| | Molecular Biology Intracellular expression profiles measured by real-time PCR tomography in the Xenopus laevis oocyte Radek Sindelka, Jiri Jonák, Rebecca Hands, Stephen A. Bustin, and Mikael Kubista Nucleic Acids Res. 2008 February; 36(2): 387–392. Published online 2008 February. doi: 10.1093/nar/gkm1024.PMCID: PMC2241880 DNA tape measurements of AraC Michael E. Rodgers and Robert Schleif Nucleic Acids Res. 2008 February; 36(2): 404–410. Published online 2008 February. doi: 10.1093/nar/gkm1030.PMCID: PMC2241862 Transcription of Satellite III non-coding RNAs is a general stress response in human cells Rut Valgardsdottir, Ilaria Chiodi, Manuela Giordano, Antonio Rossi, Silvia Bazzini, Claudia Ghigna, Silvano Riva, and Giuseppe Biamonti Nucleic Acids Res. 2008 February; 36(2): 423–434. Published online 2008 February. doi: 10.1093/nar/gkm1056.PMCID: PMC2241877 Retinoic acid modulates chromatin to potentiate tumor necrosis factor alpha signaling on the DIF2 promoter Michael Witcher, Filippa Pettersson, Daphne Dupéré-Richer, Alessandra Padovani, Leslie Summers-Deluca, Albert S. Baldwin, and Wilson H. Miller, Jr Nucleic Acids Res. 2008 February; 36(2): 435–443. Published online 2008 February. doi: 10.1093/nar/gkm1058.PMCID: PMC2241879 Structure of discontinuities in kinetoplast DNA-associated minicircles during S phase in Crithidia fasciculata Jane C. Hines and Dan S. Ray Nucleic Acids Res. 2008 February; 36(2): 444–450. Published online 2008 February. doi: 10.1093/nar/gkm1061.PMCID: PMC2241878 Chromatin-associated HMG-17 is a major regulator of homeodomain transcription factor activity modulated by Wnt/β-catenin signaling Melanie Amen, Herbert M. Espinoza, Carol Cox, Xiaowen Liang, Jianbo Wang, Todd M. E. Link, Richard G. Brennan, James F. Martin, and Brad A. Amendt Nucleic Acids Res. 2008 February; 36(2): 462–476. Published online 2008 February. doi: 10.1093/nar/gkm1047.PMCID: PMC2241859 Repair of DNA double-strand breaks within the (GAA•TTC)n sequence results in frequent deletion of the triplet-repeat sequence Laura M. Pollard, Rebecka L. Bourn, and Sanjay I. Bidichandani Nucleic Acids Res. 2008 February; 36(2): 489–500. Published online 2008 February. doi: 10.1093/nar/gkm1066.PMCID: PMC2241870 ATR-dependent pathways control hEXO1 stability in response to stalled forks Mahmoud El-Shemerly, Daniel Hess, Aswin K. Pyakurel, Said Moselhy, and Stefano Ferrari Nucleic Acids Res. 2008 February; 36(2): 511–519. Published online 2008 February. doi: 10.1093/nar/gkm1052.PMCID: PMC2241874 The RNA-dependent RNA polymerase essential for post-transcriptional gene silencing in Neurospora crassa interacts with replication protein A Tony Nolan, Germano Cecere, Carmine Mancone, Tonino Alonzi, Marco Tripodi, Caterina Catalanotto, and Carlo Cogoni Nucleic Acids Res. 2008 February; 36(2): 532–538. Published online 2008 February. doi: 10.1093/nar/gkm1071.PMCID: PMC2241871 The dual control of TFIIB recruitment by NC2 is gene specific Patrick Masson, Elisa Leimgruber, Sandrine Creton, and Martine A. Collart Nucleic Acids Res. 2008 February; 36(2): 539–549. Published online 2008 February. doi: 10.1093/nar/gkm1078.PMCID: PMC2241854 Regulating gene expression in human leukemia cells using light-activated oligodeoxynucleotides XinJing Tang, Jyothishmathi Swaminathan, Alan M. Gewirtz, and Ivan J. Dmochowski Nucleic Acids Res. 2008 February; 36(2): 559–569. Published online 2008 February. doi: 10.1093/nar/gkm1029.PMCID: PMC2241881 Nε-Formylation of lysine is a widespread post-translational modification of nuclear proteins occurring at residues involved in regulation of chromatin function Jacek R. Wiśniewski, Alexandre Zougman, and Matthias Mann Nucleic Acids Res. 2008 February; 36(2): 570–577. Published online 2008 February. doi: 10.1093/nar/gkm1057.PMCID: PMC2241850 The interaction of mammalian mitochondrial translational