Dealing with the genetic load in bacterial synthetic biology circuits: convergences with the Ohm's law.

abstract：:DISCOVER1 (DIStribution COunter VERsion 1) is a new program that can identify DNA motifs occurring with a high deviation from the expected frequency. The program generates families of patterns, each family having a common set of defined bases. Undefined bases are inserted amongst the defined bases in different ways, t...

journal_title：Nucleic acids research

authors： Valle G

更新日期：1993-11-11 00:00:00

abstract：:Bursts of free radicals produced by ionization of water in close vicinity to DNA can produce clusters of opposed DNA lesions and these are termed multiply damaged sites (MDS). How MDS are processed by the Escherichia coli DNA glycosylases, endonuclease (endo) III and endo VIII, which recognize oxidized pyrimidines, is...

journal_title：Nucleic acids research

authors： Harrison L,Hatahet Z,Purmal AA,Wallace SS

更新日期：1998-02-15 00:00:00

abstract：:Archival formalin-fixed, paraffin-embedded and ethanol-fixed tissues represent a potentially invaluable resource for gene expression analysis, as they are the most widely available material for studies of human disease. Little data are available evaluating whether RNA obtained from fixed (archival) tissues could produ...

journal_title：Nucleic acids research

authors： Karsten SL,Van Deerlin VM,Sabatti C,Gill LH,Geschwind DH

更新日期：2002-01-15 00:00:00

abstract：:RNA sequencing (RNA-Seq) is a powerful tool for analyzing the identity of cellular RNAs but is often limited by the amount of material available for analysis. In spite of extensive efforts employing existing protocols, we observed that it was not possible to obtain useful sequencing libraries from nuclear RNA derived ...

journal_title：Nucleic acids research

authors： Chu Y,Wang T,Dodd D,Xie Y,Janowski BA,Corey DR

更新日期：2015-06-23 00:00:00

abstract：:Aryldiazonium salts are shown to be useful as phototriggered structural probes for RNA mapping as well as for footprinting of RNA/protein interaction. In particular the yeast tRNA(Asp)/aspartyl-tRNA synthetase complex is shown to involve the variable loop face and the concave side of the L-shaped nucleic acid bound to...

journal_title：Nucleic acids research

authors： Garcia A,Giegé R,Behr JP

更新日期：1990-01-11 00:00:00

abstract：:We report the nucleotide sequence of the Group IV RNA bacteriophage SP. The entire sequence is 4276 nucleotides long. Four cistrons have been identified by comparison with the related Group III phage Q beta. The maturation protein contains 449 amino acids, the coat protein contains 131 amino acids, the read-through pr...

journal_title：Nucleic acids research

authors： Inokuchi Y,Jacobson AB,Hirose T,Inayama S,Hirashima A

更新日期：1988-07-11 00:00:00

abstract：:Treatment of cells with DNA damaging agents leads to induction of a variety of genes involved in different cellular processes. We have applied a lacZ-based gene trap strategy to search for new mammalian genes induced by genotoxic stress. A population of 32 x 10(3) neo r clones stably transfected with a gene trap vecto...

journal_title：Nucleic acids research

authors： Menichini P,Viaggi S,Gallerani E,Fronza G,Ottaggio L,Comes A,Ellwart JW,Abbondandolo A

更新日期：1997-12-01 00:00:00

abstract：:4'-Acylated thymidines represent a new class of DNA chain terminators, since they have been shown to act as post-incorporation chain-terminating nucleotides despite the presence of a free 3'-hydroxyl group. Here, we describe the action of the 4'-acetyl- (MeTTP) and 4'-propanoylthymidine 5'-triphosphate (EtTTP) on HIV-...

journal_title：Nucleic acids research

authors： Marx A,Amacker M,Stucki M,Hübscher U,Bickle TA,Giese B

更新日期：1998-09-01 00:00:00

abstract：:In bacteria, promoter identification by RNA polymerase is mediated by a dissociable σ factor. The housekeeping σ(70) factor of Escherichia coli recognizes two well characterized DNA sequence elements, known as the '-10' and '-35' hexamers. These elements are separated by 'spacer' DNA, the sequence of which is generall...

