Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites.

abstract：:We have studied the effect of temperature on transcription initiation in vitro at two related promoters ga/Pcon and ga/P1, which have the same nucleotide sequence around the -10 region and transcription start site, but differ in upstream sequences. One of the promoters, ga/Pcon, carries the consensus -35 hexamer, 5'TT...

journal_title：Nucleic acids research

authors： Grimes E,Busby S,Minchin S

更新日期：1991-11-25 00:00:00

abstract：:The positions of the trfA and trfB promoters of broad host range IncP plasmid RK2 (identical to RP1, RP4, R68 and R18 ) were identified by RNA polymerase protection studies, and the nucleotide sequences of the promoter regions determined. A mutation within the trfA promoter sequence is associated with loss of kilD act...

journal_title：Nucleic acids research

authors： Smith CA,Shingler V,Thomas CM

更新日期：1984-04-25 00:00:00

abstract：:dITP may be generated from dATP by a slow, nonenzymatic hydrolysis. While [3H]dITP was degraded rapidly to [3H]deoxyinosine by HeLa cell nuclear extracts, no net degradation of [3H]dITP was observed in the presence of physiological concentrations of ATP, apparently because the extract contained deoxynucleoside diphosp...

journal_title：Nucleic acids research

authors： Myrnes B,Guddal PH,Krokan H

更新日期：1982-06-25 00:00:00

abstract：:The abundance of Alu RNA is transiently increased by heat shock in human cell lines. This effect is specific to Alu repeats among Pol III transcribed genes, since the abundance of 7SL, 7SK, 5S and U6 RNAs is essentially unaffected by heat shock. The rapid induction of Alu expression precedes the heat shock induction o...

journal_title：Nucleic acids research

authors： Liu WM,Chu WM,Choudary PV,Schmid CW

更新日期：1995-05-25 00:00:00

abstract：:The Escherichia coli fmu gene product has recently been determined to be the 16S rRNA m(5)C 967 methyltransferase. As such, Fmu represents the first protein identified as an S -adenosyl-L-methionine (AdoMet)- dependent RNA m(5)C methyltransferase whose amino acid sequence is known. Using the amino acid sequence of Fmu...

journal_title：Nucleic acids research

authors： Reid R,Greene PJ,Santi DV

更新日期：1999-08-01 00:00:00

abstract：:Telomeres at the ends of eukaryotic chromosomes are essential for genome integrality and stability. In order to identify genes that sustain telomere maintenance independently of telomerase recruitment, we have exploited the phenotype of over-long telomeres in the cells that express Cdc13-Est2 fusion protein, and exami...

journal_title：Nucleic acids research

authors： Liu JC,Li QJ,He MH,Hu C,Dai P,Meng FL,Zhou BO,Zhou JQ

更新日期：2020-12-16 00:00:00

abstract：:In Trypanosoma brucei the genes are organised into long polycistronic transcription units and only three promoters for protein-encoding genes and a single terminator have been characterised. These promoters recruit a polI-like RNA polymerase for the transcription units encoding the two major stage-specific antigens of...

journal_title：Nucleic acids research

authors： Berberof M,Vanhamme L,Alexandre S,Lips S,Tebabi P,Pays E

更新日期：2000-01-15 00:00:00

abstract：:One surprisingly common element of RNA secondary structure consists of a hairpin capped by a four-base loop (or the tetraloop). Recently the 3-D structures of two RNA-tetraloops have been determined by NMR-studies. Both structures have a similar architecture: the first and the last bases of the loop form a hydrogen bo...

journal_title：Nucleic acids research

authors： Kajava A,Rüterjans H

更新日期：1993-09-25 00:00:00

abstract：:Melanotransferrin (MTf) is a tumor associated antigen found in abundance on the surface of melanoma cells. It is a transferrin-like protein found in low amount in most adult tissues and whose gene is reminiscent of house-keeping genes. With the goal of understanding the regulatory mechanisms which might explain the en...

journal_title：Nucleic acids research

authors： Duchange N,Ochoa A,Plowman GD,Rozé A,Amdjadi M,Zakin MM

更新日期：1992-06-11 00:00:00

abstract：:Bacterial small regulatory RNAs (sRNAs) are the most abundant class of post-transcriptional regulators and have been well studied in Gram-negative bacteria. Little is known about the functions and mechanisms of sRNAs in high GC Gram-positive bacteria including Mycobacterium and Streptomyces. Here, we performed an in-d...

