Nucleic Acids Research

Editorial

Claire Bird

Editorial
Nucl. Acids Res. 2007 35: 6691; doi:10.1093/nar/gkm1003 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Computational Biology

Get checked abstract Sarath Chandra Janga, Heladia Salgado, Agustino Martínez-Antonio, and Julio Collado-Vides

Coordination logic of the sensing machinery in the transcriptional regulatory network of Escherichia coli
Nucleic Acids Research Advance Access published on October 12, 2007
Nucl. Acids Res. 2007 35: 6963-6972; doi:10.1093/nar/gkm743 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Johanna Weindl, Pavol Hanus, Zaher Dawy, Juergen Zech, Joachim Hagenauer, and Jakob C. Mueller

Modeling DNA-binding of Escherichia coli ⁷⁰ exhibits a characteristic energy landscape around strong promoters
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: 7003-7010; doi:10.1093/nar/gkm720 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics

Get checked abstract 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

CG dinucleotide clustering is a species-specific property of the genome
Nucleic Acids Research Advance Access published on October 10, 2007
Nucl. Acids Res. 2007 35: 6798-6807; doi:10.1093/nar/gkm489 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract Elisabeth Zellner, Thomas Herrmann, Carsten Schulz, and Friedrich Grummt

Site-specific interaction of the murine pre-replicative complex with origin DNA: assembly and disassembly during cell cycle transit and differentiation
Nucleic Acids Research Advance Access published on October 4, 2007
Nucl. Acids Res. 2007 35: 6701-6713; doi:10.1093/nar/gkm555 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Huixian Wang and John B. Hays

Human DNA mismatch repair: coupling of mismatch recognition to strand-specific excision
Nucleic Acids Research Advance Access published on October 4, 2007
Nucl. Acids Res. 2007 35: 6727-6739; doi:10.1093/nar/gkm734 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Zehua Chen, Karen A. Lewis, Ryan K. Shultzaberger, Ilya G. Lyakhov, Ming Zheng, Bernard Doan, Gisela Storz, and Thomas D. Schneider

Discovery of Fur binding site clusters in Escherichia coli by information theory models
Nucleic Acids Research Advance Access published on October 5, 2007
Nucl. Acids Res. 2007 35: 6762-6777; doi:10.1093/nar/gkm631 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Marc Abella, Sonia Rodríguez, Sonia Paytubi, Susana Campoy, Malcolm F. White, and Jordi Barbé

The Sulfolobus solfataricus radA paralogue sso0777 is DNA damage inducible and positively regulated by the Sta1 protein
Nucleic Acids Research Advance Access published on October 5, 2007
Nucl. Acids Res. 2007 35: 6788-6797; doi:10.1093/nar/gkm782 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Laura M. Pollard, Yogesh K. Chutake, Paul M. Rindler, and Sanjay I. Bidichandani

Deficiency of RecA-dependent RecFOR and RecBCD pathways causes increased instability of the (GAA·TTC)_n sequence when GAA is the lagging strand template
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: 6884-6894; doi:10.1093/nar/gkm810 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sushuang Zheng, Stewart Shuman, and Beate Schwer

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
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: 6895-6903; doi:10.1093/nar/gkm817 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Anne Meiller, Sandra Alvarez, Pascal Drané, Christophe Lallemand, Brigitte Blanchard, Micheal Tovey, and Evelyne May

p53-dependent stimulation of redox-related genes in the lymphoid organs of -irradiated mice—identification of Haeme-oxygenase 1 as a direct p53 target gene
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: 6924-6934; doi:10.1093/nar/gkm824 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Andrew J. Wood, Déborah Bourc’his, Timothy H. Bestor, and Rebecca J. Oakey

Allele-specific demethylation at an imprinted mammalian promoter
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: 7031-7039; doi:10.1093/nar/gkm742 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes

Get checked abstract Nobutaka Hirano, Hiroyuki Ohshima, Hidenori Sakashita, and Hideo Takahashi

