| | Molecular Biology The ERCC1/XPF endonuclease is required for efficient single-strand annealing and gene conversion in mammalian cells Ali Z. Al-Minawi, Nasrollah Saleh-Gohari, and Thomas Helleday Nucleic Acids Res. 2008 January; 36(1): 1–9. Published online 2008 January. doi: 10.1093/nar/gkm888.PMCID: PMC2248766 Nuclear receptor interaction protein, a coactivator of androgen receptors (AR), is regulated by AR and Sp1 to feed forward and activate its own gene expression through AR protein stability Pei-Hong Chen, Yeou-Ping Tsao, Chih-Chiang Wang, and Show-Li Chen Nucleic Acids Res. 2008 January; 36(1): 51–66. Published online 2008 January. doi: 10.1093/nar/gkm942.PMCID: PMC2248731 Mismatch Repair proteins are recruited to replicating DNA through interaction with Proliferating Cell Nuclear Antigen (PCNA) Prerna Jasmine Masih, Dimiter Kunnev, and Thomas Melendy Nucleic Acids Res. 2008 January; 36(1): 67–75. Published online 2008 January. doi: 10.1093/nar/gkm943.PMCID: PMC2248749 The process of displacing the single-stranded DNA-binding protein from single-stranded DNA by RecO and RecR proteins Jin Inoue, Masayoshi Honda, Shukuko Ikawa, Takehiko Shibata, and Tsutomu Mikawa Nucleic Acids Res. 2008 January; 36(1): 94–109. Published online 2008 January. doi: 10.1093/nar/gkm1004.PMCID: PMC2248737 Dynamic structures of Bacillus subtilis RecN–DNA complexes Humberto Sanchez, Paula P. Cardenas, Shige H. Yoshimura, Kunio Takeyasu, and Juan C. Alonso Nucleic Acids Res. 2008 January; 36(1): 110–120. Published online 2008 January. doi: 10.1093/nar/gkm759.PMCID: PMC2248758 Distinct HDACs regulate the transcriptional response of human cyclin-dependent kinase inhibitor genes to trichostatin A and 1α,25-dihydroxyvitamin D3 Marjo Malinen, Anna Saramäki, Antti Ropponen, Tatjana Degenhardt, Sami Väisänen, and Carsten Carlberg Nucleic Acids Res. 2008 January; 36(1): 121–132. Published online 2008 January. doi: 10.1093/nar/gkm913.PMCID: PMC2248733 The C-terminal domain of Escherichia coli Hfq is required for regulation Branislav Večerek, Lukas Rajkowitsch, Elisabeth Sonnleitner, Renée Schroeder, and Udo Bläsi Nucleic Acids Res. 2008 January; 36(1): 133–143. Published online 2008 January. doi: 10.1093/nar/gkm985.PMCID: PMC2248732 SMAD3 prevents binding of NKX2.1 and FOXA1 to the SpB promoter through its MH1 and MH2 domains Parviz Minoo, Lingyan Hu, Nianling Zhu, Zea Borok, Saverio Bellusci, John Groffen, Dimitris Kardassis, and Changgong Li Nucleic Acids Res. 2008 January; 36(1): 179–188. Published online 2008 January. doi: 10.1093/nar/gkm871.PMCID: PMC2248754 Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes Ryoko Harada, Charles Vadnais, Laurent Sansregret, Lam Leduy, Ginette Bérubé, François Robert, and Alain Nepveu Nucleic Acids Res. 2008 January; 36(1): 189–202. Published online 2008 January. doi: 10.1093/nar/gkm970.PMCID: PMC2248751 Nucleolin regulates c-Jun/Sp1-dependent transcriptional activation of cPLA2α in phorbol ester-treated non-small cell lung cancer A549 cells Jen-Hui Tsou, Kwang-Yu Chang, Wei-Chiao Wang, Joseph T. Tseng, Wu-Chou Su, Liang-Yi Hung, Wen-Chang Chang, and Ben-Kuen Chen Nucleic Acids Res. 2008 January; 36(1): 217–227. Published online 2008 January. doi: 10.1093/nar/gkm1027.PMCID: PMC2248756 Incorporation of extracellular 8-oxodG into DNA and RNA requires purine nucleoside phosphorylase in MCF-7 cells Janna M. Mundt, Sang