PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update.

abstract：:The centromere complex is a multicomponent structure essential for faithful chromosome transmission. Here we show that the S. cerevisiae centromere protein Cpf1 bends centromere DNA element I (CDEI) with the bend angle ranging from 66 degrees to 71 degrees. CDEI DNA sequences that carry point mutations which lead to r...

journal_title：Nucleic acids research

authors： Niedenthal RK,Sen-Gupta M,Wilmen A,Hegemann JH

更新日期：1993-10-11 00:00:00

abstract：:We characterised the human hSuv3p protein belonging to the family of NTPases/helicases. In yeast mitochondria the hSUV3 orthologue is a component of the degradosome complex and participates in mtRNA turnover and processing, while in Caenorhabditis elegans the hSUV3 orthologue is necessary for viability of early embryo...

journal_title：Nucleic acids research

authors： Minczuk M,Piwowarski J,Papworth MA,Awiszus K,Schalinski S,Dziembowski A,Dmochowska A,Bartnik E,Tokatlidis K,Stepien PP,Borowski P

更新日期：2002-12-01 00:00:00

abstract：:DNA topoisomerases and DNA site-specific recombinases are biologically important enzymes involved in a diverse set of cellular processes. We show that replacement of a phosphodiester linkage by a 5'-bridging phosphorothioate linkage creates an efficient suicide substrate for calf thymus topoisomerase I and lambda inte...

journal_title：Nucleic acids research

authors： Burgin AB Jr,Huizenga BN,Nash HA

更新日期：1995-08-11 00:00:00

abstract：:Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position...

journal_title：Nucleic acids research

authors： Elati M,Nicolle R,Junier I,Fernández D,Fekih R,Font J,Képès F

更新日期：2013-02-01 00:00:00

abstract：:The J-binding protein 1 (JBP1) is essential for biosynthesis and maintenance of DNA base-J (β-d-glucosyl-hydroxymethyluracil). Base-J and JBP1 are confined to some pathogenic protozoa and are absent from higher eukaryotes, prokaryotes and viruses. We show that JBP1 recognizes J-containing DNA (J-DNA) through a 160-res...

journal_title：Nucleic acids research

authors： Heidebrecht T,Christodoulou E,Chalmers MJ,Jan S,Ter Riet B,Grover RK,Joosten RP,Littler D,van Luenen H,Griffin PR,Wentworth P Jr,Borst P,Perrakis A

更新日期：2011-07-01 00:00:00

abstract：:KUPS (The University of Kansas Proteomics Service) provides high-quality protein-protein interaction (PPI) data for researchers developing and evaluating computational models for predicting PPIs by allowing users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interacting protein pairs (NI...

journal_title：Nucleic acids research

authors： Chen XW,Jeong JC,Dermyer P

更新日期：2011-01-01 00:00:00

abstract：:We have previously reported the human cDNA encoding MSSP-1, a sequence-specific double- and single-stranded DNA binding protein [Negishi, Nishita, Saëgusa, Kakizaki, Galli, Kihara, Tamai, Miyajima, Iguchi-Ariga and Ariga (1994) Oncogene, 9, 1133-1143]. MSSP-1 binds to a DNA replication origin/transcriptional enhancer ...

journal_title：Nucleic acids research

authors： Takai T,Nishita Y,Iguchi-Ariga SM,Ariga H

更新日期：1994-12-25 00:00:00

abstract：:The gene for human apolipoprotein (apo) A-II has been isolated from a human genomic DNA library. The cloned fragment was approximately 14 kilobase-pair (kb) long, and extended about 9.0 kb upstream as well as 3.5 kb downstream from the apoA-II gene, which was contained within a 3.1 kb HindIII fragment of human DNA. Th...

journal_title：Nucleic acids research

authors： Lackner KJ,Law SW,Brewer HB Jr

更新日期：1985-06-25 00:00:00

abstract：:Histone variants play an important role in shaping the mammalian epigenome and their aberrant expression is frequently observed in several types of cancer. However, the mechanisms that mediate their function and the composition of the variant-containing chromatin are still largely unknown. A proteomic interrogation of...

journal_title：Nucleic acids research

authors： Sansoni V,Casas-Delucchi CS,Rajan M,Schmidt A,Bönisch C,Thomae AW,Staege MS,Hake SB,Cardoso MC,Imhof A

