| | Molecular Biology Psoralen-induced DNA adducts are substrates for the base excision repair pathway in human cells Sophie Couvé-Privat, Gaëtane Macé, Filippo Rosselli, and Murat K. Saparbaev PMCID: PMC2078531 Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions Paul Brotherton, Phillip Endicott, Juan J. Sanchez, Mark Beaumont, Ross Barnett, Jeremy Austin, and Alan Cooper PMCID: PMC2034480 Selection for efficient translation initiation biases codon usage at second amino acid position in secretory proteins Yaramah M. Zalucki, Peter M. Power, and Michael P. Jennings PMCID: PMC2034453 Low rate of replication fork progression lengthens the replication timing of a locus containing an early firing origin Marianne Bénard, Chrystelle Maric, and Gérard Pierron PMCID: PMC2034475 The tetraplex (CGG)n destabilizing proteins hnRNP A2 and CBF-A enhance the in vivo translation of fragile X premutation mRNA Samer Khateb, Pnina Weisman-Shomer, Inbal Hershco-Shani, Anna L. Ludwig, and Michael Fry PMCID: PMC2034458 Nucleosome and transcription activator antagonism at human β-globin locus control region DNase I hypersensitive sites AeRi Kim, Sang-hyun Song, Marjorie Brand, and Ann Dean PMCID: PMC2034456 Identification of eukaryotic promoter regulatory elements using nonhomologous random recombination Jeffrey B. Doyon and David R. Liu PMCID: PMC2034452 Homing endonuclease mediated gene targeting in Anopheles gambiae cells and embryos Nikolai Windbichler, Philippos Aris Papathanos, Flaminia Catteruccia, Hilary Ranson, Austin Burt, and Andrea Crisanti PMCID: PMC2034484 The p300/CBP-associated factor (PCAF) is a cofactor of ATF4 for amino acid-regulated transcription of CHOP Yoan Chérasse, Anne-Catherine Maurin, Cédric Chaveroux, Céline Jousse, Valérie Carraro, Laurent Parry, Christiane Deval, Christophe Chambon, Pierre Fafournoux, and Alain Bruhat PMCID: PMC2034469 Efficient expression of gene variants that harbour AGA codons next to the initiation codon Efraín Zamora-Romo, Luis Rogelio Cruz-Vera, Serafín Vivanco-Domínguez, Marco Antonio Magos-Castro, and Gabriel Guarneros PMCID: PMC2034473 RNA Design of extended short hairpin RNAs for HIV-1 inhibition Ying Poi Liu, Joost Haasnoot, and Ben Berkhout PMCID: PMC2034457 The U1 snRNP-associated factor Luc7p affects 5′ splice site selection in yeast and human Oscar Puig, Elisabeth Bragado-Nilsson, Terhi Koski, and Bertrand Séraphin PMCID: PMC2034479 Improved silencing properties using small internally segmented interfering RNAs Jesper B. Bramsen, Maria B. Laursen, Christian K. Damgaard, Suzy W. Lena, B. Ravindra Babu, Jesper Wengel, and Jørgen Kjems PMCID: PMC2034465 Tissue-dependent paired expression of miRNAs Seungil Ro, Chanjae Park, David Young, Kenton M. Sanders, and Wei Yan PMCID: PMC2034466 Poly(A) binding protein, C-terminally truncated by the hepatitis A virus proteinase 3C, inhibits viral translation Bo Zhang, Graziella Morace, Verena Gauss-Müller, and Yuri Kusov PMCID: PMC2034478 Structural Biology The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins S. Balaji and L. Aravind PMCID: PMC2034487 Analysis of the XPA and ssDNA-binding surfaces on the central domain of human ERCC1 reveals evidence for subfunctionalization Konstantinos Tripsianes, Gert E. Folkers, Chao Zheng, Devashish Das, Jeffrey S. Grinstead, Robert Kaptein, and Rolf Boelens PMCID: PMC2034474 Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter Alan K. Todd, Shozeb M. Haider, Gary N. Parkinson, and Stephen Neidle PMCID: PMC2034477 The checkpoint Saccharomyces cerevisiae Rad9 protein contains a tandem tudor domain that recognizes DNA 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 PMCID: PMC2034471 Molecular basis of Diamond–Blackfan anemia: structure and function analysis of RPS19 Lynn A. Gregory, Almass-Houd Aguissa-Touré, Noël Pinaud, Pierre Legrand, Pierre-Emmanuel Gleizes, and Sébastien Fribourg PMCID: PMC2034476 Methods Online Transcriptome annotation using tandem SAGE tags Eric Rivals, Anthony Boureux, Mireille Lejeune, Florence Ottones, Oscar Pecharromàn Pérez, Jorma Tarhio, Fabien Pierrat, Florence Ruffle, Thérèse Commes, and Jacques Marti PMCID: PMC2034470 Ubc9 fusion-directed SUMOylation identifies