Nucleic Acids Research

Editorial:

Editorial
Nucl. Acids Res. 2002 30: 0; doi:10.1093/nar/editorial [Print PDF] [Request Permissions]  

Articles:

Chrystelle Maric, Emma Swanston, Juliet Bailey, and Gérard Pierron

Replicational organization of three weakly expressed loci in Physarum polycephalum
Nucl. Acids Res. 2002 30: 2261-2269; doi:10.1093/nar/30.11.2261 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yuji Higaki, Daniel Schullery, Yasunobu Kawata, Maria Shnyreva, Christine Abrass, and Karol Bomsztyk

Synergistic activation of the rat laminin 1 chain promoter by the gut-enriched Kruppel-like factor (GKLF/KLF4) and Sp1
Nucl. Acids Res. 2002 30: 2270-2279; doi:10.1093/nar/30.11.2270 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Silvia Ayora, Frank Weise, Pablo Mesa, Andrzej Stasiak, and Juan C. Alonso

Bacillus subtilis bacteriophage SPP1 hexameric DNA helicase, G40P, interacts with forked DNA
Nucl. Acids Res. 2002 30: 2280-2289; doi:10.1093/nar/30.11.2280 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Robert Sijbrandi, Ulrike Fiedler, and H. Th. Marc Timmers

RNA polymerase II complexes in the very early phase of transcription are not susceptible to TFIIS-induced exonucleolytic cleavage
Nucl. Acids Res. 2002 30: 2290-2298; doi:10.1093/nar/30.11.2290 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Susanne Andreas, Frieder Schwenk, Birgit Küter-Luks, Nicole Faust, and Ralf Kühn

Enhanced efficiency through nuclear localization signal fusion on phage C31-integrase: activity comparison with Cre and FLPe recombinase in mammalian cells
Nucl. Acids Res. 2002 30: 2299-2306; doi:10.1093/nar/30.11.2299 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jinsong Ren, Xiaogang Qu, John O. Trent, and Jonathan B. Chaires

Tiny telomere DNA
Nucl. Acids Res. 2002 30: 2307-2315; doi:10.1093/nar/30.11.2307 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jérôme Salse, Benoit Piégu, Richard Cooke, and Michel Delseny

Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project
Nucl. Acids Res. 2002 30: 2316-2328; doi:10.1093/nar/30.11.2316 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Peng Liu, Amy Gucwa, Mary Louise Stover, Emily Buck, Alexander Lichtler, and David Rowe

Analysis of inhibitory action of modified U1 snRNAs on target gene expression: discrimination of two RNA targets differing by a 1 bp mismatch
Nucl. Acids Res. 2002 30: 2329-2339; doi:10.1093/nar/30.11.2329 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jiri Buzek, Leena Latonen, Sari Kurki, Karita Peltonen, and Marikki Laiho

Redox state of tumor suppressor p53 regulates its sequence-specific DNA binding in DNA-damaged cells by cysteine 277
Nucl. Acids Res. 2002 30: 2340-2348; doi:10.1093/nar/30.11.2340 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Françoise Dantzer, Luisa Luna, Magnar Bjørås, and Erling Seeberg

Human OGG1 undergoes serine phosphorylation and associates with the nuclear matrix and mitotic chromatin in vivo
Nucl. Acids Res. 2002 30: 2349-2357; doi:10.1093/nar/30.11.2349 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ana Traven, Lidija Staresincic, Milica Arneric, and Mary Sopta

The yeast protein Xtc1 functions as a direct transcriptional repressor
Nucl. Acids Res. 2002 30: 2358-2364; doi:10.1093/nar/30.11.2358 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Willy Barbot, Anne Dupressoir, Vladimir Lazar, and Thierry Heidmann

Epigenetic regulation of an IAP retrotransposon in the aging mouse: progressive demethylation and de-silencing of the element by its repetitive induction
Nucl. Acids Res. 2002 30: 2365-2373; doi:10.1093/nar/30.11.2365 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jing-Min Zhou, De-Min Zhou, Yasuomi Takagi, Yasuhiro Kasai, Atsushi Inoue, Tadashi Baba, and Kazunari Taira

Existence of efficient divalent metal ion-catalyzed and inefficient divalent metal ion-independent channels in reactions catalyzed by a hammerhead ribozyme
Nucl. Acids Res. 2002 30: 2374-2382; doi:10.1093/nar/30.11.2374 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yasuhiro Kasai, Hideki Shizuku, Yasuomi Takagi, Masaki Warashina, and Kazunari Taira

