Redundancy of primary RNA-binding functions of the bacterial transcription terminator Rho.

abstract：:The transcriptional potential of the hsp70 heat shock gene promoter is established prior to induction by stress. It has been shown previously that the TBP subunit of TFIID is associated with the TATA element and that RNA polymerase II is paused downstream from the transcription start site. In order to identify new int...

journal_title：Nucleic acids research

authors： Weber JA,Gilmour DS

更新日期：1995-08-25 00:00:00

abstract：:Natural antisense transcripts are at least partially complementary to their sense transcripts. Cis-Sense/Antisense pairs (cis-SAs) have been extensively characterized and known to play diverse regulatory roles, whereas trans-Sense/Antisense pairs (trans-SAs) in animals are poorly studied. We identified long trans-SAs ...

journal_title：Nucleic acids research

authors： Li JT,Zhang Y,Kong L,Liu QR,Wei L

更新日期：2008-09-01 00:00:00

abstract：:SPRING (http://algorithm.cs.nthu.edu.tw/tools/SPRING/) is a tool for the analysis of genome rearrangement between two chromosomal genomes using reversals and/or block-interchanges. SPRING takes two or more chromosomes as its input and then computes a minimum series of reversals and/or block-interchanges between any tw...

journal_title：Nucleic acids research

authors： Lin YC,Lu CL,Liu YC,Tang CY

更新日期：2006-07-01 00:00:00

abstract：:As the formation of ribonucleoprotein complexes is a major mechanism of angiotensin II type 1 receptor (AT1R) regulation, we sought to identify novel AT1R mRNA binding proteins. By affinity purification and mass spectroscopy, we identified TIA-1. This interaction was confirmed by colocalization of AT1R mRNA and TIA-1 ...

journal_title：Nucleic acids research

authors： Backlund M,Paukku K,Kontula KK,Lehtonen JY

更新日期：2016-04-20 00:00:00

abstract：:Nuclear factor I (NFI) is a site-specific DNA binding protein required for the replication of adenovirus type 2 DNA in vitro and in vivo. To study sequence requirements for the interaction of NFI with DNA, we have measured the binding of the protein to a variety of synthetic sites. Binding sites for NFI (FIB sites) we...

journal_title：Nucleic acids research

authors： Gronostajski RM

更新日期：1987-07-24 00:00:00

abstract：:The DNA sequence was determined for the narL gene of Escherichia coli. This gene is involved in global regulation of a number of nitrate controlled genes including frdABCD, tor, narGHJI, and adhE which are associated with bacterial respiration and fermentation. Comparison of the deduced amino acid sequence of narL to ...

journal_title：Nucleic acids research

authors： Gunsalus RP,Kalman LV,Stewart RR

更新日期：1989-03-11 00:00:00

abstract：:The continuing threat of infectious disease and future pandemics, coupled to the continuous increase of drug-resistant pathogens, makes the discovery of new and better vaccines imperative. For effective vaccine development, antigen discovery and validation is a prerequisite. The compilation of information concerning p...

journal_title：Nucleic acids research

authors： Ansari HR,Flower DR,Raghava GP

更新日期：2010-01-01 00:00:00

abstract：:The assembly of the complex that forms over the simian virus 40 origin to initiate DNA replication is not well understood. This complex is composed of the virus-coded T antigen and three cellular proteins, replication protein A (RPA), DNA polymerase alpha/primase (pol/prim) and topoisomerase I (topo I) in association ...

journal_title：Nucleic acids research

authors： Simmons DT,Gai D,Parsons R,Debes A,Roy R

更新日期：2004-02-11 00:00:00

abstract：:Systematic structure probing experiments (e.g. SHAPE) of RNA mutants such as the mutate-and-map (MaM) protocol give us a direct access into the genetic robustness of ncRNA structures. Comparative studies of homologous sequences provide a distinct, yet complementary, approach to analyze structural and functional proper...

journal_title：Nucleic acids research

authors： Reinharz V,Ponty Y,Waldispühl J

更新日期：2016-06-20 00:00:00

abstract：:RJ2.2.5, a mutant derived from the human B-lymphoma cell, Raji, is unable to express the MHC class II genes because of a recessive transcriptional defect attributed to the lack of an activator function. We report the isolation of a RJ2.2.5 revertant, namely AR, in which the expression of the mRNAs encoded by these gen...

journal_title：Nucleic acids research

authors： Ombra MN,Perfetto C,Autiero M,Anzisi AM,Pasquinelli R,Maffei A,Del Pozzo G,Guardiola J

