Common and specific amino acid residues in the prokaryotic polypeptide release factors RF1 and RF2: possible functional implications.

abstract：:The transcription regulator, tvMyb1, is the first Myb family protein identified in Trichomonas vaginalis. Using an electrophoretic mobility shift assay, we defined the amino-acid sequence from Lys(35) to Ser(141) (tvMyb1(35-141)) as the minimal DNA-binding domain, encompassing two Myb-like DNA-binding motifs (designat...

journal_title：Nucleic acids research

authors： Lou YC,Wei SY,Rajasekaran M,Chou CC,Hsu HM,Tai JH,Chen C

更新日期：2009-04-01 00:00:00

abstract：:A multivariate statistical method called correspondence analysis was used to examine the codon usage of one-hundred-and-one nuclear genes of maize (Zea mays L.). Forty percent of the variation in codon usage was due to bias toward G or C-ending versus A or U-ending codons. Differences in levels of G-ending codons show...

journal_title：Nucleic acids research

authors： Fennoy SL,Bailey-Serres J

更新日期：1993-11-25 00:00:00

abstract：:Here we analyze the effect of DNA folding on the performance of short primers and describe a simple technique for assessing hitherto uncertain values of thermodynamic parameters that determine the folding of single-stranded DNA into secondary structure. An 8mer with two degenerate positions is extended simultaneously ...

journal_title：Nucleic acids research

authors： Lvovsky L,Ioshikhes I,Raja MC,Zevin-Sonkin D,Sobolev IA,Liberzon A,Shwartzburd J,Ulanovsky LE

更新日期：1998-12-01 00:00:00

abstract：:We have purified to near homogeneity a novel nuclear protein from HeLa cells, that specifically binds to scaffold or matrix attachment region DNA elements (S/MAR DNA). The protein, designated SAF-B for scaffold attachment factor B, is an abundant component of chromatin, but not of the nuclear matrix and is expressed i...

journal_title：Nucleic acids research

authors： Renz A,Fackelmayer FO

更新日期：1996-03-01 00:00:00

abstract：:The Raf-1 proto-oncogene product is a highly regulated serine/threonine kinase that functions in signal transduction downstream from growth factor receptors and upstream from nuclear proto-oncogene products. Using a transient cotransfection assay we have found that activated Raf-1 activates expression from the HIV-LTR...

journal_title：Nucleic acids research

authors： Bruder JT,Heidecker G,Tan TH,Weske JC,Derse D,Rapp UR

更新日期：1993-11-11 00:00:00

abstract：:Plasmids p749, p106, and p150 contain cDNA inserts complementary to rat skeletal muscle actin mRNA. Nucleotide sequence analysis indicates the following sequence relationships: p749 specifies codons 171 to 360; p150 specifies codons 357 to 374 together with 120 nucleotides of the 3'-non-translated region; p106 specifi...

journal_title：Nucleic acids research

authors： Shani M,Nudel U,Zevin-Sonkin D,Zakut R,Givol D,Katcoff D,Carmon Y,Reiter J,Frischauf AM,Yaffe D

更新日期：1981-02-11 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

authors： Paz I,Kligun E,Bengad B,Mandel-Gutfreund Y

更新日期：2016-07-08 00:00:00

abstract：:Terminal deoxynucleotidyl transferase, which requires a single-stranded DNA primer under the usual assay conditions, can be made to accept double-stranded DNA as primer for the addition of either rNMP or dNMP, if Mg+2 ion is replaced by Co+2 ion. The priming efficiency in the presence of (C leads to) CO+2 ion with res...

journal_title：Nucleic acids research

authors： Roychoudhury R,Jay E,Wu R

更新日期：1976-01-01 00:00:00

abstract：:The activation of a telomere maintenance mechanism is required for cancer development in humans. While most tumors achieve this by expressing the enzyme telomerase, a fraction (5-15%) employs a recombination-based mechanism termed alternative lengthening of telomeres (ALT). Here we show that loss of the single-strande...

journal_title：Nucleic acids research

authors： Grudic A,Jul-Larsen A,Haring SJ,Wold MS,Lønning PE,Bjerkvig R,Bøe SO

更新日期：2007-01-01 00:00:00

abstract：:Protein p56 (56 amino acids) from the Bacillus subtilis phage 29 inactivates the host uracil-DNA glycosylase (UDG), an enzyme involved in the base excision repair pathway. At present, p56 is the only known example of a UDG inhibitor encoded by a non-uracil containing viral DNA. Using analytical ultracentrifugation met...

