Rapid and efficient construction of markerless deletions in the Escherichia coli genome.

abstract：:Tubercidin may be directly brominated by reaction with N-bromosuccinimide in DMF to give 5-bromotubercidin, a reversible inhibitor of RNA synthesis. When buffered with potassium acetate the major product is 6-bromotubercidin. 5,6-Dibromotubercidin is formed in minor amounts under both conditions. N-Chlorosuccinimide a...

journal_title：Nucleic acids research

authors： Bergstrom DE,Brattesani AJ

更新日期：1980-12-20 00:00:00

abstract：:We devised an indicator gene for retrotransposition based on an autocatalytic ribozyme element--the Tetrahymena thermophila 23S rRNA group I intron--which can self-splice in vitro and does not require--at variance with nuclear mRNA introns--any specific pathway and cellular component for the completion of the splicing...

journal_title：Nucleic acids research

authors： Esnault C,Casella JF,Heidmann T

更新日期：2002-06-01 00:00:00

abstract：:Triethylammonium uridine-3',5'-cyclic phosphorothioate crystallizes in space group P2(1)2(1)2(1), a = 7.177(1), b = 13.155(6), c = 21.114(7) A, C15H26N3O7PS, MW 423.4, Z = 4, dx = 1.41g/cm3. The crystal structure was solved by direct methods on the basis of 1493 counter X-ray diffraction data (CuK alpha) and refined t...

journal_title：Nucleic acids research

authors： Hinrichs W,Steifa M,Saenger W,Eckstein F

更新日期：1987-06-25 00:00:00

abstract：:Since 1992, FlyBase (flybase.org) has been an essential online resource for the Drosophila research community. Concentrating on the most extensively studied species, Drosophila melanogaster, FlyBase includes information on genes (molecular and genetic), transgenic constructs, phenotypes, genetic and physical interacti...

journal_title：Nucleic acids research

authors： Gramates LS,Marygold SJ,Santos GD,Urbano JM,Antonazzo G,Matthews BB,Rey AJ,Tabone CJ,Crosby MA,Emmert DB,Falls K,Goodman JL,Hu Y,Ponting L,Schroeder AJ,Strelets VB,Thurmond J,Zhou P,the FlyBase Consortium.

更新日期：2017-01-04 00:00:00

abstract：:Release of phosphorothioate antisense oligonucleotides (PS-ASOs) from late endosomes (LEs) is a rate-limiting step and a poorly defined process for productive intracellular ASO drug delivery. Here, we examined the role of Golgi-endosome transport, specifically M6PR shuttling mediated by GCC2, in PS-ASO trafficking and...

journal_title：Nucleic acids research

authors： Liang XH,Sun H,Hsu CW,Nichols JG,Vickers TA,De Hoyos CL,Crooke ST

更新日期：2020-02-20 00:00:00

abstract：:Using an in vitro transcription system for Saccharomyces cerevisiae RNA polymerase I, we have analyzed Pol I promoter deletion mutants and mapped the boundaries of the promoter between positions -155 and +27. The 5'-boundary of the minimal core promoter capable of transcription initiation, however, was found to lie be...

journal_title：Nucleic acids research

authors： Kulkens T,Riggs DL,Heck JD,Planta RJ,Nomura M

更新日期：1991-10-11 00:00:00

abstract：:Recent studies employing genome-wide approaches have provided an unprecedented view of the scope of L1 activities on structural variations in the human genome, and further reinforced the role of L1s as one of the major driving forces behind human genome evolution. The rapid identification of novel L1 elements by these...

journal_title：Nucleic acids research

authors： Xie Y,Rosser JM,Thompson TL,Boeke JD,An W

更新日期：2011-02-01 00:00:00

abstract：:Approaches to characterize the nucleic acid-binding properties of drugs and druglike small molecules are crucial to understanding the behavior of these compounds in cellular systems. Here, we use a Small Molecule Microarray (SMM) profiling approach to identify the preferential interaction between chlorhexidine, a wide...

journal_title：Nucleic acids research

authors： Calabrese DR,Zlotkowski K,Alden S,Hewitt WM,Connelly CM,Wilson RM,Gaikwad S,Chen L,Guha R,Thomas CJ,Mock BA,Schneekloth JS Jr

