Raman spectral studies of nucleic acids. XVII. Conformational structures of polyinosinic acid.

abstract：:The topoisomerase I (TOP1) inhibitor irinotecan triggers cell death by trapping TOP1 on DNA, generating cytotoxic protein-linked DNA breaks (PDBs). Despite its wide application in a variety of solid tumors, the mechanisms of cancer cell resistance to irinotecan remains poorly understood. Here, we generated colorectal ...

journal_title：Nucleic acids research

authors： Meisenberg C,Ashour ME,El-Shafie L,Liao C,Hodgson A,Pilborough A,Khurram SA,Downs JA,Ward SE,El-Khamisy SF

更新日期：2017-02-17 00:00:00

abstract：:The identification of genes with specific patterns of change (e.g. down-regulated and methylated) as phenotype drivers or samples with similar profiles for a given gene set as drivers of clinical outcome, requires the integration of several genomic data types for which an 'integrate by intersection' (IBI) approach is ...

journal_title：Nucleic acids research

authors： Kowalski J,Dwivedi B,Newman S,Switchenko JM,Pauly R,Gutman DA,Arora J,Gandhi K,Ainslie K,Doho G,Qin Z,Moreno CS,Rossi MR,Vertino PM,Lonial S,Bernal-Mizrachi L,Boise LH

更新日期：2016-04-20 00:00:00

abstract：:Heteroduplexes between the viral DNA of phiX174 and DNA from the replicative form (RF) of phage G4 were examined by electron microscopy. The single Eco RI site of G4-RF was utilized as a physical marker by preparing the heteroduplexes from the denatured, linear DNA obtained by restricting G4-RF with Eco RI endonucleas...

journal_title：Nucleic acids research

authors： Smiley BL,Warner RC

更新日期：1979-01-01 00:00:00

abstract：:G-quadruplexes (G4s) are non-canonical nucleic acids secondary structures that form within guanine-rich strands of regulatory genomic regions. G4s have been extensively described in the human genome, especially in telomeres and oncogene promoters; in recent years the presence of G4s in viruses has attracted increasing...

journal_title：Nucleic acids research

authors： Ruggiero E,Richter SN

更新日期：2018-04-20 00:00:00

abstract：:A novel program suite was implemented for the functional interpretation of high-throughput gene expression data based on the identification of Gene Ontology (GO) nodes. The focus of the analysis lies on the interpretation of microarray data from prokaryotes. The three well established statistical methods of the thresh...

journal_title：Nucleic acids research

authors： Scheer M,Klawonn F,Münch R,Grote A,Hiller K,Choi C,Koch I,Schobert M,Härtig E,Klages U,Jahn D

更新日期：2006-07-01 00:00:00

abstract：:Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology a...

journal_title：Nucleic acids research

authors： Kelder T,van Iersel MP,Hanspers K,Kutmon M,Conklin BR,Evelo CT,Pico AR

更新日期：2012-01-01 00:00:00

abstract：:Through a computer search of DNA databases, we have identified the homologs of the mgU6-47 snoRNA gene from the yeast Schizosaccharomyces pombe, the fly Drosophila melanogaster and human. The three box C/D-containing snoRNA genes showed no significant similarity in their sequences except for an 11 nt long complementar...

journal_title：Nucleic acids research

authors： Zhou H,Chen YQ,Du YP,Qu LH

更新日期：2002-02-15 00:00:00

abstract：:Exposure of Schizosaccharomyces pombe cells to UV light results in increased uvi15(+) gene expression at both the mRNA and protein levels, leading to elevated cell survival. This UV-induced expression of the uvi15(+) gene was reduced in Deltasty1 and Deltawis1 cells lacking the stress-activated protein kinase pathway,...

journal_title：Nucleic acids research

authors： Kim M,Lee W,Park J,Kim JB,Jang YK,Seong RH,Choe SY,Park SD

更新日期：2000-09-01 00:00:00

abstract：:Helicase-nuclease systems dedicated to DNA end resection in preparation for homologous recombination (HR) are present in all kingdoms of life. In thermophilic archaea, the HerA helicase and NurA nuclease cooperate with the highly conserved Mre11 and Rad50 proteins during HR-dependent DNA repair. Here we show that HerA...

journal_title：Nucleic acids research

authors： Blackwood JK,Rzechorzek NJ,Abrams AS,Maman JD,Pellegrini L,Robinson NP

更新日期：2012-04-01 00:00:00

abstract：:Nucleosomes, a basic structural unit of eukaryotic chromatin, play a significant role in regulating gene expression. We have developed a web tool based on DNA sequences known from empirical and theoretical studies to influence DNA bending and flexibility, and to exclude nucleosomes. NXSensor (available at http://www.s...

