| | Articles Replicational organization of three weakly expressed loci in Physarum polycephalum Chrystelle Maric, Emma Swanston, Juliet Bailey, and Gérard Pierron PMCID: PMC117180 Synergistic activation of the rat laminin γ1 chain promoter by the gut-enriched Kruppel-like factor (GKLF/KLF4) and Sp1 Yuji Higaki, Daniel Schullery, Yasunobu Kawata, Maria Shnyreva, Christine Abrass, and Karol Bomsztyk PMCID: PMC117209 Bacillus subtilis bacteriophage SPP1 hexameric DNA helicase, G40P, interacts with forked DNA Silvia Ayora, Frank Weise, Pablo Mesa, Andrzej Stasiak, and Juan C. Alonso PMCID: PMC117191 RNA polymerase II complexes in the very early phase of transcription are not susceptible to TFIIS-induced exonucleolytic cleavage Robert Sijbrandi, Ulrike Fiedler, and H. Th. Marc Timmers PMCID: PMC117193 Enhanced efficiency through nuclear localization signal fusion on phage ![[var phi]](corehtml/pmc/pmcents/x03C6.gif) C31-integrase: activity comparison with Cre and FLPe recombinase in mammalian cells Susanne Andreas, Frieder Schwenk, Birgit Küter-Luks, Nicole Faust, and Ralf Kühn PMCID: PMC117205 Tiny telomere DNA Jinsong Ren, Xiaogang Qu, John O. Trent, and Jonathan B. Chaires PMCID: PMC117210 Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project Jérôme Salse, Benoit Piégu, Richard Cooke, and Michel Delseny PMCID: PMC117207 Analysis of inhibitory action of modified U1 snRNAs on target gene expression: discrimination of two RNA targets differing by a 1 bp mismatch Peng Liu, Amy Gucwa, Mary Louise Stover, Emily Buck, Alexander Lichtler, and David Rowe PMCID: PMC117199 Redox state of tumor suppressor p53 regulates its sequence-specific DNA binding in DNA-damaged cells by cysteine 277 Jiri Buzek, Leena Latonen, Sari Kurki, Karita Peltonen, and Marikki Laiho PMCID: PMC117181 Human OGG1 undergoes serine phosphorylation and associates with the nuclear matrix and mitotic chromatin in vivo Françoise Dantzer, Luisa Luna, Magnar Bjørås, and Erling Seeberg PMCID: PMC117190 The yeast protein Xtc1 functions as a direct transcriptional repressor Ana Traven, Lidija Starešinčić, Milica Arnerić, and Mary Sopta PMCID: PMC117208 Epigenetic regulation of an IAP retrotransposon in the aging mouse: progressive demethylation and de-silencing of the element by its repetitive induction Willy Barbot, Anne Dupressoir, Vladimir Lazar, and Thierry Heidmann PMCID: PMC117196 Existence of efficient divalent metal ion-catalyzed and inefficient divalent metal ion-independent channels in reactions catalyzed by a hammerhead ribozyme Jing-Min Zhou, De-Min Zhou, Yasuomi Takagi, Yasuhiro Kasai, Atsushi Inoue, Tadashi Baba, and Kazunari Taira PMCID: PMC117202 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 Yasuhiro Kasai, Hideki Shizuku, Yasuomi Takagi, Masaki Warashina, and Kazunari Taira PMCID: PMC117203 23S rRNA assisted folding of cytoplasmic malate dehydrogenase is distinctly different from its self-folding Suparna Chandra Sanyal, Saumen Pal, Saheli Chaudhuri, and Chanchal DasGupta PMCID: PMC117201 An alternatively spliced isoform of transcriptional repressor ATF3 and its induction by stress stimuli Yoshinori Hashimoto, Chun Zhang, Junya Kawauchi, Issei Imoto, Mimi T. Adachi, Johji Inazawa, Teruo Amagasa, Tsonwin Hai, and Shigetaka Kitajima PMCID: PMC117192 eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments Gregory L. Moore and Costas D. Maranas PMCID: PMC117206 Distinct proteins encoded by alternative transcripts of the PURG gene, located contrapodal to WRN on chromosome 8, determined by differential termination/polyadenylation Hong Liu and Edward M. Johnson PMCID: PMC117198 Interactions between p53, hMSH2–hMSH6 and HMG I(Y) on Holliday junctions and bulged bases Deepa Subramanian and Jack D. Griffith PMCID: PMC117204 Design and characterization of decoy oligonucleotides containing locked nucleic acids Rita