Effect of DNA bases and backbone on sigma70 holoenzyme binding and isomerization using fork junction probes.

abstract：:Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with DNA damage. Importantly...

journal_title：Nucleic acids research

authors： Sørensen CS,Syljuåsen RG

更新日期：2012-01-01 00:00:00

abstract：:Riboswitches are RNA-based regulatory devices that mediate ligand-dependent control of gene expression. However, there has been limited success in rationally designing riboswitches. Moreover, most previous riboswitches are confined to a particular gene and only perform one-way regulation. Here, we used a library scree...

journal_title：Nucleic acids research

authors： Jin Y,Huang JD

更新日期：2011-10-01 00:00:00

abstract：:EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, and-a new addition-its transport proteins. MetaCyc is a new metabolic-pathway database that describes pathways and enzymes of many different organisms, with a microbial...

journal_title：Nucleic acids research

authors： Karp PD,Riley M,Saier M,Paulsen IT,Paley SM,Pellegrini-Toole A

更新日期：2000-01-01 00:00:00

abstract：:HbVar (http://globin.bx.psu.edu/hbvar) is one of the oldest and most appreciated locus-specific databases launched in 2001 by a multi-center academic effort to provide timely information on the genomic alterations leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records incl...

journal_title：Nucleic acids research

authors： Giardine B,Borg J,Viennas E,Pavlidis C,Moradkhani K,Joly P,Bartsakoulia M,Riemer C,Miller W,Tzimas G,Wajcman H,Hardison RC,Patrinos GP

更新日期：2014-01-01 00:00:00

abstract：:Nucleoside 3'-phosphoramidite and chlorophosphite reagents have been found to react with the lactam function of guanine. This reaction caused unsatisfactory results when oligodeoxyribonucleotides containing a large number of guanine bases were prepared in an automated solid phase synthesizer. The guanine modification ...

journal_title：Nucleic acids research

authors： Pon RT,Damha MJ,Ogilvie KK

更新日期：1985-09-25 00:00:00

abstract：:Antisense oligodeoxynucleotides (ODNs) have biological activity in treating various forms of cancer. The antisense effects of two types of 20mer ODNs, phosphorothioate-modified ODNs (S-ODNs) and S-ODNs with 12 2'-O-methyl groups (Me-S-ODNs), targeted to sites 109 and 277 of bcl-2 mRNA, were compared. Both types were a...

journal_title：Nucleic acids research

authors： Yoo BH,Bochkareva E,Bochkarev A,Mou TC,Gray DM

更新日期：2004-04-02 00:00:00

abstract：:Histone modifications are fundamental to chromatin structure and transcriptional regulation, and are recognized by a limited number of protein folds. Among these folds are PHD fingers, which are present in most chromatin modification complexes. To date, about 15 PHD finger domains have been structurally characterized,...

journal_title：Nucleic acids research

authors： Slama P,Geman D

更新日期：2011-03-01 00:00:00

abstract：:We describe a dedicated RNA motif search program and web server to identify RNA riboswitches. The Riboswitch finder analyses a given sequence using the web interface, checks specific sequence elements and secondary structure, calculates and displays the energy folding of the RNA structure and runs a number of tests in...

journal_title：Nucleic acids research

authors： Bengert P,Dandekar T

更新日期：2004-07-01 00:00:00

abstract：:The nucleotide sequences of the 5S rRNAs of the oomycete water molds Saprolegnia ferax and Pythium hydnosporum and of the chytrid water molds Blastocladiella simplex and Phlyctochytrium irregulare were determined by chemical and enzymatic partial degradation of 3' and 5' end-labelled molecules, followed by gel sequenc...

journal_title：Nucleic acids research

authors： Walker WF,Doolittle WF

更新日期：1982-09-25 00:00:00

abstract：:A small family of DNA sequences is rearranged during the development of the somatic nucleus in Tetrahymena. The family is defined by 266 bp of highly conserved sequence which restriction mapping, hybridization and sequence analysis have shown is shared by a cloned micronuclear fragment and three sequences which consti...

journal_title：Nucleic acids research

authors： Allitto BA,Karrer KM

更新日期：1986-10-24 00:00:00

abstract：:Genetic therapy holds great promise for the treatment of inherited or acquired genetic diseases; however, its breakthrough is hampered by the lack of suitable gene delivery systems. Dumbbell-shaped DNA minimal vectors represent an attractive, safe alternative to the commonly used viral vectors which are fraught with r...

