Abstract:
:The structures of the termini and their flanking regions of two human KpnI family members were investigated. The two differed in length, but the starting sequence at one terminal (defined as the 5' terminal) was found to be common to both members. The Alu family sequence was found in the 5' flanking regions. The KpnI family sequence started several base-pairs downstream from the 3' end of the Alu family sequence. In both cases, the Alu family sequence was not flanked by the direct repeat sequence common to the Alu family. These two members showed no sequence homology in 3' terminal regions. Interestingly, the Alu family plus the KpnI family unit was found to be flanked by a direct repeat sequence of several base-pair length. Based on these findings, relationship between the Alu family and KpnI family is discussed.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Miyake T,Migita K,Sakaki Ydoi
10.1093/nar/11.19.6837subject
Has Abstractpub_date
1983-10-11 00:00:00pages
6837-46issue
19eissn
0305-1048issn
1362-4962journal_volume
11pub_type
杂志文章abstract::A simple and efficient method is described to introduce structurally pre-determined mutations into recombinant genomes of filamentous phage M13. The method rests on gapped duplex DNA (gdDNA) molecules of the phage M13 genome as the key intermediate. In this gdDNA, the (+) and the (shorter) (-) strand carry different g...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.24.9441
更新日期:1984-12-21 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::The eukaryotic mismatch repair protein Msh6 shares five domains in common with other MutS members. However, it also contains several hundred additional residues at its N-terminus. A few of these residues bind to PCNA, but the functions of the other amino acids in the N-terminal region (NTR) are unknown. Here we demons...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm409
更新日期:2007-01-01 00:00:00
abstract::A linear DNA plasmid, designated pLLE1, has been isolated from a mitochondrial fraction of a strain of Lentinus edodes. pLLE1(11.0 kbp) was sensitive to the 3'----5'-acting exonuclease III and resistant to the 5'----3'-acting lambda exonuclease. It showed no homology with mitochondrial and nuclear genomic DNAs of plas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.6.1395
更新日期:1990-03-25 00:00:00
abstract::Numerous eukaryotic genes are alternatively spliced. Recently, deep transcriptome sequencing has skyrocketed proportion of alternatively spliced genes; over 95% human multi-exon genes are alternatively spliced. One fundamental question is: are all these alternative splicing (AS) events functional? To look into this is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1253
更新日期:2014-12-16 00:00:00
abstract::A simplified and economical method for the attachment of 2'-deoxyribo, ribo and arabinonucleosides onto long-chain alkylamidopropanoic acid controlled-pore glass (LCAAP-CPG, P-3) is described. In this procedure, 5'-O-tritylated nucleosides are coupled directly to LCAAP-CPG in excellent yields using 1-(3-dimethylaminop...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.13.3813
更新日期:1990-07-11 00:00:00
abstract::The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.1.55
更新日期:1999-01-01 00:00:00
abstract::The advances of next-generation sequencing technology have facilitated metagenomics research that attempts to determine directly the whole collection of genetic material within an environmental sample (i.e. the metagenome). Identification of genes directly from short reads has become an important yet challenging probl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq747
更新日期:2010-11-01 00:00:00
abstract::Single-strand specific endoribonuclease YbeY has been shown to play an important role in the processing of the 3' end of the 16S rRNA in Escherichia coli. Lack of YbeY results in the accumulation of the 17S rRNA precursor. In contrast to a previous report, we show that Sinorhizobium meliloti YbeY exhibits endoribonucl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1095
更新日期:2020-01-10 00:00:00
abstract::Holliday junction (HJ) resolving enzyme RecU is involved in DNA repair and recombination. We have determined the crystal structure of inactive mutant (D88N) of RecU from Bacillus subtilis in complex with a 12 base palindromic DNA fragment at a resolution of 3.2 Å. This structure shows the stalk region and the essentia...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1165
更新日期:2017-01-25 00:00:00
abstract::The Mouse Genome Database (MGD) forms the core of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a model organism database resource for the laboratory mouse. MGD provides essential integration of experimental knowledge for the mouse system with information annotated from both literature an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki113
更新日期:2005-01-01 00:00:00
abstract::A database (http://perso.curie.fr/tsoussi ) is described, in which over 1000 mutations in the human APC gene of tumors (colon cancer predominantly) are compiled from the literature. It includes both molecular information about the mutations and clinical data about the patients. Software has been designed to analyse al...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.1.269
更新日期:1998-01-01 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::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::Ribosome biogenesis is fundamental for cellular life, but surprisingly little is known about the underlying pathway. In eukaryotes a comprehensive collection of experimentally verified ribosome biogenesis factors (RBFs) exists only for Saccharomyces cerevisiae. Far less is known for other fungi, animals or plants, and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1137
更新日期:2014-02-01 00:00:00
