The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.

abstract：:Human thymine-DNA glycosylase (TDG) is well known to excise thymine and uracil from G.T and G.U mismatches, respectively, and was therefore proposed to play a central role in the cellular defense against genetic mutation through spontaneous deamination of 5-methylcytosine and cytosine. In this study, we characterized ...

journal_title：Nucleic acids research

authors： Hardeland U,Bentele M,Jiricny J,Schär P

更新日期：2003-05-01 00:00:00

abstract：:Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for subtyping and localization of phylogenetic breakpoints in HIV-1. Our software is based on a jumping profile Hidden Markov Model...

journal_title：Nucleic acids research

authors： Zhang M,Schultz AK,Calef C,Kuiken C,Leitner T,Korber B,Morgenstern B,Stanke M

更新日期：2006-07-01 00:00:00

abstract：:Homologous recombination provides a means for the in vivo construction of recombinant DNA molecules that may be problematic to assemble in vitro. We have investigated the efficiency of recombination within the Caenorhabditis elegans germ line as a function of the length of homology between recombining molecules. Our f...

journal_title：Nucleic acids research

authors： Kemp BJ,Hatzold J,Sternick LA,Cornman-Homonoff J,Whitaker JM,Tieu PJ,Lambie EJ

更新日期：2007-01-01 00:00:00

abstract：:Translation Initiator of Short 5' UTR (TISU) is a unique regulatory element of both transcription and translation initiation. It is present in a sizable number of genes with basic cellular functions and a very short untranslated region (5' UTR). Here, we investigated translation initiation from short 5' UTR mRNAs with...

journal_title：Nucleic acids research

authors： Elfakess R,Sinvani H,Haimov O,Svitkin Y,Sonenberg N,Dikstein R

更新日期：2011-09-01 00:00:00

abstract：:Genotoxic stress induces alternative splicing of the oncogene MDM2 generating MDM2-ALT1, an isoform attributed with tumorigenic properties. However, the mechanisms underlying this event remain unclear. Here we explore MDM2 splicing regulation by utilizing a novel minigene that mimics endogenous MDM2 splicing in respon...

journal_title：Nucleic acids research

authors： Comiskey DF Jr,Jacob AG,Singh RK,Tapia-Santos AS,Chandler DS

更新日期：2015-04-30 00:00:00

abstract：:siRNAs confer sequence specific and robust silencing of mRNA. By virtue of these properties, siRNAs have become therapeutic candidates for disease intervention. However, their use as therapeutic agents can be hampered by unintended off-target effects by either or both strands of the siRNA duplex. We report here that u...

journal_title：Nucleic acids research

authors： Vaish N,Chen F,Seth S,Fosnaugh K,Liu Y,Adami R,Brown T,Chen Y,Harvie P,Johns R,Severson G,Granger B,Charmley P,Houston M,Templin MV,Polisky B

更新日期：2011-03-01 00:00:00

abstract：:It has been recently reported that the pR plasmid enhances the UV survival in E.coli c600. In order to test whether this function may be expressed also in mammalian cells, LTA (tk- aprt-) mouse cells were cotransformed with pR plasmid DNA and ptk1 plasmid as selectable marker. Tk+ transformants were analyzed for their...

journal_title：Nucleic acids research

authors： Elli R,Marcucci L,Bosi R,Oppi C,Battaglia PA,Gigliani F

更新日期：1983-06-11 00:00:00

abstract：:Transcription initiation complexes formed by bacterial RNA polymerases (RNAPs) exhibit dramatic species-specific differences in stability, leading to different strategies of transcription regulation. The molecular basis for this diversity is unclear. Promoter complexes formed by RNAP from Thermus aquaticus (Taq) are c...

journal_title：Nucleic acids research

authors： Mekler V,Minakhin L,Kuznedelov K,Mukhamedyarov D,Severinov K

更新日期：2012-12-01 00:00:00

abstract：:50 to 55% of tobacco and barley nuclear DNA is accessible to micrococcal endonuclease digestion. The DNA fragments resulting from a mild endonuclease treatment are multiples of a basic unit of 194 +/- 6 base pairs in tobacco and 195 +/- 6 base pairs in barley. After extensive digestion, a DNA fragment of approximately...

journal_title：Nucleic acids research

authors： Philipps G,Gigot C

更新日期：1977-10-01 00:00:00

abstract：:In plants, small interfering RNAs (siRNAs) can trigger a silencing signal that may spread within a tissue to adjacent cells or even systemically to other organs. Movement of the signal is initially limited to a few cells, but in some cases the signal can be amplified and travel over larger distances. How far silencing...

