Nucleic Acids Research

Articles:

George A. Follows, Hiromi Tagoh, Pascal Lefevre, Gareth J. Morgan, and Constanze Bonifer

Differential transcription factor occupancy but evolutionarily conserved chromatin features at the human and mouse M-CSF (CSF-1) receptor loci
Nucl. Acids Res. 2003 31: 5805-5816; doi:10.1093/nar/gkg804 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kirsten M. L. Hertoghs, Jonathan H. Ellis, and Ian R. Catchpole

Use of locked nucleic acid oligonucleotides to add functionality to plasmid DNA
Nucl. Acids Res. 2003 31: 5817-5830; doi:10.1093/nar/gkg801 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Odeniel Sertil, Rachna Kapoor, Brian D. Cohen, Natalia Abramova, and Charles V. Lowry

Synergistic repression of anaerobic genes by Mot3 and Rox1 in Saccharomyces cerevisiae
Nucl. Acids Res. 2003 31: 5831-5837; doi:10.1093/nar/gkg792 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Bryce A. Mendelsohn, Ai-min Li, Claudia A. Vargas, Kristen Riehman, Alice Watson, and Judith L. Fridovich-Keil

Genetic and biochemical interactions between SCP160 and EAP1 in yeast
Nucl. Acids Res. 2003 31: 5838-5847; doi:10.1093/nar/gkg810 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Shuyi Li, Yoshihiko Takeda, Stéphanie Wragg, John Barrett, Andrew Phillips, and William S. Dynan

Modification of the ionizing radiation response in living cells by an scFv against the DNA-dependent protein kinase
Nucl. Acids Res. 2003 31: 5848-5857; doi:10.1093/nar/gkg775 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jakob T. Nielsen, Paul C. Stein, and Michael Petersen

NMR structure of an -L-LNA:RNA hybrid: structural implications for RNase H recognition
Nucl. Acids Res. 2003 31: 5858-5867; doi:10.1093/nar/gkg800 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Sven Sewitz, Paul Crellin, and Ronald Chalmers

The positive and negative regulation of Tn10 transposition by IHF is mediated by structurally asymmetric transposon arms
Nucl. Acids Res. 2003 31: 5868-5876; doi:10.1093/nar/gkg797 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Shuba Gopal, George A. M. Cross, and Terry Gaasterland

An organism-specific method to rank predicted coding regions in Trypanosoma brucei
Nucl. Acids Res. 2003 31: 5877-5885; doi:10.1093/nar/gkg798 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Chantal Guimond, Nathalie Trudel, Christian Brochu, Nathalie Marquis, Amal El Fadili, Régis Peytavi, Guylaine Briand, Dave Richard, Nadine Messier, Barbara Papadopoulou, Jacques Corbeil, Michel G. Bergeron, Danielle Légaré, and Marc Ouellette

Modulation of gene expression in Leishmania drug resistant mutants as determined by targeted DNA microarrays
Nucl. Acids Res. 2003 31: 5886-5896; doi:10.1093/nar/gkg806 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Zhaohui Feng, Wenwei Hu, Lawrence A. Chasin, and Moon-shong Tang

Effects of genomic context and chromatin structure on transcription-coupled and global genomic repair in mammalian cells
Nucl. Acids Res. 2003 31: 5897-5906; doi:10.1093/nar/gkg808 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hirokazu Handa

The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana
Nucl. Acids Res. 2003 31: 5907-5916; doi:10.1093/nar/gkg795 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Günter Ziegelin, Timo Niedenzu, Rudi Lurz, Wolfram Saenger, and Erich Lanka

Hexameric RSF1010 helicase RepA: the structural and functional importance of single amino acid residues
Nucl. Acids Res. 2003 31: 5917-5929; doi:10.1093/nar/gkg790 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

C. Maufrais, G. V. Fazakerley, J. Cadet, and Y. Boulard

Structural study of DNA duplex containing an N-(2-deoxy-ß-D-erythro-pentofuranosyl) formamide frameshift by NMR and restrained molecular dynamics
Nucl. Acids Res. 2003 31: 5930-5940; doi:10.1093/nar/gkg803 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Orit Cohen-Barak, Zanhua Yi, Nobuko Hagiwara, Koshiro Monzen, Issei Komuro, and Murray H. Brilliant

Sox6 regulation of cardiac myocyte development
Nucl. Acids Res. 2003 31: 5941-5948; doi:10.1093/nar/gkg807 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Zemfira N. Karamysheva, Andrey L. Karamyshev, Koichi Ito, Takashi Yokogawa, Kazuya Nishikawa, Yoshikazu Nakamura, and Senya Matsufuji

