Nucleic Acids Research

Molecular Biology

Get checked abstract Sophie Couvé-Privat, Gaëtane Macé, Filippo Rosselli, and Murat K. Saparbaev

Psoralen-induced DNA adducts are substrates for the base excision repair pathway in human cells
Nucleic Acids Research Advance Access published on August 21, 2007
Nucl. Acids Res. 2007 35: 5672-5682; doi:10.1093/nar/gkm592 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Paul Brotherton, Phillip Endicott, Juan J. Sanchez, Mark Beaumont, Ross Barnett, Jeremy Austin, and Alan Cooper

Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions
Nucleic Acids Research Advance Access published on August 22, 2007
Nucl. Acids Res. 2007 35: 5717-5728; doi:10.1093/nar/gkm588 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Yaramah M. Zalucki, Peter M. Power, and Michael P. Jennings

Selection for efficient translation initiation biases codon usage at second amino acid position in secretory proteins
Nucleic Acids Research Advance Access published on August 23, 2007
Nucl. Acids Res. 2007 35: 5748-5754; doi:10.1093/nar/gkm577 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Marianne Bénard, Chrystelle Maric, and Gérard Pierron

Low rate of replication fork progression lengthens the replication timing of a locus containing an early firing origin
Nucleic Acids Research Advance Access published on August 23, 2007
Nucl. Acids Res. 2007 35: 5763-5774; doi:10.1093/nar/gkm586 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Samer Khateb, Pnina Weisman-Shomer, Inbal Hershco-Shani, Anna L. Ludwig, and Michael Fry

The tetraplex (CGG)_n destabilizing proteins hnRNP A2 and CBF-A enhance the in vivo translation of fragile X premutation mRNA
Nucleic Acids Research Advance Access published on August 23, 2007
Nucl. Acids Res. 2007 35: 5775-5788; doi:10.1093/nar/gkm636 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract AeRi Kim, Sang-hyun Song, Marjorie Brand, and Ann Dean

Nucleosome and transcription activator antagonism at human ß-globin locus control region DNase I hypersensitive sites
Nucleic Acids Research Advance Access published on August 24, 2007
Nucl. Acids Res. 2007 35: 5831-5838; doi:10.1093/nar/gkm620 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Supplementary Data]  

Get checked abstract Jeffrey B. Doyon and David R. Liu

Identification of eukaryotic promoter regulatory elements using nonhomologous random recombination
Nucleic Acids Research Advance Access published on August 24, 2007
Nucl. Acids Res. 2007 35: 5851-5860; doi:10.1093/nar/gkm634 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Nikolai Windbichler, Philippos Aris Papathanos, Flaminia Catteruccia, Hilary Ranson, Austin Burt, and Andrea Crisanti

Homing endonuclease mediated gene targeting in Anopheles gambiae cells and embryos
Nucleic Acids Research Advance Access published on August 28, 2007
Nucl. Acids Res. 2007 35: 5922-5933; doi:10.1093/nar/gkm632 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yoan Chérasse, Anne-Catherine Maurin, Cédric Chaveroux, Céline Jousse, Valérie Carraro, Laurent Parry, Christiane Deval, Christophe Chambon, Pierre Fafournoux, and Alain Bruhat

The p300/CBP-associated factor (PCAF) is a cofactor of ATF4 for amino acid-regulated transcription of CHOP
Nucleic Acids Research Advance Access published on August 28, 2007
Nucl. Acids Res. 2007 35: 5954-5965; doi:10.1093/nar/gkm642 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Efraín Zamora-Romo, Luis Rogelio Cruz-Vera, Serafín Vivanco-Domínguez, Marco Antonio Magos-Castro, and Gabriel Guarneros

Efficient expression of gene variants that harbour AGA codons next to the initiation codon
Nucleic Acids Research Advance Access published on August 28, 2007
Nucl. Acids Res. 2007 35: 5966-5974; doi:10.1093/nar/gkm643 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nucleic Acid Enzymes