更新日期：1993-02-11 00:00:00

abstract：:The human RAD54B protein is a paralog of the RAD54 protein, which plays important roles in homologous recombination. RAD54B contains an N-terminal region outside the SWI2/SNF2 domain that shares less conservation with the corresponding region in RAD54. The biochemical roles of this region of RAD54B are not known, alth...

journal_title：Nucleic acids research

authors： Sarai N,Kagawa W,Fujikawa N,Saito K,Hikiba J,Tanaka K,Miyagawa K,Kurumizaka H,Yokoyama S

更新日期：2008-10-01 00:00:00

abstract：:We present a new publicly accessible web-service, RiboSoft, which implements a comprehensive hammerhead ribozyme design procedure. It accepts as input a target sequence (and some design parameters) then generates a set of ranked hammerhead ribozymes, which target the input sequence. This paper describes the implemente...

journal_title：Nucleic acids research

authors： Kharma N,Varin L,Abu-Baker A,Ouellet J,Najeh S,Ehdaeivand MR,Belmonte G,Ambri A,Rouleau G,Perreault J

更新日期：2016-02-29 00:00:00

abstract：:Understanding interactions between proteins and RNA is key to deciphering the mechanisms of many important biological processes. Here we describe RNABindR, a web-based server that identifies and displays RNA-binding residues in known protein-RNA complexes and predicts RNA-binding residues in proteins of unknown struct...

journal_title：Nucleic acids research

authors： Terribilini M,Sander JD,Lee JH,Zaback P,Jernigan RL,Honavar V,Dobbs D

更新日期：2007-07-01 00:00:00

abstract：:Many genetic manipulations are limited by difficulty in obtaining adequate levels of protein expression. Bioinformatic and experimental studies have identified nucleotide sequence features that may increase expression, however it is difficult to assess the relative influence of these features. Zebrafish embryos are ra...

journal_title：Nucleic acids research

authors： Horstick EJ,Jordan DC,Bergeron SA,Tabor KM,Serpe M,Feldman B,Burgess HA

更新日期：2015-04-20 00:00:00

abstract：:The Kruppel-like factor 5 (KLF5/IKLF) belongs to the Kruppel family of genes which bind GC-rich DNA elements and activate or repress their target genes in a promoter context and/or cellular environment-dependent manner. In the present study, we used the Gal4 fusion assay system to characterize the mechanism of transac...

journal_title：Nucleic acids research

authors： Zhang Z,Teng CT

更新日期：2003-04-15 00:00:00

abstract：:ApiDB (http://ApiDB.org) represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center (BRC) that integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises numerous veterinary and medically important parasitic protozoa including human pathogenic ...

journal_title：Nucleic acids research

authors： Aurrecoechea C,Heiges M,Wang H,Wang Z,Fischer S,Rhodes P,Miller J,Kraemer E,Stoeckert CJ Jr,Roos DS,Kissinger JC

更新日期：2007-01-01 00:00:00

abstract：:The MF alpha 1 gene of Saccharomyces cerevisiae is an alpha specific gene whose expression is regulated by two upstream activation sites (UASMF alpha 1S), which are the binding sites for activator proteins, MAT alpha 1 and MCM1. UASMF alpha 1 elements act in a synergistic fashion; lack of either element causes reduced...

journal_title：Nucleic acids research

authors： Inokuchi K,Nakayama A

更新日期：1991-06-11 00:00:00

abstract：:Human transcription factor Sp1 contains three contiguous repeats of the C2H2-type zinc finger motif and binds to the decanucleotide sequence 5'-(G/T)GGGCGG(G/A)(G/A)(C/T)-3' (GC box). In order to determine whether the three-zinc finger peptide Sp1(530-623) has selectivity for sequence outside the GC box, we used a sel...

journal_title：Nucleic acids research

authors： Nagaoka M,Shiraishi Y,Sugiura Y

更新日期：2001-12-15 00:00:00

abstract：:Post-transcriptional modifications in archaeal RNA are known to be phylogenetically distinct but relatively little is known of tRNA from the Methanococci, a lineage of methanogenic marine euryarchaea that grow over an unusually broad temperature range. Transfer RNAs from Methanococcus vannielii, Methanococcus maripalu...

journal_title：Nucleic acids research

authors： McCloskey JA,Graham DE,Zhou S,Crain PF,Ibba M,Konisky J,Söll D,Olsen GJ

更新日期：2001-11-15 00:00:00

abstract：:We show that using low denaturation temperatures (80-88 degrees C) during ligation mediated PCR (LM PCR) of bacterial DNA leads to the amplification of limited sets of the less stable DNA fragments. A set of electrophoretic patterns of such fragments obtained at different denaturation temperatures forms the PCR meltin...