Measurements of weak interactions between truncated substrates and a hammerhead ribozyme by competitive kinetic analyses: implications for the design of new and efficient ribozymes with high sequence specificity
Nucl. Acids Res. 2002 30: 2383-2389; doi:10.1093/nar/30.11.2383 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Suparna Chandra Sanyal, Saumen Pal, Saheli Chaudhuri, and Chanchal DasGupta

23S rRNA assisted folding of cytoplasmic malate dehydrogenase is distinctly different from its self-folding
Nucl. Acids Res. 2002 30: 2390-2397; doi:10.1093/nar/30.11.2390 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yoshinori Hashimoto, Chun Zhang, Junya Kawauchi, Issei Imoto, Mimi T. Adachi, Johji Inazawa, Teruo Amagasa, Tsonwin Hai, and Shigetaka Kitajima

An alternatively spliced isoform of transcriptional repressor ATF3 and its induction by stress stimuli
Nucl. Acids Res. 2002 30: 2398-2406; doi:10.1093/nar/30.11.2398 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Gregory L. Moore and Costas D. Maranas

eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments
Nucl. Acids Res. 2002 30: 2407-2416; doi:10.1093/nar/30.11.2407 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Hong Liu and Edward M. Johnson

Distinct proteins encoded by alternative transcripts of the PURG gene, located contrapodal to WRN on chromosome 8, determined by differential termination/polyadenylation
Nucl. Acids Res. 2002 30: 2417-2426; doi:10.1093/nar/30.11.2417 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Deepa Subramanian and Jack D. Griffith

Interactions between p53, hMSH2–hMSH6 and HMG I(Y) on Holliday junctions and bulged bases
Nucl. Acids Res. 2002 30: 2427-2434; doi:10.1093/nar/30.11.2427 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Rita Crinelli, Marzia Bianchi, Lucia Gentilini, and Mauro Magnani

Design and characterization of decoy oligonucleotides containing locked nucleic acids
Nucl. Acids Res. 2002 30: 2435-2443; doi:10.1093/nar/30.11.2435 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tohru Takata, Rahul Aras, Donald Tavakoli, Takafumi Ando, Asalia Z. Olivares, and Martin J. Blaser

Phenotypic and genotypic variation in methylases involved in type II restriction-modification systems in Helicobacter pylori
Nucl. Acids Res. 2002 30: 2444-2452; doi:10.1093/nar/30.11.2444 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Anastasia N. Nikolskaya and Michael Y. Galperin

A novel type of conserved DNA-binding domain in the transcriptional regulators of the AlgR/AgrA/LytR family
Nucl. Acids Res. 2002 30: 2453-2459; doi:10.1093/nar/30.11.2453 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Yaron S. N. Butterfield, Marco A. Marra, Jennifer K. Asano, Susanna Y. Chan, Ranabir Guin, Martin I. Krzywinski, Soo Sen Lee, Kim W. K. MacDonald, Carrie A. Mathewson, Teika E. Olson, Pawan K. Pandoh, Anna-Liisa Prabhu, Angelique Schnerch, Ursula Skalska, Duane E. Smailus, Jeff M. Stott, Miranda I. Tsai, George S. Yang, Scott D. Zuyderduyn, Jacqueline E. Schein, and Steven J. M. Jones

An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones
Nucl. Acids Res. 2002 30: 2460-2468; doi:10.1093/nar/30.11.2460 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yuriy Shevchenko, Gerard G. Bouffard, Yaron S. N. Butterfield, Robert W. Blakesley, James L. Hartley, Alice C. Young, Marco A. Marra, Steven J. M. Jones, Jeffrey W. Touchman, and Eric D. Green

Systematic sequencing of cDNA clones using the transposon Tn5
Nucl. Acids Res. 2002 30: 2469-2477; doi:10.1093/nar/30.11.2469 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Arthur L. Delcher, Adam Phillippy, Jane Carlton, and Steven L. Salzberg

Fast algorithms for large-scale genome alignment and comparison
Nucl. Acids Res. 2002 30: 2478-2483; doi:10.1093/nar/30.11.2478 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Qiliang Li, Miaohua Zhang, Hemei Han, Alex Rohde, and George Stamatoyannopoulos

