A novel regulatory circuit in base excision repair involving AP endonuclease 1, Creb1 and DNA polymerase beta.

abstract：:Novel techniques for high-throughput steady-state metabolomic profiling yield information about changes of nearly thousands of metabolites. Such metabolomic profiles, when analyzed together with transcriptional profiles, can reveal novel insights about underlying biological processes. While a number of conceptual appr...

journal_title：Nucleic acids research

authors： Sergushichev AA,Loboda AA,Jha AK,Vincent EE,Driggers EM,Jones RG,Pearce EJ,Artyomov MN

更新日期：2016-07-08 00:00:00

abstract：:Clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated Cas proteins comprise a prokaryotic RNA-guided adaptive immune system that interferes with mobile genetic elements, such as plasmids and phages. The type I-E CRISPR interference complex Cascade from Escherichia coli is composed of...

journal_title：Nucleic acids research

authors： Beloglazova N,Kuznedelov K,Flick R,Datsenko KA,Brown G,Popovic A,Lemak S,Semenova E,Severinov K,Yakunin AF

更新日期：2015-01-01 00:00:00

abstract：:The laminin (LM)-database, hosted at http://www.lm.lncc.br, was published in the NAR database 2011 edition. It was the first database that provided comprehensive information concerning a non-collagenous family of extracellular matrix proteins, the LMs. In its first version, this database contained a large amount of in...

journal_title：Nucleic acids research

authors： Golbert DC,Santana-van-Vliet E,Mundstein AS,Calfo V,Savino W,de Vasconcelos AT

更新日期：2014-01-01 00:00:00

abstract：:Cdc48/p97 is an evolutionary conserved ubiquitin-dependent chaperone involved in a broad array of cellular functions due to its ability to associate with multiple cofactors. Aside from its role in removing RNA polymerase II from chromatin after DNA damage, little is known about how this AAA-ATPase is involved in the t...

journal_title：Nucleic acids research

authors： Bonizec M,Hérissant L,Pokrzywa W,Geng F,Wenzel S,Howard GC,Rodriguez P,Krause S,Tansey WP,Hoppe T,Dargemont C

更新日期：2014-01-01 00:00:00

abstract：:The properties of the interaction of 5-fluorocytosine-containing DNA with the EcoRII methyltransferase were studied. The DNA used was either a polymer synthesized in vitro, or a 20-mer containing one CCA/TGG sequence. The DNA could be methylated by the enzyme. In the process the enzyme formed a tight binding adduct wi...

journal_title：Nucleic acids research

authors： Friedman S,Ansari N

更新日期：1992-06-25 00:00:00

abstract：:The activity of MHC class II promoters depends upon conserved regulatory signals one of which, the extended X-box, contains in its X2 subregion a sequence related to the cAMP response element, CRE and to the TPA response element, TRE. Accordingly, X2 is recognized by the AP-1 factor and by other c-Jun or c-Fos contain...

journal_title：Nucleic acids research

authors： Neve Ombra M,Autiero M,DeLerma Barbaro A,Barretta R,Del Pozzo G,Guardiola J

更新日期：1993-04-25 00:00:00

abstract：:I-motif DNAs have been widely employed as robust modulating components to construct reconfigurable DNA nanodevices that function well in acidic cellular environments. However, they generally display poor interactivity with fluorescent ligands under these complex conditions, illustrating a major difficulty in utilizing...

journal_title：Nucleic acids research

authors： Shi L,Peng P,Zheng J,Wang Q,Tian Z,Wang H,Li T

更新日期：2020-02-28 00:00:00

abstract：:Despite the great potential of RNAi, ectopic expression of shRNA or siRNAs holds the inherent risk of competition for critical RNAi components, thus altering the regulatory functions of some cellular microRNAs. In addition, specific siRNA sequences can potentially hinder incorporation of other siRNAs when used in a co...

journal_title：Nucleic acids research

authors： Castanotto D,Sakurai K,Lingeman R,Li H,Shively L,Aagaard L,Soifer H,Gatignol A,Riggs A,Rossi JJ

更新日期：2007-01-01 00:00:00

abstract：:The Bcl-2 protein has an anti-apoptotic effect in neuronal and other cell types. We show for the first time that the Bcl-2 promoter is activated by the neuronal survival factor nerve growth factor (NGF) and that this effect is dependent on a region of the promoter from -1472 to -1414. This activation requires the Rap-...

journal_title：Nucleic acids research

authors： Liu YZ,Boxer LM,Latchman DS

更新日期：1999-05-15 00:00:00

abstract：:The binding of nine aminoalkyl adenylates to isoleucyl-tRNA synthetase from Escherichia coli MRE 600 was measured and compared with the binding of the cognate amino acids. It was found that they bind rather tightly to the enzyme, the Kd's ranging from 3.1.10(-4) M with glycinol-AMP ester to 3.7.10(-9) M with L-isoleuc...

