Abstract:
:The replication origin (oriC) of the Escherichia coli chromosome has been cloned and the region essential for chromosomal replication has been delimited to 245 base pairs. In previous studies the ability of recombinants between oriC and ColE1-type vectors, to transform E. coli polA- strains was used to determine which nucleotides in oriC are essential for replication. In this paper we have used a different approach by isolating partial defective replication mutants of a minichromosome (pCM959) that contains oriC as the single replication origin. Our results demonstrate that many mutations are allowed within oriC that do not affect oriC function as measured by the ability to transform E. coli polA- strains. In the minimal oriC region we detected 8 mutations at positions that are conserved in the sequence of six bacterial origins. The implications of these results on previous work will be discussed. Our data also demonstrate that a mutation producing an oriC- phenotype may be suppressed by secondary mutations. An E. coli strain was found that facilitates the isolation of partially defective minichromosomes. The results with this strain indicate a specific function of the sequence surrounding the base pair at position 138.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Stuitje AR,Meijer Mdoi
10.1093/nar/11.22.8007subject
Has Abstractpub_date
1983-11-25 00:00:00pages
8007-18issue
22eissn
0305-1048issn
1362-4962journal_volume
11pub_type
杂志文章abstract::The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1044
更新日期:2012-01-01 00:00:00
abstract::TATA-binding protein (TBP) is central to the regulation of eukaryotic transcription initiation. Recruitment of TBP to target genes can be positively regulated by one of two basal transcription factor complexes: SAGA or TFIID. Negative regulation of TBP promoter association can be performed by Mot1p or the NC2 complex....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr784
更新日期:2012-02-01 00:00:00
abstract::In 4M NaCl solutions (dC-dG)n (n = 3,4; approximately 9 mM) exist as a mixture o +/- B and Z forms. The low and high field components of two 31P NMR resonances originating from internal phosphodiester groups are assigned to the GpC and CpG linkages, respectively. Low temperatures stabilize the Z-forms, which completel...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.11.4625
更新日期:1984-06-11 00:00:00
abstract::Nucleotide sequences of three cloned restriction fragments of Tetrahymena mtDNA which showed hybridization with mitochondrial tRNA have been determined. EcoRI fragment 5 (4.1 kbp) contains the tRNAphe gene sequence with anticodon GAA; Hind III fragment 6 (2.0 kbp) the tRNAhis with anticodon GTG; and EcoRI fragment 7 (...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.9.3273
更新日期:1985-05-10 00:00:00
abstract::The protein property prediction and testing database (PPT-DB) is a database housing nearly 30 carefully curated databases, each of which contains commonly predicted protein property information. These properties include both structural (i.e. secondary structure, contact order, disulfide pairing) and dynamic (i.e. orde...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm800
更新日期:2008-01-01 00:00:00
abstract::We present a www server for AUGUSTUS, a novel software program for ab initio gene prediction in eukaryotic genomic sequences. Our method is based on a generalized Hidden Markov Model with a new method for modeling the intron length distribution. This method allows approximation of the true intron length distribution m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh379
更新日期:2004-07-01 00:00:00
abstract::Native nucleotides show a hyperbolic concentration dependence of the pre-steady-state rate of incorporation while maintaining concentration-independent amplitude due to fast, largely irreversible pyrophosphate release. The kinetics of 3'-azido-2',3'-dideoxythymidine (AZT) incorporation exhibit an increase in amplitude...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm695
更新日期:2007-01-01 00:00:00
abstract::To investigate the mechanism of N4-aminocytidine-induced mutagenesis, N'-alkyl-N4-aminocytidines and N4-alkyl-N4-aminocytidines were prepared and their mutagenicity on bacteria were assayed. N'-Methyl-N4-aminocytidine, N'-(2-hydroxyethyl)-N4-aminocytidine and N',N'-dimethyl-N4-aminocytidine showed direct-acting mutage...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.24.8893
更新日期:1985-12-20 00:00:00
