Abstract:
:The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt ends. Here, we report the 1.3 Å resolution structure of the enzyme in complex with substrate DNA and a sodium or calcium ion taking the place of a catalytic magnesium ion. The structure identifies Glu54, Asp82 and Lys93 as the active site residues. This agrees with earlier bioinformatic predictions and implies that the PD and (D/E)XK motifs in the sequence are incidental. DNA recognition is very unusual: the two Met47 residues of the ThaI dimer intercalate symmetrically into the CG steps of the target sequence. They approach the DNA from the minor groove side and penetrate the base stack entirely. The DNA accommodates the intercalating residues without nucleotide flipping by a doubling of the CG step rise to twice its usual value, which is accompanied by drastic unwinding. Displacement of the Met47 side chains from the base pair midlines toward the downstream CG steps leads to large and compensating tilts of the first and second CG steps. DNA intercalation by ThaI is unlike intercalation by HincII, HinP1I or proteins that bend or repair DNA.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Firczuk M,Wojciechowski M,Czapinska H,Bochtler Mdoi
10.1093/nar/gkq834subject
Has Abstractpub_date
2011-01-01 00:00:00pages
744-54issue
2eissn
0305-1048issn
1362-4962pii
gkq834journal_volume
39pub_type
杂志文章abstract::A new method which predicts internal exon sequences in human DNA has been developed. The method is based on a splice site prediction algorithm that uses the linear discriminant function to combine information about significant triplet frequencies of various functional parts of splice site regions and preferences of ol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.24.5156
更新日期:1994-12-11 00:00:00
abstract::SITEHOUND-web (http://sitehound.sanchezlab.org) is a binding-site identification server powered by the SITEHOUND program. Given a protein structure in PDB format SITEHOUND-web will identify regions of the protein characterized by favorable interactions with a probe molecule. These regions correspond to putative ligand...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp281
更新日期:2009-07-01 00:00:00
abstract::CLASPIN is an essential mediator in the DNA replication checkpoint, responsible for ATR (ataxia telangiectasia and Rad3-related protein)-dependent activation of CHK1 (checkpoint kinase 1). Here we found a dynamic signaling pathway that regulates CLASPIN turn over. Under unperturbed conditions, the E3 ubiquitin ligase ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku978
更新日期:2014-12-01 00:00:00
abstract::Upon activation of the ERK and p38 MAPK pathways, the MSK1/2-mediated nucleosomal response, including H3 phosphorylation at serine 28 or 10, is coupled with the induction of immediate-early (IE) gene transcription. The outcome of this response, varying with the stimuli and cellular contexts, ranges from neoplastic tra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq030
更新日期:2010-06-01 00:00:00
abstract::High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku370
更新日期:2014-07-01 00:00:00
abstract::G-quadruplexes (G4s) are stable secondary structures that can lead to the stalling of replication forks and cause genomic instability. Pif1 is a 5' to 3' helicase, localized to both the mitochondria and nucleus that can unwind G4s in vitro and prevent fork stalling at G4 forming sequences in vivo. Using in vitro prime...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz608
更新日期:2019-09-19 00:00:00
abstract::The hydroxyl radical is a powerful oxidant that generates DNA lesions including the stereoisomeric R and S 5',8-cyclo-2'-deoxyadenosine (cdA) and 5',8-cyclo-2'-deoxyguanosine (cdG) pairs that have been detected in cellular DNA. Unlike some other oxidatively generated DNA lesions, cdG and cdA are repaired by the human ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku162
更新日期:2014-04-01 00:00:00
abstract::Based on the secondary structural model of MS2 RNA, it is shown that, in base-pairing regions of the RNA, there is a bias in the use of synonymous codons which favours C and/or G over U and/or A in the third codon positions, and that in non-pairing regions, there is an opposite bias which favours U and/or A over C and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.7.2073
更新日期:1979-12-11 00:00:00
abstract::We have developed an HIV nef-Escherichia coli lacZ fusion system in vitro that allows the detection of low frequency mutations, including frameshifts, deletions and insertions. A portion of the nef gene that encompasses a hypervariable region was fused in-frame with a downstream lacZalpha peptide coding region. The re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.9.1710
更新日期:1996-05-01 00:00:00
abstract::Little is known about the regulation of the DNA damage-mediated gene expression in archaea. Here we report that the addition of actinomycin D to Sulfolobus solfataricus cultures triggers the expression of the radA paralogue sso0777. Furthermore, a specific retarded band is observed when electrophoretic mobility shift ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm782
更新日期:2007-01-01 00:00:00
abstract::More than 200 assembly factors (AFs) are required for the production of ribosomes in yeast. The stepwise association and dissociation of these AFs with the pre-ribosomal subunits occurs in a hierarchical manner to ensure correct maturation of the pre-rRNAs and assembly of the ribosomal proteins. Although decades of re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1079
更新日期:2020-01-10 00:00:00
abstract::Retinoic acid-inducible gene I (RIG-I) is a pattern recognition receptor expressed in metazoan cells that is responsible for eliciting the production of type I interferons and pro-inflammatory cytokines upon detection of intracellular, non-self RNA. Structural studies of RIG-I have identified a novel Pincer domain com...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku817
更新日期:2014-10-01 00:00:00
abstract::Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky381
更新日期:2018-07-02 00:00:00
abstract::DNA helicases are required for virtually every aspect of DNA metabolism, including replication, repair, recombination and transcription. A comprehensive description of these essential biochemical processes requires detailed understanding of helicase mechanisms. These enzymes are ubiquitous, having been identified in v...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkl501
