| | Molecular Biology Inhibitory effect of a short Z-DNA forming sequence on transcription elongation by T7 RNA polymerase Jennifer V. Ditlevson, Silvia Tornaletti, Boris P. Belotserkovskii, Virginia Teijeiro, Guliang Wang, Karen M. Vasquez, and Philip C. Hanawalt PMCID: PMC2425487 The protein arginine methyltransferases CARM1 and PRMT1 cooperate in gene regulation Markus A. Kleinschmidt, Gundula Streubel, Birgit Samans, Michael Krause, and Uta-Maria Bauer PMCID: PMC2425501 An ultraconserved Hox–Pbx responsive element resides in the coding sequence of Hoxa2 and is active in rhombomere 4 Xavier Lampe, Omar Abdel Samad, Allan Guiguen, Christelle Matis, Sophie Remacle, Jacques J. Picard, Filippo M. Rijli, and René Rezsohazy PMCID: PMC2425489 Identification of a novel human Rad51 variant that promotes DNA strand exchange Jung-Young Park, Han-Wook Yoo, Bok-Ryang Kim, Raekil Park, Sang-Yun Choi, and Youngho Kim PMCID: PMC2425499 Developmentally programmed DNA splicing in Paramecium reveals short-distance crosstalk between DNA cleavage sites Ariane Gratias, Gersende Lepère, Olivier Garnier, Sarah Rosa, Sandra Duharcourt, Sophie Malinsky, Eric Meyer, and Mireille Bétermier PMCID: PMC2425466 The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK) Martine Roovers, Katarzyna H. Kaminska, Karolina L. Tkaczuk, Daniel Gigot, Louis Droogmans, and Janusz M. Bujnicki PMCID: PMC2425500 Human DNA ligases I and III, but not ligase IV, are required for microhomology-mediated end joining of DNA double-strand breaks Li Liang, Li Deng, Son C. Nguyen, Xin Zhao, Christopher D. Maulion, Changshun Shao, and Jay A. Tischfield PMCID: PMC2425475 Involvement of fission yeast Clr6-HDAC in regulation of the checkpoint kinase Cds1 Tatsuki Kunoh, Toshiyuki Habu, and Tomohiro Matsumoto PMCID: PMC2425474 Direct inhibition of the DNA-binding activity of POU transcription factors Pit-1 and Brn-3 by selective binding of a phenyl-furan-benzimidazole dication Paul Peixoto, Yang Liu, Sabine Depauw, Marie-Paule Hildebrand, David W. Boykin, Christian Bailly, W. David Wilson, and Marie-Hélène David-Cordonnier PMCID: PMC2425483 Base-pair neutral homozygotes can be discriminated by calibrated high-resolution melting of small amplicons Cameron N. Gundry, Steven F. Dobrowolski, Y. Ranae Martin, Thomas C. Robbins, Lyle M. Nay, Nathan Boyd, Thomas Coyne, Mikeal D. Wall, Carl T. Wittwer, and David H.-F. Teng PMCID: PMC2425497 Identification of transcriptional regulatory cascades in retinoic acid-induced growth arrest of HepG2 cells Misato Nakanishi, Yasuhiro Tomaru, Hisashi Miura, Yoshihide Hayashizaki, and Masanori Suzuki PMCID: PMC2425469 Purine twisted-intercalating nucleic acids: a new class of anti-gene molecules resistant to potassium-induced aggregation Manikandan Paramasivam, Susanna Cogoi, Vyacheslav V. Filichev, Niels Bomholt, Erik B. Pedersen, and Luigi E. Xodo PMCID: PMC2425464 RNA A G-tract element in apoptotic agents-induced alternative splicing Yan Hai, Wenguang Cao, Guodong Liu, Say-Pham Hong, Sherif Abou Elela, Roscoe Klinck, Jiayou Chu, and Jiuyong Xie PMCID: PMC2425498 A role for Caf1 in mRNA deadenylation and decay in trypanosomes and human cells Angela Schwede, Louise Ellis, Julia Luther, Mark Carrington, Georg Stoecklin, and Christine Clayton PMCID: PMC2425496 The HIV-1 transcriptional activator Tat has potent nucleic acid chaperoning activities in vitro Monika Kuciak, Caroline Gabus, Roland Ivanyi-Nagy, Katharina Semrad, Roman Storchak, Olivier Chaloin, Sylviane Muller, Yves Mély, and Jean-Luc Darlix PMCID: PMC2425468 Insights into anti-termination regulation of the hut operon in Bacillus subtilis: importance of the dual RNA-binding surfaces of HutP Subash C. B. Gopinath, Dhakshnamoorthy Balasundaresan, Thirumananseri Kumarevel, Tomoko S. Misono, Hiroshi Mizuno, and Penmetcha K. R. Kumar PMCID: PMC2425495 Structural Biology Structural analysis of the Sulfolobus solfataricus MCM protein N-terminal domain Wei Liu, Biagio Pucci, Mosè Rossi, Francesca M. Pisani, and Rudolf Ladenstein PMCID: PMC2425480 Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway Carmen M. Moure, Frederick S. Gimble, and Florante A. Quiocho PMCID: PMC2425494 Crystal structure of the 25 kDa subunit of human cleavage factor Im Molly Coseno, Georges Martin, Christopher Berger, Gregory Gilmartin, Walter Keller, and Sylvie Doublié PMCID: PMC2425470 Crystal structure