| | Editorial Nucleic Acids Res. 2007 November; 35(20): 6691. Published online 2007 November. doi: 10.1093/nar/gkm1003.PMCID: PMC2175330 Molecular Biology Site-specific interaction of the murine pre-replicative complex with origin DNA: assembly and disassembly during cell cycle transit and differentiation Elisabeth Zellner, Thomas Herrmann, Carsten Schulz, and Friedrich Grummt PMCID: PMC2175324 Human DNA mismatch repair: coupling of mismatch recognition to strand-specific excision Huixian Wang and John B. Hays PMCID: PMC2175295 Discovery of Fur binding site clusters in Escherichia coli by information theory models Zehua Chen, Karen A. Lewis, Ryan K. Shultzaberger, Ilya G. Lyakhov, Ming Zheng, Bernard Doan, Gisela Storz, and Thomas D. Schneider PMCID: PMC2189734 The Sulfolobus solfataricus radA paralogue sso0777 is DNA damage inducible and positively regulated by the Sta1 protein Marc Abella, Sonia Rodríguez, Sonia Paytubi, Susana Campoy, Malcolm F. White, and Jordi Barbé PMCID: PMC2175319 Deficiency of RecA-dependent RecFOR and RecBCD pathways causes increased instability of the (GAA·TTC)n sequence when GAA is the lagging strand template Laura M. Pollard, Yogesh K. Chutake, Paul M. Rindler, and Sanjay I. Bidichandani PMCID: PMC2175318 Sinefungin resistance of Saccharomyces cerevisiae arising from sam3 mutations that inactivate the AdoMet transporter or from increased expression of AdoMet synthase plus mRNA cap guanine-N7 methyltransferase Sushuang Zheng, Stewart Shuman, and Beate Schwer PMCID: PMC2175321 p53-dependent stimulation of redox-related genes in the lymphoid organs of γ-irradiated mice—identification of Haeme-oxygenase 1 as a direct p53 target gene Anne Meiller, Sandra Alvarez, Pascal Drané, Christophe Lallemand, Brigitte Blanchard, Micheal Tovey, and Evelyne May PMCID: PMC2175302 Allele-specific demethylation at an imprinted mammalian promoter Andrew J. Wood, Déborah Bourc’his, Timothy H. Bestor, and Rebecca J. Oakey PMCID: PMC2175309 RNA The small RNA repertoire of Dictyostelium discoideum and its regulation by components of the RNAi pathway Andrea Hinas, Johan Reimegård, E. Gerhart H. Wagner, Wolfgang Nellen, Victor R. Ambros, and Fredrik Söderbom PMCID: PMC2175303 C to U editing at position 32 of the anticodon loop precedes tRNA 5′ leader removal in trypanosomatids Kirk W. Gaston, Mary Anne T. Rubio, Jessica L. Spears, Irena Pastar, F. Nina Papavasiliou, and Juan D. Alfonzo PMCID: PMC2175311 Discovery of a mRNA mitochondrial localization element in Saccharomyces cerevisiae by nonhomologous random recombination and in vivo selection Jane M. Liu and David R. Liu PMCID: PMC2175308 Targeted inhibition of the hepatitis C internal ribosomal entry site genomic RNA with oligonucleotide conjugates Valérie Guerniou, Reynald Gillet, Fabienne Berrée, Bertrand Carboni, and Brice Felden PMCID: PMC2175329 Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding Sarah G. Ozanick, Janusz M. Bujnicki, Daniel S. Sem, and James T. Anderson PMCID: PMC2175304 A novel structural rearrangement of hepatitis delta virus antigenomic ribozyme Atef Nehdi, Jonathan Perreault, Jean-Denis Beaudoin, and Jean-Pierre Perreault PMCID: PMC2175327 Trans-lesion synthesis and RNaseH activity by reverse transcriptases on a true abasic RNA template Pascal A. Küpfer, Caroline Crey-Desbiolles, and Christian J. Leumann PMCID: PMC2175328 Analysis of a predicted nuclear localization signal: implications for the intracellular localization and function of the Saccharomyces cerevisiae RNA-binding protein Scp160 Melissa A. Brykailo, Laura M. McLane, Judith Fridovich-Keil, and Anita H. Corbett PMCID: PMC2175298 Anopheles gambiae miRNAs as actors of defence reaction against Plasmodium invasion Flore Winter, Sonia Edaye, Alexander Hüttenhofer, and Christine Brunel PMCID: PMC2175301 Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin Zhuoyun Zhuang, Luc Jaeger, and Joan-Emma Shea PMCID: PMC2175325 Trypanosome MTR4 is involved in rRNA processing Marina Cristodero and Christine E. Clayton PMCID: PMC2175323 Structural Biology Atomic force microscopy of DNA in solution and DNA modelling show that structural properties specify the eukaryotic replication initiation site Monique Marilley, Pascale Milani, Jean Thimonier, José Rocca-Serra, and Giuseppe Baldacci PMCID: PMC2175326 Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns Katja Petzold, Elke Duchardt, Sara Flodell, Göran