Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements.

abstract：:Directed molecular evolution and combinatorial methodologies are playing an increasingly important role in the field of protein engineering. The general approach of generating a library of partially randomized genes, expressing the gene library to generate the proteins the library encodes and then screening the protei...

journal_title：Nucleic acids research

authors： Neylon C

更新日期：2004-02-27 00:00:00

abstract：:Oligoribonucleotides with 2'-5' linkages have been synthesized on solid support. UV melting and CD experiments indicate complementary strands associate to give complexes with melting temperatures 30 to 40 degrees C lower than for duplexes formed by 3'-5' oligoribonucleotides with the same sequence. UV melting and imin...

journal_title：Nucleic acids research

authors： Kierzek R,He L,Turner DH

更新日期：1992-04-11 00:00:00

abstract：:Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes conformational changes resulting in DNA strand separation to form a transcription bubble and ...

journal_title：Nucleic acids research

authors： Duchi D,Gryte K,Robb NC,Morichaud Z,Sheppard C,Brodolin K,Wigneshweraraj S,Kapanidis AN

更新日期：2018-01-25 00:00:00

abstract：:We examined the 3'-flanking regions required for accurate 3'-end formation of wheat histone H3 mRNA using gene expression in transformed sunflower cells. The introduction of mutations into the conserved sequence AATGGAAATG in the 3'-flanking region of plant histone genes, located 22 bp upstream from the polyadenylatio...

journal_title：Nucleic acids research

authors： Ohtsubo N,Iwabuchi M

更新日期：1994-03-25 00:00:00

abstract：:The wobble uridine of certain bacterial and mitochondrial tRNAs is modified, at position 5, through an unknown reaction pathway that utilizes the evolutionarily conserved MnmE and GidA proteins. The resulting modification (a methyluridine derivative) plays a critical role in decoding NNG/A codons and reading frame mai...

journal_title：Nucleic acids research

authors： Moukadiri I,Prado S,Piera J,Velázquez-Campoy A,Björk GR,Armengod ME

更新日期：2009-11-01 00:00:00

abstract：:The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt ends. Here, we report the 1.3 Å resolution structure of the enzyme in complex with substrate DNA and a sodium or calcium ion taking the place of a catalytic magnesium ion. The structure identifies Glu54, Asp82 and Lys93 as t...

journal_title：Nucleic acids research

authors： Firczuk M,Wojciechowski M,Czapinska H,Bochtler M

更新日期：2011-01-01 00:00:00

abstract：:Short DNA sequence motifs have been identified in viral and cellular enhancers which represent the binding sites for a variety of trans- acting factors. One such HeLa cell factor, EBP1, has been purified and shown to bind to sequences in the SV40 enhancer. The PRDII element in the human beta-interferon gene regulatory...

journal_title：Nucleic acids research

authors： Clark L,Hay RT

更新日期：1989-01-25 00:00:00

abstract：:As opposed to the vast majority of prokaryotic repressors, the immunity repressor of temperate Escherichia coli phage P2 (C) recognizes non-palindromic direct repeats of DNA rather than inverted repeats. We have determined the crystal structure of P2 C at 1.8 Å. This constitutes the first structure solved from the fam...

journal_title：Nucleic acids research

authors： Massad T,Skaar K,Nilsson H,Damberg P,Henriksson-Peltola P,Haggård-Ljungquist E,Högbom M,Stenmark P

更新日期：2010-11-01 00:00:00

abstract：:EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, and-a new addition-its transport proteins. MetaCyc is a new metabolic-pathway database that describes pathways and enzymes of many different organisms, with a microbial...

journal_title：Nucleic acids research

authors： Karp PD,Riley M,Saier M,Paulsen IT,Paley SM,Pellegrini-Toole A

更新日期：2000-01-01 00:00:00

abstract：:Biological pathways can provide key information on the organization of biological systems. ArrayXPath (http://www.snubi.org/software/ArrayXPath/) is a web-based service for mapping and visualizing microarray gene-expression data for integrated biological pathway resources using Scalable Vector Graphics (SVG). By integ...