journal_title：Nucleic acids research

authors： de Felippes FF,Ott F,Weigel D

更新日期：2011-04-01 00:00:00

abstract：:Ionizing radiation induces clustered DNA damage, which presents a challenge to the cellular repair machinery. The repair efficiency of a single-strand break (SSB) is approximately 4x less than that for repair of an abasic (AP) site when in a bistranded cluster containing 8-oxoG. To explore whether this difference in r...

journal_title：Nucleic acids research

authors： Mourgues S,Lomax ME,O'Neill P

更新日期：2007-01-01 00:00:00

abstract：:Global run-on sequencing (GRO-seq) is a recent addition to the series of high-throughput sequencing methods that enables new insights into transcriptional dynamics within a cell. However, GRO-sequencing presents new algorithmic challenges, as existing analysis platforms for ChIP-seq and RNA-seq do not address the uniq...

journal_title：Nucleic acids research

authors： Allison KA,Kaikkonen MU,Gaasterland T,Glass CK

更新日期：2014-02-01 00:00:00

abstract：:The role of the enzyme poly(adenosine diphosphate-ribose) polymerase (PADPRP) in DNA repair at the level of the gene was investigated with human HeLa cells in which PADPRP antisense transcripts are inducible with dexamethasone. After such induction, the cellular content of PADPRP is reduced by 90%. DNA damage and its ...

journal_title：Nucleic acids research

authors： Stevnsner T,Ding R,Smulson M,Bohr VA

更新日期：1994-11-11 00:00:00

abstract：:MicroRNA (miRNA) 5'-isoforms, or 5'-isomiRs, are small-RNA species that originate from the same genomic loci as the major miRNAs with their 5' ends shifted from the 5' ends of the miRNAs by a few nucleotides. Although 5'-isomiRs have been reported, their origins, properties and potential functions remain to be examine...

journal_title：Nucleic acids research

authors： Xia J,Zhang W

更新日期：2014-02-01 00:00:00

abstract：:In many organisms (e.g., gram-positive eubacteria) Gin-tRNA is not formed by direct glutaminylation of tRNAGln but by a specific transamidation of Glu-tRNAGln. We wondered whether a similar transamidation pathway also operates in the formation of Asn-tRNA in these organisms. Therefore we tested in S-100 preparations o...

journal_title：Nucleic acids research

authors： Kim SI,Nalaskowska M,Germond JE,Pridmore D,Söll D

更新日期：1996-07-15 00:00:00

abstract：:We developed an algorithm named ViReMa (Viral-Recombination-Mapper) to provide a versatile platform for rapid, sensitive and nucleotide-resolution detection of recombination junctions in viral genomes using next-generation sequencing data. Rather than mapping read segments of pre-defined lengths and positions, ViReMa ...

journal_title：Nucleic acids research

authors： Routh A,Johnson JE

更新日期：2014-01-01 00:00:00

abstract：:The selective and potent inhibition of mitochondrial translation in Saccharomyces cerevisiae by pentamidine suggests a novel antimicrobial action for this drug. Electrophoresis mobility shift assay, T1 ribonuclease footprinting, hydroxyl radical footprinting and isothermal titration calorimetry collectively demonstrat...

journal_title：Nucleic acids research

authors： Sun T,Zhang Y

更新日期：2008-03-01 00:00:00

abstract：:The rates of acid-catalyzed hydrolysis of a hypermodified nucleoside, wyosine and its 5'-monophosphate were determined at various pH, temperature and buffer concentrations. The results show that despite distinct differences in structure and the glycosyl bond stability, the hydrolysis of wyosine proceeds via cleavage o...

journal_title：Nucleic acids research

authors： Golankiewicz B,Zielonacka-Lis E,Folkman W

更新日期：1985-04-11 00:00:00

abstract：:RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions (UTRs). Yet, the underlying mechanisms and coding requirements for efficient co-transcriptional folding remain unclear. Traditional a...

journal_title：Nucleic acids research

authors： Xayaphoummine A,Viasnoff V,Harlepp S,Isambert H

更新日期：2007-01-01 00:00:00

abstract：:Generally, the presence of a consensus sequence in the promoter of a gene is taken as indication for regulation by the transcription factor that binds to this sequence. In light of the recent developments in genome research, we were interested to what extent this supposition is valid. We examined the relationship betw...

