VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics.

abstract：:In Xenopus oocytes in vitro transcribed mouse U7 RNA is assembled into small nuclear ribonucleoproteins (snRNPs) that are functional in histone RNA 3' processing. If the special Sm binding site of U7 (AAUUUGUCUAG, U7 Sm WT) is converted into the canonical Sm sequence derived from the major snRNAs (AAUUUUUGGAG, U7 Sm O...

journal_title：Nucleic acids research

authors： Stefanovic B,Hackl W,Lührmann R,Schümperli D

更新日期：1995-08-25 00:00:00

abstract：:Modified bases, such as O6-methylguanines, are produced in cells exposed to alkylating agents and cause apoptosis. In human cells treated with N-methyl-N-nitrosourea, we detected a protein complex composed of MutSalpha, MutLalpha and PCNA on damaged DNA by immunoprecipitation method using chromatin extracts, in which ...

journal_title：Nucleic acids research

authors： Hidaka M,Takagi Y,Takano TY,Sekiguchi M

更新日期：2005-10-04 00:00:00

abstract：:Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcr...

journal_title：Nucleic acids research

authors： Voltz K,Léonard J,Touceda PT,Conyard J,Chaker Z,Dejaegere A,Godet J,Mély Y,Haacke S,Stote RH

更新日期：2016-04-20 00:00:00

abstract：:The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of bacteria, archaea and the yeast Saccharomyces cerevisiae (http://www....

journal_title：Nucleic acids research

authors： Tatusov RL,Natale DA,Garkavtsev IV,Tatusova TA,Shankavaram UT,Rao BS,Kiryutin B,Galperin MY,Fedorova ND,Koonin EV

更新日期：2001-01-01 00:00:00

abstract：:Recently, we developed a mass DNA-mediated transformation technique for the ciliated protozoan Tetrahymena thermophila that introduces transforming DNA by electroporation into conjugating cells. Other studies demonstrated that a neomycin resistance gene flanked by Tetrahymena H4-I gene regulatory sequences transformed...

journal_title：Nucleic acids research

authors： Gaertig J,Gu L,Hai B,Gorovsky MA

更新日期：1994-12-11 00:00:00

abstract：:Au (III) reacts with DNA at pH 5.6 to form a complex which is sensitive to mid-UV radiation. Cyclobutane pyrimidine dimers are produced at some 15 to 30 times the rate that they are in untreated DNA. The mechanism of photosensitization appears to involve energy absorption by Au-urine and Au-cytosine adducts which can ...

journal_title：Nucleic acids research

authors： Wilkins RJ

更新日期：1978-10-01 00:00:00

abstract：:The editing function of aminoacyl-tRNA synthetases (aaRSs) is indispensible for formation of the correct aminoacyl-tRNAs. Editing deficiency may lead to growth inhibition and the pathogenesis of various diseases. Herein, we confirmed that norvaline (Nva) but not isoleucine or valine is the major threat to the editing ...

journal_title：Nucleic acids research

authors： Ji QQ,Fang ZP,Ye Q,Chi CW,Wang ED

更新日期：2017-07-07 00:00:00

abstract：:Initiation of sporulation in Bacillus subtilis is controlled by several regulators which affect activation by phosphorylation of the key response regulator Spo0A or transcription of Spo0A-P-dependent genes. In vivo overexpression of one of these regulators, sinR , results in suppression of transcription from the Spo0A...

journal_title：Nucleic acids research

authors： Cervin MA,Lewis RJ,Brannigan JA,Spiegelman GB

更新日期：1998-08-15 00:00:00

abstract：:The PRISM web server enables fast and accurate prediction of protein-protein interactions (PPIs). The prediction algorithm is knowledge-based. It combines structural similarity and accounts for evolutionary conservation in the template interfaces. The predicted models are stored in its repository. Given two protein st...

journal_title：Nucleic acids research

authors： Baspinar A,Cukuroglu E,Nussinov R,Keskin O,Gursoy A

更新日期：2014-07-01 00:00:00

abstract：:RNA structural complexity and flexibility present a challenge for computational modeling efforts. Experimental information and bioinformatics data can be used as restraints to improve the accuracy of RNA tertiary structure prediction. Regarding utilization of restraints, the fundamental questions are: (i) What is the ...

journal_title：Nucleic acids research

authors： Wang J,Williams B,Chirasani VR,Krokhotin A,Das R,Dokholyan NV

更新日期：2019-06-20 00:00:00

abstract：:Modular primers are strings of three contiguously annealed unligated oligonucleotides (modules) as short as 5- or 6-mers, selected from a presynthesized library. It was previously found that such strings can prime DNA sequencing reactions specifically, thus eliminating the need for the primer synthesis step in DNA seq...

