| | Molecular Biology Mechanisms of activation of interferon regulator factor 3: the role of C-terminal domain phosphorylation in IRF-3 dimerization and DNA binding Anatoly I. Dragan, Victoria V. Hargreaves, Elena N. Makeyeva, and Peter L. Privalov PMCID: PMC1920236 Untangling the relationships between DNA repair pathways by silencing more than 20 DNA repair genes in human stable clones D. S. F. Biard PMCID: PMC1920239 Involvement of DNA polymerase μ in the repair of a specific subset of DNA double-strand breaks in mammalian cells Jean-Pascal Capp, François Boudsocq, Anne-Gaelle Besnard, Bernard S. Lopez, Christophe Cazaux, Jean-Sébastien Hoffmann, and Yvan Canitrot PMCID: PMC1920243 Cumulative contributions of weak DNA determinants to targeting the Drosophila dosage compensation complex Gregor D. Gilfillan, Cornelia König, Ina K. Dahlsveen, Nicky Prakoura, Tobias Straub, Rosemarie Lamm, Torsten Fauth, and Peter B. Becker PMCID: PMC1920250 Redundant role of DEAD box proteins p68 (Ddx5) and p72/p82 (Ddx17) in ribosome biogenesis and cell proliferation Carolin Jalal, Heike Uhlmann-Schiffler, and Hans Stahl PMCID: PMC1920232 Pathogen-induced binding of the soybean zinc finger homeodomain proteins GmZF-HD1 and GmZF-HD2 to two repeats of ATTA homeodomain binding site in the calmodulin isoform 4 (GmCaM4) promoter Hyeong Cheol Park, Man Lyang Kim, Sang Min Lee, Jeong Dong Bahk, Dae-Jin Yun, Chae Oh Lim, Jong Chan Hong, Sang Yeol Lee, Moo Je Cho, and Woo Sik Chung PMCID: PMC1920248 Disparate contributions of the Fanconi anemia pathway and homologous recombination in preventing spontaneous mutagenesis John M. Hinz, Peter B. Nham, Salustra S. Urbin, Irene M. Jones, and Larry H. Thompson PMCID: PMC1920256 Sp1 and Sp3 regulate basal transcription of the human APOBEC3G gene Heide Muckenfuss, Julia K. Kaiser, Erika Krebil, Marion Battenberg, Christina Schwer, Klaus Cichutek, Carsten Münk, and Egbert Flory PMCID: PMC1920263 Aprataxin, causative gene product for EAOH/AOA1, repairs DNA single-strand breaks with damaged 3′-phosphate and 3′-phosphoglycolate ends Tetsuya Takahashi, Masayoshi Tada, Shuichi Igarashi, Akihide Koyama, Hidetoshi Date, Akio Yokoseki, Atsushi Shiga, Yutaka Yoshida, Shoji Tsuji, Masatoyo Nishizawa, and Osamu Onodera PMCID: PMC1920238 C-Terminal regions of topoisomerase IIα and IIβ determine isoform-specific functioning of the enzymes in vivo René M. Linka, Andrew C.G. Porter, Arsen Volkov, Christian Mielke, Fritz Boege, and Morten O. Christensen PMCID: PMC1920234 RNA Dynamics of filamentous viral RNPs prior to egress Philip J. Santangelo and Gang Bao PMCID: PMC1920244 Reprogramming the tRNA-splicing activity of a bacterial RNA repair enzyme Niroshika Keppetipola, Jayakrishnan Nandakumar, and Stewart Shuman PMCID: PMC1920235 Mapping of mitochondrial mRNA termini in Arabidopsis thaliana: t-elements contribute to 5′ and 3′ end formation Joachim Forner, Bärbel Weber, Sabine Thuss, Steffen Wildum, and Stefan Binder PMCID: PMC1920247 Conformational changes in the expression domain of the Escherichia coli thiM riboswitch Andrea Rentmeister, Günter Mayer, Nicole Kuhn, and Michael Famulok PMCID: PMC1920254 Regulation of glutamate receptor B pre-mRNA splicing by RNA editing Vera K. Schoft, Sandy Schopoff, and Michael F. Jantsch PMCID: PMC1920255 RNA chaperone activity of L1 ribosomal proteins: phylogenetic conservation and splicing inhibition Stefan L. Ameres, Dmitry Shcherbakov, Ekaterina