更新日期：2014-06-01 00:00:00

abstract：:DNA cytosine-5 methyltransferases (C5-MTases) are valuable models to study sequence-specific modification of DNA and are becoming increasingly important tools for biotechnology. Here we describe a structure-guided rational protein design combined with random mutagenesis and selection to change the specificity of the H...

journal_title：Nucleic acids research

authors： Gerasimaite R,Vilkaitis G,Klimasauskas S

更新日期：2009-11-01 00:00:00

abstract：:High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such a...

journal_title：Nucleic acids research

authors： Hach F,Sarrafi I,Hormozdiari F,Alkan C,Eichler EE,Sahinalp SC

更新日期：2014-07-01 00:00:00

abstract：:Chromosome stability is primarily determined by telomere length. TRF1 is the core subunit of shelterin that plays a critical role in telomere organization and replication. However, the dynamics of TRF1 in scenarios of telomere-processing activities remain elusive. Using single-molecule magnetic tweezers, we here inves...

journal_title：Nucleic acids research

authors： Li X,Wang M,Zheng W,Huang W,Wang Z,Jin K,Liu L,Yu Z

更新日期：2021-01-25 00:00:00

abstract：:We developed a framework for quick and reliable construction of complex gene circuits for genetically engineering mammalian cells. Our hierarchical framework is based on a novel nucleotide addressing system for defining the position of each part in an overall circuit. With this framework, we demonstrate construction o...

journal_title：Nucleic acids research

authors： Guye P,Li Y,Wroblewska L,Duportet X,Weiss R

更新日期：2013-09-01 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

abstract：:Archival formalin-fixed, paraffin-embedded and ethanol-fixed tissues represent a potentially invaluable resource for gene expression analysis, as they are the most widely available material for studies of human disease. Little data are available evaluating whether RNA obtained from fixed (archival) tissues could produ...

journal_title：Nucleic acids research

authors： Karsten SL,Van Deerlin VM,Sabatti C,Gill LH,Geschwind DH

更新日期：2002-01-15 00:00:00

abstract：:The log kobs vs. pH profiles were determined in the intermediate acidity region for the glycosyl hydrolysis of guanosine and its 8-amino, 8-monomethylamino, 8-dimethylamino and 8-bromo derivatives. The decreased rate of the 8-amino and enhanced rate of the 8-bromo compound compared to guanosine support an A type mecha...

journal_title：Nucleic acids research

authors： Jordan F,Niv H

更新日期：1977-03-01 00:00:00

abstract：:The nucleotide sequence of a 981 bp's HincII-PvuII DNA fragment containing the 3' end of the malEFG operon in E. coli was determined. This sequence displayed a putative Rho-independent transcription termination site localized 87 bp's after the stop codon of malG. When cloned into plasmid pKG1800, the HincII-PvuII frag...

journal_title：Nucleic acids research

authors： Francoz E,Dassa E

更新日期：1988-05-11 00:00:00

abstract：:We investigated the effects of the antiviral agent distamycin A and of a distamycin derivative (FCE 24517) which possesses antineoplastic activity on the binding of some regulatory proteins to DNA. Both compounds inhibited the binding to DNA of the ubiquitous octamer binding factor OTF 1 and of the erythroid specific ...

journal_title：Nucleic acids research

authors： Broggini M,Ponti M,Ottolenghi S,D'Incalci M,Mongelli N,Mantovani R

更新日期：1989-02-11 00:00:00

abstract：:The newest genomic advances have uncovered an unprecedented degree of structural variation throughout genomes, with great amounts of data accumulating rapidly. Here we introduce InvFEST (http://invfestdb.uab.cat), a database combining multiple sources of information to generate a complete catalogue of non-redundant hu...

journal_title：Nucleic acids research

authors： Martínez-Fundichely A,Casillas S,Egea R,Ràmia M,Barbadilla A,Pantano L,Puig M,Cáceres M

更新日期：2014-01-01 00:00:00

abstract：:The centromere is a highly specialized chromosomal element that is essential for chromosome segregation during mitosis. Centromere integrity must therefore be properly preserved and is strictly dependent upon the establishment and maintenance of surrounding chromatin structure. Here we identify WDHD1, a WD40-domain an...

