| | Editorial Nucleic Acids Res. 2007 December; 35(21): 7043. Published online 2007 December. doi: 10.1093/nar/gkm1015.PMCID: PMC2175340 Molecular Biology Heme oxygenase-1 induction by NRF2 requires inactivation of the transcriptional repressor BACH1 John F. Reichard, Gregory T. Motz, and Alvaro Puga PMCID: PMC2175339 MyoD uses overlapping but distinct elements to bind E-box and tetraplex structures of regulatory sequences of muscle-specific genes Jeny Shklover, Shulamit Etzioni, Pnina Weisman-Shomer, Anat Yafe, Eyal Bengal, and Michael Fry PMCID: PMC2175354 Deaminase-independent inhibition of HIV-1 reverse transcription by APOBEC3G Yasumasa Iwatani, Denise S.B. Chan, F. Wang, Kristen Stewart Maynard, Wataru Sugiura, Angela M. Gronenborn, Ioulia Rouzina, Mark C. Williams, Karin Musier-Forsyth, and Judith G. Levin PMCID: PMC2175344 In vivo assembling of bacterial ribosomal protein L11 into yeast ribosomes makes the particles sensitive to the prokaryotic specific antibiotic thiostrepton Alberto García-Marcos, Antonio Morreale, Esther Guarinos, Elisa Briones, Miguel Remacha, Angel R. Ortiz, and Juan P. G. Ballesta PMCID: PMC2175356 3′-Azido-2′,3′-dideoxynucleoside 5′-triphosphates inhibit telomerase activity in vitro, and the corresponding nucleosides cause telomere shortening in human HL60 cells Xiaohong Liu, Hazuki Takahashi, Yoko Harada, Tsukasa Ogawara, Yuta Ogimura, Yoshiyuku Mizushina, Mineo Saneyoshi, and Toyofumi Yamaguchi PMCID: PMC2175342 General, negative feedback mechanism for regulation of Trithorax-like gene expression in vivo: new roles for GAGA factor in flies Jordi Bernués, David Piñeyro, and Ana Kosoy PMCID: PMC2175371 BCCIP regulates homologous recombination by distinct domains and suppresses spontaneous DNA damage Huimei Lu, Jingyin Yue, Xiangbing Meng, Jac A. Nickoloff, and Zhiyuan Shen PMCID: PMC2175368 Oncogenic point mutations in the Myb DNA-binding domain alter the DNA-binding properties of Myb at a physiological target gene Olga Ivanova, Daniel Braas, and Karl-Heinz Klempnauer PMCID: PMC2175353 Faithful transcription initiation from a mitochondrial promoter in transgenic plastids Alexandra-Viola Bohne, Stephanie Ruf, Thomas Börner, and Ralph Bock PMCID: PMC2175370 Replication protein A prevents accumulation of single-stranded telomeric DNA in cells that use alternative lengthening of telomeres Amra Grudic, Åsne Jul-Larsen, Stuart J. Haring, Marc S. Wold, Per Eystein Lønning, Rolf Bjerkvig, and Stig Ove Bøe PMCID: PMC2175364 Negative regulation of transcription coactivator p300 by orphan receptor TR3 Gui-deng Li, Jin-xu Fang, Hang-zi Chen, Jie Luo, Zhong-hui Zheng, Yue-mao Shen, and Qiao Wu PMCID: PMC2175348 Expression of the CTCF-paralogous cancer-testis gene, brother of the regulator of imprinted sites (BORIS), is regulated by three alternative promoters modulated by CpG methylation and by CTCF and p53 transcription factors Stéphanie Renaud, Elena M. Pugacheva, M. Dolores Delgado, Richard Braunschweig, Ziedulla Abdullaev, Dmitri Loukinov, Jean Benhattar, and Victor Lobanenkov PMCID: PMC2175345 Domain I of ribosomal protein L1 is sufficient for specific RNA binding Svetlana Tishchenko, Ekaterina Nikonova, Vladislav Kljashtorny, Olga Kostareva, Natalia Nevskaya, Wolfgang Piendl, Natalia Davydova, Victor Streltsov, Maria Garber, and Stanislav Nikonov PMCID: PMC2175363 RNA Aminoglycoside binding to the HIV-1 RNA dimerization initiation site: thermodynamics and effect on the kissing-loop to duplex conversion Serena Bernacchi, Séverine Freisz, Clarisse Maechling, Bernard Spiess, Roland Marquet, Philippe Dumas, and Eric Ennifar PMCID: PMC2175338 Interaction of SmpB with ribosome from directed hydroxyl radical probing Daisuke Kurita, Rumi Sasaki, Akira Muto, and Hyouta Himeno PMCID: PMC2175365 Virion packaging determinants and reverse transcription of SRP RNA in HIV-1 particles Chunjuan Tian, Tao Wang, Wenyan Zhang, and Xiao-Fang Yu PMCID: PMC2175372 An RNA targeted to the HIV-1 LTR promoter modulates indiscriminate off-target gene activation Marc S. Weinberg, Samantha Barichievy, Lana Schaffer, Jiang Han, and Kevin V. Morris PMCID: PMC2175361 Expression of a novel non-coding mitochondrial RNA in human proliferating cells Jaime Villegas, Veronica Burzio, Claudio Villota, Eduardo Landerer, Ronny Martinez, Marcela Santander, Rodrigo Martinez, Rodrigo Pinto, María I. Vera, Enrique Boccardo, Luisa L. Villa, and Luis O. Burzio PMCID: PMC2175360 Structural Biology Mechanistic insights from the crystal structures of a feast/famine regulatory protein from Mycobacterium tuberculosis H37Rv Tripti Shrivastava and Ravishankar Ramachandran PMCID: PMC2175373 Genomics Formation