Nucleic Acids Research

Chemistry and Synthetic Biology

Get checked abstract Nathalie Berthet, Caroline Crey-Desbiolles, Mitsuharu Kotera, and Pascal Dumy

Chemical synthesis, DNA incorporation and biological study of a new photocleavable 2'-deoxyadenosine mimic
Nucleic Acids Research Advance Access published on July 8, 2009
Nucl. Acids Res. 2009 37: 5237-5245; doi:10.1093/nar/gkp562 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Computational Biology

Get checked abstract Leonid Zamdborg and Ping Ma

Discovery of protein–DNA interactions by penalized multivariate regression
Nucleic Acids Research Advance Access published on July 3, 2009
Nucl. Acids Res. 2009 37: 5246-5254; doi:10.1093/nar/gkp554 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Aaron J. Arvey, Rajeev K. Azad, Alpan Raval, and Jeffrey G. Lawrence

Detection of genomic islands via segmental genome heterogeneity
Nucleic Acids Research Advance Access published on July 9, 2009
Nucl. Acids Res. 2009 37: 5255-5266; doi:10.1093/nar/gkp576 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gene Regulation, Chromatin and Epigenetics

Get checked abstract Caroline Conte, Nadera Ainaoui, Aurélie Delluc-Clavières, Marie P. Khoury, Rania Azar, Françoise Pujol, Yvan Martineau, Stéphane Pyronnet, and Anne-Catherine Prats

Fibroblast growth factor 1 induced during myogenesis by a transcription–translation coupling mechanism
Nucleic Acids Research Advance Access published on June 26, 2009
Nucl. Acids Res. 2009 37: 5267-5278; doi:10.1093/nar/gkp550 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Karim Bouazoune, Tina B. Miranda, Peter A. Jones, and Robert E. Kingston

Analysis of individual remodeled nucleosomes reveals decreased histone–DNA contacts created by hSWI/SNF
Nucleic Acids Research Advance Access published on June 30, 2009
Nucl. Acids Res. 2009 37: 5279-5294; doi:10.1093/nar/gkp524 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Julie Ross, Stefania Bottardi, Vincent Bourgoin, Alex Wollenschlaeger, Elliot Drobetsky, Marie Trudel, and Eric Milot

Differential requirement of a distal regulatory region for pre-initiation complex formation at globin gene promoters
Nucleic Acids Research Advance Access published on June 30, 2009
Nucl. Acids Res. 2009 37: 5295-5308; doi:10.1093/nar/gkp545 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Micaela Caserta, Eleonora Agricola, Mark Churcher, Edwige Hiriart, Loredana Verdone, Ernesto Di Mauro, and Andrew Travers

A translational signature for nucleosome positioning in vivo
Nucleic Acids Research Advance Access published on July 13, 2009
Nucl. Acids Res. 2009 37: 5309-5321; doi:10.1093/nar/gkp574 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Alexey Protsenko, Marina Zakharova, Maxim Nagornykh, Alexander Solonin, and Konstantin Severinov

Transcription regulation of restriction-modification system Ecl18kI
Nucleic Acids Research Advance Access published on July 10, 2009
Nucl. Acids Res. 2009 37: 5322-5330; doi:10.1093/nar/gkp579 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Arefeh Rouhi, C. Benjamin Lai, Tammy P. Cheng, Fumio Takei, Wayne M. Yokoyama, and Dixie L. Mager

Evidence for high bi-allelic expression of activating Ly49 receptors
Nucleic Acids Research Advance Access published on July 15, 2009
Nucl. Acids Res. 2009 37: 5331-5342; doi:10.1093/nar/gkp592 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genome Integrity, Repair and Replication

Get checked abstract Jacques Oberto, Norman Breuil, Arnaud Hecker, Francesca Farina, Céline Brochier-Armanet, Emmanuel Culetto, and Patrick Forterre

Qri7/OSGEPL, the mitochondrial version of the universal Kae1/YgjD protein, is essential for mitochondrial genome maintenance
Nucleic Acids Research Advance Access published on July 3, 2009
Nucl. Acids Res. 2009 37: 5343-5352; doi:10.1093/nar/gkp557 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Angela Rizzo, Erica Salvati, Manuela Porru, Carmen D’Angelo, Malcolm F. Stevens, Maurizio D’Incalci, Carlo Leonetti, Eric Gilson, Gabriella Zupi, and Annamaria Biroccio

Stabilization of quadruplex DNA perturbs telomere replication leading to the activation of an ATR-dependent ATM signaling pathway
Nucleic Acids Research Advance Access published on July 13, 2009
Nucl. Acids Res. 2009 37: 5353-5364; doi:10.1093/nar/gkp582 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics

