Abstract:
:Vaccinia virus DNA topoisomerase catalyzes resolution of synthetic Holliday junctions in vitro. The mechanism entails concerted transesterifications at two recognition sites, 5'-CCCTT/, that are opposed within a partially mobile four-way junction. Efficient resolution occurs on a junction with a 10 bp segment of branch mobility (5'-GCCCTTATCG) that extends 4 bp 3' of the scissile phosphate. Here we report that resolution is decreased when branch mobility is limited to an 8 bp segment extending 2 bp 3' of the cleavage site and then eliminated when branch mobility is confined to the 6 bp GCCCTT sequence 5' of the scissile phosphate. We surmise that a spacer region 3' of CCCTT is needed for simultaneous cleavage at two opposing sites at the junction. Branch mobility is not required for reaction chemistry at a junction, because topoisomerase cleaves a single CCCTT site in a non-mobile four-way junction where the scissile phosphate is at the crossover point. The junction resolvase activity of topo-isomerase may be involved in forming the hairpin telomeres of the vaccinia genome.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sekiguchi J,Cheng C,Shuman Sdoi
10.1093/nar/28.14.2658keywords:
subject
Has Abstractpub_date
2000-07-15 00:00:00pages
2658-63issue
14eissn
0305-1048issn
1362-4962journal_volume
28pub_type
杂志文章abstract::Chemically modified antisense oligonucleotides (ASOs) with phosphorothioate (PS) linkages have been extensively studied as research and therapeutic agents. PS-ASOs can enter the cell and trigger cleavage of complementary RNA by RNase H1 even in the absence of transfection reagent. A number of cell surface proteins hav...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky145
更新日期:2018-04-20 00:00:00
abstract::Hfq, a bacterial RNA-binding protein, was recently shown to contain the Sm1 motif, a characteristic of Sm and LSm proteins that function in RNA processing events in archaea and eukaryotes. In this report, comparative structural modeling was used to predict a three-dimensional structure of the Hfq core sequence. The pr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf508
更新日期:2002-09-01 00:00:00
abstract::Recent studies show that the region of DNA brought into close proximity to the fetal gamma-globin genes in deletional forms of hereditary persistence of fetal hemoglobin (HPFH) is selectively hypomethylated (and presumably active) in normal erythroid tissue. This region is normally located approximately 100 kilobases ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.13.5169
更新日期:1987-07-10 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::We report here on a quantitative technique called COBRA to determine DNA methylation levels at specific gene loci in small amounts of genomic DNA. Restriction enzyme digestion is used to reveal methylation-dependent sequence differences in PCR products of sodium bisulfite-treated DNA as described previously. We show t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.12.2532
更新日期:1997-06-15 00:00:00
abstract::Adenine, thymine and cytosine PNA monomers have been prepared using 3-amino-1,2-propanediol as a starting material. The benzoyl group was used to protect the exocyclic amines of the heterocyclic bases of A and C PNA monomers and the backbone primary amine was protected with the monomethoxytrityl group. The thymine and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.17.3357
更新日期:1996-09-01 00:00:00
abstract::We describe the unique features of an aberrantly rearranged mu immunoglobulin heavy chain gene isolated from MPC-11 cells (a gamma 2b producing Balb/c plasmacytoma). A novel rearrangement has occurred 1.5 Kb 5' of the MPC-11 mu gene (denoted 18b mu) resulting in the deletion of the majority of the repetitive switch re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.23.7751
更新日期:1982-12-11 00:00:00
abstract::In the filamentous cyanobacterium Anabaena sp. PCC 7120, the ferric uptake regulator FurA functions as a global transcriptional regulator. Despite several analyses have focused on elucidating the FurA-regulatory network, the number of target genes described for this essential transcription factor is limited to a handf...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku123
更新日期:2014-04-01 00:00:00
abstract::Two new endonuclease activities, endonuclease B and endonuclease C, obtained from yeast nuclear preparations have been separated and partially characterized. Endonuclease B has a primary requirement for Mn2+ which cannot be replaced by Mg2+ or Ca2+, and makes single-strand scissions in double-stranded DNA. Endonculeas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.7.1023
更新日期:1975-07-01 00:00:00
abstract::DNA3'pp5'G caps synthesized by the 3'-PO4/5'-OH ligase RtcB have a strong impact on enzymatic reactions at DNA 3'-OH ends. Aprataxin, an enzyme that repairs A5'pp5'DNA ends formed during abortive ligation by classic 3'-OH/5'-PO4 ligases, is also a DNA 3' de-capping enzyme, converting DNAppG to DNA3'p and GMP. By takin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv501
更新日期:2015-07-13 00:00:00
abstract::Fourteen P-element insertion mutants at the yellow (y) gene of D. melanogaster have been analysed by restriction mapping and DNA sequencing. The distribution of the insertion sites is nonrandom, with a preferred target site in the 5'-transcribed but non-translated leader of the gene. Transcription analysis indicates t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.7.3039
更新日期:1988-04-11 00:00:00
abstract::The allele frequency net database (http://www.allelefrequencies.net) is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations. The extensive variability observed in genes and alleles related to the immune system response and its signi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1128
更新日期:2011-01-01 00:00:00
abstract::A vector system is presented that allows generation of E. coli co-expression clones by a standardized, robust cloning procedure. The number of co-expressed proteins is not limited. Five 'pQLink' vectors for expression of His-tag and GST-tag fusion proteins as well as untagged proteins and for cloning by restriction en...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm067
更新日期:2007-01-01 00:00:00