journal_title：Nucleic acids research

authors： Serrano-Heras G,Ruiz-Masó JA,del Solar G,Espinosa M,Bravo A,Salas M

更新日期：2007-01-01 00:00:00

abstract：:The genes for mitoribosomal protein S12 (Mrps12) and mitochondrial seryl-tRNA ligase (Sarsm and Sars2) are oppositely transcribed from a conserved promoter region of <200 bp in both human and mouse. Using a dual reporter vector we identified an array of 4 CCAAT box elements required for efficient transcription of the ...

journal_title：Nucleic acids research

authors： Zanotto E,Shah ZH,Jacobs HT

更新日期：2007-01-01 00:00:00

abstract：:Using sedimentation and cryo electron tomography techniques, the conformations of eukaryotic polyribosomes formed in a long-term cell-free translation system were analyzed over all the active system lifetime (20-30 translation rounds during 6-8 h in wheat germ extract at 25°C). Three distinct types of the conformation...

journal_title：Nucleic acids research

authors： Afonina ZA,Myasnikov AG,Shirokov VA,Klaholz BP,Spirin AS

更新日期：2015-01-01 00:00:00

abstract：:Inducible promoters are a central regulatory component in synthetic biology, metabolic engineering, and protein production for laboratory and commercial uses. Many of these applications utilize two or more exogenous promoters, imposing a currently unquantifiable metabolic burden on the living system. Here, we engineer...

journal_title：Nucleic acids research

authors： Davey JA,Wilson CJ

更新日期：2020-09-25 00:00:00

abstract：:RNase III enzymes cleave double stranded (ds)RNA. This is an essential step for regulating the processing of mRNA, rRNA, snoRNA and other small RNAs, including siRNA and miRNA. Arabidopsis thaliana encodes nine RNase III: four DICER-LIKE (DCL) and five RNASE THREE LIKE (RTL). To better understand the molecular functio...

journal_title：Nucleic acids research

authors： Charbonnel C,Niazi AK,Elvira-Matelot E,Nowak E,Zytnicki M,de Bures A,Jobet E,Opsomer A,Shamandi N,Nowotny M,Carapito C,Reichheld JP,Vaucheret H,Sáez-Vásquez J

更新日期：2017-11-16 00:00:00

abstract：:Fluoropyrimidines, such as 5-fluorouracil (5-FU), are used extensively in cancer therapy. In the cell, 5-FU is metabolized to 5-fluorodeoxyuridylate (5-FdUMP), a tight binding covalent inhibitor of thymidylate synthase (TS). In order to create 5-FdUMP resistant enzymes to protect chemosensitive normal cells and furthe...

journal_title：Nucleic acids research

authors： Landis DM,Gerlach JL,Adman ET,Loeb LA

更新日期：1999-09-15 00:00:00

abstract：:Signal Transducers and Activators of Transcription (STAT) 5A/B regulate cytokine-inducible genes upon binding to GAS motifs. It is not known what percentage of genes with GAS motifs bind to and are regulated by STAT5. Moreover, it is not clear whether genome-wide STAT5 binding is modulated by its concentration. To cla...

journal_title：Nucleic acids research

authors： Zhu BM,Kang K,Yu JH,Chen W,Smith HE,Lee D,Sun HW,Wei L,Hennighausen L

更新日期：2012-05-01 00:00:00

abstract：:Here we report that the poor binding of methylphosphonate oligodeoxynucleosides (MP-ODNs) to their nucleic acid targets can be improved by additional inversion of the anomeric configuration (from beta to alpha) in the sugar moieties to give a new class of analogs, MP alpha-oligonucleosides. MP alpha-dT12and MP 5' alph...

journal_title：Nucleic acids research

authors： Debart F,Meyer A,Vasseur JJ,Rayner B

更新日期：1998-10-15 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

authors： Margreitter C,Petrov D,Zagrovic B

更新日期：2013-07-01 00:00:00

abstract：:Transcription of 5S RNA gene in Xenopus oocytes requires a 38 kDa transcription factor TFIIIA, which interacts with the 50 bp internal control region of the gene. We looked for TFIIIA-like polypeptides in the extracts of adult Xenopus tissues on the basis of their antigenic cross-reactivity to anti-TFIIIA antibody. Se...

