Abstract:
:A new method for evaluating some complex characteristics of the primary structure of E.coli promoters is proposed. The method, of nonparametric statistical significance, selects important conserved single-base positions in combination with 2-base coupling relations of identity and complementarity. The extended consensus of promoter characteristics thus obtained was used to scan unknown sequences for similarity with E.coli promoters. In terms of this method, a complete set of 244 E.coli promoters was shown to be structurally inconsistent. The set was then broken down into functionally homogeneous subsets of promoters to enhance the selectivity of the search for E.coli-specific promoter sequences, with a high significance level being attained.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Rozkot F,Sázelová P,Pivec Ldoi
10.1093/nar/17.12.4799subject
Has Abstractpub_date
1989-06-26 00:00:00pages
4799-815issue
12eissn
0305-1048issn
1362-4962journal_volume
17pub_type
杂志文章abstract::We define phosphovariants as genetic variations that change phosphorylation sites or their interacting kinases. Considering the essential role of phosphorylation in protein functions, it is highly likely that phosphovariants change protein functions. Therefore, a comparison of phosphovariants between individuals or be...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn1008
更新日期:2009-03-01 00:00:00
abstract::Muscleblind-like proteins (MBNLs) are regulators of RNA metabolism. During tissue differentiation the level of MBNLs increases, while their functional insufficiency plays a crucial role in myotonic dystrophy (DM). Deep sequencing of RNA molecules cross-linked to immunoprecipitated protein particles (CLIP-seq) revealed...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1158
更新日期:2017-02-28 00:00:00
abstract::We present a study of how substituent groups of naturally occurring and modified nucleotide bases affect the degree of hydration of right-handed B-DNA and left-handed Z-DNA. A comparison of poly(dG-dC) and poly(dG-dm5C) titrations with the lipotropic salts of the Hofmeister series infers that the methyl stabilization ...
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.23.5525
更新日期:1998-12-01 00:00:00
abstract::The transcriptional promoter of satellite 2 from the eastern newt, Notophthalmus viridescens, was analyzed by assaying the activity of deleted or mutated satellite 2 clones in Xenopus laevis oocytes. Two elements in the promoter were found to be important for transcription. These elements have sequences that are simil...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.22.4697
更新日期:1994-11-11 00:00:00
abstract::Oligonucleotide-directed mutagenesis was used to introduce an A to C transversion at position 523 in the 16S ribosomal RNA gene of Escherichia coli rrnB operon cloned in plasmid pKK3535. E. coli cells transformed with the mutated plasmid were resistant to streptomycin. The mutated ribosomes isolated from these cells w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.20.9631
更新日期:1988-10-25 00:00:00
abstract::An investigation of the mobility of short duplexes of DNA -octamers and decamers-on polyacrylamide gels is presented, showing that molecules containing less than one helical turn exhibit sequence dependent mobilities. Analysis of chains with different sequences indicates that any arrangement of two or more adjacent A....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.14.6803
更新日期:1988-07-25 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm908
更新日期:2008-01-01 00:00:00
abstract::Microbial biosynthetic gene clusters are a valuable source of bioactive molecules. However, because they typically represent a small fraction of genomic material in most metagenomic samples, it remains challenging to deeply sequence them. We present an approach to isolate and sequence gene clusters in metagenomic samp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa131
更新日期:2020-05-07 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1985-05-24 00:00:00
abstract::Pre-mRNA transcripts in a variety of organisms, including plants, Drosophila and Caenorhabditis elegans, contain introns which are significantly richer in adenosine and uridine residues than their flanking exons. Previous analyses using exonic and intronic replacements between two nonequivalent 5'splice sites in the 4...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.5.1071
更新日期:1997-03-01 00:00:00
abstract::Three Z-DNA-binding proteins of Mr 31, 33 and 58 kD were isolated from mature bull testis. They were obtained in a native state suitable for binding studies. These are the first examples of Z-DNA-binding proteins from a mammalian tissue. Purification involved tissue extraction with 0.35 M NaCl, cation exchange chromat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.23.9691
更新日期:1987-12-10 00:00:00
abstract::Direct visualization of DNA and proteins allows researchers to investigate DNA-protein interactions with great detail. Much progress has been made in this area as a result of increasingly sensitive single-molecule fluorescence techniques. At the same time, methods that control the conformation of DNA molecules have be...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
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更新日期:2008-08-01 00:00:00
