract：:Specific nucleic acid sequences can be detected in individual cells by in situ hybridization. However, when very few copies of a target sequence are present per cell, its signal is undetectable by flow cytometry. Although various approaches have been developed to increase fluorescence signals for in situ hybridization...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa515
更新日期：2020-09-04 00:00:00
abstract：:Multicellular organismal development is controlled by a complex network of transcription factors, promoters and enhancers. Although reliable computational and experimental methods exist for enhancer detection, prediction of their target genes remains a major challenge. On the basis of available literature and ChIP-seq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1081
更新日期：2011-04-01 00:00:00
abstract：:Denaturing gradient gel electrophoresis (DGGE) is based upon the different melting behaviors of DNA molecules in a chemical denaturant gradient according to their sequences. This technique has recently become a widespread tool to detect mutations. The introduction of a GC-clamp enables the detection of most single bas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.12.3331
更新日期：1991-06-25 00:00:00
abstract：:BIOSMILE web search (BWS), a web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object, location, manner, time, etc. After receiving keyword query input, BWS retrieves matching PubMed abstracts and lists them along ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn319
更新日期：2008-07-01 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 report the development of a new database of technology services and products for analysis of biobank samples in biomedical research. BARCdb, the Biobanking Analysis Resource Catalogue (http://www.barcdb.org), is a freely available web resource, listing expertise and molecular resource capabilities of research centr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1008
更新日期：2015-01-01 00:00:00
abstract：:An effective tool for the global analysis of both DNA methylation status and protein-chromatin interactions is a microarray constructed with sequences containing regulatory elements. One type of array suited for this purpose takes advantage of the strong association between CpG Islands (CGIs) and gene regulatory regio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki582
更新日期：2005-05-23 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