Larsson, Karin Kidd-Ljunggren, Sybren Wijmenga, and Jürgen Schleucher PMCID: PMC2175316 Crystal structure of the human FOXO3a-DBD/DNA complex suggests the effects of post-translational modification Kuang-Lei Tsai, Yuh-Ju Sun, Cheng-Yang Huang, Jer-Yen Yang, Mien-Chie Hung, and Chwan-Deng Hsiao PMCID: PMC2175300 Genomics CG dinucleotide clustering is a species-specific property of the genome Jacob L. Glass, Reid F. Thompson, Batbayar Khulan, Maria E. Figueroa, Emmanuel N. Olivier, Erin J. Oakley, Gary Van Zant, Eric E. Bouhassira, Ari Melnick, Aaron Golden, Melissa J. Fazzari, and John M. Greally PMCID: PMC2175314 Methods Online Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis Hiroyuki Kurata, Kentaro Inoue, Kazuhiro Maeda, Koichi Masaki, Yuki Shimokawa, and Quanyu Zhao PMCID: PMC2175333 Characterization of bacterial operons consisting of two tubulins and a kinesin-like gene by the novel Two-Step Gene Walking method Martin Pilhofer, Andreas Peter Bauer, Martina Schrallhammer, Lothar Richter, Wolfgang Ludwig, Karl-Heinz Schleifer, and Giulio Petroni PMCID: PMC2175320 An engineered l-arginine sensor of Chlamydia pneumoniae enables arginine-adjustable transcription control in mammalian cells and mice Shizuka Hartenbach, Marie Daoud-El Baba, Wilfried Weber, and Martin Fussenegger PMCID: PMC2175317 A comprehensive set of plasmids for vanillate- and xylose-inducible gene expression in Caulobacter crescentus Martin Thanbichler, Antonio A. Iniesta, and Lucy Shapiro PMCID: PMC2175322 A novel method for generating and screening peptides and libraries displayed on adenovirus fiber Shawn E. Lupold, Tarana A. Kudrolli, Wasim H. Chowdhury, Ping Wu, and Ronald Rodriguez PMCID: PMC2175307 Computational Biology Coordination logic of the sensing machinery in the transcriptional regulatory network of Escherichia coli Sarath Chandra Janga, Heladia Salgado, Agustino Martínez-Antonio, and Julio Collado-Vides PMCID: PMC2175315 Modeling DNA-binding of Escherichia coli σ70 exhibits a characteristic energy landscape around strong promoters Johanna Weindl, Pavol Hanus, Zaher Dawy, Juergen Zech, Joachim Hagenauer, and Jakob C. Mueller PMCID: PMC2175306 Nucleic Acid Enzymes The Ser176 of T4 endonuclease IV is crucial for the restricted and polarized dC-specific cleavage of single-stranded DNA implicated in restriction of dC-containing DNA in host Escherichia coli Nobutaka Hirano, Hiroyuki Ohshima, Hidenori Sakashita, and Hideo Takahashi PMCID: PMC2175332 Idiosyncratic features in tRNAs participating in bacterial cell wall synthesis Régis Villet, Matthieu Fonvielle, Patricia Busca, Maryline Chemama, Antoine P. Maillard, Jean-Emmanuel Hugonnet, Lionel Dubost, Arul Marie, Nathalie Josseaume, Stéphane Mesnage, Claudine Mayer, Jean-Marc Valéry, Mélanie Ethève-Quelquejeu, and Michel Arthur PMCID: PMC2175331 Dynamics of human replication factors in the elongation phase of DNA replication Yuji Masuda, Miki Suzuki, Jinlian Piao, Yongqing Gu, Toshiki Tsurimoto, and Kenji Kamiya PMCID: PMC2175312 Extent to which hairpin opening by the Artemis:DNA-PKcs complex can contribute to junctional diversity in V(D)J recombination Haihui Lu, Klaus Schwarz, and Michael R. Lieber PMCID: PMC2175297 Regulatory circuit based on autogenous activation-repression: roles of C-boxes and spacer sequences in control of the PvuII restriction-modification system Iwona Mruk, Preeti Rajesh, and Robert M. Blumenthal PMCID: PMC2175313 A novel mechanism of selectivity against AZT by the human mitochondrial DNA polymerase Jeremiah W. Hanes and Kenneth A. Johnson PMCID: PMC2175305 Protein–RNA and protein–protein interactions mediate association of human EST1A/SMG6 with telomerase Sophie Redon, Patrick Reichenbach, and Joachim Lingner PMCID: PMC2175296 Corrigendum Novel activity of eukaryotic translocase, eEF2: dissociation of the 80S ribosome into subunits with ATP but not with GTP Natalia Demeshkina, Go Hirokawa, Akira Kaji, and Hideko Kaji PMCID: PMC2175299 Corrects: Natalia Demeshkina, et al. Novel activity of eukaryotic translocase, eEF2: dissociation of the 80S ribosome into subunits with ATP but not with GTP. Nucleic Acids Res. 2007 July; 35(14): 4597–4607. Erratum Post-transcriptional nucleotide modification and alternative folding of RNA Mark Helm PMCID: PMC2175310 Corrects: Mark Helm. Post-transcriptional nucleotide modification and alternative folding of RNA. Nucleic Acids Res. 2006; 34(2): 721–733. |