constitutive and inducible SUMOylation Astrid Jakobs, Fabian Himstedt, Martin Funk, Bernhard Korn, Matthias Gaestel, and Rainer Niedenthal PMCID: PMC2034454 Direct immobilization of DNA oligomers onto the amine-functionalized glass surface for DNA microarray fabrication through the activation-free reaction of oxanine Seung Pil Pack, Nagendra Kumar Kamisetty, Mitsuru Nonogawa, Kamakshaiah Charyulu Devarayapalli, Kairi Ohtani, Kazunari Yamada, Yasuko Yoshida, Tsutomu Kodaki, and Keisuke Makino PMCID: PMC2034461 Nanoparticle-based detection and quantification of DNA with single nucleotide polymorphism (SNP) discrimination selectivity Wei Jie Qin and Lin Yue Lanry Yung PMCID: PMC2034455 Comparative assessment of plasmid and oligonucleotide DNA substrates in measurement of in vitro base excision repair activity Esther W. Hou, Rajendra Prasad, Kenjiro Asagoshi, Aya Masaoka, and Samuel H. Wilson PMCID: PMC2034467 Efficacy assessment of SNP sets for genome-wide disease association studies Andreas Wollstein, Alexander Herrmann, Michael Wittig, Michael Nothnagel, Andre Franke, Peter Nürnberg, Stefan Schreiber, Michael Krawczak, and Jochen Hampe PMCID: PMC2034459 A rapid high-throughput method for the detection and quantification of RNA editing based on high-resolution melting of amplicons Anne-Laure Chateigner-Boutin and Ian Small PMCID: PMC2034463 MLGA—a rapid and cost-efficient assay for gene copy-number analysis Magnus Isaksson, Johan Stenberg, Fredrik Dahl, Ann-Charlotte Thuresson, Marie-Louise Bondeson, and Mats Nilsson PMCID: PMC2034490 Vitamin H-regulated transgene expression in mammalian cells Wilfried Weber, William Bacchus, Marie Daoud-El Baba, and Martin Fussenegger PMCID: PMC2034481 Nucleic Acid Enzymes Properties of an unusual DNA primase from an archaeal plasmid Kirsten Beck and Georg Lipps PMCID: PMC2034472 Real-time assembly and disassembly of human RAD51 filaments on individual DNA molecules Thijn van der Heijden, Ralf Seidel, Mauro Modesti, Roland Kanaar, Claire Wyman, and Cees Dekker PMCID: PMC2034483 Allosteric control of the RNA polymerase by the elongation factor RfaH Vladimir Svetlov, Georgiy A. Belogurov, Elena Shabrova, Dmitry G. Vassylyev, and Irina Artsimovitch PMCID: PMC2034486 Physical and functional interactions between Werner syndrome helicase and mismatch-repair initiation factors Nurten Saydam, Radhakrishnan Kanagaraj, Tobias Dietschy, Patrick L. Garcia, Javier Peña-Diaz, Igor Shevelev, Igor Stagljar, and Pavel Janscak PMCID: PMC2034464 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 Amrita Machwe, Liren Xiao, Robert G. Lloyd, Edward Bolt, and David K. Orren PMCID: PMC2034489 Single-stranded DNA ligation and XLF-stimulated incompatible DNA end ligation by the XRCC4-DNA ligase IV complex: influence of terminal DNA sequence Jiafeng Gu, Haihui Lu, Albert G. Tsai, Klaus Schwarz, and Michael R. Lieber PMCID: PMC2034460 The yeast Pif1p DNA helicase preferentially unwinds RNA–DNA substrates Jean-Baptiste Boulé and Virginia A. Zakian PMCID: PMC2034482 Functional characterization of Rad18 domains for Rad6, ubiquitin, DNA binding and PCNA modification Valerie Notenboom, Richard G. Hibbert, Sarah E. van Rossum-Fikkert, Jesper V. Olsen, Matthias Mann, and Titia K. Sixma PMCID: PMC2034485 Altered target site specificity variants of the I-PpoI His-Cys box homing endonuclease Jennifer L. Eklund, Umut Y. Ulge, Jennifer Eastberg, and Raymond J. Monnat, Jr PMCID: PMC2034468 CTnDOT integrase performs ordered homology-dependent and homology-independent strand exchanges Karolina Malanowska, Sumiko Yoneji, Abigail A. Salyers, and Jeffrey F. Gardner PMCID: PMC2034462 Human tryptophanyl-tRNA synthetase is switched to a tRNA-dependent mode for tryptophan activation by mutations at V85 and I311 Li-Tao Guo, Xiang-Long Chen, Bo-Tao Zhao, Yi Shi, Wei Li, Hong Xue, and You-Xin Jin PMCID: PMC2034488 Corrigendum Base-specific spin-labeling of RNA for structure determination Nelly Piton, Yuguang Mu, Gerhard Stock, Thomas F. Prisner, Olav Schiemann, and Joachim W. Engels PMCID: PMC2034491 Corrects: Nelly Piton, et al. Base-specific spin-labeling of RNA for structure determination. Nucleic Acids Res. 2007 May; 35(9): 3128–3143. |
