Nucleic Acids Research

Chemistry

Get checked abstract Peter Sandin, Karl Börjesson, Hong Li, Jerker Mårtensson, Tom Brown, L. Marcus Wilhelmsson, and Bo Albinsson

Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue
Nucleic Acids Research Advance Access published on November 14, 2007
Nucl. Acids Res. 2008 36: 157-167; doi:10.1093/nar/gkm1006 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Sébastien Tremblay and J. Richard Wagner

Dehydration, deamination and enzymatic repair of cytosine glycols from oxidized poly(dG-dC) and poly(dI-dC)
Nucleic Acids Research Advance Access published on November 21, 2007
Nucl. Acids Res. 2008 36: 284-293; doi:10.1093/nar/gkm1013 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Computational Biology

Get checked abstract Sarah A. Harris, Charles A. Laughton, and Tanniemola B. Liverpool

Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: 21-29; doi:10.1093/nar/gkm891 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genomics

Get checked abstract Véronique Bourdeau, Julie Deschênes, David Laperrière, Malika Aid, John H. White, and Sylvie Mader

Mechanisms of primary and secondary estrogen target gene regulation in breast cancer cells
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: 76-93; doi:10.1093/nar/gkm945 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Steve G. Hershman, Qijun Chen, Julia Y. Lee, Marina L. Kozak, Peng Yue, Li-San Wang, and F. Brad Johnson

Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: 144-156; doi:10.1093/nar/gkm986 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract Ali Z. Al-Minawi, Nasrollah Saleh-Gohari, and Thomas Helleday

The ERCC1/XPF endonuclease is required for efficient single-strand annealing and gene conversion in mammalian cells
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2008 36: 1-9; doi:10.1093/nar/gkm888 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Pei-Hong Chen, Yeou-Ping Tsao, Chih-Chiang Wang, and Show-Li Chen

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
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: 51-66; doi:10.1093/nar/gkm942 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Prerna Jasmine Masih, Dimiter Kunnev, and Thomas Melendy

Mismatch Repair proteins are recruited to replicating DNA through interaction with Proliferating Cell Nuclear Antigen (PCNA)
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: 67-75; doi:10.1093/nar/gkm943 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jin Inoue, Masayoshi Honda, Shukuko Ikawa, Takehiko Shibata, and Tsutomu Mikawa

The process of displacing the single-stranded DNA-binding protein from single-stranded DNA by RecO and RecR proteins
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: 94-109; doi:10.1093/nar/gkm1004 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Humberto Sanchez, Paula P. Cardenas, Shige H. Yoshimura, Kunio Takeyasu, and Juan C. Alonso

Dynamic structures of Bacillus subtilis RecN–DNA complexes
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: 110-120; doi:10.1093/nar/gkm759 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Marjo Malinen, Anna Saramäki, Antti Ropponen, Tatjana Degenhardt, Sami Väisänen, and Carsten Carlberg

Distinct HDACs regulate the transcriptional response of human cyclin-dependent kinase inhibitor genes to trichostatin A and 1,25-dihydroxyvitamin D₃
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: 121-132; doi:10.1093/nar/gkm913 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Branislav Vecerek, Lukas Rajkowitsch, Elisabeth Sonnleitner, Renée Schroeder, and Udo Bläsi

The C-terminal domain of Escherichia coli Hfq is required for regulation
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: 133-143; doi:10.1093/nar/gkm985 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Parviz Minoo, Lingyan Hu, Nianling Zhu, Zea Borok, Saverio Bellusci, John Groffen, Dimitris Kardassis, and Changgong Li

SMAD3 prevents binding of NKX2.1 and FOXA1 to the SpB promoter through its MH1 and MH2 domains
Nucleic Acids Research Advance Access published on November 14, 2007
Nucl. Acids Res. 2008 36: 179-188; doi:10.1093/nar/gkm871 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Ryoko Harada, Charles Vadnais, Laurent Sansregret, Lam Leduy, Ginette Bérubé, François Robert, and Alain Nepveu

Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes
Nucleic Acids Research Advance Access published on November 14, 2007
Nucl. Acids Res. 2008 36: 189-202; doi:10.1093/nar/gkm970 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract 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

Nucleolin regulates c-Jun/Sp1-dependent transcriptional activation of cPLA₂ in phorbol ester-treated non-small cell lung cancer A549 cells
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: 217-227; doi:10.1093/nar/gkm1027 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Janna M. Mundt, Sang Soo Hah, Rhoda A. Sumbad, Vern Schramm, and Paul T. Henderson

