Abstract：
:Remodelling protein nucleic acid interfaces is an important biological task, which is often carried out by nucleic acid stimulated ATPases of the Swi2/Snf2 superfamily. Here we study the mechano-chemical cycle of such an ATPase, namely the catalytic domain of the Sulfolobus solfataricus Rad54 homologue (SsoRad54cd), by means of fluorescence resonance energy transfer (FRET). The results of the FRET studies show that the enzyme can be found in (at least) two different possible conformations in solution. An open conformation, consistent with a recently reported crystal structure, is converted into a closed conformation after DNA binding. Upon subsequent binding of ATP no further change in conformation can be detected by the FRET measurements. Instead, a FRET detectable conformational change occurs after ATP hydrolysis and prior to ADP release, suggesting a powerstroke that is linked to phosphate release. Based on these data we will present a new model for the mechano-chemical cycle of this enzyme. This scheme in turn provides a working model for understanding the function of other members of the Swi2/Snf2 family.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Lewis R,Dürr H,Hopfner KP,Michaelis Jdoi
10.1093/nar/gkn040subject
Has Abstractpub_date
2008-04-01 00:00:00pages
1881-90issue
6eissn
0305-1048issn
1362-4962pii
gkn040journal_volume
36pub_type
杂志文章abstract：:Sequences from -3500 to +1365 of the chicken histone H5 gene have been analyzed for the presence of cis-acting elements in H5 expressing (transformed CFU-E) and non-expressing cells (fibroblasts). The region from -3500 to -115 had little effect on transcription. Proximal upstream sequences contain a negative element (...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.18.7495
更新日期：1989-09-25 00:00:00
abstract：:Abasic sites (AP-sites) are frequent DNA lesions, arising by spontaneous base hydrolysis or as intermediates of base excision repair (BER). The hemiacetal at the anomeric centre renders them chemically reactive, which presents a challenge to biochemical and structural investigation. Chemically more stable AP-site anal...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1520
更新日期：2016-03-18 00:00:00
abstract：:The interpretation of data-driven experiments in genomics often involves a search for biological categories that are enriched for the responder genes identified by the experiments. However, knowledge bases such as the Gene Ontology (GO) contain hundreds or thousands of categories with very high overlap between categor...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq045
更新日期：2010-06-01 00:00:00
abstract：:Given the inherent limitations of in silico studies relying solely on DNA sequence analysis, the functional characterization of mammalian promoters and associated cis-regulatory elements requires experimental support, which demands cloning and analysis of putative promoter regions. Focusing on human chromosome 21, we ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq402
更新日期：2010-10-01 00:00:00
abstract：:It has been recently reported that the pR plasmid enhances the UV survival in E.coli c600. In order to test whether this function may be expressed also in mammalian cells, LTA (tk- aprt-) mouse cells were cotransformed with pR plasmid DNA and ptk1 plasmid as selectable marker. Tk+ transformants were analyzed for their...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.11.3679
更新日期：1983-06-11 00:00:00
abstract：:Starting from a synthetic E. coli promoter with the consensus sequences at -35 and -10 regions, a sequence CAT frequently occurred in the RNA start points of natural promoters was introduced in the downstream of the consensus sequences, and the sequences around the RNA start points as well as the relative positions of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.11.4085
更新日期：1985-06-11 00:00:00
abstract：:Evidence will be presented to show that the reagents 3a-c (X = O) obtained by the reaction of 2-chlorophenylphosphorodichloridate with 1-hydroxybenzotriazole or 1-hydroxy-6-trifluoromethyl (6-nitro) benzotriazoles, respectively, do not give, under normal coupling conditions, phosphorylation of the lactam functions in ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.14.5885
更新日期：1986-07-25 00:00:00
abstract：:We have cloned and mapped the sequences extending 38 kb 3' of the c-myc gene. This region is found to be highly repetitive in nature and hybridizes extensively with a BLUR 8 Alu probe. Unique sequence probes derived from this region were used to map the chromosomal breakpoints of a number of lymphoma cell lines with t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.10.4037
更新日期：1986-05-27 00:00:00
abstract：:In this paper, we report the cloning and sequencing of the C. elegans histidyl-tRNA synthetase gene. The complete genomic sequence, and most of the cDNA sequence, of this gene is now determined. The gene size including flanking and coding regions is 2230 nucleotides long. Three small introns (45-50 bp long) are found ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.18.4344
更新日期：1993-09-11 00:00:00
abstract：:Using an in vitro transcription system for Saccharomyces cerevisiae RNA polymerase I, we have analyzed Pol I promoter deletion mutants and mapped the boundaries of the promoter between positions -155 and +27. The 5'-boundary of the minimal core promoter capable of transcription initiation, however, was found to lie be...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.19.5363
更新日期：1991-10-11 00:00:00
abstract：:The variation of the proton chemical shifts due to the formation intermolecular hydrogen bonds is computed for a number of complexes which can be formed between the bases of the nucleic acids. The shifts expected for the isolated base pairs, in particular for the G-N1 H, T(or U)-N3H protons and the protons of the amin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.1.99
更新日期：1977-01-01 00:00:00
abstract：:The RSC complex of Saccharomyces cerevisiae is closely related to the SWI/SNF complex. Both complexes are involved in remodeling chromatin structure and they share conserved components. The RSC proteins Sth1, Rsc8/Swh3, Sfh1 and Rsc6 are homologs of the SWI/SNF proteins Swi2/Snf2, Swi3, Snf5 and Swp73 respectively. To...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.16.3739
更新日期：1998-08-15 00:00:00