and genotoxicity of a guanine–cytosine intrastrand cross-link lesion in vivo Haizheng Hong, Huachuan Cao, and Yinsheng Wang PMCID: PMC2175358 Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor Salim Charaniya, Sarika Mehra, Wei Lian, Karthik P. Jayapal, George Karypis, and Wei-Shou Hu PMCID: PMC2175336 Chemistry DNA multiplex hybridization on microarrays and thermodynamic stability in solution: a direct comparison Daniel J. Fish, M. Todd Horne, Greg P. Brewood, Jim P. Goodarzi, Saba Alemayehu, Ashwini Bhandiwad, Robert P. Searles, and Albert S. Benight PMCID: PMC2175334 Superior structure stability and selectivity of hairpin nucleic acid probes with an l-DNA stem Youngmi Kim, Chaoyong James Yang, and Weihong Tan PMCID: PMC2175343 Methods Online A versatile method for the preparation of conjugates of peptides with DNA/PNA/analog by employing chemo-selective click reaction in water Khirud Gogoi, Meenakshi V. Mane, Sunita S. Kunte, and Vaijayanti A. Kumar PMCID: PMC2175367 Heat-resistant DNA tile arrays constructed by template-directed photoligation through 5-carboxyvinyl-2′-deoxyuridine Miho Tagawa, Koh-ichiroh Shohda, Kenzo Fujimoto, Tadashi Sugawara, and Akira Suyama PMCID: PMC2175349 Yeast two-hybrid interaction partner screening through in vivo Cre-mediated Binary Interaction Tag generation Alex R. Hastie and Steven C. Pruitt PMCID: PMC2189736 A yeast two-hybrid system reconstituting substrate recognition of the von Hippel-Lindau tumor suppressor protein Claudia Bex, Katja Knauth, Silvia Dambacher, and Alexander Buchberger PMCID: PMC2175351 Quantitative analysis of the binding affinity of poly(ADP-ribose) to specific binding proteins as a function of chain length Jörg Fahrer, Ramon Kranaster, Matthias Altmeyer, Andreas Marx, and Alexander Bürkle PMCID: PMC2175335 A ligation assay for multiplex analysis of CpG methylation using bisulfite-treated DNA Christina Dahl and Per Guldberg PMCID: PMC2175362 Using force spectroscopy analysis to improve the properties of the hairpin probe Liu Yang, Kemin Wang, Weihong Tan, Huimin Li, Xiaohai Yang, Changbei Ma, and Hongxing Tang PMCID: PMC2175366 A sensitive procedure to detect alternatively spliced mRNA in pooled-tissue samples Germán Gastón Leparc and Robi David Mitra PMCID: PMC2175357 Kinetic studies of Escherichia coli AlkB using a new fluorescence-based assay for DNA demethylation Todd W. Roy and A. S. Bhagwat PMCID: PMC2175350 A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip® whole-genome resequencing platform Gagan A. Pandya, Michael H. Holmes, Sirisha Sunkara, Andrew Sparks, Yun Bai, Kathleen Verratti, Kelly Saeed, Pratap Venepally, Behnam Jarrahi, Robert D. Fleischmann, and Scott N. Peterson PMCID: PMC2175352 Computational Biology SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB Elmar Pruesse, Christian Quast, Katrin Knittel, Bernhard M. Fuchs, Wolfgang Ludwig, Jörg Peplies, and Frank Oliver Glöckner PMCID: PMC2175337 TREMOR—a tool for retrieving transcriptional modules by incorporating motif covariance Larry N. Singh, Li-San Wang, and Sridhar Hannenhalli PMCID: PMC2189735 Nucleic Acid Enzymes Escherichia coli RNA polymerase-associated SWI/SNF protein RapA: evidence for RNA-directed binding and remodeling activity Brian A. McKinley and Maxim V. Sukhodolets PMCID: PMC2175355 Involvement of phage ϕ29 DNA polymerase and terminal protein subdomains in conferring specificity during initiation of protein-primed DNA replication Patricia Pérez-Arnaiz, Elisa Longás, Laurentino Villar, José M. Lázaro, Margarita Salas, and Miguel de Vega PMCID: PMC2175359 Real-time measurements of the nucleation, growth and dissociation of single Rad51–DNA nucleoprotein filaments Judith Miné, Ludovic Disseau, Masayuki Takahashi, Giovanni Cappello, Marie Dutreix, and Jean-Louis Viovy PMCID: PMC2175369 Thermodynamics of DNA target site recognition by homing endonucleases Jennifer H. Eastberg, Audrey McConnell Smith, Lei Zhao, Justin Ashworth, Betty W. Shen, and Barry L. Stoddard PMCID: PMC2175346 Automethylation of G9a and its implication in wider substrate specificity and HP1 binding Hang Gyeong Chin, Pierre-Olivier Estève, Mihika Pradhan, Jack Benner, Debasis Patnaik, Michael F. Carey, and Sriharsa Pradhan PMCID: PMC2175347 Erratum Efficient splicing correction by PNA conjugation to an R6-Penetratin delivery peptide Saïd Abes, John J. Turner, Gabriela D. Ivanova, David Owen, Donna Williams, Andrey Arzumanov, Philippe Clair, Michael J. Gait, and Bernard Lebleu PMCID: PMC2175341 Corrects: Saïd Abes, et al. Efficient splicing correction by PNA conjugation to an R6-Penetratin delivery peptide. Nucleic Acids Res. 2007 July; 35(13): 4495–4502. |
