A neutron investigation of yeast valyl-tRNA synthetase interaction with tRNAs.

abstract：:Single-nucleotide polymorphisms (SNPs) are often linked to critical phenotypes such as diseases or responses to vaccines, medications and environmental factors. However, the specific molecular mechanisms by which a causal SNP acts is usually not obvious. Changes in RNA secondary structure emerge as a possible explanat...

journal_title：Nucleic acids research

authors： Salari R,Kimchi-Sarfaty C,Gottesman MM,Przytycka TM

更新日期：2013-01-07 00:00:00

abstract：:The multifunctional RNA-dependent RNA polymerase L protein of vesicular stomatitis virus catalyzes unconventional pre-mRNA capping via the covalent enzyme-pRNA intermediate formation, which requires the histidine-arginine (HR) motif in the polyribonucleotidyltransferase domain. Here, the effects of cap-defective mutat...

journal_title：Nucleic acids research

authors： Ogino T

更新日期：2014-10-29 00:00:00

abstract：:The modulation of GLI2, an oncogenic transcription factor commonly upregulated in cancer, is in many cases not due to genetic defects, suggesting dysregulation through alternative mechanisms. The identity of these molecular events remains for the most part unknown. Here, we identified TFII-I as a novel repressor of GL...

journal_title：Nucleic acids research

authors： McCleary-Wheeler AL,Paradise BD,Almada LL,Carlson AJ,Marks DL,Vrabel A,Vera RE,Sigafoos AN,Olson RL,Fernandez-Zapico ME

更新日期：2020-07-27 00:00:00

abstract：:Several different computational problems have been solved using DNA as a medium. However, the DNA computations that have so far been carried out have examined a relatively small number of possible sequence solutions in order to find correct sequence solutions. We have encoded a search algorithm in DNA that required th...

journal_title：Nucleic acids research

authors： James KD,Boles AR,Henckel D,Ellington AD

更新日期：1998-11-15 00:00:00

abstract：:Prion proteins (PrPs) cause prion diseases, such as bovine spongiform encephalopathy. The conversion of a normal cellular form (PrP(C)) of PrP into an abnormal form (PrP(Sc)) is thought to be associated with the pathogenesis. An RNA aptamer that tightly binds to and stabilizes PrP(C) is expected to block this conversi...

journal_title：Nucleic acids research

authors： Mashima T,Nishikawa F,Kamatari YO,Fujiwara H,Saimura M,Nagata T,Kodaki T,Nishikawa S,Kuwata K,Katahira M

更新日期：2013-01-01 00:00:00

abstract：:The splicing factor Sam68 is upregulated in many human cancers, including prostate cancer (PCa) where it promotes cell proliferation and survival. Nevertheless, in spite of its frequent upregulation in cancer, the mechanism(s) underlying its expression are largely unknown. Herein, bioinformatics analyses identified th...

journal_title：Nucleic acids research

authors： Caggiano C,Pieraccioli M,Panzeri V,Sette C,Bielli P

更新日期：2019-07-09 00:00:00

abstract：:IMGT, the international ImMunoGeneTics database (http://imgt.cines. fr:8104 ), is a high-quality integrated database specialising in Immunoglobulins (Ig), T cell Receptors (TcR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species, created in 1989 by Marie-Paule Lefranc, Université Montpellie...

journal_title：Nucleic acids research

authors： Ruiz M,Giudicelli V,Ginestoux C,Stoehr P,Robinson J,Bodmer J,Marsh SG,Bontrop R,Lemaitre M,Lefranc G,Chaume D,Lefranc MP

更新日期：2000-01-01 00:00:00

abstract：:The crystal structure of the DNA dodecamer duplex CATGGGCCCATG lies on a structural continuum along the transition between A- and B-DNA. The dodecamer possesses the normal vector plot and inclination values typical of B-DNA, but has the crystal packing, helical twist, groove width, sugar pucker, slide and x-displaceme...

journal_title：Nucleic acids research

authors： Ng HL,Dickerson RE

更新日期：2002-09-15 00:00:00

abstract：:Bacterial Hfq is a protein that plays an important role in the regulation of genes in cooperation with sRNAs. Escherichia coli Hfq (EcHfq) has two or more sites that bind RNA(s) including U-rich and/or the poly(A) tail of mRNA. However, functional and structural information about Bacillus subtilis Hfq (BsHfq) includin...

journal_title：Nucleic acids research

authors： Someya T,Baba S,Fujimoto M,Kawai G,Kumasaka T,Nakamura K

更新日期：2012-02-01 00:00:00

abstract：:The secondary structures of the 5'-untranslated region (5'-UTR) of five different tymoviruses have been determined by structure probing, computer prediction and sequence comparison. Despite large sequence differences, there are remarkable similarities in the secondary structure. In all viruses two or four hairpins are...

