Abstract：
:The Cox protein from bacteriophage P2 forms oligomeric filaments and it has been proposed that DNA can be wound up around these filaments, similar to how histones condense DNA. We here use fluorescence microscopy to study single DNA-Cox complexes in nanofluidic channels and compare how the Cox homologs from phages P2 and WΦ affect DNA. By measuring the extension of nanoconfined DNA in absence and presence of Cox we show that the protein compacts DNA and that the binding is highly cooperative, in agreement with the model of a Cox filament around which DNA is wrapped. Furthermore, comparing microscopy images for the wild-type P2 Cox protein and two mutants allows us to discriminate between compaction due to filament formation and compaction by monomeric Cox. P2 and WΦ Cox have similar effects on the physical properties of DNA and the subtle, but significant, differences in DNA binding are due to differences in binding affinity rather than binding mode. The presented work highlights the use of single DNA molecule studies to confirm structural predictions from X-ray crystallography. It also shows how a small protein by oligomerization can have great impact on the organization of DNA and thereby fulfill multiple regulatory functions.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Frykholm K,Berntsson RP,Claesson M,de Battice L,Odegrip R,Stenmark P,Westerlund Fdoi
10.1093/nar/gkw352subject
Has Abstractpub_date
2016-09-06 00:00:00pages
7219-27issue
15eissn
0305-1048issn
1362-4962pii
gkw352journal_volume
44pub_type
杂志文章abstract：:More than 20 different heterogeneous nuclear ribonucleoproteins (hnRNPs) are associated with pre-mRNAs in the nucleus of mammalian cells and these proteins appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. The arrangement of hnRNP proteins on pre-mRNAs is likely to be unique f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.6.1059
更新日期：1994-03-25 00:00:00
abstract：:It is informative to detect highly conserved positions in proteins and nucleic acid sequence/structure since they are often indicative of structural and/or functional importance. ConSurf (http://consurf.tau.ac.il) and ConSeq (http://conseq.tau.ac.il) are two well-established web servers for calculating the evolutionar...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq399
更新日期：2010-07-01 00:00:00
abstract：:Nucleotide excision repair (NER) mechanism is the major pathway responsible for the removal of a large variety of bulky lesions from the genome. Two different NER subpathways have been identified, i.e. the transcription-coupled and the global genome repair pathways. For DNA-damage induced by ultraviolet light both tra...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.23.4653
更新日期：1996-12-01 00:00:00
abstract：:Activating sequence factor 1 (ASF-1) is a nuclear DNA-binding activity that is found in monocots and dicots. It interacts with several TGACG-containing elements that have been characterized from viral and T-DNA genes, the prototypes of which are the as-1 element of the CaMV 35S promoter and the ocs element from the oc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.18.3778
更新日期：1995-09-25 00:00:00
abstract：:In this report we have analyzed the role of antisense transcription in the control of LEF1 transcription factor expression. A natural antisense transcript (NAT) is transcribed from a promoter present in the first intron of LEF1 gene and undergoes splicing in mesenchymal cells. Although this locus is silent in epitheli...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv502
更新日期：2015-07-13 00:00:00
abstract：:We have isolated the gene coding for the U2 analogue in trypanosomes. The 148 nucleotide long U2 RNA is capped and transcribed from a single copy gene. The 5' half of the molecule is highly homologous to mammalian U2 RNA, while the 3' half does not show any significant sequence homology with the mammalian counterpart....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.22.8893
更新日期：1986-11-25 00:00:00
abstract：:Gene Ontology (GO) is the most widely accepted attempt to construct a unified and structured vocabulary for the description of genes and their products in any organism. Annotation by GO terms is performed in most of the current genome projects, which besides generality has the advantage of being very convenient for co...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg582
更新日期：2003-07-01 00:00:00
abstract：:Pax-5, a member of the paired domain family of transcription factors, is a key regulator of B lymphocyte-specific transcription and differentiation. A major target of Pax-5-mediated activation is the mb-1 gene, which encodes the essential transmembrane signaling protein Ig-alpha. Pax-5 recruits three members of the Et...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg785
更新日期：2003-10-01 00:00:00
abstract：:A computer program, BRUCE, was developed for the identification of transfer-messenger RNA (tmRNA) genes. The program employs heuristic algorithms to search for a tRNA(Ala)-like secondary structure surrounding a short sequence encoding the tag peptide. In the 57 completely sequenced bacterial genomes where tmRNA genes ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf459
更新日期：2002-08-01 00:00:00
abstract：:Accurate maps and DNA sequences for human subtelomere regions, along with detailed knowledge of subtelomere variation and long-range telomere-terminal haplotypes in individuals, are critical for understanding telomere function and its roles in human biology. Here, we use a highly automated whole genome mapping technol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx017
更新日期：2017-05-19 00:00:00
abstract：:Eukaryotic genomes contain many endogenous retroviral sequences (ERVs). ERVs are often severely mutated, therefore difficult to detect. A platform independent (Java) program package, RetroTector (ReTe), was constructed. It has three basic modules: (i) detection of candidate long terminal repeats (LTRs), (ii) detection...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm515
更新日期：2007-01-01 00:00:00
abstract：:The transactivator responsive region (TAR) present in the 5'-NTR of the HIV-1 genome represents a potential target for antiretroviral intervention and a model system for the development of specific inhibitors of RNA-protein interaction. Earlier, we have shown that an anti-TAR polyamide nucleotide analog (PNA(TAR)) con...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki743
更新日期：2005-08-02 00:00:00
abstract：:Polyploidy, the presence of multiple sets of chromosomes that are similar but not identical, complicates both chromosome walking and assembly of sequence-ready contigs for many plant taxa including a large number of economically-significant crops. Traditional 'dot-blot hybridization' or PCR-based assays for identifyin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.7.e23