journal_title：Nucleic acids research

authors： Chung HJ,Kim M,Park CH,Kim J,Kim JH

更新日期：2004-07-01 00:00:00

abstract：:The cDNA encoding the human RNA lariat debranching enzyme (hDBR1) was identified and cloned by searching the Expressed Sequence Tag (EST) database and screening a HeLa cDNA library, based on predicted amino acid sequence homologies with the Saccharomyces cerevisiae, Schizosaccharomyces pombe and Caenorhabditis elegans...

journal_title：Nucleic acids research

authors： Kim JW,Kim HC,Kim GM,Yang JM,Boeke JD,Nam K

更新日期：2000-09-15 00:00:00

abstract：:The rDNA cluster in Saccharomyces cerevisiae is located 450 kb from the left end and 610 kb from the right end of chromosome XII and consists of approximately 150 tandemly repeated copies of a 9.1 kb rDNA unit. To explore the biological significance of this specific chromosomal context, chromosome XII was split at bot...

journal_title：Nucleic acids research

authors： Kim YH,Ishikawa D,Ha HP,Sugiyama M,Kaneko Y,Harashima S

更新日期：2006-05-31 00:00:00

abstract：:Mutations of the KRAS proto-oncogene are associated with several tumor types, which is why it is being considered as a target for anti-cancer drug development. The human KRAS promoter contains a nuclease hypersensitive element (NHE), which can bind to nuclear proteins and is believed to form G-quadruplex structures. P...

journal_title：Nucleic acids research

authors： Podbevšek P,Plavec J

更新日期：2016-01-29 00:00:00

abstract：:A 34 base-pair (bp) fragment spanning sequences -154 to -120 of the promoter of the CHO1 gene (structural gene for phosphatidylserine synthase) from the yeast Saccharomyces cerevisiae has been shown to place transcription of a promoter-less Escherichia coli lacZ gene under control of the phospholipid precursors inosit...

journal_title：Nucleic acids research

authors： Bailis AM,Lopes JM,Kohlwein SD,Henry SA

更新日期：1992-03-25 00:00:00

abstract：:Previously we identified Rrp1 and Rrp2 as two proteins required for the Sfr1/Swi5-dependent branch of homologous recombination (HR) in Schizosaccharomyces pombe. Here we use a yeast two-hybrid approach to demonstrate that Rrp1 and Rrp2 can interact with each other and with Swi5, an HR mediator protein. Rrp1 and Rrp2 f...

journal_title：Nucleic acids research

authors： Dziadkowiec D,Kramarz K,Kanik K,Wisniewski P,Carr AM

更新日期：2013-09-01 00:00:00

abstract：:Eucaryotic ribosome biogenesis involves many cis-acting sequences and trans-acting factors, including snoRNAS: We have used directed mutagenesis of rDNA plasmids in yeast to identify critical sequence and structural elements within and flanking the ITS2-proximal stem. This base paired structure, present in the mature ...

journal_title：Nucleic acids research

authors： Côté CA,Peculis BA

更新日期：2001-05-15 00:00:00

abstract：:The current version of PLMItRNA has been realized to constitute a database for tRNA molecules and genes identified in the mitochondria of all green plants ( Viridiplantae ). It is the enlargement of a previous database originally restricted to seed plants [Ceci,L.R., Volpicella,M., Liuni,S., Volpetti,V., Licciulli,F. ...

journal_title：Nucleic acids research

authors： Volpetti V,Gallerani R,De Benedetto C,Liuni S,Licciulli F,Ceci LR

更新日期：2000-01-01 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

authors： Buzayan JM,Hampel A,Bruening G

更新日期：1986-12-22 00:00:00

abstract：:RNA polymerase I-catalyzed synthesis of the Schizosaccharomyces pombe approximately 37S pre-rRNAs was shown to be sensitive to regulatory sequences located several kilobases upstream of the initiation site for the rRNA gene. An in vitro transcription system for RNA polymerase I-catalyzed RNA synthesis was established ...

journal_title：Nucleic acids research

authors： Liu Z,Zhao A,Chen L,Pape L

更新日期：1997-02-01 00:00:00

abstract：:The signal recognition particle database (SRPDB) is located at the University of Texas Health Science Center at Tyler and includes tabulations of SRP RNA, SRP protein and SRP receptor sequences. The sequences are annotated with links to the primary databases. They are ordered alphabetically or phylogenetically and are...