abstract::The small nucleolar RNA U3 is essential for viability in yeast. We have previously shown that U3 can be cross-linked in vivo to the pre-rRNA in the 5' external transcribed spacer (ETS), at +470. This ETS region contains 10 nucleotides of perfect complementarity to U3. In a genetic background where the mutated rDNA is ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.20.4057
更新日期:1994-10-11 00:00:00
abstract::We have examined the absorption and circular dichroism spectra of intact Penicillium chrysogenum virus, empty capsid particles, and isolated double-stranded RNA. The absorbance at 260 nm of intact virus was less than 4% hypochromic relative to the absorbances of the free double-stranded RNA and free viral protein, ind...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.1.175
更新日期:1983-01-11 00:00:00
abstract::Procaryotic DNA polymerases contain an associated 3'----5' exonuclease activity which provides a proofreading function and contributes substantially to replication fidelity. DNA polymerases of the eucaryotic herpes-type viruses contain similar associated exonuclease activities. We have investigated the fidelity of pol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.3.1185
更新日期:1987-02-11 00:00:00
abstract::WorfDB (Worm ORFeome DataBase; http://worfdb.dfci.harvard.edu) was created to integrate and disseminate the data from the cloning of complete set of approximately 19 000 predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans (also referred to as the 'worm ORFeome'). WorfDB serves as a central ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg092
更新日期:2003-01-01 00:00:00
abstract::The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1095
更新日期:2018-01-04 00:00:00
abstract::A non-enzymic protein factor that increases the in vitro rate of synthesis by HeLa DNA polymerase alpha 15- to 30-fold with denatured DNA as template has been partially purified from the cytoplasmic fraction of HeLa cells. The stimulatory effect is highly specific for HeLa DNA polymerase alpha and for DNA templates th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.1.221
更新日期:1978-01-01 00:00:00
abstract::The basal transcription factor TFE enhances transcription initiation by catalysing DNA strand-separation, a process that varies with temperature and ionic strength. Canonical TFE forms a heterodimeric complex whose integrity and function critically relies on a cubane iron-sulphur cluster residing in the TFEβ subunit. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1302
更新日期:2018-03-16 00:00:00
abstract::The 5' and 3' untranslated regions of eukaryotic mRNAs (UTRs) play crucial roles in the post-transcriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and message stability. UTRdb is a curated database of 5' and 3' untran...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp902
更新日期:2010-01-01 00:00:00
abstract::The MalaCards human disease database (http://www.malacards.org/) is an integrated compendium of annotated diseases mined from 68 data sources. MalaCards has a web card for each of ∼20 000 disease entries, in six global categories. It portrays a broad array of annotation topics in 15 sections, including Summaries, Symp...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkw1012
更新日期:2017-01-04 00:00:00
abstract::Heterotrimeric eukaryotic/archaeal translation initiation factor 2 (e/aIF2) binds initiator methionyl-tRNA and plays a key role in the selection of the start codon on messenger RNA. tRNA binding was extensively studied in the archaeal system. The γ subunit is able to bind tRNA, but the α subunit is required to reach h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1180
更新日期:2013-01-01 00:00:00
abstract::The 3'-untranslated region (UTR) of tobacco mosaic virus (TMV), which terminates in a tRNA-like structure, functionally substitutes for a poly(A) tail in both plant and animal cells. The addition of the TMV 3'-UTR to chimeric mRNA constructs increases their expression up to 100-fold, increasing both translational effi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.18.5031
更新日期:1991-09-25 00:00:00
abstract::The discovery of hydroxymethyl-, formyl- and carboxylcytosine, generated through oxidation of methylcytosine by TET dioxygenases, raised the question how these modifications contribute to epigenetic regulation. As they are subjected to complex regulation in vivo, we dissected links to gene expression with in vitro mod...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku552
更新日期:2014-07-01 00:00:00
abstract::PASMet (Prediction, Analysis and Simulation of Metabolic networks) is a web-based platform for proposing and verifying mathematical models to understand the dynamics of metabolism. The advantages of PASMet include user-friendliness and accessibility, which enable biologists and biochemists to easily perform mathematic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw415
更新日期:2016-07-08 00:00:00
abstract::Constitutive expression of major histocompatibility complex class II (MHC II) antigens normally occurs in B-lymphocytes and antigen presenting cells of the monocyte/macrophage lineage. However, many malignant tumours and transformed cells express these proteins aberrantly. We demonstrate here that the MHC II DR alpha ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.18.4881
更新日期:1992-09-25 00:00:00
abstract::Bulky lesions in the template strand block the progression of RNA polymerase II (RNAP II) and are repaired more rapidly than lesions in the non-transcribed strand, which do not block transcription. In order to better understand the basis of this transcription-coupled repair we developed an in vitro system with purifie...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.4.787
更新日期:1997-02-15 00:00:00
abstract::Digital PCR provides high sensitivity and unprecedented accuracy in DNA quantification, but current approaches require dedicated instrumentation and have limited opportunities for multiplexing. Here, we present an isothermal platform for digital enumeration of DNA reaction products in multiplex via standard fluorescen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa419
更新日期:2020-07-27 00:00:00
abstract::A linear method for the search of eukaryotic nuclear tRNA genes in DNA databases is described. Based on a modified version of the general weight matrix procedure, our algorithm relies on the recognition of two intragenic control regions known as A and B boxes, a transcription termination signal, and on the evaluation ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.7.1247
更新日期:1994-04-11 00:00:00