Abstract:
:This paper examines theoretically the effects that restraints on the tertiary structure of a superhelical DNA domain exert on the energetics of linking and the onset of conformational transitions. The most important tertiary constraint arises from the nucleosomal winding of genomic DNA in vivo. Conformational transitions are shown to occur at equilibrium at less extreme superhelicities in DNA whose tertiary structure is restrained than in unrestrained molecules where the residual linking difference alpha res (that part of the superhelical deformation which is not absorbed by transitions) may be freely partitioned between twisting and bending. In the extreme case of a rigidly held tertiary structure, this analysis predicts that the B-Z transition will occur at roughly half the superhelix density needed to drive the same transition in solution, other factors remaining fixed. This suggests that superhelical transitions may occur at more moderate superhelical deformations in vivo than in solution. The influence on transition behavior of the tertiary structural restraints imposed by gel conditions also are discussed.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Benham CJdoi
10.1093/nar/15.23.9985subject
Has Abstractpub_date
1987-12-10 00:00:00pages
9985-95issue
23eissn
0305-1048issn
1362-4962journal_volume
15pub_type
杂志文章,评审abstract::We have sequenced the 0.7-kb-long fragment of Drosophila DNA which ensures the autonomous replication of plasmids in yeast. Deletion mapping has shown the ARS element to consist of at least two domains: the core having the consensus 11-bp sequence TAAATATAAAT and the enhancer which is no more than 90 bp long and is lo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.3.1169
更新日期:1988-02-11 00:00:00
abstract::Chromatin assembly factor 1 (CAF-1) is a histone H3-H4 chaperone that deposits newly synthesized histone (H3-H4)2 tetramers during replication-coupled nucleosome assembly. However, how CAF-1 functions in this process is not yet well understood. Here, we report the crystal structure of C terminus of Cac1 (Cac1C), a sub...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw106
更新日期:2016-06-20 00:00:00
abstract::Variable regions within ribosomal RNAs frequently vary in length as a result of incorporating products of slippage. This makes constructing secondary structure models problematic because base homology is difficult or impossible to establish between species. Here, we model such a region by comparing the results of the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.7.1689
更新日期:1998-04-01 00:00:00
abstract::A 5',7-methylguanosine cap is a quintessential feature of RNA polymerase II-transcribed RNAs, and a textbook aspect of co-transcriptional RNA processing. The cap is bound by the cap-binding complex (CBC), canonically consisting of nuclear cap-binding proteins 1 and 2 (NCBP1/2). Interest in the CBC has recently renewed...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa743
更新日期:2020-10-09 00:00:00
abstract::Synthesis of (p)ppRNA-DNA chains by purified HeLa cell DNA primase-DNA polymerase alpha (pol alpha-primase) was compared with those synthesized by a multiprotein form of DNA polymerase alpha (pol alpha 2) using unique single-stranded DNA templates containing the origin of replication for simian virus 40 (SV40) DNA. Th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.18.7305
更新日期:1986-09-25 00:00:00
abstract::Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell M...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky152
更新日期:2018-05-18 00:00:00
abstract::The alcohol dehydrogenase (Adh) gene of D. melanogaster is transcribed from two different promoters during fly development: the distal (adult) and the proximal (embryonic-larval). Certain aspects of Adh gene regulation are represented in Drosophila continuous cell lines. We have used Drosophila tissue culture cells in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.19.7903
更新日期:1987-10-12 00:00:00
abstract::We recently compared the efficiency of six picornaviral internal ribosome entry segments (IRESes) and the hepatitis C virus (HCV) IRES for their ability to drive internal initiation of translationin vitro. Here we present the results of a similar comparison performed in six different cultured cell lines infected with ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.5.925
更新日期:1997-03-01 00:00:00
abstract::DNA supercoiling is an important regulator of gene activity. The transmission of transcription-generated supercoiling wave along a DNA helix provides a way for a gene being transcribed to communicate with and regulate its neighboring genes. Currently, the dynamic behavior of supercoiling transmission remains unclear o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky534
更新日期:2018-08-21 00:00:00
abstract::Antisense oligodeoxynucleotides targeted to Ha-ras mRNA have been designed to discriminate between the codon 12-mutated oncogene and the normal proto-oncogene. An in vitro assay using two different sources of RNase H (rabbit reticulocyte lysates and nuclear extract from HeLa cells) was used to characterize oligonucleo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.17.3411
更新日期:1995-09-11 00:00:00
abstract::We have determined the NMR solution structures of the quadruplexes formed by d(TGLGLT) and d(TL4T), where L denotes LNA (locked nucleic acid) modified G-residues. Both structures are tetrameric, parallel and right-handed and the native global fold of the corresponding DNA quadruplex is retained upon introduction of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl144
更新日期:2006-04-13 00:00:00
abstract::By successively assembling genetic parts such as BioBrick according to grammatical models, complex genetic constructs composed of dozens of functional blocks can be built. However, usually every category of genetic parts includes a few or many parts. With increasing quantity of genetic parts, the process of assembling...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx859
更新日期:2017-12-15 00:00:00
