| | Molecular Biology Role of Elg1 protein in double strand break repair Hideaki Ogiwara, Ayako Ui, Takemi Enomoto, and Masayuki Seki PMCID: PMC1802592 Improved nuclear localization of DNA-binding polyamides Nicholas G. Nickols, Claire S. Jacobs, Michelle E. Farkas, and Peter B. Dervan PMCID: PMC1802595 SECIS elements in the coding regions of selenoprotein transcripts are functional in higher eukaryotes Heiko Mix, Alexey V. Lobanov, and Vadim N. Gladyshev PMCID: PMC1802603 Chloroplast phosphoglycerate kinase, a gluconeogenetic enzyme, is required for efficient accumulation of Bamboo mosaic virus Jen-Wen Lin, Min-Pey Ding, Yau-Heiu Hsu, and Ching-Hsiu Tsai PMCID: PMC1802604 Ascorbate acts as a highly potent inducer of chromate mutagenesis and clastogenesis: linkage to DNA breaks in G2 phase by mismatch repair Mindy Reynolds, Lauren Stoddard, Ivan Bespalov, and Anatoly Zhitkovich PMCID: PMC1802609 Glucocorticoid-induced leucine zipper (GILZ)/NF-κB interaction: role of GILZ homo-dimerization and C-terminal domain Barbara Di Marco, Michela Massetti, Stefano Bruscoli, Antonio Macchiarulo, Rosa Di Virgilio, Enrico Velardi, Valerio Donato, Graziella Migliorati, and Carlo Riccardi PMCID: PMC1802615 Two primate-specific small non-protein-coding RNAs in transgenic mice: neuronal expression, subcellular localization and binding partners Tasneem Khanam, Timofey S. Rozhdestvensky, Marsha Bundman, Chenna R. Galiveti, Sergej Handel, Valentina Sukonina, Ursula Jordan, Jürgen Brosius, and Boris V. Skryabin PMCID: PMC1802616 Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes Michal Krawczyk, Elisa Leimgruber, Queralt Seguín-Estévez, Isabelle Dunand-Sauthier, Emmanuèle Barras, and Walter Reith PMCID: PMC1802633 Analysis of the DNA-binding sequence specificity of the archaeal transcriptional regulator Ss-LrpB from Sulfolobus solfataricus by systematic mutagenesis and high resolution contact probing Eveline Peeters, Carine Wartel, Dominique Maes, and Daniel Charlier PMCID: PMC1802622 A novel E4BP4 element drives circadian expression of mPeriod2 Tomoya Ohno, Yoshiaki Onishi, and Norio Ishida PMCID: PMC1802629 The bidirectional promoter of two genes for the mitochondrial translational apparatus in mouse is regulated by an array of CCAAT boxes interacting with the transcription factor NF-Y Ernesto Zanotto, Zahid H. Shah, and Howard T. Jacobs PMCID: PMC1802594 RNA Cold shock domain proteins and glycine-rich RNA-binding proteins from Arabidopsis thaliana can promote the cold adaptation process in Escherichia coli Jin Sun Kim, Su Jung Park, Kyung Jin Kwak, Yeon Ok Kim, Joo Yeol Kim, Jinkyung Song, Boseung Jang, Che-Hun Jung, and Hunseung Kang PMCID: PMC1802614 Incorporation of 5-fluorouracil into U2 snRNA blocks pseudouridylation and pre-mRNA splicing in vivo Xinliang Zhao and Yi-Tao Yu PMCID: PMC1802618 Interplay of ‘induced fit’ and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch Jonas Noeske, Janina Buck, Boris Fürtig, Hamid R. Nasiri, Harald Schwalbe, and Jens Wöhnert PMCID: PMC1802621 Reduced splicing efficiency induced by synonymous substitutions may generate a substrate for natural selection of new splicing isoforms: the case of CFTR exon 12 Michela Raponi, Francisco E. Baralle, and Franco Pagani PMCID: PMC1802620 Encoding folding paths of RNA switches A. Xayaphoummine, V. Viasnoff, S. Harlepp, and H. Isambert PMCID: PMC1802593 Structural Biology Modulating role of RNA structure in alternative splicing of a critical exon in the spinal muscular atrophy genes Natalia N. Singh, Ravindra N. Singh, and Elliot J. Androphy PMCID: PMC1802598 L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy Hendrik R. A. Jonker, Serge Ilin, S. Kaspar Grimm, Jens Wöhnert, and Harald Schwalbe PMCID: PMC1802607 Selenium derivatization of nucleic acids for crystallography Jiansheng Jiang, Jia Sheng, Nicolas Carrasco, and Zhen Huang PMCID: PMC1802610 Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides Shu-ichi Nakano, Toshimasa Kirihata, Satoshi Fujii, Hiroshi Sakai, Masayasu Kuwahara, Hiroaki Sawai, and Naoki Sugimoto PMCID: PMC1802612 Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases Yi-Ting Wang, Wei-Jen Yang, Chia-Lung Li, Lyudmila G. Doudeva, and Hanna S. Yuan PMCID: PMC1802626 Genomics G-quadruplexes in promoters throughout the human genome Julian L. Huppert and Shankar Balasubramanian PMCID: PMC1802602 GISMO—gene identification using a support vector machine for ORF classification Lutz Krause, Alice C. McHardy, Tim W. Nattkemper, Alfred