journal_title：Nucleic acids research

authors： Luykx P,Bajić IV,Khuri S

更新日期：2006-07-01 00:00:00

abstract：:DNA cytosine-5 methyltransferases (C5-MTases) are valuable models to study sequence-specific modification of DNA and are becoming increasingly important tools for biotechnology. Here we describe a structure-guided rational protein design combined with random mutagenesis and selection to change the specificity of the H...

journal_title：Nucleic acids research

authors： Gerasimaite R,Vilkaitis G,Klimasauskas S

更新日期：2009-11-01 00:00:00

abstract：:Antigenic variation of the pilus is an essential component of Neisseria gonorrhoeae pathogenesis. Unidirectional recombination of silent pilin DNA into an expressed pilin gene allows for substantial sequence variation of this highly immunogenic surface structure. While the RecA protein is required for pilin gene recom...

journal_title：Nucleic acids research

authors： Wainwright LA,Frangipane JV,Seifert HS

更新日期：1997-04-01 00:00:00

abstract：:In synthetic circuits, CRISPR-Cas systems have been used effectively for endpoint changes from an initial state to a final state, such as in logic gates. Here, we use deactivated Cas9 (dCas9) and deactivated Cas12a (dCas12a) to construct dynamic RNA ring oscillators that cycle continuously between states over time in ...

journal_title：Nucleic acids research

authors： Kuo J,Yuan R,Sánchez C,Paulsson J,Silver PA

更新日期：2020-08-20 00:00:00

abstract：:The FALC-Loop web server provides an online interface for protein loop modeling by employing an ab initio loop modeling method called FALC (fragment assembly and analytical loop closure). The server may be used to construct loop regions in homology modeling, to refine unreliable loop regions in experimental structures...

journal_title：Nucleic acids research

authors： Ko J,Lee D,Park H,Coutsias EA,Lee J,Seok C

更新日期：2011-07-01 00:00:00

abstract：:Single-stranded guanosine-rich oligodeoxyribonucleotides (GROs) have a propensity to form quadruplex structures that are stabilized by G-quartets. In addition to intense speculation about the role of G-quartet formation in vivo, there is considerable interest in the therapeutic potential of quadruplex oligonucleotides...

journal_title：Nucleic acids research

authors： Dapić V,Abdomerović V,Marrington R,Peberdy J,Rodger A,Trent JO,Bates PJ

更新日期：2003-04-15 00:00:00

abstract：:Upon endocytosis, most oligodeoxynucleotides (ODNs) accumulate in vesicular compartments; a tiny number of them cross the vesicle membrane, reach the cytosol and by passive diffusion enter the nucleus where they are entrapped. So far, the compartment in which an antisense ODN interacts with its mRNA target has not bee...

journal_title：Nucleic acids research

authors： Meunier L,Mayer R,Monsigny M,Roche AC

更新日期：1999-07-01 00:00:00

abstract：:ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Information About a Microarray Experiment) requirements and stores well-annotated raw and normalized data. As of November 2004, ArrayExpress contains data from approximately 12,000 hybridizations covering 35 species. Data can be s...

journal_title：Nucleic acids research

authors： Parkinson H,Sarkans U,Shojatalab M,Abeygunawardena N,Contrino S,Coulson R,Farne A,Lara GG,Holloway E,Kapushesky M,Lilja P,Mukherjee G,Oezcimen A,Rayner T,Rocca-Serra P,Sharma A,Sansone S,Brazma A

更新日期：2005-01-01 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：:The human Werner syndrome protein, WRN, is a member of the RecQ helicase family and contains 3'-->5' helicase and 3'-->5' exonuclease activities. Recently, we showed that the exonuclease activity of WRN is greatly stimulated by the human Ku heterodimer protein. We have now mapped this interaction physically and functi...

journal_title：Nucleic acids research

authors： Karmakar P,Snowden CM,Ramsden DA,Bohr VA

更新日期：2002-08-15 00:00:00

abstract：:To explain the activation of transcription by a remote enhancer, two models are most often considered, namely looping and scanning. A scanning model, also referred to as 'polymerase entry site' model predicts that for two adjacent promoters the one proximal to an enhancer would be preferentially activated. Preferentia...

journal_title：Nucleic acids research

authors： Heuchel R,Matthias P,Schaffner W

更新日期：1989-11-25 00:00:00

abstract：:In the filamentous cyanobacterium Anabaena sp. PCC 7120, the ferric uptake regulator FurA functions as a global transcriptional regulator. Despite several analyses have focused on elucidating the FurA-regulatory network, the number of target genes described for this essential transcription factor is limited to a handf...