Get checked abstract Kirsten Beck and Georg Lipps

Properties of an unusual DNA primase from an archaeal plasmid
Nucleic Acids Research Advance Access published on August 20, 2007
Nucl. Acids Res. 2007 35: 5635-5645; doi:10.1093/nar/gkm625 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Thijn van der Heijden, Ralf Seidel, Mauro Modesti, Roland Kanaar, Claire Wyman, and Cees Dekker

Real-time assembly and disassembly of human RAD51 filaments on individual DNA molecules
Nucleic Acids Research Advance Access published on August 20, 2007
Nucl. Acids Res. 2007 35: 5646-5657; doi:10.1093/nar/gkm629 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Vladimir Svetlov, Georgiy A. Belogurov, Elena Shabrova, Dmitry G. Vassylyev, and Irina Artsimovitch

Allosteric control of the RNA polymerase by the elongation factor RfaH
Nucleic Acids Research Advance Access published on August 21, 2007
Nucl. Acids Res. 2007 35: 5694-5705; doi:10.1093/nar/gkm600 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Nurten Saydam, Radhakrishnan Kanagaraj, Tobias Dietschy, Patrick L. Garcia, Javier Peña-Diaz, Igor Shevelev, Igor Stagljar, and Pavel Janscak

Physical and functional interactions between Werner syndrome helicase and mismatch-repair initiation factors
Nucleic Acids Research Advance Access published on August 22, 2007
Nucl. Acids Res. 2007 35: 5706-5716; doi:10.1093/nar/gkm500 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Amrita Machwe, Liren Xiao, Robert G. Lloyd, Edward Bolt, and David K. Orren

Replication fork regression in vitro by the Werner syndrome protein (WRN): Holliday junction formation, the effect of leading arm structure and a potential role for WRN exonuclease activity
Nucleic Acids Research Advance Access published on August 23, 2007
Nucl. Acids Res. 2007 35: 5729-5747; doi:10.1093/nar/gkm561 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jiafeng Gu, Haihui Lu, Albert G. Tsai, Klaus Schwarz, and Michael R. Lieber

Single-stranded DNA ligation and XLF-stimulated incompatible DNA end ligation by the XRCC4-DNA ligase IV complex: influence of terminal DNA sequence
Nucleic Acids Research Advance Access published on August 23, 2007
Nucl. Acids Res. 2007 35: 5755-5762; doi:10.1093/nar/gkm579 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Jean-Baptiste Boulé and Virginia A. Zakian

The yeast Pif1p DNA helicase preferentially unwinds RNA–DNA substrates
Nucleic Acids Research Advance Access published on August 24, 2007
Nucl. Acids Res. 2007 35: 5809-5818; doi:10.1093/nar/gkm613 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Valerie Notenboom, Richard G. Hibbert, Sarah E. van Rossum-Fikkert, Jesper V. Olsen, Matthias Mann, and Titia K. Sixma

Functional characterization of Rad18 domains for Rad6, ubiquitin, DNA binding and PCNA modification
Nucleic Acids Research Advance Access published on August 24, 2007
Nucl. Acids Res. 2007 35: 5819-5830; doi:10.1093/nar/gkm615 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Jennifer L. Eklund, Umut Y. Ulge, Jennifer Eastberg, and Raymond J. Monnat, Jr

Altered target site specificity variants of the I-PpoI His-Cys box homing endonuclease
Nucleic Acids Research Advance Access published on August 24, 2007
Nucl. Acids Res. 2007 35: 5839-5850; doi:10.1093/nar/gkm624 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Karolina Malanowska, Sumiko Yoneji, Abigail A. Salyers, and Jeffrey F. Gardner

CTnDOT integrase performs ordered homology-dependent and homology-independent strand exchanges
Nucleic Acids Research Advance Access published on August 24, 2007
Nucl. Acids Res. 2007 35: 5861-5873; doi:10.1093/nar/gkm637 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Li-Tao Guo, Xiang-Long Chen, Bo-Tao Zhao, Yi Shi, Wei Li, Hong Xue, and You-Xin Jin

