Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis.

abstract：:Genomic DNA of African trypanosomes contains a hypermodified thymidine residue termed base J (beta-d-glucosyl-HOMedU). This modified base is localized primarily to repetitive DNA, namely the telomeres, and is implicated in the regulation of antigenic variation. The base is synthesized in a two-step pathway. Initially,...

journal_title：Nucleic acids research

authors： Cliffe LJ,Kieft R,Southern T,Birkeland SR,Marshall M,Sweeney K,Sabatini R

更新日期：2009-04-01 00:00:00

abstract：:A search of sequence information in the GenBank files shows that tracts of 15-30 contiguous purines are greatly overrepresented in all eukaryotic species examined, ranging from yeast to human. Such an overabundance does not occur in prokaryotic sequences. The large increase in the number of oligopurine tracts cannot b...

journal_title：Nucleic acids research

authors： Behe MJ

更新日期：1995-02-25 00:00:00

abstract：:To successfully infect plants, viruses must counteract small RNA-based host defense responses. During infection of Arabidopsis, Cauliflower mosaic pararetrovirus (CaMV) is transcribed into pregenomic 35S and subgenomic 19S RNAs. The 35S RNA is both reverse transcribed and also used as an mRNA with highly structured 60...

journal_title：Nucleic acids research

authors： Blevins T,Rajeswaran R,Aregger M,Borah BK,Schepetilnikov M,Baerlocher L,Farinelli L,Meins F Jr,Hohn T,Pooggin MM

更新日期：2011-07-01 00:00:00

abstract：:Two new beta-lactoglobulin (BLG)/human serum albumin (HSA) hybrid gene vectors were constructed and tested for expression in COS-7 cells and in transgenic mice. The HSA sequences were inserted between the second and sixth BLG exons. Transient transfection experiments with these vectors as well as a series of additiona...

journal_title：Nucleic acids research

authors： Barash I,Nathan M,Kari R,Ilan N,Shani M,Hurwitz DR

更新日期：1996-02-15 00:00:00

abstract：:1731, a Drosophila retrotransposon was first described as having a transcription activity which was negatively regulated by 20-hydroxyecdysone (20-OH), the steroid molting hormone of insects. Using constructions expressing the bacterial chloramphenicol-acetyltransferase (CAT) gene under the control of the entire or de...

journal_title：Nucleic acids research

authors： Ziarczyk P,Best-Belpomme M

更新日期：1991-10-25 00:00:00

abstract：:High-throughput sequencing of 16S rRNA gene amplicons (16S-seq) has become a widely deployed method for profiling complex microbial communities but technical pitfalls related to data reliability and quantification remain to be fully addressed. In this work, we have developed and implemented a set of synthetic 16S rRNA...

journal_title：Nucleic acids research

authors： Tourlousse DM,Yoshiike S,Ohashi A,Matsukura S,Noda N,Sekiguchi Y

更新日期：2017-02-28 00:00:00

abstract：:Bacterial small RNAs (sRNAs) are a heterogeneous group of post-transcriptional regulators that often act at the heart of large networks. Hundreds of sRNAs have been discovered by genome-wide screens and most of these sRNAs exert their functions by base-pairing with target mRNAs. However, studies addressing the molecul...

journal_title：Nucleic acids research

authors： Fröhlich KS,Förstner KU,Gitai Z

更新日期：2018-11-16 00:00:00

abstract：:Rap1 is an essential DNA-binding factor from the yeast Saccharomyces cerevisiae involved in transcription and telomere maintenance. Its binding to DNA targets Rap1 at particular loci, and may optimize its ability to form functional macromolecular assemblies. It is a modular protein, rich in large potentially unfolded ...

journal_title：Nucleic acids research

authors： Matot B,Le Bihan YV,Lescasse R,Pérez J,Miron S,David G,Castaing B,Weber P,Raynal B,Zinn-Justin S,Gasparini S,Le Du MH

更新日期：2012-04-01 00:00:00

abstract：:Comparative analysis of mutants using transfection is complicated by clones exhibiting variable levels of gene expression due to copy number differences and genomic position effects. Recombinase-mediated cassette exchange (RMCE) can overcome these problems by introducing the target gene into pre-determined chromosomal...

journal_title：Nucleic acids research

authors： Wong ET,Kolman JL,Li YC,Mesner LD,Hillen W,Berens C,Wahl GM

更新日期：2005-10-04 00:00:00

abstract：:These studies employed the synthetic linear DNA, poly dGdC, in the B and cobalt hexammine chloride (Co)-induced Z form to determine the effect of conformation on protein-DNA interactions. The rate of the reaction of the restriction endonucleases, Hha I and Cfo I, are reduced with Z DNA as compared to B DNA. The abilit...