of trioxacarcin A covalently bound to DNA Roland Pfoh, Hartmut Laatsch, and George M. Sheldrick PMCID: PMC2425490 Genomics Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs Aristotelis Tsirigos and Isidore Rigoutsos PMCID: PMC2425492 Chemistry Enzymatic synthesis of structure-free DNA with pseudo-complementary properties Georges Lahoud, Victor Timoshchuk, Alexandre Lebedev, Miguel de Vega, Margarita Salas, Khalil Arar, Ya-Ming Hou, and Howard Gamper PMCID: PMC2425472 Methods Online Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping Christoph Bock, Jörn Walter, Martina Paulsen, and Thomas Lengauer PMCID: PMC2425484 UniPrime: a workflow-based platform for improved universal primer design Michaël Bekaert and Emma C. Teeling PMCID: PMC2425486 Chemical mapping of cytosines enzymatically flipped out of the DNA helix Dalia Daujotytė, Zita Liutkevičiūtė, Gintautas Tamulaitis, and Saulius Klimašauskas PMCID: PMC2425465 Enhanced identification and biological validation of differential gene expression via Illumina whole-genome expression arrays through the use of the model-based background correction methodology Liang-Hao Ding, Yang Xie, Seongmi Park, Guanghua Xiao, and Michael D. Story PMCID: PMC2425463 Microarray-based global mapping of integration sites for the retrotransposon, intracisternal A-particle, in the mouse genome Takashi Takabatake, Hiroshi Ishihara, Yasushi Ohmachi, Izumi Tanaka, Masako M. Nakamura, Katsuyoshi Fujikawa, Tokuhisa Hirouchi, Shizuko Kakinuma, Yoshiya Shimada, Yoichi Oghiso, and Kimio Tanaka PMCID: PMC2425471 Assessment of gene expression in many samples using vertical arrays Rosa Ana Risques, Gaelle Rondeau, Martin Judex, Michael McClelland, and John Welsh PMCID: PMC2425485 Gel-based oligonucleotide microarray approach to analyze protein–ssDNA binding specificity Olga A. Zasedateleva, Andrey L. Mikheikin, Alexander Y. Turygin, Dmitry V. Prokopenko, Alexander V. Chudinov, Elena E. Belobritskaya, Vladimir R. Chechetkin, and Alexander S. Zasedatelev PMCID: PMC2425478 Terminal proteins of Streptomyces chromosome can target DNA into eukaryotic nuclei Hsiu-Hui Tsai, Chih-Hung Huang, Alan M. Lin, and Carton W. Chen PMCID: PMC2425503 Computational Biology CSI-Tree: a regression tree approach for modeling binding properties of DNA-binding molecules based on cognate site identification (CSI) data Sündüz Keleş, Christopher L. Warren, Clayton D. Carlson, and Aseem Z. Ansari PMCID: PMC2425502 Accuracy and application of the motif expression decomposition method in dissecting transcriptional regulation Zhihua Zhang and Jianzhi Zhang PMCID: PMC2425491 A model of base-call resolution on broad-spectrum pathogen detection resequencing DNA microarrays Anthony P. Malanoski, Baochuan Lin, and David A. Stenger PMCID: PMC2425482 Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach Lei Li, Chenggang Wu, Haiming Huang, Kaizhong Zhang, Jacob Gan, and Shawn S.-C. Li PMCID: PMC2425477 Large-scale computational and statistical analyses of high transcription potentialities in 32 prokaryotic genomes Christine Sinoquet, Sylvain Demey, and Frédérique Braun PMCID: PMC2425493 High-throughput functional annotation and data mining with the Blast2GO suite Stefan Götz, Juan Miguel García-Gómez, Javier Terol, Tim D. Williams, Shivashankar H. Nagaraj, María José Nueda, Montserrat Robles, Manuel Talón, Joaquín Dopazo, and Ana Conesa PMCID: PMC2425479 Designating eukaryotic orthology via processed transcription units Meng-Ru Ho, Wen-Jung Jang, Chun-houh Chen, Lan-Yang Ch'ang, and Wen-chang Lin PMCID: PMC2425467 A new pheromone trail-based genetic algorithm for comparative genome assembly Fangqing Zhao, Fanggeng Zhao, Tao Li, and Donald A. Bryant PMCID: PMC2425481 Nucleic Acid Enzymes Conserved residues in the δ subunit help the E. coli clamp loader, γ complex, target primer-template DNA for clamp assembly Siying Chen, Maria Magdalena Coman, Miho Sakato, Michael O’Donnell, and Manju M. Hingorani PMCID: PMC2425476 Coordinate 5′ and 3′ endonucleolytic trimming of terminally blocked blunt DNA double-strand break ends by Artemis nuclease and DNA-dependent protein kinase Steven M. Yannone, Imran S. Khan, Rui-Zhe Zhou, Tong Zhou, Kristoffer Valerie, and Lawrence F. Povirk PMCID: PMC2425473 Rapid unwinding of triplet repeat hairpins by Srs2 helicase of Saccharomyces cerevisiae Alok Dhar and Robert S. Lahue PMCID: PMC2425488 |