journal_title：Nucleic acids research

authors： Masny A,Płucienniczak A

更新日期：2003-09-15 00:00:00

abstract：:Approximately 2% of the Dictyostelium discoideum genome consists of multiple copies of a retrotransposable element termed DRE (Dictyostelium Repetitive Element). These elements have always been found integrated in a position and orientation-specific manner 50 +/- 4 nucleotides upstream of the coding region of tRNA gen...

journal_title：Nucleic acids research

authors： Marschalek R,Hofmann J,Schumann G,Dingermann T

更新日期：1992-12-11 00:00:00

abstract：:The TWIST1 bHLH transcription factor controls embryonic development and cancer processes. Although molecular and genetic analyses have provided a wealth of data on the role of bHLH transcription factors, very little is known on the molecular mechanisms underlying their binding affinity to the E-box sequence of the pro...

journal_title：Nucleic acids research

authors： Bouard C,Terreux R,Honorat M,Manship B,Ansieau S,Vigneron AM,Puisieux A,Payen L

更新日期：2016-06-20 00:00:00

abstract：:Gold nanoparticle labels, combined with UV-visible optical absorption spectroscopic methods, are employed to probe the temperature-dependent solution properties of DNA triple helices. By using oligonucleotide-nanoparticle conjugates to characterize triplex denaturation, for the first time triplex to duplex melting tra...

journal_title：Nucleic acids research

authors： Murphy D,Eritja R,Redmond G

更新日期：2004-04-23 00:00:00

abstract：:Homozygosity for a natural deletion variant of the HIV-coreceptor molecule CCR5, CCR5Δ32, confers resistance toward HIV infection. Allogeneic stem cell transplantation from a CCR5Δ32-homozygous donor has resulted in the first cure from HIV ('Berlin patient'). Based thereon, genetic disruption of CCR5 using designer nu...

journal_title：Nucleic acids research

authors： Mock U,Machowicz R,Hauber I,Horn S,Abramowski P,Berdien B,Hauber J,Fehse B

更新日期：2015-06-23 00:00:00

abstract：:Cryptic splice sites are used only when use of a natural splice site is disrupted by mutation. To determine the features that distinguish authentic from cryptic 5' splice sites (5'ss), we systematically analyzed a set of 76 cryptic 5'ss derived from 46 human genes. These cryptic 5'ss have a similar frequency distribut...

journal_title：Nucleic acids research

authors： Roca X,Sachidanandam R,Krainer AR

更新日期：2003-11-01 00:00:00

abstract：:Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration o...

journal_title：Nucleic acids research

authors： Cantacessi C,Jex AR,Hall RS,Young ND,Campbell BE,Joachim A,Nolan MJ,Abubucker S,Sternberg PW,Ranganathan S,Mitreva M,Gasser RB

更新日期：2010-09-01 00:00:00

abstract：:The catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs) is a member of a sub-family of phosphatidylinositol (PI) 3-kinases termed PIK-related kinases. A distinguishing feature of this sub-family is the presence of a conserved C-terminal region downstream of a PI 3-kinase domain. Mutants defective in DNA-P...

journal_title：Nucleic acids research

authors： Priestley A,Beamish HJ,Gell D,Amatucci AG,Muhlmann-Diaz MC,Singleton BK,Smith GC,Blunt T,Schalkwyk LC,Bedford JS,Jackson SP,Jeggo PA,Taccioli GE

更新日期：1998-04-15 00:00:00

abstract：:Lysinomicin, a naturally-occurring pseudodisaccharide, inhibits translation in prokaryotes. We report that lysinomicin (and three related compounds) are able to inhibit the self-splicing of group I introns, thus identifying pseudodisaccharides as a novel class of group I intron splicing inhibitors. Lysinomicin inhibit...

journal_title：Nucleic acids research

authors： Rogers J,Davies J

更新日期：1994-11-25 00:00:00

abstract：:A simple and effective modified ethanol precipitation-based protocol is described for the preparation of DNA from ancient human bones. This method is fast and requires neither hazardous chemicals nor special devices. After the powdering and incubating of the bone samples Dextran Blue was added as a carrier for removin...

journal_title：Nucleic acids research

authors： Kalmár T,Bachrati CZ,Marcsik A,Raskó I

更新日期：2000-06-15 00:00:00

abstract：:RNA polymerase II (pol II) utilizes a complex interaction network to select and incorporate correct nucleoside triphosphate (NTP) substrates with high efficiency and fidelity. Our previous 'synthetic nucleic acid substitution' strategy has been successfully applied in dissecting the function of nucleic acid moieties i...

journal_title：Nucleic acids research

authors： Hwang CS,Xu L,Wang W,Ulrich S,Zhang L,Chong J,Shin JH,Huang X,Kool ET,McKenna CE,Wang D

更新日期：2016-05-05 00:00:00