initiation factor 3 with ribosomes: evolution of terminal extensions in IF3mt Md. Emdadul Haque, Domenick Grasso, and Linda L. Spremulli Nucleic Acids Res. 2008 February; 36(2): 589–597. Published online 2008 February. doi: 10.1093/nar/gkm1072.PMCID: PMC2241858 Overlapping activator sequences determined for two oppositely oriented promoters in halophilic Archaea Martina Bauer, Larissa Marschaus, Muriel Reuff, Verena Besche, Simone Sartorius-Neef, and Felicitas Pfeifer Nucleic Acids Res. 2008 February; 36(2): 598–606. Published online 2008 February. doi: 10.1093/nar/gkm1077.PMCID: PMC2241852 Escherichia coli low-copy-number plasmid R1 centromere parC forms a U-shaped complex with its binding protein ParR C. Hoischen, M. Bussiek, J. Langowski, and S. Diekmann Nucleic Acids Res. 2008 February; 36(2): 607–615. Published online 2008 February. doi: 10.1093/nar/gkm672.PMCID: PMC2241845 Functional endogenous LINE-1 retrotransposons are expressed and mobilized in rat chloroleukemia cells Alexander Kirilyuk, Genrich V. Tolstonog, Annette Damert, Ulrike Held, Silvia Hahn, Roswitha Löwer, Christian Buschmann, Axel V. Horn, Peter Traub, and Gerald G. Schumann Nucleic Acids Res. 2008 February; 36(2): 648–665. Published online 2008 February. doi: 10.1093/nar/gkm1045.PMCID: PMC2241872 RNA Rho-independent transcription terminators inhibit RNase P processing of the secG leuU and metT tRNA polycistronic transcripts in Escherichia coli Bijoy K. Mohanty and Sidney R. Kushner Nucleic Acids Res. 2008 February; 36(2): 364–375. Published online 2008 February. doi: 10.1093/nar/gkm991.PMCID: PMC2241853 Nuclear RNA export factor 7 is localized in processing bodies and neuronal RNA granules through interactions with shuttling hnRNPs Jun Katahira, Takashi Miki, Keizo Takano, Mitsuji Maruhashi, Masanori Uchikawa, Taro Tachibana, and Yoshihiro Yoneda Nucleic Acids Res. 2008 February; 36(2): 616–628. Published online 2008 February. doi: 10.1093/nar/gkm556.PMCID: PMC2241847 Epstein–Barr virus-encoded microRNA miR-BART2 down-regulates the viral DNA polymerase BALF5 Stephanie Barth, Thorsten Pfuhl, Alfredo Mamiani, Claudia Ehses, Klaus Roemer, Elisabeth Kremmer, Christoph Jäker, Julia Höck, Gunter Meister, and Friedrich A. Grässer Nucleic Acids Res. 2008 February; 36(2): 666–675. Published online 2008 February. doi: 10.1093/nar/gkm1080.PMCID: PMC2241876 Studies on the mechanism of inhibition of bacterial ribonuclease P by aminoglycoside derivatives Steven A. Kawamoto, Christopher G. Sudhahar, Cynthia L. Hatfield, Jing Sun, Edward J. Behrman, and Venkat Gopalan Nucleic Acids Res. 2008 February; 36(2): 697–704. Published online 2008 February. doi: 10.1093/nar/gkm1088.PMCID: PMC2241863 Structural Biology Interplay of ion binding and attraction in DNA condensed by multivalent cations Brian A. Todd and Donald C. Rau Nucleic Acids Res. 2008 February; 36(2): 501–510. Published online 2008 February. doi: 10.1093/nar/gkm1038.PMCID: PMC2241864 Alternative splicing and protein structure evolution Fabian Birzele, Gergely Csaba, and Ralf Zimmer Nucleic Acids Res. 2008 February; 36(2): 550–558. Published online 2008 February. doi: 10.1093/nar/gkm1054.PMCID: PMC2241867 Chemistry The formation pathway of tetramolecular G-quadruplexes Caroline Bardin and Jean Louis Leroy Nucleic Acids Res. 2008 February; 36(2): 477–488. Published online 2008 February. doi: 10.1093/nar/gkm1050.PMCID: PMC2241855 Methods Online Use of a multi-thermal washer for DNA microarrays simplifies probe design and gives robust genotyping assays Jesper Petersen, Lena Poulsen, Sarunas Petronis, Henrik Birgens, and Martin Dufva Nucleic Acids Res. 2008 February; 36(2): e10. Published online 2008 February. doi: 10.1093/nar/gkm1081.PMCID: PMC2241873 Model-based variance-stabilizing transformation for Illumina microarray data Simon M. Lin, Pan Du, Wolfgang Huber, and Warren A. Kibbe