journal_title：Nucleic acids research

authors： Hamoen LW,Smits WK,de Jong A,Holsappel S,Kuipers OP

更新日期：2002-12-15 00:00:00

abstract：:The sequence of 110 nucleotides adjacent to the 3'-end of Neurospora crassa 25S-rRNA has been derived by chemical sequencing methods. Sequences present between 40 and 85 nucleotides of the 3'-end were found to complement sequences at the 3'- and 5'-ends of 5.8S-rRNA. Interaction was shown to occur between 5.8S-rRNA an...

journal_title：Nucleic acids research

authors： Kelly JM,Cox RA

更新日期：1981-03-11 00:00:00

abstract：:The availability of the complete sequence of the Saccharomyces cerevisiae genome has allowed a comprehensive analysis of the genes encoding cytoplasmic ribosomal proteins in this organism. On the basis of this complete inventory a new nomenclature for the yeast ribosomal proteins is presented. ...

journal_title：Nucleic acids research

authors： Mager WH,Planta RJ,Ballesta JG,Lee JC,Mizuta K,Suzuki K,Warner JR,Woolford J

更新日期：1997-12-15 00:00:00

abstract：:Antigenic variation of the pilus is an essential component of Neisseria gonorrhoeae pathogenesis. Unidirectional recombination of silent pilin DNA into an expressed pilin gene allows for substantial sequence variation of this highly immunogenic surface structure. While the RecA protein is required for pilin gene recom...

journal_title：Nucleic acids research

authors： Wainwright LA,Frangipane JV,Seifert HS

更新日期：1997-04-01 00:00:00

abstract：:The universal L-shaped tertiary structure of tRNAs is maintained with the help of nucleotide modifications within the D- and T-loops, and these modifications are most extensive within hyperthermophilic species. The obligate-commensal Nanoarchaeum equitans and its phylogenetically-distinct host Ignicoccus hospitalis gr...

journal_title：Nucleic acids research

authors： Rose S,Auxilien S,Havelund JF,Kirpekar F,Huber H,Grosjean H,Douthwaite S

更新日期：2020-07-09 00:00:00

abstract：:A 15-mer DNA aptamer (named TBA) adopts a G-quadruplex structure that strongly inhibits fibrin-clot formation by binding to thrombin. We have performed thermodynamic analysis, binding affinity and biological activity studies of TBA variants modified by unlocked nucleic acid (UNA) monomers. UNA-U placed in position U3,...

journal_title：Nucleic acids research

authors： Pasternak A,Hernandez FJ,Rasmussen LM,Vester B,Wengel J

更新日期：2011-02-01 00:00:00

abstract：:Mammalian gene promoters for transcription by RNA polymerase II are typically organized in the following order: upstream sequence motif(s)/TATA box/initiation site. Here we report studies in which the order, orientation and DNA sequences of these three elements are varied to determine how these affect polarity of tran...

journal_title：Nucleic acids research

authors： Xu LC,Thali M,Schaffner W

更新日期：1991-12-25 00:00:00

abstract：:MeCP2 is a methyl-CpG binding protein that can repress transcription of nearby genes. In humans, mutations in the MECP2 gene are the major cause of Rett syndrome. By searching expressed sequence tag (EST) databases we have found a novel MeCP2 splice isoform (MeCP2alpha) which encodes a distinct N-terminus. We demonstr...

journal_title：Nucleic acids research

authors： Kriaucionis S,Bird A

更新日期：2004-03-19 00:00:00

abstract：:The homeobox-containing gene Hex is expressed in several cell types, including thyroid follicular cells, in which it regulates the transcription of tissue- specific genes. In this study the regulation of Hex promoter activity was investigated. Using co- transfection experiments, we demonstrated that the transcriptiona...

journal_title：Nucleic acids research

authors： Puppin C,D'Elia AV,Pellizzari L,Russo D,Arturi F,Presta I,Filetti S,Bogue CW,Denson LA,Damante G

更新日期：2003-04-01 00:00:00

abstract：:Hidden Markov models (HMMs) and their variants are widely used in Bioinformatics applications that analyze and compare biological sequences. Designing a novel application requires the insight of a human expert to define the model's architecture. The implementation of prediction algorithms and algorithms to train the m...

journal_title：Nucleic acids research

authors： Lam TY,Meyer IM

更新日期：2009-11-01 00:00:00

abstract：:Signal recognition particle (SRP) is a stable cytoplasmic ribonucleoprotein complex that serves to translocate secretory proteins across membranes during translation. The SRP Database (SRPDB) provides compilations of SRP components, ordered alphabetically and phylogenetically. Alignments emphasize phylogenetically-sup...

journal_title：Nucleic acids research

authors： Gorodkin J,Knudsen B,Zwieb C,Samuelsson T

更新日期：2001-01-01 00:00:00