Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL.

abstract：:The oncogene BMI1 encodes a polycomb group transcription factor that is required for embryonic development and self-renewal of stem cells. Despite these important functions little is known about the regulation of BMI1 expression. A cDNA microarray based search for target genes of E2F-1 in neuroblastoma cells expressin...

journal_title：Nucleic acids research

authors： Nowak K,Kerl K,Fehr D,Kramps C,Gessner C,Killmer K,Samans B,Berwanger B,Christiansen H,Lutz W

更新日期：2006-03-31 00:00:00

abstract：:Understanding the normal state of human tissue transcriptome profiles is essential for recognizing tissue disease states and identifying disease markers. Recently, the Human Protein Atlas and the FANTOM5 consortium have each published extensive transcriptome data for human samples using Illumina-sequenced RNA-Seq and ...

journal_title：Nucleic acids research

authors： Yu NY,Hallström BM,Fagerberg L,Ponten F,Kawaji H,Carninci P,Forrest AR,Fantom Consortium.,Hayashizaki Y,Uhlén M,Daub CO

更新日期：2015-08-18 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：:Structures of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 have been determined by NMR spectroscopy under low salt conditions. All protons and phosphorus nuclei resonances have been assigned. Signals of H5'/5" have been assigned stereospecifically. All 3JH,H and 3JP,H coupling constants have been measured. The structures were dete...

journal_title：Nucleic acids research

authors： Popenda M,Biala E,Milecki J,Adamiak RW

更新日期：1997-11-15 00:00:00

abstract：:The UGA suppressor tRNA produced by Schizosaccharomyces pombe strain sup3-e was purified to homogeneity. It can be aminoacylated with a serine by a crude aminoacyl-tRNA synthetase preparation from S. pombe cells. By combining post-labeling fingerprinting and gel sequencing methods the nucleotide sequence of this tRNA ...

journal_title：Nucleic acids research

authors： Rafalski A,Kohli J,Agris P,Söll D

更新日期：1979-06-25 00:00:00

abstract：:Single nucleotide polymorphisms (SNPs) are, together with copy number variation, the primary source of variation in the human genome. SNPs are associated with altered response to drug treatment, susceptibility to disease and other phenotypic variation. Furthermore, during genetic screens for disease-associated mutatio...

journal_title：Nucleic acids research

authors： Reumers J,Conde L,Medina I,Maurer-Stroh S,Van Durme J,Dopazo J,Rousseau F,Schymkowitz J

更新日期：2008-01-01 00:00:00

abstract：:Successful use and reliability of microarray technology is highly dependent on several factors, including surface chemistry parameters and accessibility of cDNA targets to the DNA probes fixed onto the surface. Here, we show that functionalisation of glass slides with homemade dendrimers allow production of more sensi...

journal_title：Nucleic acids research

authors： Le Berre V,Trévisiol E,Dagkessamanskaia A,Sokol S,Caminade AM,Majoral JP,Meunier B,François J

更新日期：2003-08-15 00:00:00

abstract：:From a recombinant lambda phage, we have determined a 387 bp sequence containing a mouse lysine tRNA gene. The putative lys tRNA (anticodon UUU) differs from rabbit liver lys tRNA at five positions. The flanking regions of the mouse gene are not generally homologous to published human and Drosophila lys tRNA genes. Ho...

journal_title：Nucleic acids research

authors： Han JH,Harding JD

更新日期：1983-04-11 00:00:00

abstract：:The DNA-binding protein RdgC has been identified as an inhibitor of RecA-mediated homologous recombination in Escherichia coli. In Neisseria species, RdgC also has a role in virulence-associated antigenic variation. We have previously solved the crystal structure of the E. coli RdgC protein and shown it to form a toro...

journal_title：Nucleic acids research

authors： Briggs GS,Yu J,Mahdi AA,Lloyd RG

更新日期：2010-10-01 00:00:00

abstract：:We analysed the genetic stability of two subtelomeric genes of the human malaria parasite Plasmodium falciparum. A PCR based assay, using a telomere and a target-gene specific primer was used to detect potential chromosome rearrangements. We show that chromosome breakage and the formation of new telomeres occur freque...

journal_title：Nucleic acids research

authors： Scherf A,Mattei D

更新日期：1992-04-11 00:00:00

abstract：:We report a crystal structure that shows an antibiotic that extracts a nucleobase from a DNA molecule 'caught in the act' after forming a covalent bond but before departing with the base. The structure of trioxacarcin A covalently bound to double-stranded d(AACCGGTT) was determined to 1.78 A resolution by MAD phasing ...