journal_title：Nucleic acids research

authors： Flossdorf J,Marutzky R,Messer K,Kula MR

更新日期：1977-03-01 00:00:00

abstract：:DNA polymerase (Pol) beta null mouse embryonic fibroblasts provide a useful cell system to investigate the effects of alterations in base excision repair (BER) on genome stability. These cells are characterized by hypersensitivity to the cytotoxic effects of methyl methanesulfonate (MMS) and by decreased repair of the...

journal_title：Nucleic acids research

authors： Pascucci B,Russo MT,Crescenzi M,Bignami M,Dogliotti E

更新日期：2005-01-12 00:00:00

abstract：:Synthesis of HIV GagPol involves a proportion of ribosomes translating a U6A shift site at the distal end of the gag gene performing a programmed -1 ribosomal frameshift event to enter the overlapping pol gene. In vitro studies here show that at the same shift motif HIV reverse transcriptase generates -1 and +1 indels...

journal_title：Nucleic acids research

authors： Penno C,Kumari R,Baranov PV,van Sinderen D,Atkins JF

更新日期：2017-09-29 00:00:00

abstract：:Trinucleotide exchange (TriNEx) is a method for generating novel molecular diversity during directed evolution by random substitution of one contiguous trinucleotide sequence for another. Single trinucleotide sequences were deleted at random positions in a target gene using the engineered transposon MuDel that were su...

journal_title：Nucleic acids research

authors： Baldwin AJ,Busse K,Simm AM,Jones DD

更新日期：2008-08-01 00:00:00

abstract：:Nucleobase analogs 5-methylisocytosine ((Me)isoC) and isoguanine (isoG) form a non-natural base pair in duplex nucleic acids with base pairing specificity orthogonal to the natural nucleobase pairs. Sequencing reactions were conducted with oligodeoxyribonucleotides (ODNs) containing d(Me)isoC and disoG using modified ...

journal_title：Nucleic acids research

authors： Ahle JD,Barr S,Chin AM,Battersby TR

更新日期：2005-06-02 00:00:00

abstract：:Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized Pseudomonas aeruginosa and Pseudomonas putida. Unlike these bacteria, the Acinetobacter ADP1 is highly competent for natural transformation which affords extraordinary convenience for ...

journal_title：Nucleic acids research

authors： Barbe V,Vallenet D,Fonknechten N,Kreimeyer A,Oztas S,Labarre L,Cruveiller S,Robert C,Duprat S,Wincker P,Ornston LN,Weissenbach J,Marlière P,Cohen GN,Médigue C

更新日期：2004-10-28 00:00:00

abstract：:Thermally induced structural transition in the d(TTTTATAATAAA) d(TTTATTATAAAA) heteroduplex is characterized by UV-spectroscopy and differential scanning calorimetry. At low salt (less than 0.1 M) the occurrence of a cooperative transition in the lower temperature range, followed by a broad transition connected with s...

journal_title：Nucleic acids research

authors： Bolewska K,Zielenkiewicz A,Wierzchowski KL

更新日期：1984-04-11 00:00:00

abstract：:The Immune Epitope Database Analysis Resource (IEDB-AR, http://tools.iedb.org/) is a companion website to the IEDB that provides computational tools focused on the prediction and analysis of B and T cell epitopes. All of the tools are freely available through the public website and many are also available through a RE...

journal_title：Nucleic acids research

authors： Dhanda SK,Mahajan S,Paul S,Yan Z,Kim H,Jespersen MC,Jurtz V,Andreatta M,Greenbaum JA,Marcatili P,Sette A,Nielsen M,Peters B

更新日期：2019-07-02 00:00:00

abstract：:The convergently transcribed restriction (R) and methylase (M) genes of the Restriction-Modification system Esp1396I are tightly regulated by a controller (C) protein that forms part of the CR operon. We have mapped the transcriptional start sites from each promoter and examined the regulatory role of C.Esp1396I in vi...

journal_title：Nucleic acids research

authors： Bogdanova E,Zakharova M,Streeter S,Taylor J,Heyduk T,Kneale G,Severinov K

更新日期：2009-06-01 00:00:00

abstract：:We report the complete DNA sequence of the short repeat region in the genome of herpes simplex virus type 1, as 6633 base pairs of composition 79.5% G+C. This contains immediate early gene 3, encoding the IE175 protein, an important transcriptional activator of later virus genes. The IE175 coding region was identified...

journal_title：Nucleic acids research

authors： McGeoch DJ,Dolan A,Donald S,Brauer DH

更新日期：1986-02-25 00:00:00

abstract：:We have sequenced 14 introns from the ciliate Tetrahymena thermophila and include these in an analysis of the 27 intron sequences available from seven T. thermophila protein-encoding genes. Consensus 5' and 3' splice junctions were determined and found to resemble the junctions of other nuclear pre-mRNA introns. Uniqu...