journal_title：Nucleic acids research

authors： González A,Angarica VE,Sancho J,Fillat MF

更新日期：2014-04-01 00:00:00

abstract：:Use of antisense oligonucleotides is a versatile strategy for achieving control of gene expression. Unfortunately, the interpretation of antisense-induced phenotypes is sometimes difficult, and chemical modifications that improve the potency and specificity of antisense action would be useful. The introduction of lock...

journal_title：Nucleic acids research

authors： Braasch DA,Liu Y,Corey DR

更新日期：2002-12-01 00:00:00

abstract：:DXZ4 is an X-linked macrosatellite composed of 12-100 tandemly arranged 3-kb repeat units. In females, it adopts opposite chromatin arrangements at the two alleles in response to X-chromosome inactivation. In males and on the active X chromosome, it is packaged into heterochromatin, but on the inactive X chromosome (X...

journal_title：Nucleic acids research

authors： Moseley SC,Rizkallah R,Tremblay DC,Anderson BR,Hurt MM,Chadwick BP

更新日期：2012-02-01 00:00:00

abstract：:Naturally occurring RNAs are known to exhibit a high degree of modularity, whereby specific structural modules (or motifs) can be mixed and matched to create new molecular architectures. The modular nature of RNA also affords researchers the ability to characterize individual structural elements in controlled syntheti...

journal_title：Nucleic acids research

authors： Mitchell C,Polanco JA,DeWald L,Kress D,Jaeger L,Grabow WW

更新日期：2019-07-09 00:00:00

abstract：:Using cyanoethyldiisopropylamino phosphoramidite chemistry, four oligonucleotides constituting a part of the sequence of the initiator t-RNA from B. subtilis were synthesized. For the protection of the exocyclic amino functions of bases, phenoxyacetyl group was used for adenine and guanine, and acetyl group was prefer...

journal_title：Nucleic acids research

authors： Chaix C,Duplaa AM,Molko D,Téoule R

更新日期：1989-09-25 00:00:00

abstract：:The multifunctional HCV core protein consists of a hydrophilic RNA interacting D1 domain and a hydrophobic D2 domain interacting with membranes and lipid droplets. The core D1 domain was found to possess nucleic acid annealing and strand transfer properties. To further understand these chaperone properties, we investi...

journal_title：Nucleic acids research

authors： Sharma Kk,Didier P,Darlix JL,de Rocquigny H,Bensikaddour H,Lavergne JP,Pénin F,Lessinger JM,Mély Y

更新日期：2010-06-01 00:00:00

abstract：:A simple method, primer specific and mispair extension analysis (PSMEA) with pfu DNA polymerase was developed for genotyping. PSMEA is based on the unique properties of 3'-->5' exonuclease proofreading activity. In the presence of an incomplete set of dNTPs, pfu was found to be extremely discriminative in nucleotide i...

journal_title：Nucleic acids research

authors： Hu YW,Balaskas E,Kessler G,Issid C,Scully LJ,Murphy DG,Rinfret A,Giulivi A,Scalia V,Gill P

更新日期：1998-11-01 00:00:00

abstract：:The yeast retrotransposon Ty encodes proteins that assemble into virus-like particles (Ty-VLPs) which can be readily purified. We have recently shown that expression of the pl protein encoded by the TYA gene of Ty is sufficient for particle formation. In this paper we show that when a heterologous coding sequence, hum...

journal_title：Nucleic acids research

authors： Malim MH,Adams SE,Gull K,Kingsman AJ,Kingsman SM

更新日期：1987-09-25 00:00:00

abstract：:The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provide...

journal_title：Nucleic acids research

authors： Markowitz VM,Chen IM,Palaniappan K,Chu K,Szeto E,Grechkin Y,Ratner A,Jacob B,Huang J,Williams P,Huntemann M,Anderson I,Mavromatis K,Ivanova NN,Kyrpides NC

更新日期：2012-01-01 00:00:00

abstract：:We have partially purified replicating simian virus 40 (SV40) chromosomes in a form which allows continued DNA synthesis in vitro. We first prepare a soluble DNA-synthesizing system from SV40-infected monkey cells and then sediment the components through a neutral sucrose gradient of extremely low ionic strength. Repl...

journal_title：Nucleic acids research

authors： Edenberg HJ,Waqar MA,Huberman JA

更新日期：1977-09-01 00:00:00