abstract::Recently, a cDNA from the hepatitis C virus (HCV) RNA genome has been isolated in the USA from a chronically infected chimpanzee. In order to isolate HCV cDNA derived from human material, RNA was extracted from plasma of a Japanese blood donor implicated in post-transfusion non-A, non-B hepatitis and HCV cDNA was synt...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.24.10367
更新日期:1989-12-25 00:00:00
abstract::Increasing numbers of proteins, nucleic acids and other molecular entities have been explored as therapeutic targets, hundreds of which are targets of approved and clinical trial drugs. Knowledge of these targets and corresponding drugs, particularly those in clinical uses and trials, is highly useful for facilitating...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1014
更新日期:2010-01-01 00:00:00
abstract::Single-cell RNA-sequencing (scRNA-seq) enables the characterization of transcriptomic profiles at the single-cell resolution with increasingly high throughput. However, it suffers from many sources of technical noises, including insufficient mRNA molecules that lead to excess false zero values, termed dropouts. Comput...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa506
更新日期:2020-09-04 00:00:00
abstract::The high similarity of tunicates and vertebrates during their development coupled with the transparency of tunicate larvae, their well-studied cell lineages and the availability of simple and efficient transgenesis methods makes of this subphylum an ideal system for the investigation of vertebrate physiological and de...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj064
更新日期:2006-01-01 00:00:00
abstract::We described here an approach for mapping proteins on any sequence of genomic DNA. UV-induced DNA-protein crosslinking within whole cells and the 'protein image' hybridization technique (1) were applied to test the proteins bound to different regions of the D. melanogaster hsp-70 gene. The histone H1-DNA association w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.4.1031
更新日期:1993-02-25 00:00:00
abstract::Plant specialized metabolites are chemically highly diverse, play key roles in host-microbe interactions, have important nutritional value in crops and are frequently applied as medicines. It has recently become clear that plant biosynthetic pathway-encoding genes are sometimes densely clustered in specific genomic lo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx305
更新日期:2017-07-03 00:00:00
abstract::Interaction detection methods have led to the discovery of thousands of interactions between proteins, and discerning relevance within large-scale data sets is important to present-day biology. Here, a spectral method derived from graph theory was introduced to uncover hidden topological structures (i.e. quasi-cliques...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg340
更新日期:2003-05-01 00:00:00
abstract::Nucleosomes released from oviduct nuclei during brief micrococcal nuclease digestions are enriched in transcribed sequences (bloom K.S. and Anderson, J.N. (1978) Cell, 15, 141-150). Such nucleosomes released into this 1Sf supernatant fraction are enriched in proteins HMG14, 17 and a third lower molecular weight protei...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.12.2761
更新日期:1981-06-25 00:00:00
abstract::Reversible methylation of the N6 or N1 position of adenine in RNA has recently been shown to play significant roles in regulating the functions of RNA. RNA can also be alkylated upon exposure to endogenous and exogenous alkylating agents. Here we examined how regio-specific methylation at the hydrogen bonding edge of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx515
更新日期:2017-09-06 00:00:00
abstract::The Blocks Database contains multiple alignments of conserved regions in protein families which can be searched by e-mail (blocks@blocks.fhcrc.org) and World Wide Web (http://blocks.fhcrc.org/ ) servers to classify protein and nucleotide sequences. Recent enhancements to the servers include: (i) improved calculation o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.1.222
更新日期:1997-01-01 00:00:00
abstract::A method is described to simultaneously amplify and sequence DNA using a new class of nucleotides containing boron. During the polymerase chain reaction, boron-modified nucleotides, i.e. 2'-deoxynucleoside 5'-alpha-[P-borano]-triphosphates, are incorporated into the product DNA. The boranophosphate linkages are resist...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.8.1611
更新日期:1997-04-15 00:00:00