journal_title：Nucleic acids research

authors： Samuelsson T,Zwieb C

更新日期：1999-01-01 00:00:00

abstract：:Reconstructing full-length transcript isoforms from sequence fragments (such as ESTs) is a major interest and challenge for bioinformatic analysis of pre-mRNA alternative splicing. This problem has been formulated as finding traversals across the splice graph, which is a directed acyclic graph (DAG) representation of ...

journal_title：Nucleic acids research

authors： Xing Y,Yu T,Wu YN,Roy M,Kim J,Lee C

更新日期：2006-06-06 00:00:00

abstract：:MicroRNAs (miRNAs) can group together along the human genome to form stable secondary structures made of several hairpins hosting miRNAs in their stems. The few known examples of such structures are all involved in cancer development. A large scale computational analysis of human chromosomes crossing sequence analysis...

journal_title：Nucleic acids research

authors： Mathelier A,Carbone A

更新日期：2013-04-01 00:00:00

abstract：:Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (I...

journal_title：Nucleic acids research

authors： Lu XM,Batugedara G,Lee M,Prudhomme J,Bunnik EM,Le Roch KG

更新日期：2017-07-27 00:00:00

abstract：:The major immediate early regulatory region of human cytomegalovirus (HCMV) has a complex set of DNA sites through which both cellular and viral factors coordinately regulate immediate early gene expression. In undifferentiated human teratocarcinoma (T2) cells we have previously shown that major immediate early gene e...

journal_title：Nucleic acids research

authors： Kothari S,Baillie J,Sissons JG,Sinclair JH

更新日期：1991-04-25 00:00:00

abstract：:Actinomycin D (ActD) is a small molecule with strong antibiotic and anticancer activity. However, its biologically relevant DNA-binding mechanism has never been resolved, with some studies suggesting that the primary binding mode is intercalation, and others suggesting that single-stranded DNA binding is most importan...

journal_title：Nucleic acids research

authors： Paramanathan T,Vladescu I,McCauley MJ,Rouzina I,Williams MC

更新日期：2012-06-01 00:00:00

abstract：:SV40 DNA form I is expressed efficiently after its injection into the nuclei of Xenopus laevis oocytes, resulting in the synthesis of RNA and protein products of both viral late and early transcription units. However it was observed that injection of SV40 genes cloned into pBR322 or related plasmids yielded vastly red...

journal_title：Nucleic acids research

authors： Michaeli T,Prives C

更新日期：1987-02-25 00:00:00

abstract：:Reverse gyrase is a peculiar DNA topoisomerase, specific of hyperthermophilic Archaea and Bacteria, which has the unique ability of introducing positive supercoiling into DNA molecules. Although the function of the enzyme has not been established directly, it has been suggested to be involved in DNA protection and rep...

journal_title：Nucleic acids research

authors： Valenti A,Napoli A,Ferrara MC,Nadal M,Rossi M,Ciaramella M

更新日期：2006-04-14 00:00:00

abstract：:Cellular liquid-liquid phase separation (LLPS) results in the formation of dynamic granules that play an important role in many biological processes. On a molecular level, the clustering of proteins into a confined space results from an indefinite network of intermolecular interactions. Here, we introduce and exploit ...

journal_title：Nucleic acids research

authors： Schütz S,Nöldeke ER,Sprangers R

更新日期：2017-06-20 00:00:00

abstract：:Several electrophoretic and chromatographic systems have been investigated and compared for sequence analysis of oligodeoxyribonucleotides. Three systems were found to be useful for the separation of a series of sequential degradation products resulting from a labeled oligonucleotide: (I) 2-D electrophoresisdagger; (I...

journal_title：Nucleic acids research

authors： Jay E,Bambara R,Padmanabhan R,Wu R

更新日期：1974-03-01 00:00:00

abstract：:The Mouse Genome Database (MGD) (http://www.informatics.jax.org) one component of a community database resource for the laboratory mouse, a key model organism for interpreting the human genome and for understanding human biology. MGD strives to provide an extensively integrated information resource with experimental d...

journal_title：Nucleic acids research

authors： Blake JA,Richardson JE,Bult CJ,Kadin JA,Eppig JT,Mouse Genome Database Group.

更新日期：2003-01-01 00:00:00