journal_title：Nucleic acids research

authors： Soslau G,Parker J,Nelson JW

更新日期：1986-09-25 00:00:00

abstract：:The D. melanogaster Adh gene is transcribed from two different promoters; a proximal (larval) promoter is active during late embryonic and larval stages, and a distal (adult) promoter is active primarily in third instar larvae and in adult flies (1). Genetic analyses suggest that several species of the mulleri subgrou...

journal_title：Nucleic acids research

authors： Fischer JA,Maniatis T

更新日期：1985-10-11 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：:RNA molecules of > 20 nucleotides have been the focus of numerous recent NMR structural studies. Several investigators have used the UNCG family of hairpins to ensure proper folding. We show that th UUCG hairpin has a minimum requirement of a two base-pair stem. Hairpins with a CG loop closing base pair and an initial...

journal_title：Nucleic acids research

authors： Molinaro M,Tinoco I Jr

更新日期：1995-08-11 00:00:00

abstract：:Major efforts are underway to elucidate the spatial distribution of ribosomal RNAs (rRNAs) in the ribosome. An especially informative approach is the identification of likely base-base tertiary interactions within the RNA by phylogenetic comparison. Herein evidence is presented for three heretofore unrecognized candid...

journal_title：Nucleic acids research

authors： Haselman T,Camp DG,Fox GE

更新日期：1989-03-25 00:00:00

abstract：:Although the thermophilic bacterium Thermus aquaticus grows optimally at 70 degrees C and cannot grow at moderate temperatures, its DNA polymerase I has significant activity at 20-37 degrees C. This activity is a bane to some PCRs, since it catalyzes non-specific priming. We report mutations of Klentaq (an N-terminal ...

journal_title：Nucleic acids research

authors： Kermekchiev MB,Tzekov A,Barnes WM

更新日期：2003-11-01 00:00:00

abstract：:BmFTZ-F1 is a Bombyx mori homologue of FTZ-F1, a positive regulator of the fushi tarazu gene of Drosophila melanogaster. In order to determine the sequence recognized with this factor, we made three sets of oligonucleotide mixture which contain 4 possible nucleotides at different positions within the previously propos...

journal_title：Nucleic acids research

authors： Ueda H,Hirose S

更新日期：1991-07-11 00:00:00

abstract：:NELF and DSIF act together to inhibit transcription elongation in vitro, and are implicated in causing promoter proximal pausing on the hsp70 gene in Drosophila. Here, further characterization of Drosophila NELF is provided. Drosophila NELF has four subunits similar to subunits of human NELF. The amino acid sequences ...

journal_title：Nucleic acids research

authors： Wu CH,Lee C,Fan R,Smith MJ,Yamaguchi Y,Handa H,Gilmour DS

更新日期：2005-03-01 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：:The Nucleolar Proteome Database (NOPdb) archives data on >700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli, the most prominent nuclear organelle. Each protein entry is annotated with information about its corresponding gene, its domain st...

journal_title：Nucleic acids research

authors： Leung AK,Trinkle-Mulcahy L,Lam YW,Andersen JS,Mann M,Lamond AI

更新日期：2006-01-01 00:00:00

abstract：:The diverse localization of transcripts in cells suggests that there are many specific RNA-protein interactions that have yet to be identified. Progress has been limited, however, by the lack of a robust method to detect and isolate the RNA-binding proteins. Here we describe the use of an RNA aptamer, scaffolded to a ...

journal_title：Nucleic acids research

authors： Iioka H,Loiselle D,Haystead TA,Macara IG

更新日期：2011-04-01 00:00:00

abstract：:Transcription of the bacteriophage Mu mom operon requires transactivation by the phage-encoded C protein. DNase I footprinting showed that in the absence of C, Escherichia coli RNA polymerase E(sigma)70 (RNAP) binds to the mom promoter (Pmom) region at a site, P2 (from -64 to -11 with respect to the transcription star...

journal_title：Nucleic acids research

authors： Sun W,Hattman S

更新日期：1996-10-15 00:00:00

abstract：:Escherichia coli Exonuclease I (ExoI) digests single-stranded DNA (ssDNA) in the 3'-5' direction in a highly processive manner. The crystal structure of ExoI, determined previously in the absence of DNA, revealed a C-shaped molecule with three domains that form a central positively charged groove. The active site is a...