journal_title：Nucleic acids research

authors： Singh SS,Typas A,Hengge R,Grainger DC

更新日期：2011-07-01 00:00:00

abstract：:1731, a Drosophila retrotransposon was first described as having a transcription activity which was negatively regulated by 20-hydroxyecdysone (20-OH), the steroid molting hormone of insects. Using constructions expressing the bacterial chloramphenicol-acetyltransferase (CAT) gene under the control of the entire or de...

journal_title：Nucleic acids research

authors： Ziarczyk P,Best-Belpomme M

更新日期：1991-10-25 00:00:00

abstract：:In a gene targeting experiment, the generation of a targeting construct often requires complex DNA manipulations. We developed a set of cassettes and plasmids useful for creating targeting vectors to modify the mammalian genome. A positive selection marker cassette (PGK/EM7p-npt), which included dual prokaryotic and e...

journal_title：Nucleic acids research

authors： Aoyama M,Agari K,Sun-Wada GH,Futai M,Wada Y

更新日期：2005-03-22 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：:From a sarkosyl-insoluble outer membrane fraction prepared from the Helicobacter pylori strain ATCC 43504, 19 proteins could be sequenced N-terminally by Edman degradation. Oligonucleotides were deduced and used for screening of a genomic library. From the isolated genes, five code for different members of a H.pylori ...

journal_title：Nucleic acids research

authors： Peck B,Ortkamp M,Diehl KD,Hundt E,Knapp B

更新日期：1999-08-15 00:00:00

abstract：:The paper describes an improved method for the synthesis of oligodeoxyribonucleotides using phosphoramidite chemistry. Our procedure relies on novel phosphoramidite intermediates, the deoxyribonucleoside-3'-morpholine-methoxyphosphins. These compounds are extremely stable and can be purified readily. Condensation reac...

journal_title：Nucleic acids research

authors： Dörper T,Winnacker EL

更新日期：1983-05-11 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：:The interactions between beef tRNATrp with avian myeloblastosis reverse transcriptase have been studied by statistical chemical modifications of phosphate (ethylnitrosourea) and cytidine (dimethyl sulfate) residues, as well as by digestion of complexed tRNA by Cobra venom nuclease and Neurospora crassa endonuclease. R...

journal_title：Nucleic acids research

authors： Garret M,Romby P,Giegé R,Litvak S

更新日期：1984-03-12 00:00:00

abstract：:The Est3 subunit of yeast telomerase, which adopts a predicted OB-fold, is essential for telomere replication. To assess the possible contributions that Est3 might make to enzyme catalysis, we compared telomerase activity from wild type and est3-Delta strains of Saccharomyces castellii, which revealed that loss of the...

journal_title：Nucleic acids research

authors： Lee J,Mandell EK,Rao T,Wuttke DS,Lundblad V

更新日期：2010-04-01 00:00:00

abstract：:We show herein the transcription of a processed gene that originated from a spliced transcript. Recently, we isolated the human and murine homologues of the yeast chromatin protein, SPT4. The Supt4h gene is spliced normally from five exons encoded by chromosome 11. Here we show that a related sequence on chromosome 10...

journal_title：Nucleic acids research

authors： Chiang PW,Zhang R,Stubbs L,Zhang L,Zhu L,Kurnit DM

更新日期：1998-11-01 00:00:00

abstract：:Understanding the evolutionary and genomic mechanisms responsible for turning the soil-derived saprophytic mycobacteria into lethal intracellular pathogens is a critical step towards the development of strategies for the control of mycobacterial diseases. In this context, Mycobacterium indicus pranii (MIP) is of speci...

journal_title：Nucleic acids research

authors： Saini V,Raghuvanshi S,Khurana JP,Ahmed N,Hasnain SE,Tyagi AK,Tyagi AK

更新日期：2012-11-01 00:00:00

abstract：:Heptadecaoligodeoxyribonucleotides containing one or more of the bases, 6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one (P), 2-amino-6-methoxyaminopurine (K), and hypoxanthine (I) and combinations of P with K and I have been synthesised on a DNA synthesiser. The stability of duplexes containing these basemodified ol...