Incorporation of extracellular 8-oxodG into DNA and RNA requires purine nucleoside phosphorylase in MCF-7 cells
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: 228-236; doi:10.1093/nar/gkm1032 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract M. Rederstorff, V. Allamand, P. Guicheney, C. Gartioux, P. Richard, D. Chaigne, A. Krol, and A. Lescure

Ex vivo correction of selenoprotein N deficiency in rigid spine muscular dystrophy caused by a mutation in the selenocysteine codon
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: 237-244; doi:10.1093/nar/gkm1033 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Mi Ae Park, Yeong-Jae Seok, Gajin Jeong, and Jong-Soo Lee

SUMO1 negatively regulates BRCA1-mediated transcription, via modulation of promoter occupancy
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: 263-283; doi:10.1093/nar/gkm969 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract K. Hatch, C. Danilowicz, V. Coljee, and M. Prentiss

Measurement of the salt-dependent stabilization of partially open DNA by Escherichia coli SSB protein
Nucleic Acids Research Advance Access published on November 21, 2007
Nucl. Acids Res. 2008 36: 294-299; doi:10.1093/nar/gkm1014 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract David Nord and Britt-Marie Sjöberg

Unconventional GIY-YIG homing endonuclease encoded in group I introns in closely related strains of the Bacillus cereus group
Nucleic Acids Research Advance Access published on November 21, 2007
Nucl. Acids Res. 2008 36: 300-310; doi:10.1093/nar/gkm1016 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Dong Li, Liang Da, Hong Tang, Tsaiping Li, and Mujun Zhao

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
Nucleic Acids Research Advance Access published on November 22, 2007
Nucl. Acids Res. 2008 36: 330-341; doi:10.1093/nar/gkm1028 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sung Won Choi, Arihiro Kano, and Atsushi Maruyama

Activation of DNA strand exchange by cationic comb-type copolymers: effect of cationic moieties of the copolymers
Nucleic Acids Research Advance Access published on November 22, 2007
Nucl. Acids Res. 2008 36: 342-351; doi:10.1093/nar/gkm1035 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nucleic Acid Enzymes

Get checked abstract Lisa M. Sharpe Elles and Olke C. Uhlenbeck

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
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: 41-50; doi:10.1093/nar/gkm926 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Dilantha Gunawardana, Heung-Chin Cheng, and Kenwyn R. Gayler

Identification of functional domains in Arabidopsis thaliana mRNA decapping enzyme (AtDcp2)
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: 203-216; doi:10.1093/nar/gkm1002 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sven Nottebaum, Lin Tan, Dominika Trzaska, Hannah C. Carney, and Robert O. J. Weinzierl

The RNA polymerase factory: a robotic in vitro assembly platform for high-throughput production of recombinant protein complexes
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: 245-252; doi:10.1093/nar/gkm1044 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA

Get checked abstract Andrew D.S. Cameron, Milica Volar, Laura A. Bannister, and Rosemary J. Redfield

RNA secondary structure regulates the translation of sxy and competence development in Haemophilus influenzae
Nucleic Acids Research Advance Access published on November 2, 2007
Nucl. Acids Res. 2008 36: 10-20; doi:10.1093/nar/gkm915 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Karine Gendron, Johanie Charbonneau, Dominic Dulude, Nikolaus Heveker, Gerardo Ferbeyre, and Léa Brakier-Gingras

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
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: 30-40; doi:10.1093/nar/gkm906 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Stephen M. Lewis, Sonia Cerquozzi, Tyson E. Graber, Nicoleta Hosszu Ungureanu, Meghan Andrews, and Martin Holcik

The eIF4G homolog DAP5/p97 supports the translation of select mRNAs during endoplasmic reticulum stress
Nucleic Acids Research Advance Access published on November 14, 2007
Nucl. Acids Res. 2008 36: 168-178; doi:10.1093/nar/gkm1007 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yusuke Kobayashi, Mitsuhiro Matsuo, Koji Sakamoto, Tatsuya Wakasugi, Kyoji Yamada, and Junichi Obokata

Two RNA editing sites with cis-acting elements of moderate sequence identity are recognized by an identical site-recognition protein in tobacco chloroplasts
Nucleic Acids Research Advance Access published on November 21, 2007
Nucl. Acids Res. 2008 36: 311-318; doi:10.1093/nar/gkm1026 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jonelle L. Mattiacio and Laurie K. Read

