Abstract:
:In spermidine-condensed calf thymus DNA preparations, torus-shaped condensates were shown by transmission electron microscopy to exist under the hydrated conditions of the freeze fracture experiment. Using extremely low Pt metal deposition levels (9 A Pt/C) high-contrast replicas of the spermidine-DNA toruses were obtained that showed circumferential wrapping of single DNA double helix-size surface fibres. Stereoscopic analysis of high magnification stereomicrographs established some details of the three-dimensional organization of two DNA double helix sections winding circumferentially on the inner surface of one such torus. These measurements demonstrate the usefulness of stereoscopic analysis of these high macromolecular organization magnification. Measurements on a number of torus-shaped complexes (n = 16) yielded these average dimensions: inner circumference (1840 +/- 204 A) outer circumference (2800 +/- 222 A), torus ring thickness (143 +/- 18 A). These data support a continuous circumferential DNA-winding model of torus organization proposed by Marx & Reynolds.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Marx KA,Ruben GCdoi
10.1093/nar/11.6.1839subject
Has Abstractpub_date
1983-03-25 00:00:00pages
1839-54issue
6eissn
0305-1048issn
1362-4962journal_volume
11pub_type
杂志文章abstract::Proteins that bind to DNA are found in all areas of genetic activity within the cell. To help understand how these proteins perform their various functions, it is useful to analyse which residues are involved in binding to the DNA and how they interact with the bases and sugar-phosphate backbone of nucleic acids. Here...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.24.4940
更新日期:1997-12-15 00:00:00
abstract::A straightforward enzymatic protocol for converting regular DNA into pseudo-complementary DNA could improve the performance of oligonucleotide microarrays by generating readily hybridizable structure-free targets. Here we screened several highly destabilizing analogs of G and C for one that could be used with 2-aminoa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn797
更新日期:2008-12-01 00:00:00
abstract::ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org/modelle...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1144
更新日期:2014-01-01 00:00:00
abstract::Gene expression is a multi-step process involving many layers of regulation. The main regulators of the pathway are DNA and RNA binding proteins. While over the years, a large number of DNA and RNA binding proteins have been identified and extensively studied, it is still expected that many other proteins, some with y...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw454
更新日期:2016-07-08 00:00:00
abstract::We have detected a set of transcripts in Drosophila melanogaster cells which are homologous to repeating elements within the 'non-transcribed' spacer region of rDNA. The RNA molecules range from 240 to 1680 nucleotides, differing in length by an integral value of 240 nucleotides. We have sequenced several AluI fragmen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.1.11
更新日期:1983-01-11 00:00:00
abstract::The rat alpha- and bovine alpha s1-casein genes have been isolated and their 5' sequences determined. The rat alpha-, beta-, gamma- and bovine alpha s1-casein genes contain similar 5' exon arrangements in which the 5' noncoding, signal peptide and casein kinase phosphorylation sequences are each encoded by separate ex...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.4.1883
更新日期:1986-02-25 00:00:00
abstract::Post-translational modifications (PTMs) play a key role in numerous cellular processes by directly affecting structure, dynamics and interaction networks of target proteins. Despite their importance, our understanding of protein PTMs at the atomistic level is still largely incomplete. Molecular dynamics (MD) simulatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt416
更新日期:2013-07-01 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
abstract::Improving the accuracy of prediction of gene starts is one of a few remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of relatively strong sequence patterns identifying true translation initiation sites. In the current paper we show that the accuracy of gene s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.12.2607
更新日期:2001-06-15 00:00:00
abstract::Cell cycle checkpoints induced by DNA damage play an integral role in preservation of genomic stability by allowing cells to limit the propagation of deleterious mutations. The retinoblastoma tumor suppressor (RB) is crucial for the maintenance of the DNA damage checkpoint function because it elicits cell cycle arrest...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg919
更新日期:2004-01-02 00:00:00
abstract::Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1074
更新日期:2012-01-01 00:00:00
abstract::Analysis of the human protein-tyrosine phosphatase (PTP) PTPRJ mRNA detected three in-frame AUGs at the 5'-end (starting at nt +14, +191 and +356) with no intervening stop codons. This tandem AUG arrangement is conserved between humans and the mouse and is unique among the genes of the classical PTPs. Until now it was...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn391
更新日期:2008-08-01 00:00:00
abstract::Giant chromatin-modifying complexes regulate gene transcription in eukaryotes by acting on chromatin substrates and 'setting' the histone code. The histone deacetylase (HDAC)-associated mammalian Sin3 corepressor complex regulates a wide variety of genes involved in all aspects of cellular physiology. The recruitment ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp051
更新日期:2009-04-01 00:00:00
abstract::The satellite RNA of tobacco ringspot virus (STobRV RNA) replicates and becomes encapsidated in association with tobacco ringspot virus. Previous results show that the infected tissue produces multimeric STobRV RNAs of both polarities. RNA that is complementary to encapsidated STobRV RNA, designated as having the (-) ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.24.9729
更新日期:1986-12-22 00:00:00
abstract::In eukaryotic cells, the shortening and removal of the poly(A) tail of cytoplasmic mRNA by deadenylase enzymes is a critical step in post-transcriptional gene regulation. The ribonuclease activity of deadenylase enzymes is attributed to either a DEDD (Asp-Glu-Asp-Asp) or an endonuclease-exonuclease-phosphatase domain....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt972