journal_title：Nucleic acids research

authors： Pfoh R,Laatsch H,Sheldrick GM

更新日期：2008-06-01 00:00:00

abstract：:The human immunodeficiency virus (HIV) and other retroviruses show extensive genomic variation, which is primarily due to error-prone replication by the viral reverse transcriptase (RT) enzymes. RT errors include misincorporation with subsequent extension of the mismatched terminal base, and extension of realigned pri...

journal_title：Nucleic acids research

authors： Das AT,Berkhout B

更新日期：1995-04-25 00:00:00

abstract：:CAG repeats occur predominantly in the coding regions of human genes, which suggests their functional importance. In some genes, these sequences can undergo pathogenic expansions leading to neurodegenerative polyglutamine (poly-Q) diseases. The mutant transcripts containing expanded CAG repeats possibly contribute to ...

journal_title：Nucleic acids research

authors： Kiliszek A,Kierzek R,Krzyzosiak WJ,Rypniewski W

更新日期：2010-12-01 00:00:00

abstract：:We have previously isolated two different aFGF cDNA clones from kidney and brain. The two corresponding mRNA, designated aFGF 1.A and 1.B, are the predominant species in kidney and brain, respectively. During the characterization of aFGF mRNA in glioblastoma cells, we demonstrated that aFGF mRNA in U1242MG and D65MG g...

journal_title：Nucleic acids research

authors： Payson RA,Canatan H,Chotani MA,Wang WP,Harris SE,Myers RL,Chiu IM

更新日期：1993-02-11 00:00:00

abstract：:Here, we present an update of Breast Cancer Now Tissue Bank bioinformatics, a rich platform for the sharing, mining, integration and analysis of breast cancer data. Its modalities provide researchers with access to a centralised information gateway from which they can access a network of bioinformatic resources to que...

journal_title：Nucleic acids research

authors： Gadaleta E,Pirrò S,Dayem Ullah AZ,Marzec J,Chelala C

更新日期：2018-01-04 00:00:00

abstract：:Two hexamer DNA fragments containing a carcinogenic modified base, O6-methyl guanine, have been synthesized by a solid-phase phosphotriester method, in which the unmodified guanine residues present were O6 protected with the 4-nitrophenylethyl group. These two alkylated oligonucleotides were found to have similar Tm's...

journal_title：Nucleic acids research

authors： Kuzmich S,Marky LA,Jones RA

更新日期：1983-05-25 00:00:00

abstract：:Modification of chromatin and related transcription factors by histone deacetylases (HDACs) is one of the major strategies for controlling gene expression in eukaryotes. The HDAC domains of class IIa HDACs repress the respective target genes by interacting with the C-terminal region of the silencing mediator for retin...

journal_title：Nucleic acids research

authors： Park SY,Kim GS,Hwang HJ,Nam TH,Park HS,Song J,Jang TH,Lee YC,Kim JS

更新日期：2018-12-14 00:00:00

abstract：:Lateral ribosomal stalk is responsible for binding and recruiting translation factors during protein synthesis. The eukaryotic stalk consists of one P0 protein with two copies of P1•P2 heterodimers to form a P0(P1•P2)₂ pentameric P-complex. Here, we have solved the structure of full-length P1•P2 by nuclear magnetic re...

journal_title：Nucleic acids research

authors： Lee KM,Yusa K,Chu LO,Yu CW,Oono M,Miyoshi T,Ito K,Shaw PC,Wong KB,Uchiumi T

更新日期：2013-10-01 00:00:00

abstract：:A very high rate of multidrug resistance (MDR) seen among Gram-negative bacteria such as Escherichia, Klebsiella, Salmonella, Shigella, etc. is a major threat to public health and safety. One of the major virulent determinants of Gram-negative bacteria is capsular polysaccharide or K antigen located on the bacterial o...

journal_title：Nucleic acids research

authors： Kunduru BR,Nair SA,Rathinavelan T

更新日期：2016-01-04 00:00:00

abstract：:PIR-International is an association of macromolecular sequence data collection centers dedicated to fostering international cooperation as an essential element in the development of scientific databases. A major objective of PIR-International is to continue the development of the Protein Sequence Database as an essent...

journal_title：Nucleic acids research

authors： George DG,Barker WC,Mewes HW,Pfeiffer F,Tsugita A

更新日期：1994-09-01 00:00:00

abstract：:In order to facilitate the direct computation of the sizes of DNA fragments separated by gel electrophoresis, we have written and evaluated programmes for the Hewlett-Packard 41C programmable calculator. The sizes estimated for DNA fragments of known length using some of these programmes were found to be more accurate...