Nucleic Acids Res. 2008 February; 36(2): e11. Published online 2008 February. doi: 10.1093/nar/gkm1075.PMCID: PMC2241869 Gene Ontology annotation quality analysis in model eukaryotes Teresia J. Buza, Fiona M. McCarthy, Nan Wang, Susan M. Bridges, and Shane C. Burgess Nucleic Acids Res. 2008 February; 36(2): e12. Published online 2008 February. doi: 10.1093/nar/gkm1167.PMCID: PMC2241866 Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data Christiaan Klijn, Henne Holstege, Jeroen de Ridder, Xiaoling Liu, Marcel Reinders, Jos Jonkers, and Lodewyk Wessels Nucleic Acids Res. 2008 February; 36(2): e13. Published online 2008 February. doi: 10.1093/nar/gkm1143.PMCID: PMC2241875 Computational Biology Indirect readout in drug-DNA recognition: role of sequence-dependent DNA conformation Marcos J. Araúzo-Bravo and Akinori Sarai Nucleic Acids Res. 2008 February; 36(2): 376–386. Published online 2008 February. doi: 10.1093/nar/gkm892.PMCID: PMC2241865 Identifying foldable regions in protein sequence from the hydrophobic signal Chi N.I. Pang, Kuang Lin, Merridee A. Wouters, Jaap Heringa, and Richard A. George Nucleic Acids Res. 2008 February; 36(2): 578–588. Published online 2008 February. doi: 10.1093/nar/gkm1070.PMCID: PMC2241846 Efficient siRNA selection using hybridization thermodynamics Zhi John Lu and David H. Mathews Nucleic Acids Res. 2008 February; 36(2): 640–647. Published online 2008 February. doi: 10.1093/nar/gkm920.PMCID: PMC2241856 Nucleic Acid Enzymes Cordycepin-hypersensitive growth links elevated polyphosphate levels to inhibition of poly(A) polymerase in Saccharomyces cerevisiae Sandra Holbein, Florian M. Freimoser, Thomas P. Werner, Agnieszka Wengi, and Bernhard Dichtl Nucleic Acids Res. 2008 February; 36(2): 353–363. Published online 2008 February. doi: 10.1093/nar/gkm990.PMCID: PMC2241851 The N-terminal domain of TWINKLE contributes to single-stranded DNA binding and DNA helicase activities Géraldine Farge, Teresa Holmlund, Julia Khvorostova, Reza Rofougaran, Anders Hofer, and Maria Falkenberg Nucleic Acids Res. 2008 February; 36(2): 393–403. Published online 2008 February. doi: 10.1093/nar/gkm1025.PMCID: PMC2241861 The Leu22Pro tumor-associated variant of DNA polymerase beta is dRP lyase deficient Shibani Dalal, Anna Chikova, Joachim Jaeger, and Joann B. Sweasy Nucleic Acids Res. 2008 February; 36(2): 411–422. Published online 2008 February. doi: 10.1093/nar/gkm1053.PMCID: PMC2241857 Magnesium-binding studies reveal fundamental differences between closely related RNA triphosphatases Marie F. Soulière, Jean-Pierre Perreault, and Martin Bisaillon Nucleic Acids Res. 2008 February; 36(2): 451–461. Published online 2008 February. doi: 10.1093/nar/gkm1067.PMCID: PMC2241848 Mechanisms of covalent self-assembly of the Azoarcus ribozyme from four fragment oligonucleotides Will E. Draper, Eric J. Hayden, and Niles Lehman Nucleic Acids Res. 2008 February; 36(2): 520–531. Published online 2008 February. doi: 10.1093/nar/gkm1055.PMCID: PMC2241849 The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferases Nicolas Leulliot, Markus T. Bohnsack, Marc Graille, David Tollervey, and Herman Van Tilbeurgh Nucleic Acids Res. 2008 February; 36(2): 629–639. Published online 2008 February. doi: 10.1093/nar/gkm1074.PMCID: PMC2241868 Structure–function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement Souad Naji, Michela G. Bertero, Patrizia Spitalny, Patrick Cramer, and Michael Thomm Nucleic Acids Res. 2008 February; 36(2): 676–687. Published online 2008 February. doi: 10.1093/nar/gkm1086.PMCID: PMC2241882 DNA polymerase kappa produces interrupted mutations and displays polar pausing within mononucleotide microsatellite sequences Suzanne E. Hile and Kristin A. Eckert Nucleic Acids Res. 2008 February; 36(2): 688–696. Published online 2008 February. doi: 10.1093/nar/gkm1089.PMCID: PMC2241860 |