| | Front-Matter/Back-Matter Nucleic Acids Research: VOLUME 36 ISSUE 18 2008 PMCID: PMC2566880 Nucleic Acids Res. 2008 October; 36(18): ii. Published online 2008 October. doi: 10.1093/nar/gkn789.PMCID: PMC2566890 Nucleic Acids Res. 2008 October; 36(18): iii. Published online 2008 October. doi: 10.1093/nar/gkn780.PMCID: PMC2566883 Gene regulation, Chromatin and Epigenetics Transcriptional mechanism for the paired miR-433 and miR-127 genes by nuclear receptors SHP and ERRγ Guisheng Song and Li Wang PMCID: PMC2566885 Expanded binding specificity of the human histone chaperone NASP Huanyu Wang, Scott T. R. Walsh, and Mark R. Parthun PMCID: PMC2566879 The CaMV transactivator/viroplasmin interferes with RDR6-dependent trans-acting and secondary siRNA pathways in Arabidopsis Padubidri V. Shivaprasad, Rajendran Rajeswaran, Todd Blevins, James Schoelz, Frederick Meins, Jr, Thomas Hohn, and Mikhail M. Pooggin PMCID: PMC2566869 S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum Gaëlle André, Sergine Even, Harald Putzer, Pierre Burguière, Christian Croux, Antoine Danchin, Isabelle Martin-Verstraete, and Olga Soutourina PMCID: PMC2566862 Genome Integrity, Repair and Replication Editing of misaligned 3′-termini by an intrinsic 3′–5′ exonuclease activity residing in the PHP domain of a family X DNA polymerase Benito Baños, José M. Lázaro, Laurentino Villar, Margarita Salas, and Miguel de Vega PMCID: PMC2566882 Loss of DNA ligase IV prevents recognition of DNA by double-strand break repair proteins XRCC4 and XLF Sumithra Jayaram, Gary Ketner, Noritaka Adachi, and Les A. Hanakahi PMCID: PMC2566893 The SET and transposase domain protein Metnase enhances chromosome decatenation: regulation by automethylation Elizabeth A. Williamson, Kanwaldeep Kaur Rasila, Lori Kwan Corwin, Justin Wray, Brian D. Beck, Virginia Severns, Charlotte Mobarak, Suk-Hee Lee, Jac A. Nickoloff, and Robert Hromas PMCID: PMC2566874 Mutagenicity of tamoxifen DNA adducts in human endometrial cells and in silico prediction of p53 mutation hotspots Evagelos Liapis, Keith I.E. McLuckie, Paul D. Lewis, Peter B. Farmer, and Karen Brown PMCID: PMC2566887 Molecular Biology RAG2's non-core domain contributes to the ordered regulation of V(D)J recombination John D. Curry and Mark S. Schlissel PMCID: PMC2566892 The human mitochondrial ribosome recycling factor is essential for cell viability Joanna Rorbach, Ricarda Richter, Hans J. Wessels, Mateusz Wydro, Marcin Pekalski, Murtada Farhoud, Inge Kühl, Mauricette Gaisne, Nathalie Bonnefoy, Jan A. Smeitink, Robert N. Lightowlers, and Zofia M.A. Chrzanowska-Lightowlers PMCID: PMC2566884 Dicistronic tRNA–5S rRNA genes in Yarrowia lipolytica: an alternative TFIIIA-independent way for expression of 5S rRNA genes Joël Acker, Christophe Ozanne, Rym Kachouri-Lafond, Claude Gaillardin, Cécile Neuvéglise, and Christian Marck PMCID: PMC2566860 A single amino acid substitution in ORF1 dramatically decreases L1 retrotransposition and provides insight into nucleic acid chaperone activity Sandra L. Martin, Diane Bushman, Fei Wang, Patrick Wai-Lun Li, Ann Walker, Jessica Cummiskey, Dan Branciforte, and Mark C. Williams PMCID: PMC2566875 Phosphate coordination and movement of DNA in the Tn5 synaptic complex: role of the (R)YREK motif Vadim A. Klenchin, Agata Czyz, Igor Y. Goryshin, Richard Gradman, Scott Lovell, Ivan Rayment, and William S. Reznikoff PMCID: PMC2566895 Cosegregation of novel mitochondrial 16S rRNA gene mutations with the age-associated T414G variant in human cybrids Peter Seibel, Chiara Di Nunno, Christian Kukat, Ingo Schäfer, Roberto Del Bo, Andreina Bordoni, Giacomo P. Comi, Astrid Schön, Ferdinando Capuano, Dominga Latorre, and Gaetano Villani PMCID: PMC2566888 14-3-3 activation of DNA binding of p53 by enhancing its association into tetramers Sridharan Rajagopalan, Agnes M. Jaulent, Mark Wells, Dmitry B. Veprintsev, and Alan R. Fersht PMCID: PMC2566891 Evolutionary conservation supports ancient origin for Nudt16, a