| | Chemistry and Synthetic Biology Assembling of G-strands into novel tetra-molecular parallel G4-DNA nanostructures using avidin–biotin recognition Natalia Borovok, Natalie Iram, Dragoslav Zikich, Jamal Ghabboun, Gideon I. Livshits, Danny Porath, and Alexander B. Kotlyar PMCID: PMC2528189 Editorial-Publication Charges Editorial-Publication Charges Claire Bird, Keith Fox, and Rich Roberts PMCID: PMC2528181 Gene Regulation, Chromatin and Epigenetics Chromatin profiling across the human tumour necrosis factor gene locus reveals a complex, cell type-specific landscape with novel regulatory elements Jennifer M. Taylor, Kate Wicks, Claire Vandiedonck, and Julian C. Knight PMCID: PMC2528168 A high-throughput percentage-of-binding strategy to measure binding energies in DNA–protein interactions: application to genome-scale site discovery Xiaohu Wang, Haichun Gao, Yufeng Shen, George M. Weinstock, Jizhong Zhou, and Timothy Palzkill PMCID: PMC2528174 The splice variants of UBF differentially regulate RNA polymerase I transcription elongation in response to ERK phosphorylation Victor Y. Stefanovsky and Tom Moss PMCID: PMC2528179 Molecular Biology DNA repair of clustered lesions in mammalian cells: involvement of non-homologous end-joining Svitlana Malyarchuk, Reneau Castore, and Lynn Harrison PMCID: PMC2528178 Srs2 removes deadly recombination intermediates independently of its interaction with SUMO-modified PCNA Cyrille Le Breton, Pauline Dupaigne, Thomas Robert, Eric Le Cam, Serge Gangloff, Francis Fabre, and Xavier Veaute PMCID: PMC2528196 WRN Exonuclease activity is blocked by specific oxidatively induced base lesions positioned in either DNA strand Zuzanna Bukowy, Jeanine A. Harrigan, Dale A. Ramsden, Barbara Tudek, Vilhelm A. Bohr, and Tinna Stevnsner PMCID: PMC2528166 Multimolecular complex of Par-4 and E2F1 binding to Smac promoter contributes to glutamate-induced apoptosis in human- bone mesenchymal stem cells Chao Lu, Jie-Qing Chen, Guo-Ping Zhou, Sheng-Hua Wu, Ya-Fei Guan, and Chuan-Shun Yuan PMCID: PMC2528162 Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis Melda Tozluoğlu, Ezgi Karaca, Turkan Haliloglu, and Ruth Nussinov PMCID: PMC2528188 DNA organization by the apicoplast-targeted bacterial histone-like protein of Plasmodium falciparum E. V. S. Raghu Ram, Rangeetha Naik, Munia Ganguli, and Saman Habib PMCID: PMC2528193 XRCC1 protects against the lethality of induced oxidative DNA damage in nondividing neural cells Avanti Kulkarni, Daniel R. McNeill, Marc Gleichmann, Mark P. Mattson, and David M. Wilson, III PMCID: PMC2528184 RNA A unique conformation of the anticodon stem-loop is associated with the capacity of tRNAfMet to initiate protein synthesis Pierre Barraud, Emmanuelle Schmitt, Yves Mechulam, Frédéric Dardel, and Carine Tisné PMCID: PMC2528185 The G-quartet containing FMRP binding site in FMR1 mRNA is a potent exonic splicing enhancer Marie-Cécile Didiot, Zhaoxia Tian, Céline Schaeffer, Murugan Subramanian, Jean-Louis Mandel, and Hervé Moine PMCID: PMC2528169 Imaging and characterizing influenza A virus mRNA transport in living cells Wei Wang, Zong-Qiang Cui, Han Han, Zhi-Ping Zhang, Hong-Ping Wei, Ya-Feng Zhou, Ze Chen, and Xian-En Zhang PMCID: PMC2528172 60S ribosomal subunit assembly dynamics defined by semi-quantitative mass spectrometry of purified complexes Alice Lebreton, Jean-Claude Rousselle, Pascal Lenormand, Abdelkader Namane, Alain Jacquier, Micheline Fromont-Racine, and Cosmin Saveanu PMCID: PMC2528192 Structural Biology The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity Hélène Walbott, Nicolas Leulliot, Henri Grosjean, and Béatrice Golinelli-Pimpaneau PMCID: PMC2528175 Molecular dynamics of a κB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation Cameron Mura and J. Andrew McCammon PMCID: PMC2528173 Selective recognition of pyrimidine–pyrimidine DNA mismatches