journal_title：Nucleic acids research

authors： Korada SK,Johns TD,Smith CE,Jones ND,McCabe KA,Bell CE

更新日期：2013-06-01 00:00:00

abstract：:Autosomal dominant and/or recessive progressive external ophthalmoplegia (ad/arPEO) is associated with mtDNA mutagenesis. It can be caused by mutations in three nuclear genes, encoding the adenine nucleotide translocator 1, the mitochondrial helicase Twinkle or DNA polymerase gamma (POLG). How mutations in these genes...

journal_title：Nucleic acids research

authors： Wanrooij S,Luoma P,van Goethem G,van Broeckhoven C,Suomalainen A,Spelbrink JN

更新日期：2004-06-04 00:00:00

abstract：:The enterovirus 71 (EV71) 3Dpol is an RNA-dependent RNA polymerase (RdRP) that plays the central role in the viral genome replication, and is an important target in antiviral studies. Here, we report a crystal structure of EV71 3Dpol elongation complex (EC) at 1.8 Å resolution. The structure reveals that the 5'-end gu...

journal_title：Nucleic acids research

authors： Shi W,Ye HQ,Deng CL,Li R,Zhang B,Gong P

更新日期：2020-02-20 00:00:00

abstract：:DNA double-strand breaks (DSBs) are repaired by either the non-homologous end joining (NHEJ) or homologous recombination (HR) pathway. Pathway choice is determined by the generation of 3΄ single-strand DNA overhangs at the break that are initiated by the action of the Mre11-Rad50-Xrs2 (MRX) complex to direct repair to...

journal_title：Nucleic acids research

authors： Wiest NE,Houghtaling S,Sanchez JC,Tomkinson AE,Osley MA

更新日期：2017-06-02 00:00:00

abstract：:The possible role of LG-1, a Tetrahymena specific HMG protein found in the macronuclear chromatin (Hamana, K. and Iwai, K. (1979) J. Biochem. 86, 789-794), was examined in relation to the chromatin structure. The chromatin isolated from cells synchronized at different stages of the cell cycle contained about one molec...

journal_title：Nucleic acids research

authors： Hamana K,Zama M

更新日期：1980-11-25 00:00:00

abstract：:The transactivator Staf, which contains seven contiguous zinc fingers of the C(2)-H(2)type, exerts its effects on gene expression by binding to specific targets in vertebrate small nuclear RNA (snRNA) and snRNA-type gene promoters. Here, we have investigated the interaction of the Staf zinc finger domain with the opti...

journal_title：Nucleic acids research

authors： Schaub M,Krol A,Carbon P

更新日期：2000-05-15 00:00:00

abstract：:The development of biosensors based on DNA hybridization requires a more precise knowledge of the thermodynamics of the hybridization at a solid interface. In particular, the selectivity of hybridization can be affected by a lot of parameters such as the single-strand (ss)DNA density, the pH, the ionic strength or the...

journal_title：Nucleic acids research

authors： Meunier-Prest R,Raveau S,Finot E,Legay G,Cherkaoui-Malki M,Latruffe N

更新日期：2003-12-01 00:00:00

abstract：:The nucleotide sequence of Drosophila melanogaster methionine tRNAi was determined to be: pA-G-C-A-G-A-G-U-m1G-m2G-C-G-C-A-G-U-G-G-A-A-G-C-G-U-m2G-C-U-G-G-G-C-C-C-A-U-t6A-A-C-C-C-A-G-A-G-m7G-D-m5C-C-C-G-A-G-G-A-U-C-G-m1A-A-A-C-C-U-U-G-C-U-C-U-G-C-U-A-C-C-A(OH). It differs from vertebrate initiator tRNAs in only 6 out ...

journal_title：Nucleic acids research

authors： Silverman S,Heckman J,Cowling GJ,Delaney AD,Dunn RJ,Gillam IC,Tener GM,Söll D,RajBhandary UL

更新日期：1979-02-01 00:00:00

abstract：:Combinatorial interactions of sequence-specific trans-acting factors with localized genomic cis-element clusters are the principal mechanism for regulating tissue-specific and developmental gene expression. With the emergence of expanding numbers of genome-wide expression analyses, the identification of the cis-elemen...

journal_title：Nucleic acids research

authors： Jegga AG,Gupta A,Gowrisankar S,Deshmukh MA,Connolly S,Finley K,Aronow BJ

更新日期：2005-07-01 00:00:00