abstract::In the virion core of retroviruses, the genomic RNA is tightly associated with nucleocapsid (NC) protein molecules, forming the nucleocapsid structure. NC protein, a highly basic protein with two zinc fingers, is indispensable for RNA dimerization, encapsidation and the initiation of reverse transcription in avian, mu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.4.831
更新日期:1993-02-25 00:00:00
abstract::Laser microirradiation is a powerful tool for real-time single-cell analysis of the DNA damage response (DDR). It is often found, however, that factor recruitment or modification profiles vary depending on the laser system employed. This is likely due to an incomplete understanding of how laser conditions/dosages affe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv976
更新日期:2016-02-18 00:00:00
abstract::The VS ribozyme trans-cleavage substrate interacts with the catalytic RNA via tertiary interactions. To study the role of phosphate groups in the ribozyme-substrate interaction, 18 modified substrates were synthesized, where an epimeric phosphorothioate replaces one of the phosphate diester linkages. Sites in the stem...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh957
更新日期:2004-12-01 00:00:00
abstract::Understanding the normal state of human tissue transcriptome profiles is essential for recognizing tissue disease states and identifying disease markers. Recently, the Human Protein Atlas and the FANTOM5 consortium have each published extensive transcriptome data for human samples using Illumina-sequenced RNA-Seq and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv608
更新日期:2015-08-18 00:00:00
abstract::Apurinic/apyrimidinic endonuclease 1 (APE1), an essential protein in mammals, is involved in base excision DNA repair (BER) and in regulation of gene expression, acting as a redox co-activator of several transcription factors. Recent findings highlight a novel role for APE1 in RNA metabolism, which is modulated by nuc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq691
更新日期:2010-12-01 00:00:00
abstract::2'-O-(2-methoxyethyl) (2'-MOE) RNA possesses favorable pharmocokinetic properties that make it a promising option for the design of oligonucleotide drugs. Telomerase is a ribonucleoprotein that is up-regulated in many types of cancer, but its potential as a target for chemotherapy awaits the development of potent and ...
journal_title:Nucleic acids research
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doi:10.1093/nar/29.8.1683
更新日期:2001-04-15 00:00:00
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
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更新日期:1997-12-15 00:00:00
abstract:UNLABELLED:Synonymous codon usage biases are associated with various biological factors, such as gene expression level, gene length, gene translation initiation signal, protein amino acid composition, protein structure, tRNA abundance, mutation frequency and patterns, and GC compositions. Quantification of codon usage ...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2007-07-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1998-06-15 00:00:00
abstract::An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the map...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw026
更新日期:2016-05-05 00:00:00
abstract::Phosphorylation of the cellular single-stranded DNA-binding protein, replication protein A (RPA), occurs during normal mitotic cell cycle progression and also in response to genotoxic stress. In budding yeast, these reactions require the ATM homolog Mec1, a central regulator of the DNA replication and DNA damage check...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.23.4808
更新日期:2001-12-01 00:00:00
abstract::To elucidate the general constraints imposed on the structure of the D- and T-loops in functional tRNAs, active suppressor tRNAs were selected in vivo from a combinatorial tRNA gene library in which several nucleotide positions of these loops were randomized. Analysis of the nucleotide sequences of the selected clones...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg448
更新日期:2003-07-15 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::In this paper, we report investigations, based on circular dichroism, nuclear magnetic resonance spectroscopy and electrophoresis methods, on three oligonucleotide sequences, each containing one 3'-3' and two 5'-5' inversion of polarity sites, and four G-runs with a variable number of residues, namely two, three and f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx566
更新日期:2017-08-21 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::Three computer programs are described which may be used to translate a DNA sequence into a protein sequence, back translate the protein sequence into an ambiguous DNA sequence, and then do pattern searching in the ambiguous sequence. The programs are written in the C programming language, have been compiled to run on ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.1part2.819
更新日期:1984-01-11 00:00:00
abstract::Hfq, a bacterial RNA-binding protein, was recently shown to contain the Sm1 motif, a characteristic of Sm and LSm proteins that function in RNA processing events in archaea and eukaryotes. In this report, comparative structural modeling was used to predict a three-dimensional structure of the Hfq core sequence. The pr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf508
更新日期:2002-09-01 00:00:00