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
Nucleic Acids Research Advance Access published on October 2, 2007
Nucl. Acids Res. 2007 35: 6692-6700; doi:10.1093/nar/gkm722 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract 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

Idiosyncratic features in tRNAs participating in bacterial cell wall synthesis
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: 6870-6883; doi:10.1093/nar/gkm778 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yuji Masuda, Miki Suzuki, Jinlian Piao, Yongqing Gu, Toshiki Tsurimoto, and Kenji Kamiya

Dynamics of human replication factors in the elongation phase of DNA replication
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: 6904-6916; doi:10.1093/nar/gkm822 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Haihui Lu, Klaus Schwarz, and Michael R. Lieber

Extent to which hairpin opening by the Artemis:DNA-PKcs complex can contribute to junctional diversity in V(D)J recombination
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: 6917-6923; doi:10.1093/nar/gkm823 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Iwona Mruk, Preeti Rajesh, and Robert M. Blumenthal

Regulatory circuit based on autogenous activation-repression: roles of C-boxes and spacer sequences in control of the PvuII restriction-modification system
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: 6935-6952; doi:10.1093/nar/gkm837 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jeremiah W. Hanes and Kenneth A. Johnson

A novel mechanism of selectivity against AZT by the human mitochondrial DNA polymerase
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: 6973-6983; doi:10.1093/nar/gkm695 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sophie Redon, Patrick Reichenbach, and Joachim Lingner

Protein–RNA and protein–protein interactions mediate association of human EST1A/SMG6 with telomerase
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: 7011-7022; doi:10.1093/nar/gkm724 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA

Get checked abstract Andrea Hinas, Johan Reimegård, E. Gerhart H. Wagner, Wolfgang Nellen, Victor R. Ambros, and Fredrik Söderbom

The small RNA repertoire of Dictyostelium discoideum and its regulation by components of the RNAi pathway
Nucleic Acids Research Advance Access published on October 4, 2007
Nucl. Acids Res. 2007 35: 6714-6726; doi:10.1093/nar/gkm707 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Kirk W. Gaston, Mary Anne T. Rubio, Jessica L. Spears, Irena Pastar, F. Nina Papavasiliou, and Juan D. Alfonzo

C to U editing at position 32 of the anticodon loop precedes tRNA 5' leader removal in trypanosomatids
Nucleic Acids Research Advance Access published on October 4, 2007
Nucl. Acids Res. 2007 35: 6740-6749; doi:10.1093/nar/gkm745 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jane M. Liu and David R. Liu

Discovery of a mRNA mitochondrial localization element in Saccharomyces cerevisiae by nonhomologous random recombination and in vivo selection
Nucleic Acids Research Advance Access published on October 4, 2007
Nucl. Acids Res. 2007 35: 6750-6761; doi:10.1093/nar/gkm777 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Valérie Guerniou, Reynald Gillet, Fabienne Berrée, Bertrand Carboni, and Brice Felden

Targeted inhibition of the hepatitis C internal ribosomal entry site genomic RNA with oligonucleotide conjugates
Nucleic Acids Research Advance Access published on October 5, 2007
Nucl. Acids Res. 2007 35: 6778-6787; doi:10.1093/nar/gkm770 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sarah G. Ozanick, Janusz M. Bujnicki, Daniel S. Sem, and James T. Anderson

Conserved amino acids in each subunit of the heteroligomeric tRNA m¹A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding
Nucleic Acids Research Advance Access published on October 10, 2007
Nucl. Acids Res. 2007 35: 6808-6819; doi:10.1093/nar/gkm574 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Atef Nehdi, Jonathan Perreault, Jean-Denis Beaudoin, and Jean-Pierre Perreault

A novel structural rearrangement of hepatitis delta virus antigenomic ribozyme
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: 6820-6831; doi:10.1093/nar/gkm674 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Pascal A. Küpfer, Caroline Crey-Desbiolles, and Christian J. Leumann