abstract：:A complete physical map of the spinach mitochondrial genome has been established. The entire sequence content of 327 kilobase pairs (kb) is postulated to occur as a single circular molecule. Two directly repeated elements of approximately 6 kb, located on this "master chromosome", are proposed to participate in an int...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.14.5651
更新日期：1986-07-25 00:00:00
abstract：:We have developed an improved method for photofootprinting in vivo which utilizes the thermostable DNA polymerase from T. aquaticus (Taq) in a primer extension assay. UV light is used to introduce photoproducts into the genomic DNA of intact yeast cells. The photoproducts are then detected and mapped at the nucleotide...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.1.171
更新日期：1989-01-11 00:00:00
abstract：:The TWIST1 bHLH transcription factor controls embryonic development and cancer processes. Although molecular and genetic analyses have provided a wealth of data on the role of bHLH transcription factors, very little is known on the molecular mechanisms underlying their binding affinity to the E-box sequence of the pro...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw334
更新日期：2016-06-20 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：: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：:Two similar, but not identical, models have been proposed for the amino acid-base pair contacts in the CAP-DNA complex ('Model I,' Weber, I. and Steitz, T., Proc. Natl. Acad. Sci. USA, 81, 3973-3977, 1984; 'Model II,' Ebright, et al., Proc. Natl. Acad. Sci. USA, 81, 7274-7278, 1984). One difference between the two mod...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.23.6853
更新日期：1990-12-11 00:00:00
abstract：:DEAD-box helicases catalyze the non-processive unwinding of double-stranded RNA (dsRNA) at the expense of adenosine triphosphate (ATP) hydrolysis. Nucleotide and RNA binding and unwinding are mediated by the RecA domains of the helicase core, but their cooperation in these processes remains poorly understood. We there...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku747
更新日期：2014-01-01 00:00:00
abstract：:In silico prediction of transcription factor binding sites (TFBSs) is central to the task of gene regulatory network elucidation. Genomic DNA sequence information provides a basis for these predictions, due to the sequence specificity of TF-binding events. However, DNA sequence alone is an impoverished source of infor...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn866
更新日期：2009-01-01 00:00:00
abstract：:In eukaryotes, RNA-binding proteins that contain multiple K homology (KH) domains play a key role in coordinating the different steps of RNA synthesis, metabolism and localization. Understanding how the different KH modules participate in the recognition of the RNA targets is necessary to dissect the way these protein...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks368
更新日期：2012-08-01 00:00:00
abstract：:We report the first investigation of oligoribonucleotides containing a few 1-(2-deoxy-2-alpha-C-hydroxymethyl-beta-D-ribofuranosyl)thymine units (or 2'-hm-dT, abbreviated in this work as 'H'). Both the 2'-CH2O-phosphoramidite and 3'-O-phosphoramidite derivatives of H were synthesized and incorporated into both 2',5'-R...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki1003
更新日期：2005-12-23 00:00:00
abstract：:MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression. They are characterized by specific maturation processes defined by canonical and non-canonical biogenic pathways. Analysis of ∼0.5 billion sequences from mouse data sets derived from different tissues, developmental stages and cell types, partly...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1474
更新日期：2013-03-01 00:00:00
abstract：:As a trial practical application, we have applied optimized microfabricated electrophoresis devices, combined with enzymatic mutation detection methods, to the determination of single nucleotide polymorphism (SNP) sites in the p53 suppressor gene. Using clinical samples, we have achieved robust assays with quality fac...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.9.e43
更新日期：2000-05-01 00:00:00
abstract：:Recent advances in next-generation sequencing technologies and genome assembly algorithms have enabled the accumulation of a huge volume of genome sequences from various species. This has provided new opportunities for large-scale comparative genomics studies. Identifying and utilizing synteny blocks, which are genomi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw310
更新日期：2016-07-08 00:00:00
abstract：:We present the LGA (Local-Global Alignment) method, designed to facilitate the comparison of protein structures or fragments of protein structures in sequence dependent and sequence independent modes. The LGA structure alignment program is available as an online service at http://PredictionCenter.llnl.gov/local/lga. D...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg571
更新日期：2003-07-01 00:00:00
abstract：:PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. In the past two years, PubChem made substantial improvements. Data from more than 100 new data sources were added to PubChem...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa971
更新日期：2021-01-08 00:00:00
abstract：:Previous work has demonstrated that the yeast SPT3 gene is required for transcription from delta sequences, the long terminal repeats that flank yeast Ty elements. In spt3 null mutants, transcription fails to initiate in delta sequences and instead initiates farther downstream. Null mutations in SPT3 cause other mutan...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.17.6885
更新日期：1986-09-11 00:00:00
abstract：:Linkage analysis is a successful procedure to associate diseases with specific genomic regions. These regions are often large, containing hundreds of genes, which make experimental methods employed to identify the disease gene arduous and expensive. We present two methods to prioritize candidates for further experimen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl707
更新日期：2006-01-01 00:00:00
abstract：:The cellular response to DNA double-strand breaks (DSBs) is initiated by the Mre11-Rad50-Xrs2 (MRX) complex that has structural and catalytic functions. MRX association at DSBs is counteracted by Rif2, which is known to interact with Rap1 that binds telomeric DNA through two tandem Myb-like domains. Whether and how Ra...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz1203
更新日期：2020-03-18 00:00:00