Antizyme frameshifting as a functional probe of eukaryotic translational termination
Nucl. Acids Res. 2003 31: 5949-5956; doi:10.1093/nar/gkg789 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christophe Gangneux, Maryvonne Daveau, Martine Hiron, Céline Derambure, John Papaconstantinou, and Jean-Philippe Salier

The inflammation-induced down-regulation of plasma Fetuin-A (2HS-Glycoprotein) in liver results from the loss of interaction between long C/EBP isoforms at two neighbouring binding sites
Nucl. Acids Res. 2003 31: 5957-5970; doi:10.1093/nar/gkg788 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nikolay Korolev, Alexander P. Lyubartsev, Aatto Laaksonen, and Lars Nordenskiöld

A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations
Nucl. Acids Res. 2003 31: 5971-5981; doi:10.1093/nar/gkg802 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Steffen Schubert, Deniz C. Gül, Hans-Peter Grunert, Heinz Zeichhardt, Volker A. Erdmann, and Jens Kurreck

RNA cleaving ‘10-23’ DNAzymes with enhanced stability and activity
Nucl. Acids Res. 2003 31: 5982-5992; doi:10.1093/nar/gkg791 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ricardo Krüger and Marcin Filutowicz

Protein- and ATP-dependent transitions from ‘closed’ to ‘open’ complexes at the ori of plasmid R6K
Nucl. Acids Res. 2003 31: 5993-6003; doi:10.1093/nar/gkg809 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Thomas M. Schinecker, Rebecca A. Perlow, Suse Broyde, Nicholas E. Geacintov, and David A. Scicchitano

Human RNA polymerase II is partially blocked by DNA adducts derived from tumorigenic benzo[c]phenanthrene diol epoxides: relating biological consequences to conformational preferences
Nucl. Acids Res. 2003 31: 6004-6015; doi:10.1093/nar/gkg771 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Vsevolod J. Makeev, Alexander P. Lifanov, Anna G. Nazina, and Dmitri A. Papatsenko

Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information
Nucl. Acids Res. 2003 31: 6016-6026; doi:10.1093/nar/gkg799 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Shiau-Yin Wu, Kevin Culligan, Meindert Lamers, and John Hays

Dissimilar mispair-recognition spectra of Arabidopsis DNA-mismatch-repair proteins MSH2·MSH6 (MutS) and MSH2·MSH7 (MutS)
Nucl. Acids Res. 2003 31: 6027-6034; doi:10.1093/nar/gkg780 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Rajat Banerjee, Amit Kumar Mandal, Rajesh Saha, Soumi Guha, Soma Samaddar, Anusree Bhattacharyya, and Siddhartha Roy

Solvation change and ion release during aminoacylation by aminoacyl-tRNA synthetases
Nucl. Acids Res. 2003 31: 6035-6042; doi:10.1093/nar/gkg779 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

David C. Samuels, Richard J. Boys, Daniel A. Henderson, and Patrick F. Chinnery

A compositional segmentation of the human mitochondrial genome is related to heterogeneities in the guanine mutation rate
Nucl. Acids Res. 2003 31: 6043-6052; doi:10.1093/nar/gkg784 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Esti Yeger-Lotem and Hanah Margalit

Detection of regulatory circuits by integrating the cellular networks of protein–protein interactions and transcription regulation
Nucl. Acids Res. 2003 31: 6053-6061; doi:10.1093/nar/gkg787 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

NAR Methods Online:

Michael Motz, Gregor Sagner, Svante Pääbo, and Christian Kilger

Sequential DEXAS: a method for obtaining DNA sequences from genomic DNA and blood in one reaction
Nucl. Acids Res. 2003 31: e121; doi:10.1093/nar/gng112 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ales Tichopad, Michael Dilger, Gerhard Schwarz, and Michael W. Pfaffl

Standardized determination of real-time PCR efficiency from a single reaction set-up
Nucl. Acids Res. 2003 31: e122; doi:10.1093/nar/gng122 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yuanli Zhang, Dabing Zhang, Wenquan Li, Jianqun Chen, Yufa Peng, and Wei Cao

A novel real-time quantitative PCR method using attached universal template probe
Nucl. Acids Res. 2003 31: e123; doi:10.1093/nar/gng123 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ann H. Y. Kwan, Robert Czolij, Joel P. Mackay, and Merlin Crossley

Pentaprobe: a comprehensive sequence for the one-step detection of DNA-binding activities
Nucl. Acids Res. 2003 31: e124; doi:10.1093/nar/gng124 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Bénédicte Géron-Landre, Thibaut Roulon, Pierre Desbiolles, and Christophe Escudé

Sequence-specific fluorescent labeling of double-stranded DNA observed at the single molecule level
Nucl. Acids Res. 2003 31: e125; doi:10.1093/nar/gng125 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Corrigenda:

Corrigendum
Nucl. Acids Res. 2003 31: 6062; doi:10.1093/nar/GKG837 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

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