Importance in catalysis of a magnesium ion with very low affinity for a hammerhead ribozyme.

abstract：:Differential expression analysis of RNA sequencing (RNA-seq) data typically relies on reconstructing transcripts or counting reads that overlap known gene structures. We previously introduced an intermediate statistical approach called differentially expressed region (DER) finder that seeks to identify contiguous regi...

journal_title：Nucleic acids research

authors： Collado-Torres L,Nellore A,Frazee AC,Wilks C,Love MI,Langmead B,Irizarry RA,Leek JT,Jaffe AE

更新日期：2017-01-25 00:00:00

abstract：:Accurate mapping of spliced RNA-Seq reads to genomic DNA has been known as a challenging problem. Despite significant efforts invested in developing efficient algorithms, with the human genome as a primary focus, the best solution is still not known. A recently introduced tool, TrueSight, has demonstrated better perfo...

journal_title：Nucleic acids research

authors： Burns PD,Li Y,Ma J,Borodovsky M

更新日期：2014-02-01 00:00:00

abstract：:The high-mobility-group A2 protein (HMGA2) plays important functional roles in transcriptional regulation, DNA replication and chromatin structure. In this study, the effect of histone deacetylase inhibition on the transcriptional activity of the Hmga2 gene was investigated in vivo both at the endogenous gene level an...

journal_title：Nucleic acids research

authors： Ferguson M,Henry PA,Currie RA

更新日期：2003-06-15 00:00:00

abstract：:Traditional chromatin analysis methods only test one locus at the time or use different templates for each locus, making a standardized analysis of large genomic regions or many co-regulated genes at different loci a difficult task. On the other hand, genome-wide high-resolution mapping of chromatin accessibility empl...

journal_title：Nucleic acids research

authors： Basheer A,Berger H,Reyes-Dominguez Y,Gorfer M,Strauss J

更新日期：2009-04-01 00:00:00

abstract：:IMP (Integrative Multi-species Prediction), originally released in 2012, is an interactive web server that enables molecular biologists to interpret experimental results and to generate hypotheses in the context of a large cross-organism compendium of functional predictions and networks. The system provides biologists...

journal_title：Nucleic acids research

authors： Wong AK,Krishnan A,Yao V,Tadych A,Troyanskaya OG

更新日期：2015-07-01 00:00:00

abstract：:A repeated non-coding DNA sequence d(TTAGGG)n is present in the telomeric ends of all human chromosomes. These repeats can adopt multiple inter and intramolecular non-B-DNA conformations that may play an important role in biological processes. Two intramolecular structures of the telomeric oligonucleotide dAGGG(TTAGGG...

journal_title：Nucleic acids research

authors： He Y,Neumann RD,Panyutin IG

更新日期：2004-10-08 00:00:00

abstract：:The transcription factor HIV-TF1, which binds to a region about 60 bp upstream from the enhancer of the human immunodeficiency virus-1 (HIV-1), was purified from human B cells. HIV-TF1 had a molecular weight of 39,000. Binding of HIV-TF1 to the HIV long terminal repeat (LTR) activated transcription from the HIV promot...

journal_title：Nucleic acids research

authors： Maekawa T,Sudo T,Kurimoto M,Ishii S

更新日期：1991-09-11 00:00:00

abstract：:It has been postulated that a myriad of long noncoding RNAs (lncRNAs) contribute to gene regulation. In fission yeast, glucose starvation triggers lncRNA transcription across promoter regions of stress-responsive genes including fbp1 (fructose-1,6-bisphosphatase1). At the fbp1 promoter, this transcription promotes chr...

journal_title：Nucleic acids research

authors： Takemata N,Oda A,Yamada T,Galipon J,Miyoshi T,Suzuki Y,Sugano S,Hoffman CS,Hirota K,Ohta K

更新日期：2016-06-20 00:00:00

abstract：:G-quadruplexes (G4s) are nucleic acid structure motifs that are of significance in chemistry and biology. The function of G4s is often governed by their interaction with G4-binding proteins. Few categories of G4-specific tools have been developed to inhibit G4-protein interactions; however, until now there is no aptam...

journal_title：Nucleic acids research

authors： Umar MI,Kwok CK

更新日期：2020-10-09 00:00:00

abstract：:Here we advocate the use of 2-dimensional data representation in the context of the informational approach of sequence analysis (Claverie & Bougueleret (1986) Nucleic Acids Research 14, 179-196) by applying these methods to the problem of intron/exon discrimination. Two main findings are reported: i) oligonucleotide p...

