Abstract:
UNLABELLED:Partial cleavage of DNA with the restriction endonuclease NotI (5'...GC/GGCCGC...3') is an important technique for genomic mapping. However, partial genomic cleavage with this enzyme is impaired by the agarose matrix in which the DNA must be suspended. To solve this problem we have purified the blocking methylase M. BspRI (5'...GGmCC...3') for competition digests with NotI. The resulting methylase-limited partial DNA cleavage is shown to be superior to standard techniques on bacterial genomic DNA. ABBREVIATIONS:bp, base-pair; kb, one thousand base-pairs; Mb, one million base-pairs; Tris, Tris(hydroxy-methyl)aminomethane; EDTA, (ethylenedinitrilo)tetraacetic; beta-ME, beta-mercaptoethanol; PMSF, phenyl methyl-sulfonyl fluoride; PEG, polyethyleneglycol (MW = 8000); 3H, tritium; SAM, S-adenosylmethionine; KGB, potassium glutamate buffer; DTT, dithiothreitol; IPTG, isopropyl-beta-D-thiogalactopyranoside; BSA, bovine serum albumin.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Hanish J,McClelland Mdoi
10.1093/nar/18.11.3287subject
Has Abstractpub_date
1990-06-11 00:00:00pages
3287-91issue
11eissn
0305-1048issn
1362-4962journal_volume
18pub_type
杂志文章abstract::HotSpot Wizard is a web server used for the automated identification of hotspots in semi-rational protein design to give improved protein stability, catalytic activity, substrate specificity and enantioselectivity. Since there are three orders of magnitude fewer protein structures than sequences in bioinformatic datab...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky417
更新日期:2018-07-02 00:00:00
abstract::The equilibrium binding of ethidium bromide to native DNAs and to poly(dG-dC) X poly(dG-dC) has been studied by both phase partition and direct spectrophotometric techniques. The binding isotherms obtained from both experimental techniques show that ethidium binds in a cooperative manner to E. coli DNA. On the other h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.24.8211
更新日期:1982-12-20 00:00:00
abstract::The advent of RNA-sequencing and microarray technologies has led to rapid growth of transcriptome data generated for a wide range of organisms, under various cellular, organ and individual conditions. Since the number of possible combinations of intercellular and extracellular conditions is almost unlimited, catalogin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1155
更新日期:2019-01-08 00:00:00
abstract::Among a collection of 74 aprt mutations induced by treatment of plateau phase Chinese hamster ovary CHO cells with the radiomimetic DNA double-strand cleaving agent neocarzinostatin, nine were large-scale rearrangements. Molecular analysis indicated that all nine were highly conservative, non-homologous reciprocal exc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf369
更新日期:2002-06-15 00:00:00
abstract::We have previously reported that transcription from a distal promoter (promoter B) of the estrogen receptor alpha (ERalpha) gene is responsible for the increased expression of ERalpha in human breast carcinomas. This paper first characterized the promoter B region in terms of transient transfection experiments with lu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.3.903
更新日期:1999-02-01 00:00:00
abstract::Argonaute (AGO) proteins have a well-established role in post-transcriptional regulation of gene expression as key component of the RNA silencing pathways. Recent evidence involves AGO proteins in mammalian nuclear processes such as transcription and splicing, though the mechanistic aspects of AGO nuclear functions re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1387
更新日期:2015-02-18 00:00:00
abstract::The cytosine base in DNA undergoes hydrolytic deamination at a considerable rate when UV radiation induces formation of a cyclobutane pyrimidine dimer (CPD) with an adjacent pyrimidine base. We have synthesized a phosphoramidite building block of a cis-syn cyclobutane thymine-uracil dimer (T[]U), which is the deaminat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh342
更新日期:2004-03-12 00:00:00
abstract::Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1286
更新日期:2013-02-01 00:00:00
abstract::The 3' splice site of the second intron (I2) of the human apolipoprotein-AII gene, (GT)16GGGCAG, is unique in that, although fully functional, a stretch of alternating guanine and thymine residues replaces the polypyrimidine tract usually associated with 3' splice junctions. The transient expression of successive 5' d...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.9.3787
更新日期:1987-05-11 00:00:00
abstract::The environmental carcinogen benzo[a]pyrene (BP) is metabolized to reactive diol epoxides that bind to cellular DNA by predominantly forming N2-guanine adducts (G*). Mutation hotspots for these adducts are frequently found in 5'- ... GG ... dinucleotide sequences, but their origins are poorly understood. Here we used ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm022
更新日期:2007-01-01 00:00:00
abstract::RNA-binding proteins (RBPs) play important roles in the post-transcriptional control of RNAs. Identifying RBP binding sites and characterizing RBP binding preferences are key steps toward understanding the basic mechanisms of the post-transcriptional gene regulation. Though numerous computational methods have been dev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1025
更新日期:2016-02-29 00:00:00
abstract::In prokaryotes and archaea transfer ribonucleic acid (tRNA) stability as well as cellular UV protection relies on the post-transcriptional modification of uracil at position 8 (U8) of tRNAs by the 4-thiouridine synthetase ThiI. Here, we report three crystal structures of ThiI from Thermotoga maritima in complex with a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku249
更新日期:2014-06-01 00:00:00
abstract::Minigenes encoding the peptide Met-Arg-Arg have been used to study the mechanism of toxicity of AGA codons proximal to the start codon or prior to the termination codon in bacteria. The codon sequences of the 'mini-ORFs' employed were initiator, combinations of AGA and CGA, and terminator. Both, AGA and CGA are low-us...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh784
更新日期:2004-08-18 00:00:00