更新日期：2018-04-06 00:00:00

abstract：:DNA polymerase beta (polbeta), a member of the X family of DNA polymerases, is the major polymerase in the base excision repair pathway. Using in vitro selection, we obtained RNA aptamers for polbeta from a variable pool of 8 x 10(12) individual RNA sequences containing 30 random nucleotides. A total of 60 individual ...

journal_title：Nucleic acids research

authors： Gening LV,Klincheva SA,Reshetnjak A,Grollman AP,Miller H

更新日期：2006-05-17 00:00:00

abstract：:Transcription start and termination sites were mapped in the E. coli replication origin, oriC. Outward transcription from within oriC (promoters Pori-r and Pori-l) was found to start in vivo at position 178 for Pori-l and at positions 294 and 304 for Pori-r, respectively. These transcripts were terminated after 100-15...

journal_title：Nucleic acids research

authors： Schauzu MA,Kücherer C,Kölling R,Messer W,Lother H

更新日期：1987-03-25 00:00:00

abstract：:Mammalian mitochondrial ribosomes evolved from bacterial ribosomes by reduction of ribosomal RNAs, increase of ribosomal protein content, and loss of guanine nucleotides. Guanine is the base most sensitive to oxidative damage. By systematically comparing high-quality, small ribosomal subunit RNA sequence alignments an...

journal_title：Nucleic acids research

authors： Hosseini M,Roy P,Sissler M,Zirbel CL,Westhof E,Leontis N

更新日期：2018-11-16 00:00:00

abstract：:Bisulfite genomic sequencing is the most widely used technique to analyze the 5-methylation of cytosines, the prevalent covalent DNA modification in mammals. The process is based on the selective transformation of unmethylated cytosines to uridines. Then, the investigated genomic regions are PCR amplified, subcloned a...

journal_title：Nucleic acids research

authors： Tusnády GE,Simon I,Váradi A,Arányi T

更新日期：2005-01-13 00:00:00

abstract：:From gene expression to nanotechnology, understanding and controlling DNA requires a detailed knowledge of its higher order structure and dynamics. Here we take advantage of the environment-sensitive photoisomerization of cyanine dyes to probe local and global changes in DNA structure. We report that a covalently atta...

journal_title：Nucleic acids research

authors： Morten MJ,Lopez SG,Steinmark IE,Rafferty A,Magennis SW

更新日期：2018-11-30 00:00:00

abstract：:We have used heteroduplex analysis to investigate the sequences surrounding the germline C gamma 1 and C gamma 3 genes, and to compare them with those surrounding the C mu gene. We detected an inverted pseudogene 5' to the C gamma 3 gene and 50-65% homologous to it. A 400 bp region of the C gamma 1 and C gamma 3 3' fl...

journal_title：Nucleic acids research

authors： Tyler BM,Adams JM

更新日期：1980-12-11 00:00:00

abstract：:The mRNA encoding repressor cI of phage lambda is the only known E. coli message which starts directly with the initiation AUG codon. The ability of in vitro synthesized cI mRNA fragments (150 or 400 nts) to form ternary initiation complexes has been studied using the toeprint method. In the presence of tRNA(Met)f, th...

journal_title：Nucleic acids research

authors： Balakin AG,Skripkin EA,Shatsky IN,Bogdanov AA

更新日期：1992-02-11 00:00:00

abstract：:The EMBL Data Library was the first internationally supported central resource for nucleic acid sequence data. Working in close collaboration with its American counterpart, GenBank (1), the library prepares and makes available to the scientific community a comprehensive collection of the published nucleic acid sequenc...

journal_title：Nucleic acids research

authors： Hamm GH,Cameron GN

更新日期：1986-01-10 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：:Recognition of genomic binding sites by transcription factors can occur through base-specific recognition, or by recognition of variations within the structure of the DNA macromolecule. In this article, we investigate what information can be retrieved from local DNA structural properties that is relevant to transcript...

journal_title：Nucleic acids research

authors： Meysman P,Dang TH,Laukens K,De Smet R,Wu Y,Marchal K,Engelen K

更新日期：2011-01-01 00:00:00

abstract：:In previous studies, we reported that fractionation of HeLa cell nuclear extracts on glycerol gradients revealed an endogenous ∼10S particle that contained galectin-3 and U1 snRNP and this particle was sufficient to load the galectin polypeptide onto a pre-mRNA substrate. We now document that this interaction between ...