journal_title：Nucleic acids research

authors： Hellendoorn K,Michiels PJ,Buitenhuis R,Pleij CW

更新日期：1996-12-15 00:00:00

abstract：:The development of complex methods in molecular biology is a laborious, costly, iterative and often intuition-bound process where optima are sought in a multidimensional parameter space through step-by-step optimizations. The difficulty of miniaturizing reactions under the microliter volumes usually handled in multiwe...

journal_title：Nucleic acids research

authors： Poulain S,Arnaud O,Kato S,Chen I,Ishida H,Carninci P,Plessy C

更新日期：2020-04-17 00:00:00

abstract：:The Deciphering the Mechanisms of Developmental Disorders (DMDD) consortium is a research programme set up to identify genes in the mouse, which if mutated (or knocked-out) result in embryonic lethality when homozygous, and initiate the study of why disruption of their function has such profound effects on embryo deve...

journal_title：Nucleic acids research

authors： Wilson R,McGuire C,Mohun T,DMDD Project.

更新日期：2016-01-04 00:00:00

abstract：:We present a simple and highly accurate computational method for operon prediction, based on intergenic distances and functional relationships between the protein products of contiguous genes, as defined by STRING database (Jensen,L.J., Kuhn,M., Stark,M., Chaffron,S., Creevey,C., Muller,J., Doerks,T., Julien,P., Roth,...

journal_title：Nucleic acids research

authors： Taboada B,Verde C,Merino E

更新日期：2010-07-01 00:00:00

abstract：:The J-binding protein 1 (JBP1) is essential for biosynthesis and maintenance of DNA base-J (β-d-glucosyl-hydroxymethyluracil). Base-J and JBP1 are confined to some pathogenic protozoa and are absent from higher eukaryotes, prokaryotes and viruses. We show that JBP1 recognizes J-containing DNA (J-DNA) through a 160-res...

journal_title：Nucleic acids research

authors： Heidebrecht T,Christodoulou E,Chalmers MJ,Jan S,Ter Riet B,Grover RK,Joosten RP,Littler D,van Luenen H,Griffin PR,Wentworth P Jr,Borst P,Perrakis A

更新日期：2011-07-01 00:00:00

abstract：:Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons. Enhancers, as well as their associated target genes, and transcription factors (TFs) that bind to them, are highly associated with human disease and biological processes. Alt...

journal_title：Nucleic acids research

authors： Bai X,Shi S,Ai B,Jiang Y,Liu Y,Han X,Xu M,Pan Q,Wang F,Wang Q,Zhang J,Li X,Feng C,Li Y,Wang Y,Song Y,Feng K,Li C

更新日期：2020-01-08 00:00:00

abstract：:We present a new coarse grained method for the simulation of duplex DNA. The algorithm uses a generalized multi-harmonic model that can represent any multi-normal distribution of helical parameters, thus avoiding caveats of current mesoscopic models for DNA simulation and representing a breakthrough in the field. The ...

journal_title：Nucleic acids research

authors： Walther J,Dans PD,Balaceanu A,Hospital A,Bayarri G,Orozco M

更新日期：2020-03-18 00:00:00

abstract：:Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell M...

journal_title：Nucleic acids research

authors： Smyth RP,Smith MR,Jousset AC,Despons L,Laumond G,Decoville T,Cattenoz P,Moog C,Jossinet F,Mougel M,Paillart JC,von Kleist M,Marquet R

更新日期：2018-05-18 00:00:00

abstract：:Partial acid cleavage, comparative HPLC tryptic peptide mapping and amino acid sequencing of the C1 and C2 proteins of HeLa heterogeneous nuclear ribonucleoprotein (hnRNP) particles demonstrate that proteins C1 and C2 differ in primary structure by the presence of a 13 amino acid insert sequence in C2. This C2 insert ...

journal_title：Nucleic acids research

authors： Merrill BM,Barnett SF,LeStourgeon WM,Williams KR

更新日期：1989-11-11 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：:Clustered regularly interspaced short palindromic repeats (CRISPR), in combination with CRISPR associated (cas) genes, constitute CRISPR-Cas bacterial adaptive immune systems. To generate immunity, these systems acquire short sequences of nucleic acids from foreign invaders and incorporate these into their CRISPR arra...

journal_title：Nucleic acids research

authors： Richter C,Dy RL,McKenzie RE,Watson BN,Taylor C,Chang JT,McNeil MB,Staals RH,Fineran PC

更新日期：2014-07-01 00:00:00

abstract：:We present web servers for analysis of non-coding RNA sequences on the basis of their secondary structures. Software tools for structural multiple sequence alignments, structural pairwise sequence alignments and structural motif findings are available from the integrated web server and the individual stand-alone web s...