abstract::Synthesis of (p)ppRNA-DNA chains by purified HeLa cell DNA primase-DNA polymerase alpha (pol alpha-primase) was compared with those synthesized by a multiprotein form of DNA polymerase alpha (pol alpha 2) using unique single-stranded DNA templates containing the origin of replication for simian virus 40 (SV40) DNA. Th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.18.7305
更新日期:1986-09-25 00:00:00
abstract::The DNA replication, plasmid segregation and transactivation functions of Epstein-Barr nuclear antigen 1 (EBNA1) require the binding of EBNA1 to specific DNA recognition sites in the two non-contiguous functional elements of the Epstein-Barr virus latent origin of replication, oriP . EBNA1 molecules bound to these ele...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.19.4462
更新日期:1998-10-01 00:00:00
abstract::Lateral ribosomal stalk is responsible for binding and recruiting translation factors during protein synthesis. The eukaryotic stalk consists of one P0 protein with two copies of P1•P2 heterodimers to form a P0(P1•P2)₂ pentameric P-complex. Here, we have solved the structure of full-length P1•P2 by nuclear magnetic re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt636
更新日期:2013-10-01 00:00:00
abstract::The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes, and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1010
更新日期:2021-01-08 00:00:00
abstract::Many strains of E. coli K12 restrict DNA containing cytosine methylation such as that present in plant and animal genomes. Such restriction can severely inhibit the efficiency of cloning genomic DNAs. We have quantitatively evaluated a total of 39 E. coli strains for their tolerance to cytosine methylation in phage an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.9.3469
更新日期:1989-05-11 00:00:00
abstract::The conditions under which Drosophila melanogaster are grown markedly influence the amount of the hypermodified nucleoside Q found in certain tRNAs. This effect on Q biosynthesis was found in both the wild-type and the suppressor of sable [su(s)2] mutant. Suppressed vermilion flies [su(s)2v; bw] with 78% of the tyrosi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.11.3919
更新日期:1977-11-01 00:00:00
abstract::The solubility of adult beta-globin chromatin (beta A chromatin) from immature chicken red blood cells can be controlled by the presence or absence of n-butyrate in a cell incubation medium. In the absence of n-butyrate, only a small percentage (approximately 4%) of the total beta A chromatin is in a soluble chromatin...
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
abstract::We previously proposed that the first enzyme for histidine biosynthesis in Salmonellatyphimurium plays a role in regulating expression of the histidine operon and that in order to play this role the enzyme must form a complex with histidyl-tRNA. Among the many observations that led to these conclusions were 1) that re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.7.881
更新日期:1974-07-01 00:00:00
abstract::The budding yeast Saccharomyces cerevisiae is proving to be an useful and accurate model for eukaryotic DNA replication. It contains both DNA polymerase alpha (I) and delta (III). Recently, proliferating cell nuclear antigen (PCNA), which in mammalian cells is an auxiliary subunit of DNA polymerase delta and is essent...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.2.261
更新日期:1990-01-25 00:00:00
abstract::The heterodimeric subunit, SRP9/14, of the signal recognition particle (SRP) has previously been found to bind to scAlu and scB1 RNAs in vitro and to exist in large excess over SRP in anthropoid cells. Here we show that human and mouse SRP9/14 bind with high affinities to other Alu-like RNAs of different evolutionary ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.2.318
更新日期:1997-01-15 00:00:00
abstract::Here, we present an update of Breast Cancer Now Tissue Bank bioinformatics, a rich platform for the sharing, mining, integration and analysis of breast cancer data. Its modalities provide researchers with access to a centralised information gateway from which they can access a network of bioinformatic resources to que...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx913
更新日期:2018-01-04 00:00:00
abstract::A method is described which allows selection of sequences which can substitute for the normal AATAAA hexanucleotide involved in polyadenylation of SV40 late mRNAs. Plaques were generated from viral DNA lacking the motif, forcing acquisition of substitute sequences. Four variants were characterized. All displayed wild-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.22.8053
更新日期:1985-11-25 00:00:00
abstract::We have overproduced and purified wild type regA protein, a translational repressor encoded by bacteriophage T4. The repressor activity of the cloned regA protein has been tested on four known regA target genes (T4 genes: 44, 45, rpbA and regA) using in vitro coupled transcription-translation reactions. We have demons...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.23.10047
更新日期:1989-12-11 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::One surprisingly common element of RNA secondary structure consists of a hairpin capped by a four-base loop (or the tetraloop). Recently the 3-D structures of two RNA-tetraloops have been determined by NMR-studies. Both structures have a similar architecture: the first and the last bases of the loop form a hydrogen bo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.19.4556
更新日期:1993-09-25 00:00:00
abstract::The archaeal exosome is a phosphorolytic 3'-5' exoribonuclease complex. In a reverse reaction it synthesizes A-rich RNA tails. Its RNA-binding cap comprises the eukaryotic orthologs Rrp4 and Csl4, and an archaea-specific subunit annotated as DnaG. In Sulfolobus solfataricus DnaG and Rrp4 but not Csl4 show preference f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku969
更新日期:2014-11-10 00:00:00
abstract::Toscana virus (TOSV) is an arthropod-borne human pathogen responsible for seasonal outbreaks of fever and meningoencephalitis in the Mediterranean basin. TOSV is a segmented negative-strand RNA virus (sNSV) that belongs to the genus phlebovirus (family Phenuiviridae, order Bunyavirales), encompassing other important h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz838
更新日期:2019-11-18 00:00:00