journal_title：Nucleic acids research

authors： Beskin AD,Zevin-Sonkin D,Sobolev IA,Ulanovsky LE

更新日期：1995-08-11 00:00:00

abstract：:Double stranded cDNA of cucumber pale fruit viroid ( CPFV ) has been cloned by the method of Okayama and Berg (Mol.Cell.Biol.2,161-170 (1982] and the complete nucleotide sequence was established. The covalently closed circular molecules of single-stranded CPFV RNA consists of 303 nucleotides. The nucleotide sequence o...

journal_title：Nucleic acids research

authors： Sano T,Uyeda I,Shikata E,Ohno T,Okada Y

更新日期：1984-04-25 00:00:00

abstract：:Eukaryotes produce multiple products from a single gene locus by alternative splicing, translation or promoter usage as mechanisms expanding the complexity of their proteome. Trithorax proteins, including the Arabidopsis Trithorax-like protein ATX1, are histone modifiers regulating gene activity. Here, we report that ...

journal_title：Nucleic acids research

authors： Ndamukong I,Lapko H,Cerny RL,Avramova Z

更新日期：2011-06-01 00:00:00

abstract：:The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparativ...

journal_title：Nucleic acids research

authors： Arnaud MB,Chibucos MC,Costanzo MC,Crabtree J,Inglis DO,Lotia A,Orvis J,Shah P,Skrzypek MS,Binkley G,Miyasato SR,Wortman JR,Sherlock G

更新日期：2010-01-01 00:00:00

abstract：:T-region transfer from wild-type Agrobacterium strains is thought to be an orientated process, starting at the right border repeat and terminating at the left border repeat of the T-region. Here we demonstrate that a right border repeat in the inverted orientation relative to the onc-genes can also mediate transfer of...

journal_title：Nucleic acids research

authors： van Haaren MJ,Sedee NJ,de Boer HA,Schilperoort RA,Hooykaas PJ

更新日期：1988-11-11 00:00:00

abstract：:Bacteriophage T4 Dda helicase has recently been shown to be active as a monomer for unwinding of short duplex oligonucleotides and for displacing streptavidin from 3'-biotinylated oligonucleotides. However, its activity for streptavidin displacement and DNA unwinding has been shown to increase as the number of Dda mol...

journal_title：Nucleic acids research

authors： Byrd AK,Raney KD

更新日期：2006-05-31 00:00:00

abstract：:Translin and translin-associated factor-x are highly conserved in eukaroytes; they can form heteromeric complexes (known as C3POs) and participate in various nucleic acid metabolism pathways. In humans and Drosophila, C3POs cleave the fragmented siRNA passenger strands and facilitate the activation of RNA-induced sile...

journal_title：Nucleic acids research

authors： Zhang J,Liu H,Yao Q,Yu X,Chen Y,Cui R,Wu B,Zheng L,Zuo J,Huang Z,Ma J,Gan J

更新日期：2016-11-02 00:00:00

abstract：:In this paper, we report investigations, based on circular dichroism, nuclear magnetic resonance spectroscopy and electrophoresis methods, on three oligonucleotide sequences, each containing one 3'-3' and two 5'-5' inversion of polarity sites, and four G-runs with a variable number of residues, namely two, three and f...

journal_title：Nucleic acids research

authors： Virgilio A,Russo A,Amato T,Russo G,Mayol L,Esposito V,Galeone A

更新日期：2017-08-21 00:00:00

abstract：:Gene expression profiling has gradually become a routine procedure for disease diagnosis and classification. In the past decade, many computational methods have been proposed, resulting in great improvements on various levels, including feature selection and algorithms for classification and clustering. In this study,...

journal_title：Nucleic acids research

authors： Ren X,Wang Y,Zhang XS,Jin Q

更新日期：2013-08-01 00:00:00

abstract：:Little is known about the function of most non-coding RNAs (ncRNAs). The majority of long ncRNAs (lncRNAs) is expressed at very low levels and it is a matter of intense debate whether these can be of functional relevance. Here, we identified lncRNAs regulating the viability of lung cancer cells in a high-throughput RN...

journal_title：Nucleic acids research

authors： Seiler J,Breinig M,Caudron-Herger M,Polycarpou-Schwarz M,Boutros M,Diederichs S