abstract::Detection of cell-free DNA in liquid biopsies offers great potential for use in non-invasive prenatal testing and as a cancer biomarker. Fetal and tumor DNA fractions however can be extremely low in these samples and ultra-sensitive methods are required for their detection. Here, we report an extremely simple and fast...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw224
更新日期:2016-06-20 00:00:00
abstract::The repetitive zinc finger domain of transcription factor IIIA binds 5S DNA and 5S RNA with similar affinity. Site directed mutagenesis of the Xenopus borealis somatic 5S RNA gene has been used to produce a series of derivatives of 5S RNA containing local sequence substitutions or sequence deletions. Gel mobility shif...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.11.2639
更新日期:1992-06-11 00:00:00
abstract::Insertion of the four major nucleotides at the 5'-side of the anticodon triplet of E. coli tRNAMetf was performed by joining of the half molecules obtained by limited digestion with RNase A and the chemically synthesized tetranucleotide pN-C-A-U using RNA ligase. Insertion of U-U at the 5'-side or A and A-A at the 3'-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.10.3685
更新日期:1985-05-24 00:00:00
abstract::The editing function of aminoacyl-tRNA synthetases (aaRSs) is indispensible for formation of the correct aminoacyl-tRNAs. Editing deficiency may lead to growth inhibition and the pathogenesis of various diseases. Herein, we confirmed that norvaline (Nva) but not isoleucine or valine is the major threat to the editing ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx487
更新日期:2017-07-07 00:00:00
abstract::Evidence will be presented to show that the allyl group is suitable for the protection of a 3'-terminal phosphodiester function. The latter will be demonstrated by the synthesis, via a phosphotriester approach, of two cyclic tetraribonucleotides [r(AAAA) and r(UAMe2UAMe2)], two cyclic hexadeoxyribonucleotides [d(CGCGC...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.10.4607
更新日期:1988-05-25 00:00:00
abstract::Exome sequencing strategy is promising for finding novel mutations of human monogenic disorders. However, pinpointing the casual mutation in a small number of samples is still a big challenge. Here, we propose a three-level filtration and prioritization framework to identify the casual mutation(s) in exome sequencing ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1257
更新日期:2012-04-01 00:00:00
abstract::Previous studies have shown that (i) several RNAs induced by heat shock of Drosophila melanogaster cells are homologous to tandemly repeated alpha beta units found in cloned segments of D. melanogaster DNA, and (ii) the alpha beta sequences are present both at a major heat shock locus, 87Cl, and the chromocenter of po...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.20.5297
更新日期:1981-10-24 00:00:00
abstract::The functionalisation of oligodeoxynucleotides and oligoribonucleotides by incorporation of 2'-amido-2'-deoxyribonucleosides, possibly containing a reporter group via the 2'-amido bond, was examined. Therefore 2'-acetamido-ribonucleosides containing a small methyl group at the 2'-amido bond were synthesized as model c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.1.51
更新日期:1995-01-11 00:00:00
abstract::RNA exhibits a large diversity of conformations. Three thousand nucleotides of 23S and 5S ribosomal RNA from a structure of the large ribosomal subunit were analyzed in order to classify their conformations. Fourier averaging of the six 3D distributions of torsion angles and analyses of the resulting pseudo electron m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh333
更新日期:2004-03-11 00:00:00
abstract::In order to facilitate the direct computation of the sizes of DNA fragments separated by gel electrophoresis, we have written and evaluated programmes for the Hewlett-Packard 41C programmable calculator. The sizes estimated for DNA fragments of known length using some of these programmes were found to be more accurate...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.1part2.845
更新日期:1984-01-11 00:00:00
abstract::The increasing availability of multi-omic platforms poses new challenges to data analysis. Joint visualization of multi-omics data is instrumental in better understanding interconnections across molecular layers and in fully utilizing the multi-omic resources available to make biological discoveries. We present here P...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky466
更新日期:2018-07-02 00:00:00