更新日期：2000-04-01 00:00:00
abstract：:Genome-wide association studies (GWAS) have become a preferred method to identify new genetic susceptibility loci. This technique aims to understanding the molecular etiology of common diseases, but in many cases, it has led to the identification of loci with no obvious biological relevance. Herein, we show that previ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks169
更新日期：2012-06-01 00:00:00
abstract：:The DNA sequence of a 354 basepair EcoRI-HindIII fragment of plasmid pMB9 which has originally been derived from plasmid pSC101 has been resolved. This fragment contains a promoter for transcription directed towards the EcoRI site. Escherichia coli RNA polymerase binds to a region within the EcoRI-HindIII fragment whi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.7.1535
更新日期：1980-04-11 00:00:00
abstract：:RNA pseudoknots are functional structure elements with key roles in viral and cellular processes. Prediction of a pseudoknotted minimum free energy structure is an NP-complete problem. Practical algorithms for RNA structure prediction including restricted classes of pseudoknots suffer from high runtime and poor accura...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq021
更新日期：2010-04-01 00:00:00
abstract：:We have studied the effect of selenium on the expression of a cellular glutathione peroxidase, GSHPx-1, in transfected MCF-7 cells and in doxorubicin-resistant (Adrr) MCF-7 cells. A GSHPx-1 cDNA with a Rous Sarcoma virus promoter was transfected into a human mammary carcinoma cell line, MCF-7, which has very low endog...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.6.1531
更新日期：1990-03-25 00:00:00
abstract：:Cloned ribosomal DNA (rDNA) of Locusta migratoria was analyzed by restriction site mapping and SI nuclease experiments. The repeat unit is 18 kb long. The nontranscribed spacer region (NTS) is very large (11 kb) and homogeneous in length, but many of the restriction sites are heterogeneous among the repeat units. Two ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.4.1251
更新日期：1985-02-25 00:00:00
abstract：:We devised an indicator gene for retrotransposition based on an autocatalytic ribozyme element--the Tetrahymena thermophila 23S rRNA group I intron--which can self-splice in vitro and does not require--at variance with nuclear mRNA introns--any specific pathway and cellular component for the completion of the splicing...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.11.e49
更新日期：2002-06-01 00:00:00
abstract：:In Escherichia coli, the MnmEG complex modifies transfer RNAs (tRNAs) decoding NNA/NNG codons. MnmEG catalyzes two different modification reactions, which add an aminomethyl (nm) or carboxymethylaminomethyl (cmnm) group to position 5 of the anticodon wobble uridine using ammonium or glycine, respectively. In tRNA(cmnm...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1228
更新日期：2014-02-01 00:00:00
abstract：:Evidence is presented that the editing mechanisms of aminoacyl-tRNA synthetase operate by two alternative pathways: pre-transfer, by hydrolysis of the non-cognate aminoacyl adenylate; post-transfer, by hydrolysis of the mischarged tRNA. The methionyl-tRNA synthetases from Escherichia coli and Bacillus stearothermophil...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.13.3105
更新日期：1981-07-10 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：:The origin of replication of the c-myc gene in HeLa cells was previously identified at low resolution within 3.5 kb 5' to the P1 promoter, based on replication fork polarity and the location of DNA nascent strands. To define the initiation events in the c-myc origin at higher resolution the template bias of nascent DN...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.10.1887
更新日期：1996-05-15 00:00:00
abstract：:Light-inducible systems allow spatiotemporal control of a variety of biological activities. Here, we report newly optimized optogenetic tools to induce transcription with light in mammalian cells, using the Arabidopsis photoreceptor Flavin Kelch-repeat F-box 1 (FKF1) and its binding partner GIGANTEA (GI) as well as CR...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx804
更新日期：2017-11-16 00:00:00
abstract：:Evidence has emerged that repair of clustered DNA lesions may be compromised, possibly leading to the formation of double-strand breaks (DSB) and, thus, to deleterious events. The first repair event occurring at a multiply damaged site (MDS) is of major importance and will largely contribute to the hazardousness of MD...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm190
更新日期：2007-01-01 00:00:00
abstract：:An examination, using reversed-phase chromatography and cyanogen bromide treatment, of tRNATyr, tRNAHis, tRNAAsn, and tRNAAsp from SV40-transformed mouse fibroblasts grown to different cell densities, untransformed cells grown to confluence, and mouse liver indicates that: (1) The tissue cultured mouse fibroblasts exa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.7.2513
更新日期：1978-07-01 00:00:00
abstract：:Ditercalinium, an antitumor bifunctional intercalator which forms a high affinity reversible complex with DNA, was found to be specifically cytotoxic for polA and lig7 E. coli strains. In the polA strain, the cytotoxic effect of ditercalinium was suppressed by the uvrA mutation. DNA single strand breaks accumulated in...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.3.1063
更新日期：1988-02-11 00:00:00
abstract：:In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3'- and 5'-ends of 261 yeast genes by run-on. The results obtained indicate that the 3'/5' run-on ratio varies among the genes studied by over 12 log(2) units. This ratio seem...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq215
更新日期：2010-08-01 00:00:00
abstract：:High-resolution structures of proteins remain the most valuable source for understanding their function in the cell and provide leads for drug design. Since the availability of sufficient protein structures to tackle complex problems such as modeling backbone moves or docking remains a problem, alternative approaches ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq972
更新日期：2011-01-01 00:00:00
abstract：:Oligonucleotides synthesized in array format suffer from contamination by truncated species. We have developed a method to invert DNA molecules in situ after completed synthesis. Reactive functions at the 5'-ends of the oligonucleotides are permitted to react with functions on the support before the 3'-ends are releas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.24.4710
更新日期：1999-12-15 00:00:00