更新日期：2017-05-19 00:00:00

abstract：:Analyses of secondary structures proposed for ribosomal RNA's show that, of the different kinds of base pairs directly adjoining the ends of postulated double-helical regions, only A-G with A at the 5' end significantly exceeds the number expected for a random base distribution. An A(syn)-G(trans) hydrogen-bonded base...

journal_title：Nucleic acids research

authors： Traub W,Sussman JL

更新日期：1982-04-24 00:00:00

abstract：:In nematodes, the 22 nucleotide (nt) spliced leader (SL) is normally encoded by a multi-copy, tandemly reiterated SL gene and is trans-spliced from SL-RNA onto the 5' end of a subset of mRNAs. We have found that the SL is also encoded at multiple (> 100) orphon genomic sites in the parasitic nematode Angiostrongylus c...

journal_title：Nucleic acids research

authors： Joshua GW,Perler FB,Wang CC

更新日期：1995-03-25 00:00:00

abstract：:The TGGCA protein, the chicken homologue of HeLa cell NF-I, was purified to homogeneity from liver tissue by a procedure which includes preparative mobility shift electrophoresis (PMSE) as the final step. PMSE was here adjusted for the isolation of the TGGCA protein, but can be used as a general method to characterize...

journal_title：Nucleic acids research

authors： Rupp RA,Sippel AE

更新日期：1987-12-10 00:00:00

abstract：:Complete genomes of three closely related Gram-positive bacteria Streptococcus pyogenes, Streptococcus pneumoniae and Lactococcus lactis are analyzed for abundances of short DNA sequence motifs (frequent words). The character and extent of frequent words are strikingly different among these genomes. The frequent words...

journal_title：Nucleic acids research

authors： Mrázek J,Gaynon LH,Karlin S

更新日期：2002-10-01 00:00:00

abstract：:Toxin-antitoxin systems are widespread in bacteria and archaea. They perform diverse functional roles, including the generation of persistence, maintenance of genetic loci and resistance to bacteriophages through abortive infection. Toxin-antitoxin systems have been divided into three types, depending on the nature of...

journal_title：Nucleic acids research

authors： Blower TR,Short FL,Rao F,Mizuguchi K,Pei XY,Fineran PC,Luisi BF,Salmond GP

更新日期：2012-07-01 00:00:00

abstract：:Partial restriction digestion is used to map restriction sites and the location of genes within yeast artificial chromosomes (YACs). Locus-specific probes are hybridised to the partially digested YAC DNA and the fragments to which they hybridise are compared with the pattern of partial digestion products that include ...

journal_title：Nucleic acids research

authors： Shields DC,Butler A,Mosurski KR,Walsh MT,Whitehead AS

更新日期：1996-11-15 00:00:00

abstract：:RNA G-quadruplexes (G4s) are secondary structures proposed to function as regulators of post-transcriptional mRNA localisation and translation. G4s within some neuronal mRNAs are known to control distal localisation and local translation, contributing to distinct local proteomes that facilitate the synaptic remodellin...

journal_title：Nucleic acids research

authors： Maltby CJ,Schofield JPR,Houghton SD,O'Kelly I,Vargas-Caballero M,Deinhardt K,Coldwell MJ

更新日期：2020-09-25 00:00:00

abstract：:The hybridization of complementary strands of DNA is the underlying principle of all microarray-based techniques for the analysis of DNA variation. In this paper, we study how probe immobilization at surfaces, specifically probe density, influences the kinetics of target capture using surface plasmon resonance (SPR) s...

journal_title：Nucleic acids research

authors： Peterson AW,Heaton RJ,Georgiadis RM

更新日期：2001-12-15 00:00:00

abstract：:Most type II restriction-modification (R-M) systems produce separate endonuclease (REase) and methyltransferase (MTase) proteins. After R-M genes enter a new cell, MTase activity must appear before REase or the host chromosome will be cleaved. Temporal control of these genes thus has life-or-death consequences. PvuII ...

journal_title：Nucleic acids research

authors： Mruk I,Blumenthal RM

更新日期：2009-02-01 00:00:00

abstract：:RNase D was recently reported as a new enzymatic activity associated with HIV-1 reverse transcriptase (RT), cleaving RNA at two positions within the double-stranded region of the tRNA primer-viral RNA template complex (Ben-Artzi et al., Proc. Natl. Acad. Sci. USA 89 (1992) 927-931). This would make RNase D a fourth di...

journal_title：Nucleic acids research

authors： Hostomsky Z,Hudson GO,Rahmati S,Hostomska Z

更新日期：1992-11-11 00:00:00