nuclear-localized, RNA-binding, RNA-decapping enzyme Melissa J. Taylor and Brenda A. Peculis PMCID: PMC2566886 RNA Effect of asymmetric terminal structures of short RNA duplexes on the RNA interference activity and strand selection Masayuki Sano, Malgorzata Sierant, Makoto Miyagishi, Mahito Nakanishi, Yasuomi Takagi, and Shizuyo Sutou PMCID: PMC2566866 Structural Biology Protein–DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins Shandar Ahmad, Ozlem Keskin, Akinori Sarai, and Ruth Nussinov PMCID: PMC2566867 Rigid spin-labeled nucleoside Ç: a nonperturbing EPR probe of nucleic acid conformation Pavol Cekan, Alyssa L. Smith, Nivrutti Barhate, Bruce H. Robinson, and Snorri Th. Sigurdsson PMCID: PMC2566876 Genomics Megasatellites: a peculiar class of giant minisatellites in genes involved in cell adhesion and pathogenicity in Candida glabrata Agnès Thierry, Christiane Bouchier, Bernard Dujon, and Guy-Franck Richard PMCID: PMC2566889 Methods Online Recombineering-mediated tagging of Drosophila genomic constructs for in vivo localization and acute protein inactivation Koen J. T. Venken, Jaroslaw Kasprowicz, Sabine Kuenen, Jiekun Yan, Bassem A. Hassan, and Patrik Verstreken PMCID: PMC2566861 Prioritization of candidate cancer genes—an aid to oncogenomic studies Simon J. Furney, Borja Calvo, Pedro Larrañaga, Jose A. Lozano, and Nuria Lopez-Bigas PMCID: PMC2566894 Studying copy number variations using a nanofluidic platform Jian Qin, Robert C. Jones, and Ramesh Ramakrishnan PMCID: PMC2566873 Advantages of q-PCR as a method of screening for gene targeting in mammalian cells using conventional and whole BAC-based constructs Julio Gómez-Rodríguez, Valance Washington, Jun Cheng, Amalia Dutra, Evgenia Pak, Pentao Liu, Daniel W. McVicar, and Pamela L. Schwartzberg PMCID: PMC2566865 NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs Dany Morisset, David Dobnik, Sandrine Hamels, Jana Žel, and Kristina Gruden PMCID: PMC2566881 DNA methylation determination by liquid chromatography–tandem mass spectrometry using novel biosynthetic [U-15N]deoxycytidine and [U-15N]methyldeoxycytidine internal standards Eoin P. Quinlivan and Jesse F. Gregory, III PMCID: PMC2566864 Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers Zongzhi Liu, Todd Z. DeSantis, Gary L. Andersen, and Rob Knight PMCID: PMC2566877 An artificial processivity clamp made with streptavidin facilitates oriented attachment of polymerase–DNA complexes to surfaces John G. K. Williams, David L. Steffens, Jon P. Anderson, Teresa M. Urlacher, Donald T. Lamb, Daniel L. Grone, and Jolene C. Egelhoff PMCID: PMC2566871 Computational Biology The whole alignment and nothing but the alignment: the problem of spurious alignment flanks Martin C. Frith, Yonil Park, Sergey L. Sheetlin, and John L. Spouge PMCID: PMC2566872 Dissociation of minor groove binders from DNA: insights from metadynamics simulations Attilio Vittorio Vargiu, Paolo Ruggerone, Alessandra Magistrato, and Paolo Carloni PMCID: PMC2566863 KnotInFrame: prediction of −1 ribosomal frameshift events Corinna Theis, Jens Reeder, and Robert Giegerich PMCID: PMC2566878 Nucleic Acid Enzymes The putative RNase P motif in the DEAD box helicase Hera is dispensable for efficient interaction with RNA and helicase activity Martin H. Linden, Roland K. Hartmann, and Dagmar Klostermeier PMCID: PMC2566870 The reverse gyrase helicase-like domain is a nucleotide-dependent switch that is attenuated by the topoisomerase domain Yoandris del Toro Duany, Stefan P. Jungblut, Andreas S. Schmidt, and Dagmar Klostermeier PMCID: PMC2566858 Identification of two conserved aspartic acid residues required for DNA digestion by a novel thermophilic Exonuclease VII in Thermotoga maritima Andres A. Larrea, Ilene M. Pedroso, Arun Malhotra, and Richard S. Myers PMCID: PMC2566859 Serial analysis of mutation spectra (SAMS): a new approach for the determination of mutation spectra of site-specific DNA damage and their sequence dependence Huafeng Fang and John-Stephen Taylor PMCID: PMC2566868 |