abstract::Treatment of the ciliated protozoan Tetrahymena thermophila with 8-methoxypsoralen combined with long wavelength ultraviolet irradiation (UVA, lambda approximately 360 nm) resulted in a dose dependent equal inhibition of the synthesis of rRNA, 5.8S, 5S and tRNA. Similar results were obtained with 3-carbethoxy-8-methox...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.3.921
更新日期:1987-02-11 00:00:00
abstract::A type II restriction endonuclease, DraI, isolated from Deinococcus radiophilus ATCC 27603 recognises the palindromic hexanucleotide sequence (formula; see text) and cleaves it, as indicated by the arrows, to produce blunt-ended fragments. The yield of enzyme is 100 to 1000 times that of the only other known type II r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.16.5467
更新日期:1983-08-25 00:00:00
abstract::From the general views of the eukaryotic transcription systems, L1 (or L1-like) retrotransposons that encode some proteins are unusual. L1, unlike other protein-coding elements, is transcribed through an internal promoter. And the L1 internal promoter, unlike other internal promoters, is thought to be RNA polymerase I...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.18.3704
更新日期:1995-09-25 00:00:00
abstract::Defined DNA substrates containing discrete abasic sites or paired abasic sites set 1, 3, 5 and 7 bases apart on opposite strands were constructed to examine the reactivity of S1, mung bean and P1 nucleases towards abasic sites. None of the enzymes acted on the substrate containing discrete abasic sites. Under conditio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.19.3805
更新日期:1995-10-11 00:00:00
abstract::Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, uses chemical energy to translocate single-stranded RNA genomic precursors into the procapsid. We previously dissected th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt713
更新日期:2013-11-01 00:00:00
abstract::NF-IL6beta regulates gene expression and plays function roles in many tissues. The EGF-regulated cyclooxygenase-2 (cox-2) expression is mediated through p38(MAPK) signaling pathway and positively correlates with NF-IL6beta expression in A431 cells. NF-IL6beta coordinated with c-Jun on cox-2 transcriptional activation ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj422
更新日期:2006-01-05 00:00:00
abstract::The 16S ribosomal RNA mutation database (16SMDB) provides a list of mutated positions in 16S ribosomal RNA from Escherichia coli and the identity of each alteration. Information provided for each mutation includes: (i) a brief description of the phenotype(s) associated with each mutation; (ii) whether a mutant phenoty...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.1.166
更新日期:1996-01-01 00:00:00
abstract::A key issue when designing and using DNA-targeting nucleases is specificity. Ideally, an optimal DNA-targeting tool has only one recognition site within a genomic sequence. In practice, however, almost all designer nucleases available today can accommodate one to several mutations within their target site. The ability...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku155
更新日期:2014-04-01 00:00:00
abstract::The method employed to determine the sequence of a T1 RNase fragment, A-A-A-A-A-U-A-A-C-A-A-U-A-C-A-Gp, from Novikoff rat hepatoma 18S ribosomal RNA is described. This method is applicable to any oligoribonucleotide produced by specific endonucleases that leave the newly cleaved 5'-end free for labeling with polynucle...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.2.339
更新日期:1977-02-01 00:00:00
abstract::The molecular basis for the DNA binding specificity of the thyroid transcription factor 1 homeodomain (TTF-1HD) has been investigated. Methylation and ethylation interference experiments show that the TTF-1HD alone recapitulates the DNA binding properties of the entire protein. Studies carried out with mutant derivati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.15.3075
更新日期:1994-08-11 00:00:00
abstract::Six 1',5'-anhydrohexitol uridine triphosphates were synthesized with aromatic substitutions appended via a carboxamide linker to the 5-position of their bases. An improved method for obtaining such 5-substituted hexitol nucleosides and nucleotides is described. The incorporation profile of the nucleotide analogues int...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz008
更新日期:2019-03-18 00:00:00
abstract::We have established a sensitive, monoclonal antibody (Mab)-based procedure permitting the selective enrichment of sequences containing the miscoding alkylation product O6-ethylguanine (O6-EtGua) from mammalian DNA. H5 rat hepatoma cells were reacted with the N-nitroso carcinogen N-ethyl-N-nitrosourea in vitro, to give...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.16.4467
更新日期:1991-08-25 00:00:00
abstract::Type I toxin-antitoxin (TA) systems have been identified in a wide range of bacterial genomes. Here, we report the characterization of a new type I TA system present on the chromosome of the major human gastric pathogen, Helicobacter pylori. We show that the aapA1 gene encodes a 30 amino acid peptide whose artificial ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1343
更新日期:2017-05-05 00:00:00
abstract::Carbohydrate-binding proteins play crucial roles across all organisms and viruses. The complexity of carbohydrate structures, together with inconsistencies in how their 3D structures are reported, has led to difficulties in characterizing the protein-carbohydrate interfaces. In order to better understand protein-carbo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz860
更新日期:2020-01-08 00:00:00
abstract::Recognition of genomic binding sites by transcription factors can occur through base-specific recognition, or by recognition of variations within the structure of the DNA macromolecule. In this article, we investigate what information can be retrieved from local DNA structural properties that is relevant to transcript...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1071
更新日期:2011-01-01 00:00:00