Soo Hah, Rhoda A. Sumbad, Vern Schramm, and Paul T. Henderson Nucleic Acids Res. 2008 January; 36(1): 228–236. Published online 2008 January. doi: 10.1093/nar/gkm1032.PMCID: PMC2248762 Ex vivo correction of selenoprotein N deficiency in rigid spine muscular dystrophy caused by a mutation in the selenocysteine codon M. Rederstorff, V. Allamand, P. Guicheney, C. Gartioux, P. Richard, D. Chaigne, A. Krol, and A. Lescure Nucleic Acids Res. 2008 January; 36(1): 237–244. Published online 2008 January. doi: 10.1093/nar/gkm1033.PMCID: PMC2248747 SUMO1 negatively regulates BRCA1-mediated transcription, via modulation of promoter occupancy Mi Ae Park, Yeong-Jae Seok, Gajin Jeong, and Jong-Soo Lee Nucleic Acids Res. 2008 January; 36(1): 263–283. Published online 2008 January. doi: 10.1093/nar/gkm969.PMCID: PMC2248730 Measurement of the salt-dependent stabilization of partially open DNA by Escherichia coli SSB protein K. Hatch, C. Danilowicz, V. Coljee, and M. Prentiss Nucleic Acids Res. 2008 January; 36(1): 294–299. Published online 2008 January. doi: 10.1093/nar/gkm1014.PMCID: PMC2248746 Unconventional GIY-YIG homing endonuclease encoded in group I introns in closely related strains of the Bacillus cereus group David Nord and Britt-Marie Sjöberg Nucleic Acids Res. 2008 January; 36(1): 300–310. Published online 2008 January. doi: 10.1093/nar/gkm1016.PMCID: PMC2248736 CpG methylation plays a vital role in determining tissue- and cell-specific expression of the human cell-death-inducing DFF45-like effector A gene through the regulation of Sp1/Sp3 binding Dong Li, Liang Da, Hong Tang, Tsaiping Li, and Mujun Zhao Nucleic Acids Res. 2008 January; 36(1): 330–341. Published online 2008 January. doi: 10.1093/nar/gkm1028.PMCID: PMC2248752 Activation of DNA strand exchange by cationic comb-type copolymers: effect of cationic moieties of the copolymers Sung Won Choi, Arihiro Kano, and Atsushi Maruyama Nucleic Acids Res. 2008 January; 36(1): 342–351. Published online 2008 January. doi: 10.1093/nar/gkm1035.PMCID: PMC2248768 RNA RNA secondary structure regulates the translation of sxy and competence development in Haemophilus influenzae Andrew D.S. Cameron, Milica Volar, Laura A. Bannister, and Rosemary J. Redfield Nucleic Acids Res. 2008 January; 36(1): 10–20. Published online 2008 January. doi: 10.1093/nar/gkm915.PMCID: PMC2248739 The presence of the TAR RNA structure alters the programmed -1 ribosomal frameshift efficiency of the human immunodeficiency virus type 1 (HIV-1) by modifying the rate of translation initiation Karine Gendron, Johanie Charbonneau, Dominic Dulude, Nikolaus Heveker, Gerardo Ferbeyre, and Léa Brakier-Gingras Nucleic Acids Res. 2008 January; 36(1): 30–40. Published online 2008 January. doi: 10.1093/nar/gkm906.PMCID: PMC2248755 The eIF4G homolog DAP5/p97 supports the translation of select mRNAs during endoplasmic reticulum stress Stephen M. Lewis, Sonia Cerquozzi, Tyson E. Graber, Nicoleta Hosszu Ungureanu, Meghan Andrews, and Martin Holcik Nucleic Acids Res. 2008 January; 36(1): 168–178. Published online 2008 January. doi: 10.1093/nar/gkm1007.PMCID: PMC2248753 Two RNA editing sites with cis-acting elements of moderate sequence identity are recognized by an identical site-recognition protein in tobacco chloroplasts Yusuke Kobayashi, Mitsuhiro Matsuo, Koji Sakamoto, Tatsuya Wakasugi, Kyoji Yamada, and Junichi Obokata Nucleic Acids