journal_title：Nucleic acids research

authors： Mai J,Rao C,Watt J,Sun X,Lin C,Zhang L,Liu J

更新日期：2019-05-07 00:00:00

abstract：:TFIIH is a multisubunit factor essential for transcription initiation and promoter escape of RNA polymerase II and for the opening of damaged DNA double strands in nucleotide excision repair (NER). In this study, we have analyzed at which step of the transcription cycle TFIIH is essential for transcription by RNA poly...

journal_title：Nucleic acids research

authors： Assfalg R,Lebedev A,Gonzalez OG,Schelling A,Koch S,Iben S

更新日期：2012-01-01 00:00:00

abstract：:DNA double-strand breaks are repaired by end-joining or homologous recombination. A key-committing step of recombination is DNA end resection. In resection, phosphorylated CtIP first promotes the endonuclease of MRE11-RAD50-NBS1 (MRN). Subsequently, CtIP also stimulates the WRN/BLM-DNA2 pathway, coordinating thus both...

journal_title：Nucleic acids research

authors： Howard SM,Ceppi I,Anand R,Geiger R,Cejka P

更新日期：2020-06-04 00:00:00

abstract：:DNA replication of phi29 and related phages takes place via a strand displacement mechanism, a process that generates large amounts of single-stranded DNA (ssDNA). Consequently, phage-encoded ssDNA-binding proteins (SSBs) are essential proteins during phage phi29-like DNA replication. In the present work we analyze th...

journal_title：Nucleic acids research

authors： Gascón I,Lázaro JM,Salas M

更新日期：2000-05-15 00:00:00

abstract：:This review presents detailed information about the structure of triplet repeat RNA and addresses the simple sequence repeats of normal and expanded lengths in the context of the physiological and pathogenic roles played in human cells. First, we discuss the occurrence and frequency of various trinucleotide repeats in...

journal_title：Nucleic acids research

authors： Krzyzosiak WJ,Sobczak K,Wojciechowska M,Fiszer A,Mykowska A,Kozlowski P

更新日期：2012-01-01 00:00:00

abstract：:The mode of action of regulated promoters is largely determined by kinetic parameters which govern the interaction between promoters and proteins involved in induction and repression of transcription. To gain insight into the interplay between positively and negatively acting transcriptional regulators, in this case A...

journal_title：Nucleic acids research

authors： Lutz R,Lozinski T,Ellinger T,Bujard H

更新日期：2001-09-15 00:00:00

abstract：:While most of the recent improvements in multiple sequence alignment accuracy are due to better use of vertical information, which include the incorporation of consistency-based pairwise alignments and the use of profile alignments, we observe that it is possible to further improve accuracy by taking into account alig...

journal_title：Nucleic acids research

authors： Lu Y,Sze SH

更新日期：2009-02-01 00:00:00

abstract：:Exposure to genotoxic agents, such as ionizing radiation (IR), produces double-strand breaks, repaired predominantly in mammalian cells by non-homologous end-joining (NHEJ). Ku70 was identified as an interacting partner of a proteolytic Cyclin E (CycE) fragment, p18CycE. p18CycE endogenous generation during IR-induced...

journal_title：Nucleic acids research

authors： Chatterjee P,Plesca D,Mazumder S,Boutros J,Yannone SM,Almasan A

更新日期：2013-12-01 00:00:00

abstract：:A single base change in 16S rRNA (C726 to G) has previously been shown to have a dramatic effect on protein synthesis in E. coli (1). This paper more specifically details the effects of the mutation on mRNA binding and translation-termination. The in vitro technique of toeprinting (2) was used to demonstrate that 30S ...

journal_title：Nucleic acids research

authors： Prescott CD,Göringer HU

更新日期：1990-09-25 00:00:00

abstract：:Restriction endonucleases HindII and TaqI, but not SalI, were found to efficiently cleave synthetic hexadecanucleotide duplexes which contained either an A/C or a G/T mismatch within their respective restriction sites. Double-stranded M13 DNAs with identical mismatches were also cleaved under the assay conditions. The...

journal_title：Nucleic acids research

authors： Jiricny J,Martin D

更新日期：1986-03-11 00:00:00

abstract：:The database of 3D interacting domains (3did) is a collection of protein interactions for which high-resolution 3D structures are known. 3did exploits structural information to provide the crucial molecular details necessary for understanding how protein interactions occur. Besides interactions between globular domain...

journal_title：Nucleic acids research

authors： Stein A,Panjkovich A,Aloy P

更新日期：2009-01-01 00:00:00

abstract：:We have determined the NMR solution structures of the quadruplexes formed by d(TGLGLT) and d(TL4T), where L denotes LNA (locked nucleic acid) modified G-residues. Both structures are tetrameric, parallel and right-handed and the native global fold of the corresponding DNA quadruplex is retained upon introduction of th...