Crinelli, Marzia Bianchi, Lucia Gentilini, and Mauro Magnani PMCID: PMC117200 Phenotypic and genotypic variation in methylases involved in type II restriction-modification systems in Helicobacter pylori Tohru Takata, Rahul Aras, Donald Tavakoli, Takafumi Ando, Asalia Z. Olivares, and Martin J. Blaser PMCID: PMC117188 A novel type of conserved DNA-binding domain in the transcriptional regulators of the AlgR/AgrA/LytR family Anastasia N. Nikolskaya and Michael Y. Galperin PMCID: PMC117183 An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones 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 PMCID: PMC117194 Systematic sequencing of cDNA clones using the transposon Tn5 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 PMCID: PMC117195 Fast algorithms for large-scale genome alignment and comparison Arthur L. Delcher, Adam Phillippy, Jane Carlton, and Steven L. Salzberg PMCID: PMC117189 Evidence that DNase I hypersensitive site 5 of the human β-globin locus control region functions as a chromosomal insulator in transgenic mice Qiliang Li, Miaohua Zhang, Hemei Han, Alex Rohde, and George Stamatoyannopoulos PMCID: PMC117184 The C-terminal region of Escherichia coli UvrC contributes to the flexibility of the UvrABC nucleotide excision repair system 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 PMCID: PMC117173 Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes Huai-chun Wang and Donal A. Hickey PMCID: PMC117185 ADA3-containing complexes associate with estrogen receptor alpha Arndt Benecke, Claudine Gaudon, Jean-Marie Garnier, Elmar vom Baur, Pierre Chambon, and Régine Losson PMCID: PMC117179 Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes Nathaniel Echols, Paul Harrison, Suganthi Balasubramanian, Nicholas M. Luscombe, Paul Bertone, Zhaolei Zhang, and Mark Gerstein PMCID: PMC117176 A novel family of mobile genetic elements is limited to the germline genome in Tetrahymena thermophila Jeffrey D. Wuitschick, Jill A. Gershan, Andrew J. Lochowicz, Shuqiang Li, and Kathleen M. Karrer PMCID: PMC117186 Transfer RNA determinants for translational editing by Escherichia coli valyl-tRNA synthetase Keith D. Tardif and Jack Horowitz PMCID: PMC117182 Dominant genetic screen for cofactors that enhance antisense RNA-mediated gene silencing in fission yeast Mitch Raponi and Greg M. Arndt PMCID: PMC117174 Novel products generated from 2′-deoxyguanosine by hypochlorous acid or a myeloperoxidase–H2O2–Cl– system: identification of diimino-imidazole and amino-imidazolone nucleosides Toshinori Suzuki, Mitsuharu Masuda, Marlin D. Friesen, Bernard Fenet, and Hiroshi Ohshima PMCID: PMC117197 Acridine-modified, clamp-forming antisense oligonucleotides synergize with cisplatin to inhibit c-Myc expression and B16-F0 tumor progression Delisha A. Stewart, Xiaohou Xu, Shelia D. Thomas, and Donald M. Miller PMCID: PMC117175 Tracing the evolution of RNA structure in ribosomes Gustavo Caetano-Anollés PMCID: PMC117177 Sequential binding of UV DNA damage binding factor and degradation of the p48 subunit as early events after UV irradiation Vesna RapiM-Otrin, Mary P. McLenigan, Dawn C. Bisi, Martin Gonzalez, and Arthur S. Levine PMCID: PMC117178 Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics Kui Lin, Yuyu Kuang, Jeremiah S. Joseph, and Prasanna R. Kolatkar PMCID: PMC117187 NAR Methods Online A Tetrahymena thermophila ribozyme-based indicator gene to detect transposition of marked retroelements in mammalian cells Cécile Esnault, Jean-François Casella, and Thierry Heidmann PMCID: PMC117211 Ranking: a closer look on globalisation methods for normalisation of gene expression arrays Torsten C. Kroll and Stefan Wölfl PMCID: PMC117212 Optimization of oligonucleotide-based DNA microarrays Angela Relógio, Christian Schwager, Alexandra Richter, Wilhelm Ansorge, and Juan Valcárcel PMCID: PMC117213 |