更新日期:2006-01-01 00:00:00
abstract::Targeted genome engineering requires nucleases that introduce a highly specific double-strand break in the genome that is either processed by homology-directed repair in the presence of a homologous repair template or by non-homologous end-joining (NHEJ) that usually results in insertions or deletions. The error-prone...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt080
更新日期:2013-04-01 00:00:00
abstract::The Eco57I restriction endonuclease and methylase were purified to homogeneity from the E.coli RR1 strain carrying the eco57IRM genes on a recombinant plasmid. The molecular weight of the denaturated methylase is 63 kDa. The restriction endonuclease exists in a monomeric form with an apparent molecular weight of 104-1...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.22.6043
更新日期:1992-11-25 00:00:00
abstract::Purified 15 S globin mRNA-protein (mRNP) complexes obtained by EDTA dissociation of duck reticulocytes polyribosomes were digested with the calcium dependant Staphylococcus aureus nuclease (EC 3. 1. 4. 7.). 25% of the globin mRNA sequences were resistant to extensive nuclease digestion as determined by TCA precipitati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.8.2787
更新日期:1979-06-25 00:00:00
abstract::Chelation of divalent cations by 5 mM EDTA and subsequent removal by dialysis from a cytoplasmic HeLa cell extract leads to a complete loss of 5S rRNA transcription without affecting tRNA synthesis. Transcription complexes for 5S RNA can no longer be assembled in such a zinc-depleted extract and this ability can be fu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.23.8971
更新日期:1984-12-11 00:00:00
abstract::The interactions between beef tRNATrp with avian myeloblastosis reverse transcriptase have been studied by statistical chemical modifications of phosphate (ethylnitrosourea) and cytidine (dimethyl sulfate) residues, as well as by digestion of complexed tRNA by Cobra venom nuclease and Neurospora crassa endonuclease. R...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.5.2259
更新日期:1984-03-12 00:00:00
abstract::Maintenance of stem-cell identity requires proper regulation of enhancer activity. Both transcription factors OCT4/SOX2/NANOG and histone methyltransferase complexes MLL/SET1 were shown to regulate enhancer activity, but how they are regulated in embryonic stem cells (ESCs) remains further studies. Here, we report a t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkab034
更新日期:2021-01-27 00:00:00
abstract::How DNA sequence variation influences gene expression remains poorly understood. Diploid organisms have two homologous copies of their DNA sequence in the same nucleus, providing a rich source of information about how genetic variation affects a wealth of biochemical processes. However, few computational methods have ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz176
更新日期:2019-06-20 00:00:00
abstract::The use of the ammonia deprotection step to introduce (15)N labels at specific exocyclic amino positions of adenine, cytosine, guanine or 2-aminopurine of oligodeoxynucleotides is described. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.15.2982
更新日期:1994-08-11 00:00:00
abstract::A novel program suite was implemented for the functional interpretation of high-throughput gene expression data based on the identification of Gene Ontology (GO) nodes. The focus of the analysis lies on the interpretation of microarray data from prokaryotes. The three well established statistical methods of the thresh...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl329
更新日期:2006-07-01 00:00:00
abstract::DNA repair is required to maintain genome stability in stem cells and early embryos. At critical junctures, oxidative damage to DNA requires the base excision repair (BER) pathway. Since early zebrafish embryos lack the major polymerase in BER, DNA polymerase ß, repair proceeds via replicative polymerases, even though...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1142
更新日期:2011-04-01 00:00:00
abstract::The proportion of cytosines methylated in the DNA of nucleosome oligomers and of core particles appears indistinguishable from that of total nuclear DNA from CHO cells. However the DNA in nucleoprotein which is initially released from nuclei by treatment with very low levels of micrococcal nuclease and the first 10% o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.9.3097
更新日期:1977-09-01 00:00:00
abstract::Oriented DNA films prepared by the wet-spinning technique have been complexed with several ligands: the anthracycline antibiotic violamycin BI, the dipeptide L-carnosine, and the oligopeptide antibiotic netropsin. The formation of the DNA-ligand complexes is accompanied by dramatic changes of the conformational flexib...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.23.9165
更新日期:1984-12-11 00:00:00
abstract::We have modeled local DNA sequence parameters to search for DNA architectural motifs involved in transcription regulation and promotion within the Xenopus laevis ribosomal gene promoter and the intergenic spacer (IGS) sequences. The IGS was found to be shaped into distinct topological domains. First, intrinsic bends s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.18.3433
更新日期:2000-09-15 00:00:00
abstract::PIR-International is an association of macromolecular sequence data collection centers dedicated to fostering international cooperation as an essential element in the development of scientific databases. A major objective of PIR-International is to continue the development of the Protein Sequence Database as an essent...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:
更新日期:1994-09-01 00:00:00
abstract::Previous studies have implicated the DE-1 (-111/-106) and alpha A-CRYBP1 (-66/-57) sites for activity of the mouse alpha A-crystallin promoter in transiently transfected lens cells. Here we have used the bacterial chloramphenicol acetyltransferase (CAT) reporter gene to test the functional importance of the putative D...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.11.2633
更新日期:1993-06-11 00:00:00
abstract::Transcription initiation complexes formed by bacterial RNA polymerases (RNAPs) exhibit dramatic species-specific differences in stability, leading to different strategies of transcription regulation. The molecular basis for this diversity is unclear. Promoter complexes formed by RNAP from Thermus aquaticus (Taq) are c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks973
更新日期:2012-12-01 00:00:00