Abstract:
:Fundamental aspects of the biochemistry of Type III restriction endonucleases remain unresolved despite being characterized by numerous research groups in the past decades. One such feature is the subunit stoichiometry of these hetero-oligomeric enzyme complexes, which has important implications for the reaction mechanism. In this study, we present a series of results obtained by native mass spectrometry and size exclusion chromatography with multi-angle light scattering consistent with a 1:2 ratio of Res to Mod subunits in the EcoP15I, EcoPI and PstII complexes as the main holoenzyme species and a 1:1 stoichiometry of specific DNA (sDNA) binding by EcoP15I and EcoPI. Our data are also consistent with a model where ATP hydrolysis activated by recognition site binding leads to release of the enzyme from the site, dissociation from the substrate via a free DNA end and cleavage of the DNA. These results are discussed critically in the light of the published literature, aiming to resolve controversies and discuss consequences in terms of the reaction mechanism.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Butterer A,Pernstich C,Smith RM,Sobott F,Szczelkun MD,Tóth Jdoi
10.1093/nar/gku122subject
Has Abstractpub_date
2014-04-01 00:00:00pages
5139-50issue
8eissn
0305-1048issn
1362-4962pii
gku122journal_volume
42pub_type
杂志文章abstract::Cells of the central nervous system (CNS) are prone to the devastating consequences of trinucleotide repeat (TNR) expansion. Some CNS cells, including astrocytes, show substantial TNR instability in affected individuals. Since astrocyte enrichment occurs in brain regions sensitive to neurodegeneration and somatic TNR ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl614
更新日期:2006-01-01 00:00:00
abstract::The properties of the interaction of 5-fluorocytosine-containing DNA with the EcoRII methyltransferase were studied. The DNA used was either a polymer synthesized in vitro, or a 20-mer containing one CCA/TGG sequence. The DNA could be methylated by the enzyme. In the process the enzyme formed a tight binding adduct wi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.12.3241
更新日期:1992-06-25 00:00:00
abstract::The linking number of DNA in minichromosomes increases by 2 turns during SV40 assembly. Changes in temperature also influence the average linking number of the total intracellular forms of SV40 DNA. When the isolated minichromosomes assembled in vivo are incubated with topoisomerase I at 33 degrees C in vitro, the lin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.9.3703
更新日期:1987-05-11 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn511
更新日期:2008-11-01 00:00:00
abstract::This review presents detailed information about the structure of triplet repeat RNA and addresses the simple sequence repeats of normal and expanded lengths in the context of the physiological and pathogenic roles played in human cells. First, we discuss the occurrence and frequency of various trinucleotide repeats in...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkr729
更新日期:2012-01-01 00:00:00
abstract::The restriction endonuclease (R.BsuFI) of Bacillus subtilis recognizes the target DNA sequence 5' CCGG. The R.BsuFI gene was found in close proximity to the cognate M.BsuFI gene, which had previously been characterized (1). Cloning of the R.BsuFI gene in E.coli was only possible with the M.BsuFI Mtase gene present on ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.23.6457
更新日期:1991-12-11 00:00:00
abstract::We demonstrate a single DNA molecule optical mapping assay able to resolve a specific Escherichia coli strain from other strains. The assay is based on competitive binding of the fluorescent dye YOYO-1 and the AT-specific antibiotic netropsin. The optical map is visualized by stretching the DNA molecules in nanofluidi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku556
更新日期:2014-09-01 00:00:00
abstract::To explain the activation of transcription by a remote enhancer, two models are most often considered, namely looping and scanning. A scanning model, also referred to as 'polymerase entry site' model predicts that for two adjacent promoters the one proximal to an enhancer would be preferentially activated. Preferentia...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.22.8931
更新日期:1989-11-25 00:00:00
abstract::The frequencies of each of the 257 468 complete protein coding sequences (CDSs) have been compiled from the taxonomical divisions of the GenBank DNA sequence database. The sum of the codons used by 8792 organisms has also been calculated. The data files can be obtained from the anonymous ftp sites of DDBJ, Kazusa and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.1.292
更新日期:2000-01-01 00:00:00
abstract::We have recently described three group I introns inserted into a single gene, orf142, of the staphylococcal bacteriophage Twort and suggested the presence of at least two additional self-splicing introns in this phage genome. Here we report that two previously uncharacterized introns, 429 and 1087 nt in length, interr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.9.1935
更新日期:2002-05-01 00:00:00
abstract::We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5'-alternative splicing, 3'-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki129
更新日期:2005-01-01 00:00:00