Human tryptophanyl-tRNA synthetase is switched to a tRNA-dependent mode for tryptophan activation by mutations at V85 and I311
Nucleic Acids Research Advance Access published on August 28, 2007
Nucl. Acids Res. 2007 35: 5934-5943; doi:10.1093/nar/gkm633 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

RNA

Get checked abstract Ying Poi Liu, Joost Haasnoot, and Ben Berkhout

Design of extended short hairpin RNAs for HIV-1 inhibition
Nucleic Acids Research Advance Access published on August 21, 2007
Nucl. Acids Res. 2007 35: 5683-5693; doi:10.1093/nar/gkm596 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Oscar Puig, Elisabeth Bragado-Nilsson, Terhi Koski, and Bertrand Séraphin

The U1 snRNP-associated factor Luc7p affects 5' splice site selection in yeast and human
Nucleic Acids Research Advance Access published on August 28, 2007
Nucl. Acids Res. 2007 35: 5874-5885; doi:10.1093/nar/gkm505 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jesper B. Bramsen, Maria B. Laursen, Christian K. Damgaard, Suzy W. Lena, B. Ravindra Babu, Jesper Wengel, and Jørgen Kjems

Improved silencing properties using small internally segmented interfering RNAs
Nucleic Acids Research Advance Access published on August 28, 2007
Nucl. Acids Res. 2007 35: 5886-5897; doi:10.1093/nar/gkm548 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Seungil Ro, Chanjae Park, David Young, Kenton M. Sanders, and Wei Yan

Tissue-dependent paired expression of miRNAs
Nucleic Acids Research Advance Access published on August 28, 2007
Nucl. Acids Res. 2007 35: 5944-5953; doi:10.1093/nar/gkm641 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Bo Zhang, Graziella Morace, Verena Gauss-Müller, and Yuri Kusov

Poly(A) binding protein, C-terminally truncated by the hepatitis A virus proteinase 3C, inhibits viral translation
Nucleic Acids Research Advance Access published on August 28, 2007
Nucl. Acids Res. 2007 35: 5975-5984; doi:10.1093/nar/gkm645 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Structural Biology

Get checked abstract S. Balaji and L. Aravind

The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins
Nucleic Acids Research Advance Access published on August 21, 2007
Nucl. Acids Res. 2007 35: 5658-5671; doi:10.1093/nar/gkm558 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Konstantinos Tripsianes, Gert E. Folkers, Chao Zheng, Devashish Das, Jeffrey S. Grinstead, Robert Kaptein, and Rolf Boelens

Analysis of the XPA and ssDNA-binding surfaces on the central domain of human ERCC1 reveals evidence for subfunctionalization
Nucleic Acids Research Advance Access published on August 24, 2007
Nucl. Acids Res. 2007 35: 5789-5798; doi:10.1093/nar/gkm503 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Alan K. Todd, Shozeb M. Haider, Gary N. Parkinson, and Stephen Neidle

Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter
Nucleic Acids Research Advance Access published on August 24, 2007
Nucl. Acids Res. 2007 35: 5799-5808; doi:10.1093/nar/gkm609 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Nathalie Lancelot, Gaëlle Charier, Joël Couprie, Isabelle Duband-Goulet, Béatrice Alpha-Bazin, Eric Quémeneur, Emilie Ma, Marie-Claude Marsolier-Kergoat, Virginie Ropars, Jean-Baptiste Charbonnier, Simona Miron, Constantin T. Craescu, Isabelle Callebaut, Bernard Gilquin, and Sophie Zinn-Justin

The checkpoint Saccharomyces cerevisiae Rad9 protein contains a tandem tudor domain that recognizes DNA
Nucleic Acids Research Advance Access published on August 28, 2007
Nucl. Acids Res. 2007 35: 5898-5912; doi:10.1093/nar/gkm607 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Lynn A. Gregory, Almass-Houd Aguissa-Touré, Noël Pinaud, Pierre Legrand, Pierre-Emmanuel Gleizes, and Sébastien Fribourg

Molecular basis of Diamond–Blackfan anemia: structure and function analysis of RPS19
Nucleic Acids Research Advance Access published on August 28, 2007
Nucl. Acids Res. 2007 35: 5913-5921; doi:10.1093/nar/gkm626 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Corrigendum

