Abstract:
:The structure of eukaryotic chromatin has been investigated by isolating and analyzing the "accessible" DNA fraction of rat liver chromatin. This DNA fraction has been isolated by titrating the chromatin with the protese-resistant D isomer of polylysine to bind the "accessible" DNA sites. After removal of chromosomal proteins by digestion with pronase, all DNA not protected from attack by bound polylysine was removed by digestion with DNase. Even after exhaustive treatment with pronase and DNase approximately 30% of the chromatin DNA remains resistant to nuclease attack. Analysis of the isolated DNA shows it to be mainly double-stranded with an average size of 200-250 base pairs. The DNA is slightly A-T rich and contains both repetitive and "single-copy" nuleotide sequences. The results suggest that there are extensive regions in chromatin where the DNA is not tightly complexed with protein. Furthermore, the DNA of these regions is similar in gross properties to the DNA of the total genome.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Arnold EA,Wahn U,Young KEdoi
10.1093/nar/2.5.667keywords:
subject
Has Abstractpub_date
1975-05-01 00:00:00pages
667-81issue
5eissn
0305-1048issn
1362-4962journal_volume
2pub_type
杂志文章abstract::This paper describes a method for predicting a supersecondary structural motif, beta-hairpins, in a protein sequence. The method was trained and tested on a set of 5102 hairpins and 5131 non-hairpins, obtained from a non-redundant dataset of 2880 proteins using the DSSP and PROMOTIF programs. Two machine-learning tech...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki588
更新日期:2005-07-01 00:00:00
abstract::The DNA-binding protein RdgC has been identified as an inhibitor of RecA-mediated homologous recombination in Escherichia coli. In Neisseria species, RdgC also has a role in virulence-associated antigenic variation. We have previously solved the crystal structure of the E. coli RdgC protein and shown it to form a toro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq509
更新日期:2010-10-01 00:00:00
abstract::The rol-6 gene is trans-spliced to the 22 nt leader, SL1, 173 nt downstream of the transcription start. We have analyzed splicing in transformants carrying extrachromosomal arrays of rol-6 with mutations in the trans-splice acceptor site. This site is a close match to the consensus, UUUCAG, that is highly conserved in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.4.913
更新日期:1993-02-25 00:00:00
abstract::Polyaromatic molecules with amino chain substituents, upon binding with DNA, selectively catalyze exchange of the A.T base pair protons with bulk water protons. The amine-catalyzed exchange is mediated by compounds which are A.T and G.C base sequence specific, intercalators, and outside binders. A mechanism for the se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.20.8511
更新日期:1987-10-26 00:00:00
abstract::In Arabidopsis thaliana, endogenous trans-acting and exogenous siRNA pathways are initiated by the interaction of DRB4 with trigger dsRNA. Further, DCL4:DRB4 complex cleaves the dsRNA into 21 bp siRNA. Understanding molecular determinants and mechanistic details of dsRNA recognition by DRB4 is vital for inducing long-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx481
更新日期:2017-08-21 00:00:00
abstract::This laboratory has established in previous studies that Pmel 17, a gene expressed specifically in melanocytes, maps near the silver coat color locus (si/si) on mouse chromosome 10. In the current study, we have focused on determining whether or not the si allele carries a mutation in Pmel 17. Pmel 17 cDNA clones, iso...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.1.154
更新日期:1995-01-11 00:00:00
abstract::The chromatin structure of a germ-line specific gene, the TPG-3 gene, one of the rainbow trout protamine genes was analyzed in various tissues. The protamine genes are expressed in early stage testis but not in late stage testis, liver or erythrocyte. Five potential CpG methylation sites in the coding and flanking reg...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.8.3385
更新日期:1987-04-24 00:00:00
abstract::A novel method of determining the number of superhelical turns of a covalently-closed plasmid DNA is described. It relies on the determination of the hyperchromicity, and hence the proportion of unstacked basepairs, of a partially heat-denatured sample which co-migrates during electrophoresis with nicked circular dupl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.2.525
更新日期:1982-01-22 00:00:00
