| | Molecular Biology Sequence-specific DNA cleavage mediated by bipyridine polyamide conjugates Philippe Simon, Fabio Cannata, Loïc Perrouault, Ludovic Halby, Jean-Paul Concordet, Alexandre Boutorine, Vladimir Ryabinin, Alexandre Sinyakov, and Carine Giovannangeli PMCID: PMC2441794 Cooperation between EZH2, NSPc1-mediated histone H2A ubiquitination and Dnmt1 in HOX gene silencing Xudong Wu, Yanhua Gong, Jiping Yue, Boqin Qiang, Jiangang Yuan, and Xiaozhong Peng PMCID: PMC2441805 TRE-dependent transcription activation by JDP2–CHOP10 association Keren Weidenfeld-Baranboim, Keren Bitton-Worms, and Ami Aronheim PMCID: PMC2441799 Characterization of genome-wide p53-binding sites upon stress response Leonie Smeenk, Simon J. van Heeringen, Max Koeppel, Marc A. van Driel, Stefanie J. J. Bartels, Robert C. Akkers, Sergei Denissov, Hendrik G. Stunnenberg, and Marion Lohrum PMCID: PMC2441782 Mechanism of high-mobility group protein B enhancement of progesterone receptor sequence-specific DNA binding Sarah C. Roemer, James Adelman, Mair E. A. Churchill, and Dean P. Edwards PMCID: PMC2441811 LINE-1 methylation status of endogenous DNA double-strand breaks Wichai Pornthanakasem, Narisorn Kongruttanachok, Chutipa Phuangphairoj, Chotika Suyarnsestakorn, Taweap Sanghangthum, Sornjarod Oonsiri, Wanpen Ponyeam, Thatchawan Thanasupawat, Oranart Matangkasombut, and Apiwat Mutirangura PMCID: PMC2441779 Streptococcus pyogenes pSM19035 requires dynamic assembly of ATP-bound ParA and ParB on parS DNA during plasmid segregation Florencia Pratto, Aslan Cicek, Wilhelm A. Weihofen, Rudi Lurz, Wolfram Saenger, and Juan C. Alonso PMCID: PMC2441792 The bHLH/Per-Arnt-Sim transcription factor SIM2 regulates muscle transcript myomesin2 via a novel, non-canonical E-box sequence Susan Woods, Alexandra Farrall, Carl Procko, and Murray L. Whitelaw PMCID: PMC2441813 Recruitment of RNA polymerase III in vivo Niall S. Kenneth, Lynne Marshall, and Robert J. White PMCID: PMC2441808 Structural polymorphism within a regulatory element of the human KRAS promoter: formation of G4-DNA recognized by nuclear proteins Susanna Cogoi, Manikandan Paramasivam, Barbara Spolaore, and Luigi E. Xodo PMCID: PMC2441797 Molecular basis for group-specific activation of the virulence regulator PlcR by PapR heptapeptides L. Bouillaut, S. Perchat, S. Arold, S. Zorrilla, L. Slamti, C. Henry, M. Gohar, N. Declerck, and D. Lereclus PMCID: PMC2441798 In vivo identification of novel STAT5 target genes Beth Basham, Manjiri Sathe, Jeffrey Grein, Terrill McClanahan, Annalisa D’Andrea, Emma Lees, and Anne Rascle PMCID: PMC2441806 Discovery of novel tumor suppressor p53 response elements using information theory Ilya G. Lyakhov, Annangarachari Krishnamachari, and Thomas D. Schneider PMCID: PMC2441790 bZIP-Type transcription factors CREB and OASIS bind and stimulate the promoter of the mammalian transcription factor GCMa/Gcm1 in trophoblast cells Steffen Wolfgang Schubert, Alexandra Abendroth, Karin Kilian, Tina Vogler, Bernhard Mayr, Ina Knerr, and Said Hashemolhosseini PMCID: PMC2441803 A single amino acid change in histone H4 enhances UV survival and DNA repair in yeast Ronita Nag, Feng Gong, Deirdre Fahy, and Michael J. Smerdon PMCID: PMC2441814 RNA Ribosomal RNAs are tolerant toward genetic insertions: evolutionary origin of the expansion segments Takeshi Yokoyama and Tsutomu Suzuki PMCID: PMC2441807 Selection of a novel class of RNA–RNA interaction motifs based on the ligase ribozyme with defined modular architecture Shoji P. Ohuchi, Yoshiya Ikawa, and Yoshikazu Nakamura PMCID: PMC2441787 Structural Biology Structural and functional insights into human Tudor-SN, a