Evidence that DNase I hypersensitive site 5 of the human ß-globin locus control region functions as a chromosomal insulator in transgenic mice
Nucl. Acids Res. 2002 30: 2484-2491; doi:10.1093/nar/30.11.2484 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Esther E. A. Verhoeven, Marian van Kesteren, John J. Turner, Gijs A. van der Marel, Jacques H. van Boom, Geri F. Moolenaar, and Nora Goosen

The C-terminal region of Escherichia coli UvrC contributes to the flexibility of the UvrABC nucleotide excision repair system
Nucl. Acids Res. 2002 30: 2492-2500; doi:10.1093/nar/30.11.2492 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Huai-chun Wang and Donal A. Hickey

Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes
Nucl. Acids Res. 2002 30: 2501-2507; doi:10.1093/nar/30.11.2501 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Arndt Benecke, Claudine Gaudon, Jean-Marie Garnier, Elmar vom Baur, Pierre Chambon, and Régine Losson

ADA3-containing complexes associate with estrogen receptor alpha
Nucl. Acids Res. 2002 30: 2508-2514; doi:10.1093/nar/30.11.2508 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nathaniel Echols, Paul Harrison, Suganthi Balasubramanian, Nicholas M. Luscombe, Paul Bertone, Zhaolei Zhang, and Mark Gerstein

Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes
Nucl. Acids Res. 2002 30: 2515-2523; doi:10.1093/nar/30.11.2515 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jeffrey D. Wuitschick, Jill A. Gershan, Andrew J. Lochowicz, Shuqiang Li, and Kathleen M. Karrer

A novel family of mobile genetic elements is limited to the germline genome in Tetrahymena thermophila
Nucl. Acids Res. 2002 30: 2524-2537; doi:10.1093/nar/30.11.2524 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Keith D. Tardif and Jack Horowitz

Transfer RNA determinants for translational editing by Escherichia coli valyl-tRNA synthetase
Nucl. Acids Res. 2002 30: 2538-2545; doi:10.1093/nar/30.11.2538 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mitch Raponi and Greg M. Arndt

Dominant genetic screen for cofactors that enhance antisense RNA-mediated gene silencing in fission yeast
Nucl. Acids Res. 2002 30: 2546-2554; doi:10.1093/nar/30.11.2546 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Toshinori Suzuki, Mitsuharu Masuda, Marlin D. Friesen, Bernard Fenet, and Hiroshi Ohshima

Novel products generated from 2'-deoxyguanosine by hypochlorous acid or a myeloperoxidase–H₂O₂–Cl^– system: identification of diimino-imidazole and amino-imidazolone nucleosides
Nucl. Acids Res. 2002 30: 2555-2564; doi:10.1093/nar/30.11.2555 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Delisha A. Stewart, Xiaohou Xu, Shelia D. Thomas, and Donald M. Miller

Acridine-modified, clamp-forming antisense oligonucleotides synergize with cisplatin to inhibit c-Myc expression and B16-F0 tumor progression
Nucl. Acids Res. 2002 30: 2565-2574; doi:10.1093/nar/30.11.2565 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Gustavo Caetano-Anollés

Tracing the evolution of RNA structure in ribosomes
Nucl. Acids Res. 2002 30: 2575-2587; doi:10.1093/nar/30.11.2575 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Vesna Rapic-Otrin, Mary P. McLenigan, Dawn C. Bisi, Martin Gonzalez, and Arthur S. Levine

Sequential binding of UV DNA damage binding factor and degradation of the p48 subunit as early events after UV irradiation
Nucl. Acids Res. 2002 30: 2588-2598; doi:10.1093/nar/30.11.2588 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kui Lin, Yuyu Kuang, Jeremiah S. Joseph, and Prasanna R. Kolatkar

Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics
Nucl. Acids Res. 2002 30: 2599-2607; doi:10.1093/nar/30.11.2599 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

NAR Methods Online:

Cécile Esnault, Jean-François Casella, and Thierry Heidmann

A Tetrahymena thermophila ribozyme-based indicator gene to detect transposition of marked retroelements in mammalian cells
Nucl. Acids Res. 2002 30: e49; doi:10.1093/nar/30.11.e49 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Torsten C. Kroll and Stefan Wölfl

Ranking: a closer look on globalisation methods for normalisation of gene expression arrays
Nucl. Acids Res. 2002 30: e50; doi:10.1093/nar/30.11.e50 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Angela Relógio, Christian Schwager, Alexandra Richter, Wilhelm Ansorge, and Juan Valcárcel

Optimization of oligonucleotide-based DNA microarrays
Nucl. Acids Res. 2002 30: e51; doi:10.1093/nar/30.11.e51 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

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