abstract::In prokaryotes and archaea transfer ribonucleic acid (tRNA) stability as well as cellular UV protection relies on the post-transcriptional modification of uracil at position 8 (U8) of tRNAs by the 4-thiouridine synthetase ThiI. Here, we report three crystal structures of ThiI from Thermotoga maritima in complex with a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku249
更新日期:2014-06-01 00:00:00
abstract::The mutation patterns at Cas9 targeted sites contain unique information regarding the nuclease activity and repair mechanisms in mammalian cells. However, analytical framework for extracting such information are lacking. Here, we present a novel computational platform called Rational InDel Meta-Analysis (RIMA) that en...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky653
更新日期:2018-09-19 00:00:00
abstract::I have used a novel single-sided specific polymerase chain reaction (PCR) strategy inspired by ligation-mediated PCR to clone fragments of divergent homeobox genes from a flatworm, the planarian Polycelis nigra. Eight homeobox-containing fragments were amplified, belonging to the Hox, msh, NK-1 and NK-2 classes. Toget...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.8.1547
更新日期:1996-04-15 00:00:00
abstract::Terminal deoxynucleotidyl transferase, which requires a single-stranded DNA primer under the usual assay conditions, can be made to accept double-stranded DNA as primer for the addition of either rNMP or dNMP, if Mg+2 ion is replaced by Co+2 ion. The priming efficiency in the presence of (C leads to) CO+2 ion with res...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.1.101
更新日期:1976-01-01 00:00:00
abstract::DNA mismatches that occur between vector homology arms and chromosomal target sequences reduce gene targeting frequencies in several species; however, this has not been reported in human cells. Here we demonstrate that even a single mismatched base pair can significantly decrease human gene targeting frequencies. In a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1303
更新日期:2014-03-01 00:00:00
abstract::Molecules of single-stranded ribosomal RNA and double-stranded replicative form of phage f2 RNA (dsRNA) adopt a compact form in solutions, containing sufficiently high concentrations of salt (NaCl) and polymer (PEG). However, only in the cases of native dsRNA molecules the compact particles are characterized by a regu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.6.1533
更新日期:1976-06-01 00:00:00
abstract::The results of differential expression analyses provide scientists with hundreds to thousands of differentially expressed genes that need to be interpreted in light of the biology of the specific system under study. This requires mapping the genes to functional classifications that can be, for example, the KEGG pathwa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt516
更新日期:2013-07-01 00:00:00
abstract::A cDNA encoding the 60 kDa subunit of mammalian splicing factor SF3a has been isolated. The deduced protein sequence reveals a 30% identity to the PRP9 splicing protein of the yeast S.cerevisiae. The highest homology is present in a zinc finger-like region in the C-terminal domain of both proteins. The PRP9 zinc finge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.24.5223
更新日期:1994-12-11 00:00:00
abstract::Escherichia coli DNA polymerase III holoenzyme is composed of 10 different subunits linked by noncovalent interactions. The polymerase activity resides in the alpha-subunit. The epsilon-subunit, which contains the proofreading exonuclease site within its N-terminal 185 residues, binds to alpha via a segment of 57 addi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn489
更新日期:2008-09-01 00:00:00
abstract::Conserved in a variety of evolutionarily divergent plant species, LOB DOMAIN (LBD) genes define a large, plant-specific family of largely unknown function. LBD genes have been implicated in a variety of developmental processes in plants, although to date, relatively few members have been assigned functions. LBD protei...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm775
更新日期:2007-01-01 00:00:00
abstract::In an RNase III-deficient strain of E. coli 23S pre-rRNA accumulates unprocessed in 50S ribosomes and in polysomes. These ribosomes provide a substrate for the analysis of rRNA maturation in vitro. S1 nuclease protection analysis of the products obtained in in vitro processing reactions demonstrates that 23S rRNA proc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.14.5041