Res. 2008 January; 36(1): 311–318. Published online 2008 January. doi: 10.1093/nar/gkm1026.PMCID: PMC2248765 Roles for TbDSS-1 in RNA surveillance and decay of maturation by-products from the 12S rRNA locus Jonelle L. Mattiacio and Laurie K. Read Nucleic Acids Res. 2008 January; 36(1): 319–329. Published online 2008 January. doi: 10.1093/nar/gkm690.PMCID: PMC2248759 Structural Biology DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics Jingyang Chen, François-Yves Dupradeau, David A. Case, Christopher J. Turner, and JoAnne Stubbe Nucleic Acids Res. 2008 January; 36(1): 253–262. Published online 2008 January. doi: 10.1093/nar/gkm622.PMCID: PMC2248740 Genomics Mechanisms of primary and secondary estrogen target gene regulation in breast cancer cells Véronique Bourdeau, Julie Deschênes, David Laperrière, Malika Aid, John H. White, and Sylvie Mader Nucleic Acids Res. 2008 January; 36(1): 76–93. Published online 2008 January. doi: 10.1093/nar/gkm945.PMCID: PMC2248750 Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae Steve G. Hershman, Qijun Chen, Julia Y. Lee, Marina L. Kozak, Peng Yue, Li-San Wang, and F. Brad Johnson Nucleic Acids Res. 2008 January; 36(1): 144–156. Published online 2008 January. doi: 10.1093/nar/gkm986.PMCID: PMC2248735 Chemistry Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue Peter Sandin, Karl Börjesson, Hong Li, Jerker Mårtensson, Tom Brown, L. Marcus Wilhelmsson, and Bo Albinsson Nucleic Acids Res. 2008 January; 36(1): 157–167. Published online 2008 January. doi: 10.1093/nar/gkm1006.PMCID: PMC2248743 Dehydration, deamination and enzymatic repair of cytosine glycols from oxidized poly(dG-dC) and poly(dI-dC) Sébastien Tremblay and J. Richard Wagner Nucleic Acids Res. 2008 January; 36(1): 284–293. Published online 2008 January. doi: 10.1093/nar/gkm1013.PMCID: PMC2248729 Methods Online Protein evolution by hypermutation and selection in the B cell line DT40 Hiroshi Arakawa, Hiroaki Kudo, Vera Batrak, Randolph B. Caldwell, Michael A. Rieger, Joachim W. Ellwart, and Jean-Marie Buerstedde Nucleic Acids Res. 2008 January; 36(1): e1. Published online 2008 January. doi: 10.1093/nar/gkm616.PMCID: PMC2248763 siRNA nanoformulation against the Ret/PTC1 junction oncogene is efficient in an in vivo model of papillary thyroid carcinoma Henri de Martimprey, Jean-Remi Bertrand, Alfredo Fusco, Massimo Santoro, Patrick Couvreur, Christine Vauthier, and Claude Malvy Nucleic Acids Res. 2008 January; 36(1): e2. Published online 2008 January. doi: 10.1093/nar/gkm1094.PMCID: PMC2248757 Comprehensive viral oligonucleotide probe design using conserved protein regions Omar J. Jabado, Yang Liu, Sean Conlan, P. Lan Quan, Hédi Hegyi, Yves Lussier, Thomas Briese, Gustavo Palacios, and W. I. Lipkin Nucleic Acids Res. 2008 January; 36(1): e3. Published online 2008 January. doi: 10.1093/nar/gkm1106.PMCID: PMC2248741 Recombineering with tolC as a Selectable/Counter-selectable Marker: remodeling the rRNA Operons of Escherichia coli Joseph A. DeVito Nucleic Acids Res. 2008 January; 36(1): e4. Published online 2008 January. doi: 10.1093/nar/gkm1084.PMCID: PMC2248734 From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing Matthias Meyer, Adrian W. Briggs, Tomislav Maricic, Barbara Höber, Barbara Höffner, Johannes Krause, Antje Weihmann, Svante Pääbo, and Michael Hofreiter Nucleic Acids Res. 2008 January; 36(1): e5. Published online 