journal_title：Nucleic acids research

authors： Bougueleret L,Tekaia F,Sauvaget I,Claverie JM

更新日期：1988-03-11 00:00:00

abstract：:It has been proposed that DNA multiply damaged sites (MDS), where more than one moiety in a local region ( approximately 1 helical turn, 10 bp) of the DNA is damaged, are lesions of enhanced biological significance. However, other than indirect measures, there are few analytical techniques that allow direct detection ...

journal_title：Nucleic acids research

authors： Bowman KJ,Pla RL,Guichard Y,Farmer PB,Jones GD

更新日期：2001-10-15 00:00:00

abstract：:Ribosomal RNA (rRNA) in intact ribosomes is cleaved into discrete products on incubation of reticulocyte lysates or L-cell extracts with ppp(A2'p)3A. Cleavage of rRNA may, therefore, provide a useful assay for 2-5A (ppp)A2'p)nA; n = 2 to 4) or for the presence of a 2-5A-dependent nuclease. The results with reticulocyt...

journal_title：Nucleic acids research

authors： Wreschner DH,James TC,Silverman RH,Kerr IM

更新日期：1981-04-10 00:00:00

abstract：:The -1 ribosomal frameshifting requires the existence of an in cis RNA slippery sequence and is promoted by a downstream stimulator RNA. An atypical RNA pseudoknot with an extra stem formed by complementary sequences within loop 2 of an H-type pseudoknot is characterized in the severe acute respiratory syndrome corona...

journal_title：Nucleic acids research

authors： Su MC,Chang CT,Chu CH,Tsai CH,Chang KY

更新日期：2005-07-29 00:00:00

abstract：:Human single-strand (ss) DNA binding proteins 1 (hSSB1) has been shown to participate in DNA damage response and maintenance of genome stability by regulating the initiation of ATM-dependent signaling. ATM phosphorylates hSSB1 and prevents hSSB1 from ubiquitin-proteasome-mediated degradation. However, the E3 ligase th...

journal_title：Nucleic acids research

authors： Chen ZW,Liu B,Tang NW,Xu YH,Ye XY,Li ZM,Niu XM,Shen SP,Lu S,Xu L

更新日期：2014-10-01 00:00:00

abstract：:Type I toxin-antitoxin (TA) systems have been identified in a wide range of bacterial genomes. Here, we report the characterization of a new type I TA system present on the chromosome of the major human gastric pathogen, Helicobacter pylori. We show that the aapA1 gene encodes a 30 amino acid peptide whose artificial ...

journal_title：Nucleic acids research

authors： Arnion H,Korkut DN,Masachis Gelo S,Chabas S,Reignier J,Iost I,Darfeuille F

更新日期：2017-05-05 00:00:00

abstract：:The GeneSpeed database (http://genespeed.uchsc.edu/) is an online database and resource tool facilitating the detailed study of protein domain homology in the transcriptomes of Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans. The population schema for the GeneSpeed database takes advanta...

journal_title：Nucleic acids research

authors： Kutchma A,Quayum N,Jensen J

更新日期：2007-01-01 00:00:00

abstract：:Eukaryotic cells possess several distinct mismatch repair pathways. A mismatch can be introduced in retroviral double-stranded DNA by a pre-existing mutation within the primer binding site (PBS) of the viral RNA genome. In order to evaluate mismatch repair of retroviral double-stranded DNA, Moloney leukemia virus (MLV...

journal_title：Nucleic acids research

authors： Tang LY,Zhang J

更新日期：2000-06-15 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：:We have developed a PCR-based short interfering RNA (siRNA) quantification method based on competition between siRNA and a homologous DNA primer for annealing to template DNA, avoiding the requirement for prior conversion of RNA to cDNA. Primers and probe were designed to amplify regions of the human papillomavirus E6...

journal_title：Nucleic acids research

authors： Liu WL,Stevenson M,Seymour LW,Fisher KD

更新日期：2009-01-01 00:00:00

abstract：:The conformational changes induced by the binding of cis-diamminedichloroplatinum(II) to poly(dG-dC).poly(dG-dC) have been studied by reaction with specific antibodies, by circular dichroism and 31P nuclear magnetic resonance. Polyclonal and monoclonal antibodies to Z-DNA bind to platinated poly(dG-dC).poly(dG-dC) at ...

journal_title：Nucleic acids research

authors： Malinge JM,Ptak M,Leng M

更新日期：1984-07-25 00:00:00

abstract：:The structural gene and the regulatory DNA sequence of the yeast Hansenula polymorpha methanol oxidase have been isolated. According to the nucleotide sequence data obtained, the structural gene encodes a 664 amino acids long protein, contains no intervening sequences, and the 5'- and 3'-non-coding region contains sev...