journal_title：Nucleic acids research

authors： Gough EJ,Gough NM

更新日期：1984-01-11 00:00:00

abstract：:Recent studies indicate that controlling the nuclear decondensation and intra-nuclear localization of plasmid DNA (pDNA) would result in an increased transfection efficiency. In the present study, we established a technology for imaging the nuclear condensation/decondensation status of pDNA in nuclear subdomains using...

journal_title：Nucleic acids research

authors： Shaheen SM,Akita H,Yamashita A,Katoono R,Yui N,Biju V,Ishikawa M,Harashima H

更新日期：2011-04-01 00:00:00

abstract：:The base pairing properties of oligonucleotide duplexes containing 8-aza-7-deaza-2'-deoxyisoguanosine, its 7-bromo or its 7-iodo derivative are described. The nucleosides were synthesized on a convergent route, protected and converted into phosphoramidites. Oligonucleotides were prepared on a solid-phase and were hybr...

journal_title：Nucleic acids research

authors： Seela F,Kröschel R

更新日期：2003-12-15 00:00:00

abstract：:A UCSD Pascal program was developed which can analyze nucleic acid dot matrices of up to 9500 X 9500 in size on the Apple II computer. Although matrices of such size consume large amounts of computer memory, this program minimizes these problems by analyzing only small strips of the matrix at a time, and then transfer...

journal_title：Nucleic acids research

authors： Zweig SE

更新日期：1984-01-11 00:00:00

abstract：:Expressed Sequence Tag-based gene expression profiling can be used to discover functionally associated genes on a large scale. Currently available web servers and tools focus on finding differentially expressed genes in different samples or tissues rather than finding co-expressed genes. To fill this gap, we have deve...

journal_title：Nucleic acids research

authors： Wu X,Walker MG,Luo J,Wei L

更新日期：2005-07-01 00:00:00

abstract：:Zar1 was one of the earliest mammalian maternal-effect genes to be identified. Embryos derived from Zar1-null female mice are blocked before zygotic genome activation; however, the underlying mechanism remains unclear. By knocking out Zar1 and its homolog Zar2 in mice, we revealed a novel function of these genes in oo...

journal_title：Nucleic acids research

authors： Rong Y,Ji SY,Zhu YZ,Wu YW,Shen L,Fan HY

更新日期：2019-12-02 00:00:00

abstract：:Human U6 small nuclear RNA (U6 snRNA), an abundant snRNA required for splicing of pre-mRNAs, contains several post-transcriptional modifications including a single m6A (N-6-methyladenosine) at position 43. This A-43 residue is critical for the function of U6 snRNA in splicing of pre-mRNAs. Yeast and plant U6 snRNAs al...

journal_title：Nucleic acids research

authors： Shimba S,Bokar JA,Rottman F,Reddy R

更新日期：1995-07-11 00:00:00

abstract：:Post-translational modifications contribute to the spliceosome dynamics by facilitating the physical rearrangements of the spliceosome. Here, we report USP15, a deubiquitinating enzyme, as a regulator of protein-protein interactions for the spliceosome dynamics. We show that PRP31, a component of U4 snRNP, is modified...

journal_title：Nucleic acids research

authors： Das T,Park JK,Park J,Kim E,Rape M,Kim EE,Song EJ

更新日期：2017-05-05 00:00:00

abstract：:In this study, we demonstrate that the lack of retinoic acid-related orphan receptor (ROR) γ or α expression in mice significantly reduced the peak expression level of Cry1, Bmal1, E4bp4, Rev-Erbα and Per2 in an ROR isotype- and tissue-selective manner without affecting the phase of their rhythmic expression. Analysis...

journal_title：Nucleic acids research

authors： Takeda Y,Jothi R,Birault V,Jetten AM

更新日期：2012-09-01 00:00:00

abstract：:The HIV-1 viral infectivity factor (Vif) allows productive infection of non-permissive cells (including most natural HIV-1 targets) by counteracting the cellular cytosine deaminases APOBEC-3G (hA3G) and hA3F. The Vif-induced degradation of these restriction factors by the proteasome has been extensively studied, but l...

journal_title：Nucleic acids research

authors： Mercenne G,Bernacchi S,Richer D,Bec G,Henriet S,Paillart JC,Marquet R

更新日期：2010-01-01 00:00:00