Pühler, Jens Stoye, and Folker Meyer PMCID: PMC1802617 Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs Yuping Luo and Siguang Li PMCID: PMC1802619 Chemistry Efficient signaling platforms built from a small catalytic DNA and doubly labeled fluorogenic substrates William Chiuman and Yingfu Li PMCID: PMC1802601 Antisense oligonucleotides containing locked nucleic acid improve potency but cause significant hepatotoxicity in animals Eric E. Swayze, Andrew M. Siwkowski, Edward V. Wancewicz, Michael T. Migawa, Tadeusz K. Wyrzykiewicz, Gene Hung, Brett P. Monia, and and C. Frank Bennett PMCID: PMC1802611 Methods Online Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool Haiyuan Yu, Katherine Nguyen, Tom Royce, Jiang Qian, Kenneth Nelson, Michael Snyder, and Mark Gerstein PMCID: PMC1802630 Human RAD18 is involved in S phase-specific single-strand break repair without PCNA monoubiquitination Naoko Shiomi, Masahiko Mori, Hideo Tsuji, Takashi Imai, Hirokazu Inoue, Satoshi Tateishi, Masaru Yamaizumi, and Tadahiro Shiomi PMCID: PMC1802632 Development of a species-specific RNA polymerase I-based shRNA expression vector M. S. Brenz Verca, Peter Weber, Christine Mayer, Cornelia Graf, Damián Refojo, Ralf Kühn, Ingrid Grummt, and Beat Lutz PMCID: PMC1802596 A semi-automated high-throughput approach to the generation of transposon insertion mutants in the nematode Caenorhabditis elegans Yohann Duverger, Jérôme Belougne, Sarah Scaglione, Dominique Brandli, Christophe Beclin, and Jonathan J. Ewbank PMCID: PMC1903375 A pHMM-ANN based discriminative approach to promoter identification in prokaryote genomic contexts Scott Mann, Jinyan Li, and Yi-Ping Phoebe Chen PMCID: PMC1802591 Increasing the sensitivity of DNA microarrays by metal-enhanced fluorescence using surface-bound silver nanoparticles Chandran R. Sabanayagam and Joseph R. Lakowicz PMCID: PMC1802600 Computational Biology More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature Istvan Ladunga PMCID: PMC1802606 High sensitivity RNA pseudoknot prediction Xiaolu Huang and Hesham Ali PMCID: PMC1802631 Dynamic use of multiple parameter sets in sequence alignment Xiaoqiu Huang and Douglas L. Brutlag PMCID: PMC1802605 Nucleic Acid Enzymes Association of Dnmt3a and thymine DNA glycosylase links DNA methylation with base-excision repair Ya-Qiang Li, Ping-Zhu Zhou, Xiu-Dan Zheng, Colum P. Walsh, and Guo-Liang Xu PMCID: PMC1802599 Nucleus-encoded plastid sigma factor SIG3 transcribes specifically the psbN gene in plastids Wafa Zghidi, Livia Merendino, Annick Cottet, Régis Mache, and Silva Lerbs-Mache PMCID: PMC1802608 Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins Veronika Németh-Pongrácz, Orsolya Barabás, Mónika Fuxreiter, István Simon, Iva Pichová, Michalea Rumlová, Helena Zábranská, Dmitri Svergun, Maxim Petoukhov, Veronika Harmat, Éva Klement, Éva Hunyadi-Gulyás, Katalin F. Medzihradszky, Emese Kónya, and Beáta G. Vértessy PMCID: PMC1802613 Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases Cécile Zaros, Jean-François Briand, Yves Boulard, Sylvie Labarre-Mariotte, M. Carmen Garcia-Lopez, Pierre Thuriaux, and Francisco Navarro PMCID: PMC1802627 Corrigenda Nucleic Acids Res. 2007 January; 35(2): 703. doi: 10.1093/nar/gkl1132.PMCID: PMC1802624 Corrects: Sarah Blair, et al. A scalable method for multiplex LED-controlled synthesis of DNA in capillaries. Nucleic Acids Res. 2006 September; 34(16): e110. Nucleic Acids Res. 2007 January; 35(2): 703. doi: 10.1093/nar/gkl760.PMCID: PMC1802628 Corrects: J P Kreivi, et al. A U1 snRNA binding site improves the efficiency of in vitro pre-mRNA splicing. Nucleic Acids Res. 1991 December 25; 19(24): 6956. Errata Structural diversity of target-specific homopyrimidine peptide nucleic acid–dsDNA complexes Thomas Bentin, Georg I. Hansen, and Peter E. Nielsen PMCID: PMC1802625 Corrects: Thomas Bentin, et al. Structural diversity of target-specific homopyrimidine peptide nucleic acid–dsDNA complexes. Nucleic Acids Res. 2006 November; 34(20): 5790–5799. Nucleic Acids Res. 2007 January; 35(2): 704. doi: 10.1093/nar/gkm048.PMCID: PMC1802634 Corrects: . Retraction Non-random, individual-specific methylation profiles are present at the sixth CTCF binding site in the human H19/IGF2 imprinting control region. PMCID: PMC1802623 Retracts: Jörg Tost, et al. Non-random, individual-specific methylation profiles are present at the sixth CTCF binding site in the human H19/IGF2 imprinting control region. Nucleic Acids Res. 2006 November; 34(19): 5438–5448. |