Roles for TbDSS-1 in RNA surveillance and decay of maturation by-products from the 12S rRNA locus
Nucleic Acids Research Advance Access published on November 21, 2007
Nucl. Acids Res. 2008 36: 319-329; doi:10.1093/nar/gkm690 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Structural Biology

Get checked abstract Jingyang Chen, François-Yves Dupradeau, David A. Case, Christopher J. Turner, and JoAnne Stubbe

DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: 253-262; doi:10.1093/nar/gkm622 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Corrigendum

Maria Nilsson, Karin Dahlman-Wright, Charlotta Karelmo, Martin Ebeling, Jan-Åke Gustafsson, and Knut R. Steffensen

Elk1 and SRF transcription factors convey basal transcription and mediate glucose response via their binding sites in the human LXRB gene promoter
Nucl. Acids Res. 2008 36: 352; doi:10.1093/nar/gkm1155 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online

Get checked abstract Hiroshi Arakawa, Hiroaki Kudo, Vera Batrak, Randolph B. Caldwell, Michael A. Rieger, Joachim W. Ellwart, and Jean-Marie Buerstedde

Protein evolution by hypermutation and selection in the B cell line DT40
Nucleic Acids Research Advance Access published on December 11, 2007
Nucl. Acids Res. 2008 36: e1; doi:10.1093/nar/gkm616 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Henri de Martimprey, Jean-Remi Bertrand, Alfredo Fusco, Massimo Santoro, Patrick Couvreur, Christine Vauthier, and Claude Malvy

siRNA nanoformulation against the Ret/PTC1 junction oncogene is efficient in an in vivo model of papillary thyroid carcinoma
Nucleic Acids Research Advance Access published on December 13, 2007
Nucl. Acids Res. 2008 36: e2; doi:10.1093/nar/gkm1094 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Omar J. Jabado, Yang Liu, Sean Conlan, P. Lan Quan, Hédi Hegyi, Yves Lussier, Thomas Briese, Gustavo Palacios, and W. I. Lipkin

Comprehensive viral oligonucleotide probe design using conserved protein regions
Nucleic Acids Research Advance Access published on December 13, 2007
Nucl. Acids Res. 2008 36: e3; doi:10.1093/nar/gkm1106 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Joseph A. DeVito

Recombineering with tolC as a Selectable/Counter-selectable Marker: remodeling the rRNA Operons of Escherichia coli
Nucleic Acids Research Advance Access published on December 15, 2007
Nucl. Acids Res. 2008 36: e4; doi:10.1093/nar/gkm1084 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Matthias Meyer, Adrian W. Briggs, Tomislav Maricic, Barbara Höber, Barbara Höffner, Johannes Krause, Antje Weihmann, Svante Pääbo, and Michael Hofreiter

From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing
Nucleic Acids Research Advance Access published on December 15, 2007
Nucl. Acids Res. 2008 36: e5; doi:10.1093/nar/gkm1095 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract S. Care, C. Bignon, M. C. Pelissier, E. Blanc, B. Canard, and B. Coutard

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
Nucleic Acids Research Advance Access published on December 15, 2007
Nucl. Acids Res. 2008 36: e6; doi:10.1093/nar/gkm1097 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Margaret F. Phillips, Matthew R. Lockett, Matthew J. Rodesch, Michael R. Shortreed, Franco Cerrina, and Lloyd M. Smith

In situ oligonucleotide synthesis on carbon materials: stable substrates for microarray fabrication
Nucleic Acids Research Advance Access published on December 15, 2007
Nucl. Acids Res. 2008 36: e7; doi:10.1093/nar/gkm1103 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract 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

Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins
Nucleic Acids Research Advance Access published on December 17, 2007
Nucl. Acids Res. 2008 36: e8; doi:10.1093/nar/gkm1117 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Zhengyao Xu, Nicholas C. O. Lee, Felix Dafhnis-Calas, Sunir Malla, Margaret C. M. Smith, and William R. A. Brown

Site-specific recombination in Schizosaccharomyces pombe and systematic assembly of a 400kb transgene array in mammalian cells using the integrase of Streptomyces phage BT1
Nucleic Acids Research Advance Access published on December 20, 2007
Nucl. Acids Res. 2008 36: e9; doi:10.1093/nar/gkm1123 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

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