abstract::Loop-loop tertiary interactions play a key role in the folding and catalytic activity of natural hammerhead ribozymes. Using a combination of NMR spectroscopy, site-directed mutagenesis and kinetic and infectivity analyses, we have examined the structure and function of loops 1 and 2 of the (+) and (-) hammerheads of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn918
更新日期:2009-02-01 00:00:00
abstract::We describe the first polyA-containing processed pseudogene reported in the chicken. It includes a 0.52 kb open reading frame which could encode a 175 amino acid protein. The putative protein shows extensive homology to the ras oncogene superfamily, being most closely related to the yeast protein YP2. It is one of the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.5.2123
更新日期:1986-03-11 00:00:00
abstract::The carbon catabolite repressor protein 4 (Ccr4)-Negative on TATA (Not) complex controls gene expression at two levels. In the nucleus, it regulates the basal transcription machinery, nuclear receptor-mediated transcription and histone modifications. In the cytoplasm, the complex is required for messenger RNA (mRNA) t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr011
更新日期:2011-05-01 00:00:00
abstract::For high-throughput in vitro protein selection using genotype (mRNA)-phenotype (protein) fusion formation and C-terminal protein labeling as a post-selection analysis, it is important to improve the stability and efficiency of mRNA templates for both technologies. Here we describe an efficient single-strand ligation (...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng078
更新日期:2003-08-01 00:00:00
abstract::Proteins engage in highly selective interactions with their macromolecular partners. Sequence variants that alter protein binding affinity may cause significant perturbations or complete abolishment of function, potentially leading to diseases. There exists a persistent need to develop a mechanistic understanding of i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw374
更新日期:2016-07-08 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::I show that the recognition sequences of Type II restriction systems are correlated with the G + C content of the host bacterial DNA. Almost all restriction systems with G + C rich tetranucleotide recognition sequences are found in species with A + T rich genomes, whereas G + C rich hexanucleotide and octanucleotide r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.5.2283
更新日期:1988-03-25 00:00:00
abstract::We present YOGY a web-based resource for orthologous proteins from nine eukaryotic organisms: Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Schizosaccharomyces pombe and Saccharomyces cerevisiae. Using a gene name from any o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl311
更新日期:2006-07-01 00:00:00
abstract::The interaction of the high mobility group proteins, HMG14 and HMG17, with nucleosome core particles has been studied. The results show that two molecules of HMG14/17 can be bound tightly but reversibly to each core particle and that their affinity for core particles is greater than their affinity for histone-free DNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.17.3757
更新日期:1980-09-11 00:00:00
abstract::Our database on large ribosomal subunit RNA contained 334 sequences in July, 1995. All sequences in the database are aligned, taking into account secondary structure. The aligned sequences are provided, together with incorporated secondary structure information, in several computer-readable formats. These data can eas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.1.92
更新日期:1996-01-01 00:00:00
abstract::Molecular dynamics simulations were performed on the duplex DNA dodecamers d(CGCGAA TT CGCG): d(CGCGAATTCGCG) and d(GCACGAA TT AAG): d(CTTAATTCGTGC), where TT denotes a cis, syn cyclobutane thymine dimer. The constant temperature and pressure algorithm of the AMBER 4.1 molecular-modeling package was used with explicit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.7.1432
更新日期:1997-04-01 00:00:00
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 mecha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku122
更新日期:2014-04-01 00:00:00
abstract::Mild ultraviolet irradiation of E. coli ribosomal subunits leads to the formation of a number of intra-RNA cross-links, in addition to the RNA-protein cross-links already reported (see refs. 9, 10). After partial ribonuclease digestion of the RNA from irradiated subunits, complexes containing these intra-RNA cross-lin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.11.2397
更新日期:1980-06-11 00:00:00
abstract::We describe mGene.web, a web service for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It offers pre-trained models for the recognition of gene structures including untranslated regions in an increasing number of organisms. With mGene.web, users have the additional possibility to tr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp479
更新日期:2009-07-01 00:00:00
abstract::Sets of genes expressed in the same tissue are believed to be under the regulation of a similar set of transcription factors, and can thus be assumed to contain similar structural patterns in their regulatory regions. Here we present a study of the structural patterns in promoters of genes expressed specifically in 26...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp866
更新日期:2010-01-01 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::It is believed that depending on the thermodynamic stability of the 5'-strand and the 3'-strand in the stem-loop structure of a precursor microRNA (pre-miRNA), cells preferentially select the less stable one (called the miRNA or guide strand) and destroy the other one (called the miRNA* or passenger strand). However, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm641
更新日期:2007-01-01 00:00:00
abstract::Cancer-associated somatic mutations outside protein-coding regions remain largely unexplored. Analyses of the TERT locus have indicated that non-coding regulatory mutations can be more frequent than previously suspected and play important roles in oncogenesis. Using a computational method called SASE-hunter, developed...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv419
更新日期:2015-06-23 00:00:00