journal_title：Nucleic acids research

authors： Csank C,Taylor FM,Martindale DW

更新日期：1990-09-11 00:00:00

abstract：:Isolated yeast mitochondria incorporate added UTP into RNA. Amongst the products formed are the two rRNAs, 4S RNA and several components presumed to be mRNAs. In omega+ strains (containing an intervening sequence in the 21S rRNA gene) besides mature 21S rRNA a transcript could be detected still containing nucleotide s...

journal_title：Nucleic acids research

authors： Groot GS,van Harten-Loosbroek N,van Ommen GJ,Pijst HL

更新日期：1981-12-11 00:00:00

abstract：:ATP-dependent type I topoisomerases from extremely thermophilic archaebacteria--reverse gyrases--drive positive supercoiling of DNA. We showed that reverse gyrase from Desulfurococcus amylolyticus breaks the DNA at specific sites and covalently binds to the 5' end. In 30 out of 31 sites located in pBR322 DNA fragments...

journal_title：Nucleic acids research

authors： Kovalsky OI,Kozyavkin SA,Slesarev AI

更新日期：1990-05-11 00:00:00

abstract：:Long-range enhancers of transcription are a key component of the genomic regulatory architecture. Recent studies have identified bi-directionally transcribed RNAs emanating from these enhancers known as eRNAs. However, it remains unclear how tightly coupled eRNA production is with enhancer activity. Through our system...

journal_title：Nucleic acids research

authors： Banerjee AR,Kim YJ,Kim TH

更新日期：2014-11-10 00:00:00

abstract：:The synthesis of cyclic di-, tri-, tetra-, penta- and hexa-thymidylic acids (16; n = 2, 3, 4, 5 and 6) and the cyclic hexadeoxyribonucleotide [d(CpCpTpApGpGp)], via the "filtration" approach, is reported. Some of the physical properties of the cyclic oligonucleotides are discussed, and their susceptibility to digestio...

journal_title：Nucleic acids research

authors： Rao MV,Reese CB

更新日期：1989-10-25 00:00:00

abstract：:In Euplotes crassus millions of telomeres are synthesized during the sexual phase of the life cycle. Since these newly synthesized telomeres are longer than normal macronuclear telomeres, they must be trimmed to the mature size. We have examined the timing and mechanism of this trimming step. We have shown that a sudd...

journal_title：Nucleic acids research

authors： Vermeesch JR,Williams D,Price CM

更新日期：1993-11-25 00:00:00

abstract：:The formation of interstrand cross-links in nucleic acids can have a strong impact on biological function of nucleic acids; therefore, many cross-linking agents have been developed for biological applications. Despite numerous studies, there remains a need for cross-linking agents that exhibit both efficiency and sele...

journal_title：Nucleic acids research

authors： Nishimoto A,Jitsuzaki D,Onizuka K,Taniguchi Y,Nagatsugi F,Sasaki S

更新日期：2013-07-01 00:00:00

abstract：:RNase E is a 472-kDa homo-tetrameric essential endoribonuclease involved in RNA processing and turnover in Escherichia coli. In its N-terminal half (NTH) is the catalytic active site, as also a substrate 5'-sensor pocket that renders enzyme activity maximal on 5'-monophosphorylated RNAs. The protein's non-catalytic C-...

journal_title：Nucleic acids research

authors： Ali N,Gowrishankar J

更新日期：2020-01-24 00:00:00

abstract：:TropGeneDB (http://tropgenedb.cirad.fr) was created to store genetic, molecular and phenotypic data on tropical crop species. The most common data stored in TropGeneDB are molecular markers, quantitative trait loci, genetic and physical maps, genetic diversity, phenotypic diversity studies and information on genetic r...

journal_title：Nucleic acids research

authors： Hamelin C,Sempere G,Jouffe V,Ruiz M

更新日期：2013-01-01 00:00:00

abstract：:High-throughput screening assays have been developed to rapidly identify small molecule inhibitors targeting catalytic group I introns. Biochemical reactions catalyzed by a self-splicing group I intron derived from Pneumocystis carinii or from bacteriophage T4 have been investigated. In vitro biochemical assays amenab...

journal_title：Nucleic acids research

authors： Mei HY,Cui M,Sutton ST,Truong HN,Chung FZ,Czarnik AW

更新日期：1996-12-15 00:00:00

abstract：:The temperature-sensitive Neurospora nuclear mutant cyt18-1 is deficient in splicing many Group I mitochondrial introns when grown at its non-permissive temperature; however, splicing of intron 1 in the coI gene of the Adiopodoume (formerly called North Africa) strain is unaffected (R.A. Collins and A.M. Lambowitz, J....

journal_title：Nucleic acids research

authors： Field DJ,Sommerfield A,Saville BJ,Collins RA

更新日期：1989-11-25 00:00:00