journal_title：Nucleic acids research

authors： Ledeboer AM,Edens L,Maat J,Visser C,Bos JW,Verrips CT,Janowicz Z,Eckart M,Roggenkamp R,Hollenberg CP

更新日期：1985-05-10 00:00:00

abstract：:An oligonucleotide hybrid is described which possesses two triple helix forming oligonucleotides which have been connected by a flexible polymeric linker chain. As a prototype, binding of this class of oligonucleotide to duplex DNA has been studied using a segment of the HSV-1 D-glycoprotein promoter, which possesses ...

journal_title：Nucleic acids research

authors： Kessler DJ,Pettitt BM,Cheng YK,Smith SR,Jayaraman K,Vu HM,Hogan ME

更新日期：1993-10-11 00:00:00

abstract：:Gene expression patterns have been demonstrated to be highly variable between similar cell types, for example lab strains and wild strains of Saccharomyces cerevisiae cultured under identical growth conditions exhibit a wide range of expression differences. We have used a genome-wide approach to characterize transcrip...

journal_title：Nucleic acids research

authors： Llinás M,Bozdech Z,Wong ED,Adai AT,DeRisi JL

更新日期：2006-02-21 00:00:00

abstract：:MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally. Previous studies, which characterized miRNA function, revealed their involvement in fundamental biological processes. Importantly, miRNA expression is deregulated in many human diseases. Specific inhibition of miRNAs usin...

journal_title：Nucleic acids research

authors： Takahashi M,Yamada N,Hatakeyama H,Murata M,Sato Y,Minakawa N,Harashima H,Matsuda A

更新日期：2013-12-01 00:00:00

abstract：:PRED(BALB/c) is a computational system that predicts peptides binding to the major histocompatibility complex-2 (H2(d)) of the BALB/c mouse, an important laboratory model organism. The predictions include the complete set of H2(d) class I (H2-K(d), H2-L(d) and H2-D(d)) and class II (I-E(d) and I-A(d)) molecules. The p...

journal_title：Nucleic acids research

authors： Zhang GL,Srinivasan KN,Veeramani A,August JT,Brusic V

更新日期：2005-07-01 00:00:00

abstract：:In the most extensive examination to date of the relationship between the pausing of reverse transcrip-tase (RT) and RNA secondary structures, pause events were found to be correlated to inverted repeats both ahead of, and behind the catalytic site in vitro. In addition pausing events were strongly associated with pol...

journal_title：Nucleic acids research

authors： Harrison GP,Mayo MS,Hunter E,Lever AM

更新日期：1998-07-15 00:00:00

abstract：:Arginyl-tRNA synthetase (ArgRS) catalyses AMP- and PPi-independent deacylation of Arg-tRNAArg in the presence of cysteine. A dipeptide, Arg-Cys, is a product of this deacylation reaction. Similar reaction with homocysteine yields Arg-Hcy. Arginine is a noncompetitive inhibitor of the cysteine-dependent deacylation whi...

journal_title：Nucleic acids research

authors： Jakubowski H

更新日期：1995-11-25 00:00:00

abstract：:The multi-protein complex WRAD, formed by WDR5, RbBP5, Ash2L and Dpy30, binds to the MLL SET domain to stabilize the catalytically active conformation required for histone H3K4 methylation. In addition, the WRAD complex contributes to the targeting of the activated complex to specific sites on chromatin. RbBP5 is cent...

journal_title：Nucleic acids research

authors： Mittal A,Hobor F,Zhang Y,Martin SR,Gamblin SJ,Ramos A,Wilson JR

更新日期：2018-04-20 00:00:00

abstract：:High-throughput chromosome conformation capture (3C) technologies, such as Hi-C, have made it possible to survey 3D genome structure. However, obtaining 3D profiles at kilobase resolution at low cost remains a major challenge. Therefore, we herein present an algorithm for precise identification of chromatin interactio...

journal_title：Nucleic acids research

authors： Zhang H,Li F,Jia Y,Xu B,Zhang Y,Li X,Zhang Z

更新日期：2017-12-15 00:00:00

abstract：:The hypothesis that DNA strands complementary to the coding strand contain in phase coding sequences has been investigated. Statistical analysis of the 50 genes of bacteriophage T7 shows no significant correlation between patterns of codon usage on the coding and non-coding strands. In Bacillus and yeast genes the cor...

journal_title：Nucleic acids research

authors： Sharp PM

更新日期：1985-02-25 00:00:00