Nikonova, Wolfgang Piendl, Renée Schroeder, and Katharina Semrad PMCID: PMC1920258 The electrostatic characteristics of G·U wobble base pairs Darui Xu, Theresa Landon, Nancy L. Greenbaum, and Marcia O. Fenley PMCID: PMC1920249 Structural Biology G-quadruplex formation in human telomeric (TTAGGG)4 sequence with complementary strand in close vicinity under molecularly crowded condition Zhong-yuan Kan, Yi Lin, Feng Wang, Xin-ying Zhuang, Yong Zhao, Dai-wen Pang, Yu-hua Hao, and Zheng Tan PMCID: PMC1920240 Three-dimensional model for the isolated recombinant influenza virus polymerase heterotrimer Eva Torreira, Guy Schoehn, Yolanda Fernández, Núria Jorba, Rob W.H. Ruigrok, Stephen Cusack, Juan Ortín, and Oscar Llorca PMCID: PMC1920261 Survey and Summary Human RNase P: a tRNA-processing enzyme and transcription factor Nayef Jarrous and Robert Reiner PMCID: PMC1920233 Genomics Comparative analysis of bacterial genomes: identification of divergent regions in mycobacterial strains using an anchor-based approach Anchal Vishnoi, Rahul Roy, and Alok Bhattacharya PMCID: PMC1931498 Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome Shurjo K. Sen, Charles T. Huang, Kyudong Han, and Mark A. Batzer PMCID: PMC1920257 Chemistry Pixantrone can be activated by formaldehyde to generate a potent DNA adduct forming agent Ben J. Evison, Oula C. Mansour, Ernesto Menta, Don R. Phillips, and Suzanne M. Cutts PMCID: PMC1920253 Enhanced oligonucleotide–nanoparticle conjugate stability using thioctic acid modified oligonucleotides Jennifer A. Dougan, Camilla Karlsson, W. Ewen Smith, and Duncan Graham PMCID: PMC1920241 Methods Online General transfer matrix formalism to calculate DNA–protein–drug binding in gene regulation: application to OR operator of phage λ Vladimir B. Teif PMCID: PMC1920246 Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method Xiangdong Meng, Stacey Thibodeau-Beganny, Tao Jiang, J. Keith Joung, and Scot A. Wolfe PMCID: PMC1920264 Quantitative multiplexing analysis of PCR-amplified ribosomal RNA genes by hierarchical oligonucleotide primer extension reaction Jer-Horng Wu and Wen-Tso Liu PMCID: PMC1920266 Selection of restriction endonucleases using artificial cells Yu Zheng and Richard J. Roberts PMCID: PMC1920265 Computational Biology Distributed control for recruitment, scanning and subunit joining steps of translation initiation Padchanee Sangthong, John Hughes, and John E. G. McCarthy PMCID: PMC1920251 Extracting binary signals from microarray time-course data Debashis Sahoo, David L. Dill, Rob Tibshirani, and Sylvia K. Plevritis PMCID: PMC1920252 SNAP: predict effect of non-synonymous polymorphisms on function Yana Bromberg and Burkhard Rost PMCID: PMC1920242 Nucleic Acid Enzymes Characterization of Agrobacterium tumefaciens DNA ligases C and D Hui Zhu and Stewart Shuman PMCID: PMC1920237 In vitro replication and thermodynamic studies of methylation and oxidation modifications of 6-thioguanine Chunang Gu and Yinsheng Wang PMCID: PMC1920245 DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity Felix Mueller-Planitz and Daniel Herschlag PMCID: PMC1920260 Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules Ji Hoon Kim and Ronald G. Larson PMCID: PMC1920259 Cell cycle regulation as a mechanism for functional separation of the apparently redundant uracil DNA glycosylases TDG and UNG2 Ulrike Hardeland, Christophe Kunz, Frauke Focke, Marta Szadkowski, and Primo Schär PMCID: PMC1920262 |