journal_title：Nucleic acids research

authors： Nielsen JT,Arar K,Petersen M

更新日期：2006-04-13 00:00:00

abstract：:Mature chicken erythrocyte polynucleosomes which are soluble at physiological ionic strength are enriched in beta-globin DNA sequences. Vitellogenin chromatin, which is not expressed in this tissue, is found in aggregation prone, salt insoluble chromatin. There is a direct correlation between the size of soluble fragm...

journal_title：Nucleic acids research

authors： Ridsdale JA,Davie JR

更新日期：1987-02-11 00:00:00

abstract：:Effective drug discovery and optimization can be accelerated by techniques capable of deconvoluting the complexities often present in targeted biological systems. We report a single-molecule approach to study the binding of an alternative splicing regulator, muscleblind-like 1 protein (MBNL1), to (CUG)n = 4,6 and the ...

journal_title：Nucleic acids research

authors： Haghighat Jahromi A,Honda M,Zimmerman SC,Spies M

更新日期：2013-07-01 00:00:00

abstract：:The FREP database (http://facts.gsc.riken.go.jp/FREP/) contains 31 396 RepeatMasker-identified non-redundant variant repeat sequences derived from 16,527 mouse cDNAs with protein-coding potential. The repeats were computationally associated with potential effects on transcriptional variation, translation, protein func...

journal_title：Nucleic acids research

authors： Nagashima T,Matsuda H,Silva DG,Petrovsky N,Konagaya A,Schönbach C,Kasukawa T,Arakawa T,Carninci P,Kawai J,Hayashizaki Y,RIKEN GER Group.,Genome Science Laoratory Members.

更新日期：2004-01-01 00:00:00

abstract：:We have studied a novel class of DNA sequences that cause DNA polymerases to pause. These sequences have the central consensus Py-G-C and are not necessarily adjacent to hairpins in the DNA template. Since most consensus sequences do not cause pauses under standard conditions, additional template features must exist t...

journal_title：Nucleic acids research

authors： Mytelka DS,Chamberlin MJ

更新日期：1996-07-15 00:00:00

abstract：:Three databases that provide data on transcriptional regulation are described. TRANSFAC is a database on transcription factors and their DNA binding sites. TRRD (Transcription Regulatory Region Database) collects information about complete regulatory regions, their regulation properties and architecture. COMPEL compri...

journal_title：Nucleic acids research

authors： Wingender E,Kel AE,Kel OV,Karas H,Heinemeyer T,Dietze P,Knüppel R,Romaschenko AG,Kolchanov NA

更新日期：1997-01-01 00:00:00

abstract：:A DNA copy of influenza A/NT/60/68 viral RNA segment 2, corresponding to protein P1, has been cloned in the E.coli plasmid pBr322. The clone is 2341 nucleotides long and represents a full-length copy of the viral RNA. In the viral complementary (plus sense) strand there is an open reading frame that is 2271 nucleotide...

journal_title：Nucleic acids research

authors： Bishop DH,Huddleston JA,Brownlee GG

更新日期：1982-02-25 00:00:00

abstract：:Helicobacter pylori is a Gram-negative bacterium that colonizes human stomach and causes gastric inflammation. The species is naturally competent and displays remarkable diversity. The presence of a large number of restriction-modification (R-M) systems in this bacterium creates a barrier against natural transformatio...

journal_title：Nucleic acids research

authors： Dwivedi GR,Sharma E,Rao DN

更新日期：2013-03-01 00:00:00

abstract：:An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the map...

journal_title：Nucleic acids research

authors： Yamagata K,Yamanishi A,Kokubu C,Takeda J,Sese J

更新日期：2016-05-05 00:00:00

abstract：:Stem cell fate decisions are controlled by a molecular network in which transcription factors and miRNAs are of key importance. To systemically investigate their impact on neural stem cell (NSC) maintenance and neuronal commitment, we performed a high-throughput mRNA and miRNA profiling and isolated functional interac...

journal_title：Nucleic acids research

authors： Palm T,Hemmer K,Winter J,Fricke IB,Tarbashevich K,Sadeghi Shakib F,Rudolph IM,Hillje AL,De Luca P,Bahnassawy L,Madel R,Viel T,De Siervi A,Jacobs AH,Diederichs S,Schwamborn JC

更新日期：2013-04-01 00:00:00