更新日期:2014-03-01 00:00:00
abstract::Upon endocytosis, most oligodeoxynucleotides (ODNs) accumulate in vesicular compartments; a tiny number of them cross the vesicle membrane, reach the cytosol and by passive diffusion enter the nucleus where they are entrapped. So far, the compartment in which an antisense ODN interacts with its mRNA target has not bee...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.13.2730
更新日期:1999-07-01 00:00:00
abstract::Single nucleotide polymorphisms (SNPs) are, together with copy number variation, the primary source of variation in the human genome. SNPs are associated with altered response to drug treatment, susceptibility to disease and other phenotypic variation. Furthermore, during genetic screens for disease-associated mutatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm979
更新日期:2008-01-01 00:00:00
abstract::The database of molecular motions, MolMovDB (http://molmovdb.org), has been in existence for the past decade. It classifies macromolecular motions and provides tools to interpolate between two conformations (the Morph Server) and predict possible motions in a single structure. In 2005, we expanded the services offered...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj046
更新日期:2006-01-01 00:00:00
abstract::Oligonucleotide models of ribosomal RNA domains are powerful tools to study the binding and molecular recognition of antibiotics that interfere with bacterial translation. Techniques such as selective chemical modification, fluorescence labeling and mutations are cumbersome for the whole ribosome but readily applicabl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq159
更新日期:2010-07-01 00:00:00
abstract::We report the use of an engineered ribozyme to produce a circular human exon in vitro. Specifically, we have designed a derivative of a yeast self-splicing group II intron that is able to catalyze the formation of a circular exon encoding the first kringle domain (K1) of the human tissue plasminogen activator protein....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.24.5085
更新日期:1997-12-15 00:00:00
abstract::UHRF1 plays multiple roles in regulating DNMT1-mediated DNA methylation maintenance during DNA replication. The UHRF1 C-terminal RING finger functions as an ubiquitin E3 ligase to establish histone H3 ubiquitination at Lys18 and/or Lys23, which is subsequently recognized by DNMT1 to promote its localization onto repli...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky104
更新日期:2018-04-06 00:00:00
abstract::Exposure to many endogenous and exogenous agents can give rise to DNA alkylation, which constitutes a major type of DNA damage. Among the DNA alkylation products, alkyl phosphotriesters have relatively high frequencies of occurrence and are resistant to repair in mammalian tissues. However, little is known about how t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky140
更新日期:2018-05-04 00:00:00
abstract::We observed overexpression and increased intra-nuclear accumulation of the PRMT5/WDR77 in breast cancer cell lines relative to immortalized breast epithelial cells. Utilizing mass spectrometry and biochemistry approaches we identified the Zn-finger protein ZNF326, as a novel interaction partner and substrate of the nu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx727
更新日期:2017-11-02 00:00:00
abstract::An accurate and highly sensitive mutation detection assay has been developed. The assay is based on the detection of mispaired and unpaired bases by immobilized mismatch binding protein (Escherichia coli MutS). The assay can detect most mismatches and all single base substitution mutations, as well as small addition o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.19.3944
更新日期:1995-10-11 00:00:00
abstract::The p53 protein is crucial for adapting programs of gene expression in response to stress. Recently, we revealed that this occurs partly through the formation of stress-specific p53 binding patterns. However, the mechanisms that generate these binding patterns remain largely unknown. It is not established whether the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1209
更新日期:2011-04-01 00:00:00
abstract::The human lymphoid cell lines Walker and Daudi constitute a particularly suitable system for studies on the chromatin structure of K light chain genes (see preceding paper). The rearranged and non-rearranged alleles of Walker cells were found to be about equally sensitive towards digestion with DNAase I. A DNAase I hy...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.18.7007
更新日期:1984-09-25 00:00:00
abstract::Ovarian poly (A) + RNA from Xenopus laevis and Xenopus borealis was used to construct two cDNA libraries which were screened for histone sequences. cDNA clones to H4 mRNA were obtained from both species and an H3 cDNA clone from Xenopus laevis. The complete DNA sequences of these clones have been determined and are pr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.12.3769
更新日期:1982-06-25 00:00:00
abstract::Chromatin immunoprecipitation (ChIP) has been used to detect binding of DNA-binding proteins to sites in nuclear and mitochondrial genomes. Here, we describe a method for detecting protein-binding sites on chloroplast DNA, using modifications to the nuclear ChIP procedures. The method was developed using the lac opera...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq413
更新日期:2010-08-01 00:00:00
abstract::We have isolated a unique fragment of the HLA-DR alpha gene and probed human genomic DNA at low stringency to search for homologous sequences. A minimum of six non-polymorphic cross-hybridizing high molecular weight fragments were found in all DNAs examined. In order to obtain molecular clones of these cross-hybridizi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.20.7515
更新日期:1985-10-25 00:00:00
abstract::ymf39 is a conserved hypothetical protein-coding gene found in mitochondrial genomes of land plants and certain protists. We speculated earlier, based on a weak sequence similarity between Ymf39 from a green alga and the atpF gene product from Bradyrhizobium, that ymf39 might code for subunit b of mitochondrial F(0)F(...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg326
更新日期:2003-05-01 00:00:00