journal_title：Nucleic acids research

authors： Hsieh CL,Lin CL,Liu H,Chang YJ,Shih CJ,Zhong CZ,Lee SC,Tan BC

更新日期：2011-05-01 00:00:00

abstract：:DNA sequences, that control expression of the spliced leader (SL) RNA gene in the parasitic protozoan Leishmania amazonensis, were mapped by block substitution mutagenesis. In the absence of a functional in vitro system for transcription, no promoter elements have yet been identified in this organism. We therefore dev...

journal_title：Nucleic acids research

authors： Agami R,Aly R,Halman S,Shapira M

更新日期：1994-06-11 00:00:00

abstract：:The secondary structure of an adenovirus associated low molecular weight RNA (VAI-RNA) has been studied by partial digestion with T1-RNase and S1-endonuclease followed by T1-fingerprint analysis. The empirical secondary structure has been compared with two computer generated models based on minimal free energy of the ...

journal_title：Nucleic acids research

authors： Monstein HJ,Philipson L

更新日期：1981-09-11 00:00:00

abstract：:Diethyl pyrocarbonate reacts with the single-stranded loops of cruciform structures with great selectivity. Adenine bases are carbethoxylated, as a result of which the backbone may be cleaved with piperidine, and the level of chemical modification at each base may be determined. We have studied the ColE1 and (A-T)34 c...

journal_title：Nucleic acids research

authors： Furlong JC,Lilley DM

更新日期：1986-05-27 00:00:00

abstract：:PROtein Domain Organization and Comparison (PRODOC) comprises several programs that enable convenient comparison of proteins as a sequence of domains. The in-built dataset currently consists of approximately 698 000 proteins from 192 organisms with complete genomic data, and all the SWISSPROT proteins obtained from th...

journal_title：Nucleic acids research

authors： Krishnadev O,Rekha N,Pandit SB,Abhiman S,Mohanty S,Swapna LS,Gore S,Srinivasan N

更新日期：2005-07-01 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：:Microarrays are an effective tool for monitoring genome-wide gene expression levels. In current microarray analyses, the majority of genes on arrays are frequently eliminated for further analysis because the changes in their expression levels (ratios) are considered to be not significant. This strategy risks failure t...

journal_title：Nucleic acids research

authors： Yano K,Imai K,Shimizu A,Hanashita T

更新日期：2006-03-14 00:00:00

abstract：:eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. Here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 euka...

journal_title：Nucleic acids research

authors： Huerta-Cepas J,Szklarczyk D,Heller D,Hernández-Plaza A,Forslund SK,Cook H,Mende DR,Letunic I,Rattei T,Jensen LJ,von Mering C,Bork P

更新日期：2019-01-08 00:00:00

abstract：:Although subtelomeric regions in humans are heterochromatic, the epigenetic nature of human telomeres remains controversial. This controversy might have been influenced by the confounding effect of subtelomeric regions and interstitial telomeric sequences (ITSs) on telomeric chromatin structure analyses. In addition, ...

journal_title：Nucleic acids research

authors： Cubiles MD,Barroso S,Vaquero-Sedas MI,Enguix A,Aguilera A,Vega-Palas MA

更新日期：2018-03-16 00:00:00

abstract：:The potency of the immune response has still to be harnessed effectively to combat human cancers. However, the discovery of T-cell targets in melanomas and other tumors has raised the possibility that cancer vaccines can be used to induce a therapeutically effective immune response against cancer. The targets, cancer-...

journal_title：Nucleic acids research

authors： Almeida LG,Sakabe NJ,deOliveira AR,Silva MC,Mundstein AS,Cohen T,Chen YT,Chua R,Gurung S,Gnjatic S,Jungbluth AA,Caballero OL,Bairoch A,Kiesler E,White SL,Simpson AJ,Old LJ,Camargo AA,Vasconcelos AT

更新日期：2009-01-01 00:00:00

abstract：:Transcription driven by the proviral promoter of the Human T-cell Leukemia Virus type I (HTLV-I) is tightly regulated by the Tax1 transactivator. This viral protein potently induces the enhancer activity of a 21 bp motif repeated three times in the promoter. We have previously shown that this induction results from th...

journal_title：Nucleic acids research

authors： Lombard-Platet G,Jalinot P

更新日期：1993-08-25 00:00:00