Get checked abstract Wei Sun, Fred A. Wright, Zhengzheng Tang, Silje H. Nordgard, Peter Van Loo, Tianwei Yu, Vessela N. Kristensen, and Charles M. Perou

Integrated study of copy number states and genotype calls using high-density SNP arrays
Nucleic Acids Research Advance Access published on July 6, 2009
Nucl. Acids Res. 2009 37: 5365-5377; doi:10.1093/nar/gkp493 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract Markella Ponticos, Clare Harvey, Tetsuro Ikeda, David Abraham, and George Bou-Gharios

JunB mediates enhancer/promoter activity of COL1A2 following TGF-β induction
Nucleic Acids Research Advance Access published on June 26, 2009
Nucl. Acids Res. 2009 37: 5378-5389; doi:10.1093/nar/gkp544 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes

Get checked abstract Anastasia Rogozina, Evgeny Zaychikov, Malcolm Buckle, Hermann Heumann, and Bianca Sclavi

DNA melting by RNA polymerase at the T7A1 promoter precedes the rate-limiting step at 37°C and results in the accumulation of an off-pathway intermediate
Nucleic Acids Research Advance Access published on July 3, 2009
Nucl. Acids Res. 2009 37: 5390-5404; doi:10.1093/nar/gkp560 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Sylvestre Grizot, Julianne Smith, Fayza Daboussi, Jesús Prieto, Pilar Redondo, Nekane Merino, Maider Villate, Séverine Thomas, Laetitia Lemaire, Guillermo Montoya, Francisco J. Blanco, Frédéric Pâques, and Philippe Duchateau

Efficient targeting of a SCID gene by an engineered single-chain homing endonuclease
Nucleic Acids Research Advance Access published on July 7, 2009
Nucl. Acids Res. 2009 37: 5405-5419; doi:10.1093/nar/gkp548 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Miloje Savic, Josip Lovric, Tatjana Ilic Tomic, Branka Vasiljevic, and Graeme L. Conn

Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics
Nucleic Acids Research Advance Access published on July 9, 2009
Nucl. Acids Res. 2009 37: 5420-5431; doi:10.1093/nar/gkp575 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jaroslav Malina, Oldrich Vrana, and Viktor Brabec

Mechanistic studies of the modulation of cleavage activity of topoisomerase I by DNA adducts of mono- and bi-functional Pt^II complexes
Nucleic Acids Research Advance Access published on July 9, 2009
Nucl. Acids Res. 2009 37: 5432-5442; doi:10.1093/nar/gkp580 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Stuart R. W. Bellamy, Yana S. Kovacheva, Ishan Haji Zulkipli, and Stephen E. Halford

Differences between Ca²⁺ and Mg²⁺ in DNA binding and release by the SfiI restriction endonuclease: implications for DNA looping
Nucleic Acids Research Advance Access published on July 13, 2009
Nucl. Acids Res. 2009 37: 5443-5453; doi:10.1093/nar/gkp569 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Niels Laurens, Stuart R. W. Bellamy, August F. Harms, Yana S. Kovacheva, Stephen E. Halford, and Gijs J. L. Wuite

Dissecting protein-induced DNA looping dynamics in real time
Nucleic Acids Research Advance Access published on July 8, 2009
Nucl. Acids Res. 2009 37: 5454-5464; doi:10.1093/nar/gkp570 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA

Get checked abstract Richard S. P. Horler and Carin K. Vanderpool

Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence
Nucleic Acids Research Advance Access published on June 16, 2009
Nucl. Acids Res. 2009 37: 5465-5476; doi:10.1093/nar/gkp501 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Caryn S. Wadler and Carin K. Vanderpool

Characterization of homologs of the small RNA SgrS reveals diversity in function
Nucleic Acids Research Advance Access published on July 20, 2009
Nucl. Acids Res. 2009 37: 5477-5485; doi:10.1093/nar/gkp591 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Sara Chirayil, Rachel Chirayil, and Kevin J. Luebke

Discovering ligands for a microRNA precursor with peptoid microarrays
Nucleic Acids Research Advance Access published on June 26, 2009
Nucl. Acids Res. 2009 37: 5486-5497; doi:10.1093/nar/gkp549 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Rosa Díaz-Toledano, Ascensión Ariza-Mateos, Alex Birk, Belén Martínez-García, and Jordi Gómez