journal_title：Nucleic acids research

authors： Yasui W,Ryoji M

更新日期：1989-07-25 00:00:00

abstract：:p73, the p53 homologue, exists as a transactivation-domain-proficient TAp73 or deficient deltaN(DN)p73 form. Expectedly, the oncogenic DNp73 that is capable of inactivating both TAp73 and p53 function, is over-expressed in cancers. However, the role of TAp73, which exhibits tumour-suppressive properties in gain or los...

journal_title：Nucleic acids research

authors： Toh WH,Logette E,Corcos L,Sabapathy K

更新日期：2008-08-01 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

authors： Besemer J,Lomsadze A,Borodovsky M

更新日期：2001-06-15 00:00:00

abstract：:The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation ...

journal_title：Nucleic acids research

authors： MacArthur J,Bowler E,Cerezo M,Gil L,Hall P,Hastings E,Junkins H,McMahon A,Milano A,Morales J,Pendlington ZM,Welter D,Burdett T,Hindorff L,Flicek P,Cunningham F,Parkinson H

更新日期：2017-01-04 00:00:00

abstract：:Non-selenocysteine-containing phospholipid hydroperoxide glutathione peroxidase (NPGPx or GPx7) is an oxidative stress sensor that modulates the antioxidative activity of its target proteins through intermolecular disulfide bond formation. Given NPGPx's role in protecting cells from oxidative damage, identification of...

journal_title：Nucleic acids research

authors： Chen PJ,Weng JY,Hsu PH,Shew JY,Huang YS,Lee WH

更新日期：2015-10-30 00:00:00

abstract：:Comparisons of proteins show that they evolve through the movement of domains. However, in many cases, the underlying mechanisms remain unclear. Here, we observed the movements of DNA recognition domains between non-orthologous proteins within a prokaryote genome. Restriction-modification (RM) systems, consisting of a...

journal_title：Nucleic acids research

authors： Furuta Y,Kobayashi I

更新日期：2012-10-01 00:00:00

abstract：:The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130,000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77,000 Thalassiosira pseudonana ESTs from seven libraries...

journal_title：Nucleic acids research

authors： Maheswari U,Mock T,Armbrust EV,Bowler C

更新日期：2009-01-01 00:00:00

abstract：:Observation and tracking of fluorescently labeled molecules and particles in living cells reveals detailed information about intracellular processes on the molecular level. Whereas light microscopic particle observation is usually limited to two-dimensional projections of short trajectory segments, we report here imag...

journal_title：Nucleic acids research

authors： Spille JH,Kaminski TP,Scherer K,Rinne JS,Heckel A,Kubitscheck U

更新日期：2015-01-01 00:00:00

abstract：:We have sequenced the 480 base pair (bp) repeating unit of the 5S RNA genes of the Dipteran fly Calliphora erythrocephala and compared this sequence to the three known 5S RNA gene sequences from the Dipteran Genus Drosophila (1,2). A striking series of five perfectly conserved homologies identically positioned within ...

journal_title：Nucleic acids research

authors： Rubacha A,Sumner W 3rd,Richter L,Beckingham K

更新日期：1984-11-12 00:00:00

abstract：:The mouse c-Ki-ras protooncogene promoter contains a homopurine-homopyrimidine domain that exhibits S1 nuclease sensitivity in vitro. We have studied the structure of this DNA region in a supercoiled state using a number of chemical probes for non-B DNA conformations including diethyl pyrocarbonate, osmium tetroxide, ...

journal_title：Nucleic acids research

authors： Pestov DG,Dayn A,Siyanova EYu,George DL,Mirkin SM

更新日期：1991-12-11 00:00:00

abstract：:The rapidly growing amount of genomic sequence data being generated and made publicly available necessitate the development of new data storage and archiving methods. The vast amount of data being shared and manipulated also create new challenges for network resources. Thus, developing advanced data compression techni...

journal_title：Nucleic acids research

authors： Chanda P,Elhaik E,Bader JS

更新日期：2012-11-01 00:00:00

abstract：:We previously showed that mRNAs synthesized from three genes that naturally lack introns contain a portion of their coding sequence, known as a cytoplasmic accumulation region (CAR), which is essential for stable accumulation of the intronless mRNAs in the cytoplasm. The CAR in each mRNA is unexpectedly large, ranging...

journal_title：Nucleic acids research

authors： Lei H,Zhai B,Yin S,Gygi S,Reed R

更新日期：2013-02-01 00:00:00