journal_title：Nucleic acids research

authors： Yu H,Jiang X,Tan KT,Hang L,Patzel V

更新日期：2015-10-15 00:00:00

abstract：:The conditions under which Drosophila melanogaster are grown markedly influence the amount of the hypermodified nucleoside Q found in certain tRNAs. This effect on Q biosynthesis was found in both the wild-type and the suppressor of sable [su(s)2] mutant. Suppressed vermilion flies [su(s)2v; bw] with 78% of the tyrosi...

journal_title：Nucleic acids research

authors： Wosnick MA,White BN

更新日期：1977-11-01 00:00:00

abstract：:The promoter of the human BCR gene, regulating the transcription of the chimeric BCR/ABL mRNA in leukemia, has been isolated and characterized. A region of 1.1 kb immediately 5' to the transcription start site was analyzed in detail by sequencing, DNase 1 footprinting, gel retardation and functional studies. These exp...

journal_title：Nucleic acids research

authors： Zhu QS,Heisterkamp N,Groffen J

更新日期：1990-12-11 00:00:00

abstract：:We have isolated from a single human liver cDNA library two clones which are highly homologous (78% over the coding region) to the major phenobarbital-inducible P450 from rat (P450IIB1). This is the first direct demonstration of the presence of the P450IIB gene subfamily in humans. This subfamily is much less extensiv...

journal_title：Nucleic acids research

authors： Miles JS,Spurr NK,Gough AC,Jowett T,McLaren AW,Brook JD,Wolf CR

更新日期：1988-07-11 00:00:00

abstract：:We report, herein, a new class of RNAi trigger molecules based on the unconventional parallel hybridization of two oligonucleotide chains. We have prepared and studied several parallel stranded (ps) duplexes, in which the parallel orientation is achieved through incorporation of isoguanine and isocytosine to form reve...

journal_title：Nucleic acids research

authors： Habibian M,Yahyaee-Anzahaee M,Lucic M,Moroz E,Martín-Pintado N,Di Giovanni LD,Leroux JC,Hall J,González C,Damha MJ

更新日期：2018-02-28 00:00:00

abstract：:We identify a novel activity of the RarA (also MgsA) protein of Escherichia coli, demonstrating that this protein functions at DNA ends to generate flaps. A AAA+ ATPase in the clamp loader clade, RarA protein is part of a highly conserved family of DNA metabolism proteins. We demonstrate that RarA binds to double-stra...

journal_title：Nucleic acids research

authors： Stanage TH,Page AN,Cox MM

更新日期：2017-03-17 00:00:00

abstract：:Electrophoretic mobility shift assays (EMSA) were used to define the regions of the INO1 promoter that interact with factors present in extracts prepared from the yeast, Saccharomyces cerevisae. These experiments identified three different types of protein:DNA complexes that assemble with the INO1 promoter. Formation ...

journal_title：Nucleic acids research

authors： Lopes JM,Henry SA

更新日期：1991-07-25 00:00:00

abstract：:The rat beta-casein gene is a member of a small gene family, encoding the principal milk proteins. In order to understand the mechanisms by which its stage- and tissue-specific expression are regulated, initially, a 14 kb genomic clone containing the entire 7.5 kb rat beta-casein gene with 3.5 kb of 5' and 3.0 kb of 3...

journal_title：Nucleic acids research

authors： Lee KF,DeMayo FJ,Atiee SH,Rosen JM

更新日期：1988-02-11 00:00:00

abstract：:Cells of the central nervous system (CNS) are prone to the devastating consequences of trinucleotide repeat (TNR) expansion. Some CNS cells, including astrocytes, show substantial TNR instability in affected individuals. Since astrocyte enrichment occurs in brain regions sensitive to neurodegeneration and somatic TNR ...

journal_title：Nucleic acids research

authors： Farrell BT,Lahue RS

更新日期：2006-01-01 00:00:00

abstract：:The antitumour antibiotics bleomycin and actinomycin are commonly used therapeutically in combination. One causes metal ion- and oxygen-dependent oxidative damage to DNA, while the other acts at the level of DNA via intercalation of its phenoxazone chromophore and probable inhibition of topoisomerases. Both drugs bind...

journal_title：Nucleic acids research

authors： Bailly C,Kénani A,Waring MJ

更新日期：1997-04-15 00:00:00

abstract：:Large-scale cooperative helix opening has been previously observed in A + T rich sequences contained in supercoiled DNA molecules at elevated temperatures. Since it is well known that helix melting of linear DNA is suppressed by addition of salt, we have investigated the effects of added salts on opening transitions i...