In vitro characterization of a miR-122-sensitive double-helical switch element in the 5' region of hepatitis C virus RNA
Nucleic Acids Research Advance Access published on July 3, 2009
Nucl. Acids Res. 2009 37: 5498-5510; doi:10.1093/nar/gkp553 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Angela Schwede, Theresa Manful, Bhaskar Anand Jha, Claudia Helbig, Natalia Bercovich, Mhairi Stewart, and Christine Clayton

The role of deadenylation in the degradation of unstable mRNAs in trypanosomes
Nucleic Acids Research Advance Access published on July 13, 2009
Nucl. Acids Res. 2009 37: 5511-5528; doi:10.1093/nar/gkp571 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Natalie Luhtala and Roy Parker

LSM1 over-expression in Saccharomyces cerevisiae depletes U6 snRNA levels
Nucleic Acids Research Advance Access published on July 13, 2009
Nucl. Acids Res. 2009 37: 5529-5536; doi:10.1093/nar/gkp572 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Laura E. Easton, Nicolas Locker, and Peter J. Lukavsky

Conserved functional domains and a novel tertiary interaction near the pseudoknot drive translational activity of hepatitis C virus and hepatitis C virus-like internal ribosome entry sites
Nucleic Acids Research Advance Access published on July 13, 2009
Nucl. Acids Res. 2009 37: 5537-5549; doi:10.1093/nar/gkp588 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Denise S. Tevis, Arvind Kumar, Chad E. Stephens, David W. Boykin, and W. David Wilson

Large, sequence-dependent effects on DNA conformation by minor groove binding compounds
Nucleic Acids Research Advance Access published on July 3, 2009
Nucl. Acids Res. 2009 37: 5550-5558; doi:10.1093/nar/gkp558 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Aurore Guédin, Patrizia Alberti, and Jean-Louis Mergny

Stability of intramolecular quadruplexes: sequence effects in the central loop
Nucleic Acids Research Advance Access published on July 6, 2009
Nucl. Acids Res. 2009 37: 5559-5567; doi:10.1093/nar/gkp563 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Graham L. Randall, Lynn Zechiedrich, and B. Montgomery Pettitt

In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form
Nucleic Acids Research Advance Access published on July 8, 2009
Nucl. Acids Res. 2009 37: 5568-5577; doi:10.1093/nar/gkp556 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Philippe Salah, Marco Bisaglia, Pascale Aliprandi, Marc Uzan, Christina Sizun, and François Bontems

Probing the relationship between Gram-negative and Gram-positive S1 proteins by sequence analysis
Nucleic Acids Research Advance Access published on July 15, 2009
Nucl. Acids Res. 2009 37: 5578-5588; doi:10.1093/nar/gkp547 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online

Get checked abstract Iouri Chepelev, Gang Wei, Qingsong Tang, and Keji Zhao

Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq
Nucleic Acids Research Advance Access published on June 15, 2009
Nucl. Acids Res. 2009 37: e106; doi:10.1093/nar/gkp507 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Dimos Gaidatzis, Kirsten Jacobeit, Edward J. Oakeley, and Michael B. Stadler

Overestimation of alternative splicing caused by variable probe characteristics in exon arrays
Nucleic Acids Research Advance Access published on June 15, 2009
Nucl. Acids Res. 2009 37: e107; doi:10.1093/nar/gkp508 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Junichi Yamaguchi, Mohammed Naimuddin, Manish Biyani, Toru Sasaki, Masayuki Machida, Tai Kubo, Takashi Funatsu, Yuzuru Husimi, and Naoto Nemoto

cDNA display: a novel screening method for functional disulfide-rich peptides by solid-phase synthesis and stabilization of mRNA–protein fusions
Nucleic Acids Research Advance Access published on June 15, 2009
Nucl. Acids Res. 2009 37: e108; doi:10.1093/nar/gkp514 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Marco Severgnini, Paola Cremonesi, Clarissa Consolandi, Giada Caredda, Gianluca De Bellis, and Bianca Castiglioni

ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design
Nucleic Acids Research Advance Access published on June 16, 2009
Nucl. Acids Res. 2009 37: e109; doi:10.1093/nar/gkp499 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Agnieszka Doroszuk, L. Basten Snoek, Emilie Fradin, Joost Riksen, and Jan Kammenga

A genome-wide library of CB4856/N2 introgression lines of Caenorhabditis elegans
Nucleic Acids Research Advance Access published on June 19, 2009
Nucl. Acids Res. 2009 37: e110; doi:10.1093/nar/gkp528 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 37 ISSUE 16 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkp922 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkp920 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkp924 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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