by distance-constrained macrocyclic bis-intercalators Matthias Bahr, Valérie Gabelica, Anton Granzhan, Marie-Paule Teulade-Fichou, and Elmar Weinhold PMCID: PMC2528167 RecR forms a ring-like tetramer that encircles dsDNA by forming a complex with RecF Masayoshi Honda, Tetsuro Fujisawa, Takehiko Shibata, and Tsutomu Mikawa PMCID: PMC2528183 The proofreading exonuclease subunit ε of Escherichia coli DNA polymerase III is tethered to the polymerase subunit α via a flexible linker Kiyoshi Ozawa, Slobodan Jergic, Ah Young Park, Nicholas E. Dixon, and Gottfried Otting PMCID: PMC2528190 Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design Joseph D. Bauman, Kalyan Das, William C. Ho, Mukta Baweja, Daniel M. Himmel, Arthur D. Clark, Jr, Deena A. Oren, Paul L. Boyer, Stephen H. Hughes, Aaron J. Shatkin, and Eddy Arnold PMCID: PMC2528191 Methods Online Chum-RNA allows preparation of a high-quality cDNA library from a single-cell quantity of mRNA without PCR amplification Takahiro Tougan, Daisuke Okuzaki, and Hiroshi Nojima PMCID: PMC2528176 Tetraalkylammonium derivatives as real-time PCR enhancers and stabilizers of the qPCR mixtures containing SYBR Green I Gouse M. Shaik, Lubica Dráberová, Peter Dráber, Michael Boubelík, and Petr Dráber PMCID: PMC2528177 SNP-specific extraction of haplotype-resolved targeted genomic regions Johannes Dapprich, Deborah Ferriola, Eleni E. Magira, Mark Kunkel, and Dimitri Monos PMCID: PMC2528194 A functional selection of viral genetic elements in cultured cells to identify hepatitis C virus RNA translation inhibitors Loic Jaffrelo, Sandrine Chabas, Sandrine Reigadas, Aude Pflieger, Czeslaw Wychowski, Julie Rumi, Michel Ventura, Jean-Jacques Toulmé, and Cathy Staedel PMCID: PMC2528164 Rational vector design and multi-pathway modulation of HEK 293E cells yield recombinant antibody titers exceeding 1 g/l by transient transfection under serum-free conditions Gaurav Backliwal, Markus Hildinger, Sebastien Chenuet, Sarah Wulhfard, Maria De Jesus, and Florian M. Wurm PMCID: PMC2528171 Functional studies on transfected cell microarray analysed by linear regression modelling Christina Sæten Fjeldbo, Kristine Misund, Clara-Cecilie Günther, Mette Langaas, Tonje Strømmen Steigedal, Liv Thommesen, Astrid Lægreid, and Torunn Bruland PMCID: PMC2528170 Electrical detection of the temperature induced melting transition of a DNA hairpin covalently attached to gold interdigitated microelectrodes Greg P. Brewood, Yaswanth Rangineni, Daniel J. Fish, Ashwini S. Bhandiwad, David R. Evans, Raj Solanki, and Albert S. Benight PMCID: PMC2528165 Computational Biology Tissue-specific splicing factor gene expression signatures Ana Rita Grosso, Anita Q. Gomes, Nuno L. Barbosa-Morais, Sandra Caldeira, Natalie P. Thorne, Godfrey Grech, Marieke von Lindern, and Maria Carmo-Fonseca PMCID: PMC2528195 Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation Jiong-Tang Li, Yong Zhang, Lei Kong, Qing-Rong Liu, and Liping Wei PMCID: PMC2528163 DNA supercoiling inhibits DNA knotting Yannis Burnier, Julien Dorier, and Andrzej Stasiak PMCID: PMC2528182 Nucleic Acid Enzymes Human topoisomerase IIα uses a two-metal-ion mechanism for DNA cleavage Joseph E. Deweese, Alex B. Burgin, and Neil Osheroff PMCID: PMC2528187 The solution structure of the amino-terminal domain of human DNA polymerase ε subunit B is homologous to C-domains of AAA+ proteins Tarmo Nuutinen, Helena Tossavainen, Kai Fredriksson, Päivi Pirilä, Perttu Permi, Helmut Pospiech, and Juhani E. Syvaoja PMCID: PMC2528186 Erratum Dynamics and consequences of DNA looping by the FokI restriction endonuclease Lucy E. Catto, Stuart R. W. Bellamy, Susan E. Retter, and Stephen E. Halford PMCID: PMC2528180 Corrects: Lucy E. Catto, et al. Dynamics and consequences of DNA looping by the FokI restriction endonuclease. Nucleic Acids Res. 2008 April; 36(6): 2073–2081. |