abstract::Lnc2Meth (http://www.bio-bigdata.com/Lnc2Meth/), an interactive resource to identify regulatory relationships between human long non-coding RNAs (lncRNAs) and DNA methylation, is not only a manually curated collection and annotation of experimentally supported lncRNAs-DNA methylation associations but also a platform t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx985
更新日期:2018-01-04 00:00:00
abstract::Hepatocyte Nuclear Factor 4 (HNF-4), a liver-enriched orphan receptor of the nuclear receptor superfamily, is required for the expression of a wide variety of liver-specific genes including apoAI. To explore the possibility that site A of the apoAI gene enhancer might also be the target for HNF-4 without the interfere...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.25.5665
更新日期:1994-12-25 00:00:00
abstract::In this study we describe a novel method to investigate the RNA-RNA interactions between a small RNA and its target that we termed 'RNA walk'. The method is based on UV-induced AMT cross-linking in vivo followed by affinity selection of the hybrid molecules and mapping the intermolecular adducts by RT-PCR or real-time...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp872
更新日期:2010-01-01 00:00:00
abstract::Traditional chromatin analysis methods only test one locus at the time or use different templates for each locus, making a standardized analysis of large genomic regions or many co-regulated genes at different loci a difficult task. On the other hand, genome-wide high-resolution mapping of chromatin accessibility empl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp037
更新日期:2009-04-01 00:00:00
abstract::Recombinase proteins assembled into helical filaments on DNA are believed to be the catalytic core of homologous recombination. The assembly, disassembly and dynamic rearrangements of this structure must drive the DNA strand exchange reactions of homologous recombination. The sensitivity of eukaryotic recombinase acti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki640
更新日期:2005-06-08 00:00:00
abstract::Cortical development is controlled by transcriptional programs, which are orchestrated by transcription factors. Yet, stable inheritance of spatio-temporal activity of factors influencing cell fate and localization in different layers is only partly understood. Here we find that deletion of Dot1l in the murine telence...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky953
更新日期:2019-01-10 00:00:00
abstract::A phosphotriester solid phase method on a polyamide support has been used to prepare oligodeoxyribonucleotides up to 12 units long. Compared to solid phase phosphodiester synthesis the new methodology is quicker, more flexible and gives 10-60-fold better overall yields. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.5.1081
更新日期:1980-03-11 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz136
更新日期:2019-05-07 00:00:00
abstract::A novel cytoplasmic gene expression system has been developed. This system differs from other expression systems in that it relies on the co-delivery of plasmid DNA and T7 RNA polymerase (RNAP) during transfection. The plasmid contains a T7 RNAP gene driven by the T7 promoter (T7 autogene) and a functional/reporter ge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.11.2114
更新日期:1994-06-11 00:00:00
abstract::We have previously described programs for a variety of types of sequence analysis (1-4). These programs have now been integrated into a single package. They are written in the standard C programming language and run on virtually any computer system with a C compiler, such as the IBM/PC and other computers running unde...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.1.443
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh018
更新日期:2004-02-03 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm762
更新日期:2008-01-01 00:00:00
abstract::We describe here the cloning, characterization and expression in E. coli of the gene coding for a DNA methylase from Spiroplasma sp. strain MQ1 (M.SssI). This enzyme methylates completely and exclusively CpG sequences. The Spiroplasma gene was transcribed in E. coli using its own promoter. Translation of the entire me...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.5.1145
更新日期:1990-03-11 00:00:00
abstract::Mutational analysis has shown that the integrity of the region in domain III of 25S rRNA that is involved in binding of ribosomal protein L25 is essential for the production of mature 25S rRNA in the yeast Saccharomyces cerevisiae. However, even structural alterations that do not noticeably affect recognition by L25, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.24.5001
更新日期:2001-12-15 00:00:00
abstract::The 'sandwich' binding format, which uses two reagents that can bind simultaneously to a given analyte, is the gold standard in diagnostics and many biochemical techniques. One of the bottlenecks in creating a sandwich assay is identifying pairs of reagents that bind non-competitively to the target. To bridge this gap...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx688
更新日期:2017-10-13 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr555
更新日期:2011-10-01 00:00:00
abstract::The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1331
更新日期:2013-02-01 00:00:00
abstract::An efficient procedure for the synthesis of unnatural alpha-anomeric oligodeoxyribonucleotides is described. This solid-phase procedure is based on the use of alpha-nucleoside phosphoramidites and alpha-nucleoside derivatized solid supports corresponding to the four natural bases and allow rapid synthesis of oligonucl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.3.833
更新日期:1988-02-11 00:00:00