Nelly Piton, Yuguang Mu, Gerhard Stock, Thomas F. Prisner, Olav Schiemann, and Joachim W. Engels

Base-specific spin-labeling of RNA for structure determination
Nucl. Acids Res. 2007 35: 5985; doi:10.1093/nar/gkm714 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online

Get checked abstract Eric Rivals, Anthony Boureux, Mireille Lejeune, Florence Ottones, Oscar Pecharromàn Pérez, Jorma Tarhio, Fabien Pierrat, Florence Ruffle, Thérèse Commes, and Jacques Marti

Transcriptome annotation using tandem SAGE tags
Nucleic Acids Research Advance Access published on August 20, 2007
Nucl. Acids Res. 2007 35: e108; doi:10.1093/nar/gkm495 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Astrid Jakobs, Fabian Himstedt, Martin Funk, Bernhard Korn, Matthias Gaestel, and Rainer Niedenthal

Ubc9 fusion-directed SUMOylation identifies constitutive and inducible SUMOylation
Nucleic Acids Research Advance Access published on August 20, 2007
Nucl. Acids Res. 2007 35: e109; doi:10.1093/nar/gkm617 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Seung Pil Pack, Nagendra Kumar Kamisetty, Mitsuru Nonogawa, Kamakshaiah Charyulu Devarayapalli, Kairi Ohtani, Kazunari Yamada, Yasuko Yoshida, Tsutomu Kodaki, and Keisuke Makino

Direct immobilization of DNA oligomers onto the amine-functionalized glass surface for DNA microarray fabrication through the activation-free reaction of oxanine
Nucleic Acids Research Advance Access published on August 21, 2007
Nucl. Acids Res. 2007 35: e110; doi:10.1093/nar/gkm619 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Wei Jie Qin and Lin Yue Lanry Yung

Nanoparticle-based detection and quantification of DNA with single nucleotide polymorphism (SNP) discrimination selectivity
Nucleic Acids Research Advance Access published on August 24, 2007
Nucl. Acids Res. 2007 35: e111; doi:10.1093/nar/gkm602 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Esther W. Hou, Rajendra Prasad, Kenjiro Asagoshi, Aya Masaoka, and Samuel H. Wilson

Comparative assessment of plasmid and oligonucleotide DNA substrates in measurement of in vitro base excision repair activity
Nucleic Acids Research Advance Access published on August 24, 2007
Nucl. Acids Res. 2007 35: e112; doi:10.1093/nar/gkm639 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Andreas Wollstein, Alexander Herrmann, Michael Wittig, Michael Nothnagel, Andre Franke, Peter Nürnberg, Stefan Schreiber, Michael Krawczak, and Jochen Hampe

Efficacy assessment of SNP sets for genome-wide disease association studies
Nucleic Acids Research Advance Access published on August 28, 2007
Nucl. Acids Res. 2007 35: e113; doi:10.1093/nar/gkm621 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Anne-Laure Chateigner-Boutin and Ian Small

A rapid high-throughput method for the detection and quantification of RNA editing based on high-resolution melting of amplicons
Nucleic Acids Research Advance Access published on August 28, 2007
Nucl. Acids Res. 2007 35: e114; doi:10.1093/nar/gkm640 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Magnus Isaksson, Johan Stenberg, Fredrik Dahl, Ann-Charlotte Thuresson, Marie-Louise Bondeson, and Mats Nilsson

MLGA—a rapid and cost-efficient assay for gene copy-number analysis
Nucleic Acids Research Advance Access published on September 6, 2007
Nucl. Acids Res. 2007 35: e115; doi:10.1093/nar/gkm651 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Wilfried Weber, William Bacchus, Marie Daoud-El Baba, and Martin Fussenegger

Vitamin H-regulated transgene expression in mammalian cells
Nucleic Acids Research Advance Access published on September 7, 2007
Nucl. Acids Res. 2007 35: e116; doi:10.1093/nar/gkm466 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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