journal_title：Nucleic acids research

authors： Lin PK,Brown DM

更新日期：1992-10-11 00:00:00

abstract：:Large-scale automatic annotation of protein sequences remains challenging in postgenomics era. E1DS is designed for annotating enzyme sequences based on a repository of 1D signatures. The employed sequence signatures are derived using a novel pattern mining approach that discovers long motifs consisted of several sequ...

journal_title：Nucleic acids research

authors： Chien TY,Chang DT,Chen CY,Weng YZ,Hsu CM

更新日期：2008-07-01 00:00:00

abstract：:Alternative RNA splicing is an essential process to yield proteomic diversity in eukaryotic cells, and aberrant splicing is often associated with numerous human diseases and cancers. We recently described serine/arginine-rich splicing factor 3 (SRSF3 or SRp20) being a proto-oncogene. However, the SRSF3-regulated splic...

journal_title：Nucleic acids research

authors： Ajiro M,Jia R,Yang Y,Zhu J,Zheng ZM

更新日期：2016-02-29 00:00:00

abstract：:U6 RNA is a member of a class of small abundant stable nuclear RNAs that are essential for splicing. In all species examined so far, the U6 RNA is a RNA polymerase III transcript. The U6 gene of the fission yeast Schizosaccharomyces pombe is unusual in that it is interrupted by an intron whose structure is similar to ...

journal_title：Nucleic acids research

authors： Potashkin J,Frendewey D

更新日期：1989-10-11 00:00:00

abstract：:Peptidome similarity analysis enables researchers to gain insights into differential peptide profiles, providing a robust tool to discriminate strain-specific peptides, true intra-species differences among biological replicates or even microorganism-phenotype variations. However, no in silico peptide fingerprinting so...

journal_title：Nucleic acids research

authors： Blanco-Míguez A,Fdez-Riverola F,Lourenço A,Sánchez B

更新日期：2017-07-03 00:00:00

abstract：:During carcinogenesis, cells are exposed to increased replication stress due to replication fork arrest at sites of DNA lesions and difficult to replicate genomic regions. Efficient fork restart and DNA repair are important for cancer cell proliferation. We previously showed that the ADP-ribosyltransferase PARP10 inte...

journal_title：Nucleic acids research

authors： Schleicher EM,Galvan AM,Imamura-Kawasawa Y,Moldovan GL,Nicolae CM

更新日期：2018-09-28 00:00:00

abstract：:Properties of a mutant bacteriophage T2 DNA [N:(6)-adenine] methyltransferase (T2 Dam MTase) have been investigated for its potential utilization in RecA-assisted restriction endonuclease (RARE) cleavage. Steady-state kinetic analyses with oligonucleotide duplexes revealed that, compared to wild-type T4 Dam, both wild...

journal_title：Nucleic acids research

authors： Minko I,Hattman S,Lloyd RS,Kossykh V

更新日期：2001-04-01 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：:An elongation cycle of a transcribing RNA polymerase (RNAP) usually consists of multiple kinetics steps, so there exist multiple kinetic checkpoints where non-cognate nucleotides can be selected against. We conducted comprehensive free energy calculations on various nucleotide insertions for viral T7 RNAP employing al...

journal_title：Nucleic acids research

authors： Long C,E C,Da LT,Yu J

更新日期：2019-05-21 00:00:00

abstract：:A series of plasmids were constructed in which a promoter was introduced into a lac-based operon fusion vector. A perfectly symmetrical oligonucleotide of 22-bp corresponding to an idealized binding site for cAMP receptor protein (CRP) of E. coli was chemically synthesized. The synthetic CRP site was placed between th...

journal_title：Nucleic acids research

authors： Morita T,Shigesada K,Kimizuka F,Aiba H

更新日期：1988-08-11 00:00:00

abstract：:Traditional Chinese medicine (TCM) is not only an effective solution for primary health care, but also a great resource for drug innovation and discovery. To meet the increasing needs for TCM-related data resources, we developed ETCM, an Encyclopedia of Traditional Chinese Medicine. ETCM includes comprehensive and sta...

journal_title：Nucleic acids research

authors： Xu HY,Zhang YQ,Liu ZM,Chen T,Lv CY,Tang SH,Zhang XB,Zhang W,Li ZY,Zhou RR,Yang HJ,Wang XJ,Huang LQ

更新日期：2019-01-08 00:00:00