journal_title：Nucleic acids research

authors： Haudek KC,Voss PG,Wang JL,Patterson RJ

更新日期：2016-07-27 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：:NONO, SFPQ and PSPC1 make up a family of proteins with diverse roles in transcription, RNA processing and DNA double-strand break (DSB) repair. To understand long-term effects of loss of NONO, we characterized murine embryonic fibroblasts (MEFs) from knockout mice. In the absence of genotoxic stress, wild-type and mut...

journal_title：Nucleic acids research

authors： Li S,Li Z,Shu FJ,Xiong H,Phillips AC,Dynan WS

更新日期：2014-09-01 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：:Unfolding of the nucleosomes in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3 and permits the selective recovery of the unfolded nucleosomes by mercury-affinity chromatography. This new technique has been used to compare the nucleosomal proteins and their postsynthetic modifications i...

journal_title：Nucleic acids research

authors： Sterner R,Boffa LC,Chen TA,Allfrey VG

更新日期：1987-06-11 00:00:00

abstract：:G-quadruplexes (G4s) are stable secondary structures that can lead to the stalling of replication forks and cause genomic instability. Pif1 is a 5' to 3' helicase, localized to both the mitochondria and nucleus that can unwind G4s in vitro and prevent fork stalling at G4 forming sequences in vivo. Using in vitro prime...

journal_title：Nucleic acids research

authors： Sparks MA,Singh SP,Burgers PM,Galletto R

更新日期：2019-09-19 00:00:00

abstract：:Upon HIV-1 infection of a target cell, the viral reverse transcriptase (RT) copies the genomic RNA to synthesize the viral DNA. The genomic RNA is within the incoming HIV-1 core where it is coated by molecules of nucleocapsid (NC) protein that chaperones the reverse transcription process. Indeed, the RT chaperoning pr...

journal_title：Nucleic acids research

authors： Grigorov B,Bocquin A,Gabus C,Avilov S,Mély Y,Agopian A,Divita G,Gottikh M,Witvrouw M,Darlix JL

更新日期：2011-07-01 00:00:00

abstract：:We recently reported that the antitumor triazoloacridone, compound C-1305, is a topoisomerase II poison with unusual properties. In this study we characterize the DNA interactions of C-1305 in vitro, in comparison with other topoisomerase II inhibitors. Our results show that C-1305 binds to DNA by intercalation and po...

journal_title：Nucleic acids research

authors： Lemke K,Wojciechowski M,Laine W,Bailly C,Colson P,Baginski M,Larsen AK,Skladanowski A

更新日期：2005-10-27 00:00:00

abstract：:A total of 10 B-lymphocyte-specific DNase I hypersensitive sites located in the chicken Ig-beta locus were divided into four regions and combinations of deletions of these regions were carried out. A decrease in transcription of the Ig-beta gene to <3% was demonstrated in cells with deletions in all four regions. The ...

journal_title：Nucleic acids research

authors： Shimada N,Matsudo H,Osano K,Arakawa H,Buerstedde JM,Matsumoto Y,Chayahara K,Torihata A,Ono M

更新日期：2006-08-11 00:00:00

abstract：:MicroArray Gene expression and Network Evaluation Toolkit (MAGNET) is a web-based application that provides tools to generate and score both protein-protein interaction networks and coexpression networks. MAGNET integrates user-provided experimental measurements with high-throughput proteomic datasets, generating weig...

journal_title：Nucleic acids research

authors： Linderman GC,Chance MR,Bebek G

更新日期：2012-07-01 00:00:00

abstract：:A type II restriction endonuclease, named CviJI, was isolated from a eukaryotic Chlorella-like green alga infected with the dsDNA containing virus IL-3A. CviJI is the first restriction endonuclease to recognize the sequence PuGCPy; CviJI cleaves DNA between the G and C. Methylation of the cytosine in PuGCPy sequences ...

journal_title：Nucleic acids research

authors： Xia YN,Burbank DE,Uher L,Rabussay D,Van Etten JL

更新日期：1987-08-11 00:00:00

abstract：:The chemical synthesis of backbone deuterium labelled [r(CGCGAAU*U*CGCG)]2 (U* = [5'-2H]U) is described. An efficient purification procedure was developed using a polymeric reverse phase (PRP) HPLC column at 60 degrees C. This procedure provided pure RNA dodecamer in the multi-milligram quantities (39% overall yield) ...

journal_title：Nucleic acids research

authors： Khare D,Orban J

更新日期：1992-10-11 00:00:00