key component linking RNA interference and editing Chia-Lung Li, Wei-Zen Yang, Yi-Ping Chen, and Hanna S. Yuan PMCID: PMC2441809 Molecular basis for the lack of enantioselectivity of human 3-phosphoglycerate kinase C. Gondeau, L. Chaloin, P. Lallemand, B. Roy, C. Périgaud, T. Barman, A. Varga, M. Vas, C. Lionne, and S. T. Arold PMCID: PMC2441801 DNA conformations and their sequence preferences Daniel Svozil, Jan Kalina, Marek Omelka, and Bohdan Schneider PMCID: PMC2441783 Survey and Summary Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses Jerzy Orlowski and Janusz M. Bujnicki PMCID: PMC2441816 Genomics Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics Riu Yamashita, Yutaka Suzuki, Nono Takeuchi, Hiroyuki Wakaguri, Takuya Ueda, Sumio Sugano, and Kenta Nakai PMCID: PMC2441802 DNA physical properties determine nucleosome occupancy from yeast to fly Vincent Miele, Cédric Vaillant, Yves d'Aubenton-Carafa, Claude Thermes, and Thierry Grange PMCID: PMC2441789 Chemistry Snap-to-it probes: chelate-constrained nucleobase oligomers with enhanced binding specificity Joel R. Morgan, Robert P. Lyon, Dean Y. Maeda, and John A. Zebala PMCID: PMC2441785 DNA binding of dinuclear iron(II) metallosupramolecular cylinders. DNA unwinding and sequence preference Jaroslav Malina, Michael J. Hannon, and Viktor Brabec PMCID: PMC2441793 Mechanistic studies on bleomycin-mediated DNA damage: multiple binding modes can result in double-stranded DNA cleavage Jingyang Chen, Manas K. Ghorai, Grace Kenney, and JoAnne Stubbe PMCID: PMC2441780 Methods Online High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis Somdeb Mitra, Inna V. Shcherbakova, Russ B. Altman, Michael Brenowitz, and Alain Laederach PMCID: PMC2441812 A simple algorithm for quantifying DNA methylation levels on multiple independent CpG sites in bisulfite genomic sequencing electropherograms Tatiana I. Leakey, Jerzy Zielinski, Rachel N. Siegfried, Eric R. Siegel, Chun-Yang Fan, and Craig A. Cooney PMCID: PMC2441810 Electrochemical detection of low-copy number salivary RNA based on specific signal amplification with a hairpin probe Fang Wei, Jianghua Wang, Wei Liao, Bernhard G. Zimmermann, David T. Wong, and Chih-Ming Ho PMCID: PMC2441804 Predicting failure rate of PCR in large genomes Reidar Andreson, Tõnu Möls, and Maido Remm PMCID: PMC2441781 Regulated gene insertion by steroid-induced ΦC31 integrase Nynne Sharma, Brian Moldt, Trine Dalsgaard, Thomas G. Jensen, and Jacob Giehm Mikkelsen PMCID: PMC2441784 The simple and rapid detection of specific PCR products from bacterial genomes using Zn finger proteins Yuko Osawa, Kazunori Ikebukuro, Hiroaki Motoki, Takafumi Matsuo, Michio Horiuchi, and Koji Sode PMCID: PMC2441800 Computational Biology 3D visualization software to analyze topological outcomes of topoisomerase reactions I. K. Darcy, R. G. Scharein, and A. Stasiak PMCID: PMC2441796 Spatial effects on the speed and reliability of protein–DNA search Zeba Wunderlich and Leonid A. Mirny PMCID: PMC2441786 Beyond tissueInfo: functional prediction using tissue expression profile similarity searches Daniel Aguilar, Lucy Skrabanek, Steven S. Gross, Baldo Oliva, and Fabien Campagne PMCID: PMC2441795 Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design Zhi John Lu and David H. Mathews PMCID: PMC2441788 SCUMBLE: a method for systematic and accurate detection of codon usage bias by maximum likelihood estimation Morten Kloster and Chao Tang PMCID: PMC2441815 Nucleic Acid Enzymes Low-fidelity DNA synthesis by human DNA polymerase theta Mercedes E. Arana, Mineaki Seki, Richard D. Wood, Igor B. Rogozin, and Thomas A. Kunkel PMCID: PMC2441791 |