journal_title：Nucleic acids research

authors： Bowater RP,Aboul-ela F,Lilley DM

更新日期：1994-06-11 00:00:00

abstract：:Cre recombinase catalyzes the cleavage and religation of DNA at loxP sites. The enzyme is a homotetramer in its functional state, and the symmetry of the protein complex enforces a pseudo-palindromic symmetry upon the loxP sequence. The Cre-lox system is a powerful tool for many researchers. However, broader applicati...

journal_title：Nucleic acids research

authors： Zhang C,Myers CA,Qi Z,Mitra RD,Corbo JC,Havranek JJ

更新日期：2015-10-15 00:00:00

abstract：:Vascular endothelial growth factor A (VEGF-A) is a master regulator of angiogenesis, vascular development and function. In this study we investigated the transcriptional regulation of VEGF-A-responsive genes in primary human aortic endothelial cells (HAECs) and human umbilical vein endothelial cells (HUVECs) using gen...

journal_title：Nucleic acids research

authors： Kaikkonen MU,Niskanen H,Romanoski CE,Kansanen E,Kivelä AM,Laitalainen J,Heinz S,Benner C,Glass CK,Ylä-Herttuala S

更新日期：2014-11-10 00:00:00

abstract：:Budding yeast telomerase is mainly activated by Tel1/Mec1 (yeast ATM/ATR) on Cdc13 from late S to G2 phase of the cell cycle. Here, we demonstrated that the telomerase-recruitment domain of Cdc13 is also phosphorylated by Cdk1 at the same cell cycle stage as the Tel1/Mec1-dependent regulation. Phosphor-specific gel an...

journal_title：Nucleic acids research

authors： Tseng SF,Shen ZJ,Tsai HJ,Lin YH,Teng SC

更新日期：2009-06-01 00:00:00

abstract：:The aminoacylation kinetics of T7 transcripts representing defined regions of Escherichia coli serine tRNAs were determined using purified E.coli seryl-tRNA synthetase (SerRS) and the kinetic values were used to estimate the relative contribution of various tRNA(Ser) domains to recognition by SerRS. The analysis revea...

journal_title：Nucleic acids research

authors： Sampson JR,Saks ME

更新日期：1993-09-25 00:00:00

abstract：:A library of three synthetic ribozymes with randomized arms, targeting NUX, GUX and NXG triplets, respectively, were used to identify ribozyme-accessible sites on the HIV-1 LTR transcript comprising positions -533 to 386. Three cleavable sites were identified at positions 109, 115 and 161. Ribozymes were designed agai...

journal_title：Nucleic acids research

authors： Bramlage B,Luzi E,Eckstein F

更新日期：2000-11-01 00:00:00

abstract：:The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a suite of database resources to support worldwide research activities in both academia and industry. With the explosive growth of multi-omics data, CNCB-NGDC is continually expanding, updating and enriching...

journal_title：Nucleic acids research

authors： CNCB-NGDC Members and Partners.

更新日期：2021-01-08 00:00:00

abstract：:This paper describes the sequence of 257 nucleotides from the 3' end of RNA 2 of barley stripe mosaic virus ( BSMV , strain Argentina Mild) including an internal oligo (A) tract localized at a distance of 236 nucleotides from the 3' end, and the 3' terminal tRNA-like structure accepting tyrosine. This sequence is show...

journal_title：Nucleic acids research

authors： Kozlov YuV,Rupasov VV,Adyshev DM,Belgelarskaya SN,Agranovsky AA,Mankin AS,Morozov SYu,Dolja VV,Atabekov JG

更新日期：1984-05-11 00:00:00

abstract：:A common goal in the discovery of rare functional DNA variants via medical resequencing is to incur a relatively lower proportion of false positive base-calls. We developed a novel statistical method for resequencing arrays (SRMA, sequence robust multi-array analysis) to increase the accuracy of detecting rare variant...

journal_title：Nucleic acids research

authors： Wang W,Shen P,Thiyagarajan S,Lin S,Palm C,Horvath R,Klopstock T,Cutler D,Pique L,Schrijver I,Davis RW,Mindrinos M,Speed TP,Scharfe C

更新日期：2011-01-01 00:00:00

abstract：:Work from a number of laboratories has indicated that the TATA box sequence can act as a basal promoter element not only for RNA polymerase II (RNAP II) transcription, but also for transcription by RNA polymerase III (RNAP III). We previously reported that, in the absence of other cis-acting elements, the canonical TA...

journal_title：Nucleic acids research

authors： Wang Y,Jensen RC,Stumph WE

更新日期：1996-08-01 00:00:00