更新日期:1985-07-25 00:00:00
abstract::DnaD and DnaB are essential DNA-replication-initiation proteins in low-G+C content Gram-positive bacteria. Here we use sensitive Hidden Markov Model-based techniques to show that the DnaB and DnaD proteins share a common structure that is evident across all their structural domains, termed DDBH1 and DDBH2 (DnaD DnaB H...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq465
更新日期:2010-11-01 00:00:00
abstract::Ribotoxins are potent inhibitors of protein biosynthesis and inactivate ribosomes from a variety of organisms. The ribotoxin alpha-sarcin cleaves the large 23S ribosomal RNA (rRNA) at the universally conserved sarcin-ricin loop (SRL) leading to complete inactivation of the ribosome and cellular death. The SRL interact...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq151
更新日期:2010-07-01 00:00:00
abstract::The FREP database (http://facts.gsc.riken.go.jp/FREP/) contains 31 396 RepeatMasker-identified non-redundant variant repeat sequences derived from 16,527 mouse cDNAs with protein-coding potential. The repeats were computationally associated with potential effects on transcriptional variation, translation, protein func...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh123
更新日期:2004-01-01 00:00:00
abstract::The specific DNA binding ligand netropsin selectively blocks dA-dT base pairs in clusters containing two or more consecutive thymine residues at the dNAase I cleavage sites of DNA. Using CD and UV absorption measurements it is shown, that at various ratios of netropsin to nucleotide concentrations and even at satuatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.13.2999
更新日期:1980-07-11 00:00:00
abstract::The codon UGA located 5' adjacent to an mRNA hairpin within fdhF mRNA promotes the incorporation of the amino acid selenocysteine into formate dehydrogenase H of Escherichia coli. The loop region of this mRNA hairpin has been shown to bind to the special elongation factor SELB, which also forms a complex with selenocy...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.20.3903
更新日期:1996-10-15 00:00:00
abstract::We have investigated the substrate specificity of the Ogg1 protein of Saccharomyces cerevisiae (yOgg1 protein) for excision of modified DNA bases from oxidatively damaged DNA substrates using gas chromatography/isotope dilution mass spectrometry. Four DNA substrates prepared by treatment with H2O2/Fe(III)-EDTA/ascorbi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.5.1228
更新日期:1998-03-01 00:00:00
abstract::PlantGDB (http://www.plantgdb.org/) is a genomics database encompassing sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript assemblies for >100 plant species, with transcripts mapped to their cognate genomic context where available, integrated with a variety of sequence analysis tool...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1041
更新日期:2008-01-01 00:00:00
abstract::A method to purify histone groups H2A+H2B and H3+H4 using dissociation with NaCl and hydroxylapatite chromatography is presented. The procedure is simple, involves mild solvents, and provides milligram quantities of histones of high purity. The histone pairs prepared by this method can regenerate chromatin-like charac...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.2.689
更新日期:1979-02-01 00:00:00
abstract::We have analyzed the molecular mechanism that makes translation of the MS2 replicase cistron dependent on the translation of the upstream coat cistron. Deletion mapping on cloned cDNA of the phage shows that the ribosomal binding site of the replicase cistron is masked by a long distance basepairing to an internal coa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.19.6955
更新日期:1985-10-11 00:00:00
abstract::To explain biochemical and genetic data on spontaneous nucleotide replacements in nucleic acid biosynthesis all the 8 mispairs in normal tautomeric forms have been considered. Possible B-conformations of DNA fragments containing each of such mispairs incorporated between Watson-Crick pairs have been found using comput...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.1.141
更新日期:1985-01-11 00:00:00
abstract::Chromatin core particles near physiological ionic strength undergo a reversible transition induced by changes in pH near neutrality. While sedimentation studies indicate no significant effect on size or shape, changes in tyrosine fluorescence anisotropy and in circular dichroism suggest a somewhat looser structure at ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.10.4351
更新日期:1984-05-25 00:00:00