2008 January. doi: 10.1093/nar/gkm1095.PMCID: PMC2248761 The translation of recombinant proteins in E. coli can be improved by in silico generating and screening random libraries of a −70/+96 mRNA region with respect to the translation initiation codon S. Care, C. Bignon, M. C. Pelissier, E. Blanc, B. Canard, and B. Coutard Nucleic Acids Res. 2008 January; 36(1): e6. Published online 2008 January. doi: 10.1093/nar/gkm1097.PMCID: PMC2248745 In situ oligonucleotide synthesis on carbon materials: stable substrates for microarray fabrication Margaret F. Phillips, Matthew R. Lockett, Matthew J. Rodesch, Michael R. Shortreed, Franco Cerrina, and Lloyd M. Smith Nucleic Acids Res. 2008 January; 36(1): e7. Published online 2008 January. doi: 10.1093/nar/gkm1103.PMCID: PMC2248760 Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins Jue Zeng, Jizhou Yan, Ting Wang, Deborah Mosbrook-Davis, Kyle T. Dolan, Ryan Christensen, Gary D. Stormo, David Haussler, Richard H. Lathrop, Rainer K. Brachmann, and Shawn M. Burgess Nucleic Acids Res. 2008 January; 36(1): e8. Published online 2008 January. doi: 10.1093/nar/gkm1117.PMCID: PMC2248728 Site-specific recombination in Schizosaccharomyces pombe and systematic assembly of a 400kb transgene array in mammalian cells using the integrase of Streptomyces phage ϕBT1 Zhengyao Xu, Nicholas C. O. Lee, Felix Dafhnis-Calas, Sunir Malla, Margaret C. M. Smith, and William R. A. Brown Nucleic Acids Res. 2008 January; 36(1): e9. Published online 2008 January. doi: 10.1093/nar/gkm1123.PMCID: PMC2248738 Computational Biology Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations Sarah A. Harris, Charles A. Laughton, and Tanniemola B. Liverpool Nucleic Acids Res. 2008 January; 36(1): 21–29. Published online 2008 January. doi: 10.1093/nar/gkm891.PMCID: PMC2248748 Nucleic Acid Enzymes Mutation of the arginine finger in the active site of Escherichia coli DbpA abolishes ATPase and helicase activity and confers a dominant slow growth phenotype Lisa M. Sharpe Elles and Olke C. Uhlenbeck Nucleic Acids Res. 2008 January; 36(1): 41–50. Published online 2008 January. doi: 10.1093/nar/gkm926.PMCID: PMC2248767 Identification of functional domains in Arabidopsis thaliana mRNA decapping enzyme (AtDcp2) Dilantha Gunawardana, Heung-Chin Cheng, and Kenwyn R. Gayler Nucleic Acids Res. 2008 January; 36(1): 203–216. Published online 2008 January. doi: 10.1093/nar/gkm1002.PMCID: PMC2248764 The RNA polymerase factory: a robotic in vitro assembly platform for high-throughput production of recombinant protein complexes Sven Nottebaum, Lin Tan, Dominika Trzaska, Hannah C. Carney, and Robert O. J. Weinzierl Nucleic Acids Res. 2008 January; 36(1): 245–252. Published online 2008 January. doi: 10.1093/nar/gkm1044.PMCID: PMC2248744 Corrigendum Elk1 and SRF transcription factors convey basal transcription and mediate glucose response via their binding sites in the human LXRB gene promoter Maria Nilsson, Karin Dahlman-Wright, Charlotta Karelmo, Martin Ebeling, Jan-Åke Gustafsson, and Knut R. Steffensen Nucleic Acids Res. 2008 January; 36(1): 352. Published online 2008 January. doi: 10.1093/nar/gkm1155.PMCID: PMC2248742 Corrects: Maria Nilsson, et al. Elk1 and SRF transcription factors convey basal transcription and mediate glucose response via their binding sites in the human LXRB gene promoter. Nucleic Acids Res. 2007 July; 35(14): 4858–4868. |