Trans-lesion synthesis and RNaseH activity by reverse transcriptases on a true abasic RNA template
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: 6846-6853; doi:10.1093/nar/gkm767 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Melissa A. Brykailo, Laura M. McLane, Judith Fridovich-Keil, and Anita H. Corbett

Analysis of a predicted nuclear localization signal: implications for the intracellular localization and function of the Saccharomyces cerevisiae RNA-binding protein Scp160
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: 6862-6869; doi:10.1093/nar/gkm776 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Flore Winter, Sonia Edaye, Alexander Hüttenhofer, and Christine Brunel

Anopheles gambiae miRNAs as actors of defence reaction against Plasmodium invasion
Nucleic Acids Research Advance Access published on October 12, 2007
Nucl. Acids Res. 2007 35: 6953-6962; doi:10.1093/nar/gkm686 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Zhuoyun Zhuang, Luc Jaeger, and Joan-Emma Shea

Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: 6995-7002; doi:10.1093/nar/gkm719 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Marina Cristodero and Christine E. Clayton

Trypanosome MTR4 is involved in rRNA processing
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: 7023-7030; doi:10.1093/nar/gkm736 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Monique Marilley, Pascale Milani, Jean Thimonier, José Rocca-Serra, and Giuseppe Baldacci

Atomic force microscopy of DNA in solution and DNA modelling show that structural properties specify the eukaryotic replication initiation site
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: 6832-6845; doi:10.1093/nar/gkm733 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Katja Petzold, Elke Duchardt, Sara Flodell, Göran Larsson, Karin Kidd-Ljunggren, Sybren Wijmenga, and Jürgen Schleucher

Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: 6854-6861; doi:10.1093/nar/gkm774 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Kuang-Lei Tsai, Yuh-Ju Sun, Cheng-Yang Huang, Jer-Yen Yang, Mien-Chie Hung, and Chwan-Deng Hsiao

Crystal structure of the human FOXO3a-DBD/DNA complex suggests the effects of post-translational modification
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: 6984-6994; doi:10.1093/nar/gkm703 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Corrigendum

Natalia Demeshkina, Go Hirokawa, Akira Kaji, and Hideko Kaji

Novel activity of eukaryotic translocase, eEF2: dissociation of the 80S ribosome into subunits with ATP but not with GTP
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: 7040; doi:10.1093/nar/gkm716 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Erratum

Mark Helm

Post-transcriptional nucleotide modification and alternative folding of RNA
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: 7041; doi:10.1093/nar/gkm819 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online

Get checked abstract Hiroyuki Kurata, Kentaro Inoue, Kazuhiro Maeda, Koichi Masaki, Yuki Shimokawa, and Quanyu Zhao

Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: e134; doi:10.1093/nar/gkm769 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Martin Pilhofer, Andreas Peter Bauer, Martina Schrallhammer, Lothar Richter, Wolfgang Ludwig, Karl-Heinz Schleifer, and Giulio Petroni

Characterization of bacterial operons consisting of two tubulins and a kinesin-like gene by the novel Two-Step Gene Walking method
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: e135; doi:10.1093/nar/gkm836 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Shizuka Hartenbach, Marie Daoud-El Baba, Wilfried Weber, and Martin Fussenegger

An engineered L-arginine sensor of Chlamydia pneumoniae enables arginine-adjustable transcription control in mammalian cells and mice
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2007 35: e136; doi:10.1093/nar/gkm652 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Martin Thanbichler, Antonio A. Iniesta, and Lucy Shapiro

A comprehensive set of plasmids for vanillate- and xylose-inducible gene expression in Caulobacter crescentus
Nucleic Acids Research Advance Access published on October 24, 2007
Nucl. Acids Res. 2007 35: e137; doi:10.1093/nar/gkm818 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Shawn E. Lupold, Tarana A. Kudrolli, Wasim H. Chowdhury, Ping Wu, and Ronald Rodriguez

A novel method for generating and screening peptides and libraries displayed on adenovirus fiber
Nucleic Acids Research Advance Access published on October 26, 2007
Nucl. Acids Res. 2007 35: e138; doi:10.1093/nar/gkm914 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

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