journal_title：Nucleic acids research

authors： Asai K,Kiryu H,Hamada M,Tabei Y,Sato K,Matsui H,Sakakibara Y,Terai G,Mituyama T

更新日期：2008-07-01 00:00:00

abstract：:We have isolated and characterized a S. pombe promoter using a functional heterologous gene product assay. Random S. pombe genomic fragments were cloned upstream from the promoterless 'lacZ gene and tested in vivo for their efficiency to promote expression of the beta-galactosidase protein in the fission yeast. An eff...

journal_title：Nucleic acids research

authors： Kudla B,Persuy MA,Gaillardin C,Heslot H

更新日期：1988-09-12 00:00:00

abstract：:Caged antisense oligodeoxynucleotides (asODNs) are synthesized by linking two ends of linear oligodeoxynucleotides using a photocleavable linker. Two of them (H30 and H40) have hairpin-like structures which show a large difference in thermal stability (Delta T(m) = 17.5 degrees C and 11.6 degrees C) comparing to uncag...

journal_title：Nucleic acids research

authors： Tang X,Su M,Yu L,Lv C,Wang J,Li Z

更新日期：2010-06-01 00:00:00

abstract：:The cDNA encoding the human RNA lariat debranching enzyme (hDBR1) was identified and cloned by searching the Expressed Sequence Tag (EST) database and screening a HeLa cDNA library, based on predicted amino acid sequence homologies with the Saccharomyces cerevisiae, Schizosaccharomyces pombe and Caenorhabditis elegans...

journal_title：Nucleic acids research

authors： Kim JW,Kim HC,Kim GM,Yang JM,Boeke JD,Nam K

更新日期：2000-09-15 00:00:00

abstract：:During protein synthesis, the nascent peptide chain traverses the peptide exit tunnel of the ribosome. We monitor the co-translational movement of the nascent peptide using a fluorescent probe attached to the N-terminus of the nascent chain. Due to fluorophore quenching, the time-dependent fluorescence signal emitted ...

journal_title：Nucleic acids research

authors： Haase N,Holtkamp W,Lipowsky R,Rodnina M,Rudorf S

更新日期：2018-12-14 00:00:00

abstract：:With the improved rapid sequencing techniques, the earlier sequence of U2 RNA of Novikoff hepatoma (Shibata et al, J. Biol. Chem. 250, 3909-3920, 1975) was reanalyzed and modified. The improved sequence of U2 RNA is 188 (or 189) nucleotides long and is in register with a characterized U2 RNA pseudogene (Denison et al,...

journal_title：Nucleic acids research

authors： Reddy R,Henning D,Epstein P,Busch H

更新日期：1981-11-11 00:00:00

abstract：:The lytic-lysogenic decision in bacteriophage 186 is governed by the 186 CI repressor protein in a unique way. The 186 CI is proposed to form a wheel-like oligomer that can mediate either wrapped or looped nucleoprotein complexes to provide the cooperative and competitive interactions needed for regulation. Although c...

journal_title：Nucleic acids research

authors： Wang H,Dodd IB,Dunlap DD,Shearwin KE,Finzi L

更新日期：2013-06-01 00:00:00

abstract：:The deoxyoligonucleotide 5' AATCGGGCATGGATT (15-mer) was synthesized containing 12 phosphoramidate linkages derived from 2 primary and 2 secondary amines. The oligonucleotides were purified by reverse phase HPLC and characterized by PAGE. The thermal stability of the duplexes derived from these compounds, when hybridi...

journal_title：Nucleic acids research

authors： Froehler B,Ng P,Matteucci M

更新日期：1988-06-10 00:00:00

abstract：:We report the use of MonoQ FPLC (Fast Protein Liquid Chromatography) for the rapid purification of a novel Type II restriction endonuclease PmaCI, from Pseudomonas maltophila, which recognises the sequence 5'-CAC decreases GTG-3'. The resulting enzyme is free of other nucleases to a level suitable for its characterisa...

journal_title：Nucleic acids research

authors： Walker JN,Dean PD,Saunders JR

更新日期：1986-02-11 00:00:00

abstract：:Rapid characterization of unknown biological samples is under the focus of many current studies. Here we report a method for screening of biological samples by optical mapping of their DNA. We use a novel, one-step chemo-enzymatic reaction to covalently bind fluorophores to DNA at the four-base recognition sites of a ...

journal_title：Nucleic acids research

authors： Grunwald A,Dahan M,Giesbertz A,Nilsson A,Nyberg LK,Weinhold E,Ambjörnsson T,Westerlund F,Ebenstein Y

更新日期：2015-10-15 00:00:00