Nucleic Acids Research

Articles:

Pamela D. Vise, Bharat Baral, Andrew J. Latos, and Gary W. Daughdrill

NMR chemical shift and relaxation measurements provide evidence for the coupled folding and binding of the p53 transactivation domain
Nucl. Acids Res. 2005 33: 2061-2077; doi:10.1093/nar/gki336 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shingo Nakahata and Sachiyo Kawamoto

Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities
Nucl. Acids Res. 2005 33: 2078-2089; doi:10.1093/nar/gki338 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nicholas S. Y. Ting, Yaping Yu, Brant Pohorelic, Susan P. Lees-Miller, and Tara L. Beattie

Human Ku70/80 interacts directly with hTR, the RNA component of human telomerase
Nucl. Acids Res. 2005 33: 2090-2098; doi:10.1093/nar/gki342 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Thijn van der Heijden, John van Noort, Hendrikje van Leest, Roland Kanaar, Claire Wyman, Nynke Dekker, and Cees Dekker

Torque-limited RecA polymerization on dsDNA
Nucl. Acids Res. 2005 33: 2099-2105; doi:10.1093/nar/gki512 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Teldja N. Azzouz, Andreas Gruber, and Daniel Schümperli

U7 snRNP-specific Lsm11 protein: dual binding contacts with the 100 kDa zinc finger processing factor (ZFP100) and a ZFP100-independent function in histone RNA 3' end processing
Nucl. Acids Res. 2005 33: 2106-2117; doi:10.1093/nar/gki516 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zhijie Li and Yi Zhang

Predicting the secondary structures and tertiary interactions of 211 group I introns in IE subgroup
Nucl. Acids Res. 2005 33: 2118-2128; doi:10.1093/nar/gki517 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Marialuisa Pellegrini-Calace and Janet M. Thornton

Detecting DNA-binding helix–turn–helix structural motifs using sequence and structure information
Nucl. Acids Res. 2005 33: 2129-2140; doi:10.1093/nar/gki349 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sergine Even, Olivier Pellegrini, Lena Zig, Valerie Labas, Joelle Vinh, Dominique Bréchemmier-Baey, and Harald Putzer

Ribonucleases J1 and J2: two novel endoribonucleases in B.subtilis with functional homology to E.coli RNase E
Nucl. Acids Res. 2005 33: 2141-2152; doi:10.1093/nar/gki505 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Cédric Feschotte, Mark T. Osterlund, Ryan Peeler, and Susan R. Wessler

DNA-binding specificity of rice mariner-like transposases and interactions with Stowaway MITEs
Nucl. Acids Res. 2005 33: 2153-2165; doi:10.1093/nar/gki509 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sergei A. Gaidamakov, Inna I. Gorshkova, Peter Schuck, Peter J. Steinbach, Hirofumi Yamada, Robert J. Crouch, and Susana M. Cerritelli

Eukaryotic RNases H1 act processively by interactions through the duplex RNA-binding domain
Nucl. Acids Res. 2005 33: 2166-2175; doi:10.1093/nar/gki510 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Korbinian Schneeberger, Ketil Malde, Eivind Coward, and Inge Jonassen

Masking repeats while clustering ESTs
Nucl. Acids Res. 2005 33: 2176-2180; doi:10.1093/nar/gki511 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Toshiaki Nakano, Atsushi Katafuchi, Ryoko Shimizu, Hiroaki Terato, Toshinori Suzuki, Hiroshi Tauchi, Keisuke Makino, Milan Skorvaga, Bennett Van Houten, and Hiroshi Ide

Repair activity of base and nucleotide excision repair enzymes for guanine lesions induced by nitrosative stress
Nucl. Acids Res. 2005 33: 2181-2191; doi:10.1093/nar/gki513 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Céline Douarre, Dennis Gomez, Hamid Morjani, Jean-Marie Zahm, Marie-Françoise O'Donohue, Lahcen Eddabra, Patrick Mailliet, Jean-François Riou, and Chantal Trentesaux

Overexpression of Bcl-2 is associated with apoptotic resistance to the G-quadruplex ligand 12459 but is not sufficient to confer resistance to long-term senescence
Nucl. Acids Res. 2005 33: 2192-2203; doi:10.1093/nar/gki514 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jason L. Parsons, Irina I. Dianova, and Grigory L. Dianov

APE1-dependent repair of DNA single-strand breaks containing 3'-end 8-oxoguanine
Nucl. Acids Res. 2005 33: 2204-2209; doi:10.1093/nar/gki518 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Daniel P. Aalberts and Nathan O. Hodas

Asymmetry in RNA pseudoknots: observation and theory
Nucl. Acids Res. 2005 33: 2210-2214; doi:10.1093/nar/gki508 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shouhong Guang and Janet E. Mertz

Pre-mRNA processing enhancer (PPE) elements from intronless genes play additional roles in mRNA biogenesis than do ones from intron-containing genes
Nucl. Acids Res. 2005 33: 2215-2226; doi:10.1093/nar/gki506 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kalin Taskov, Charles Chapple, Gregory V. Kryukov, Sergi Castellano, Alexey V. Lobanov, Konstantin V. Korotkov, Roderic Guigó, and Vadim N. Gladyshev

Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome?
Nucl. Acids Res. 2005 33: 2227-2238; doi:10.1093/nar/gki507 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Katri Mäkeläinen and Kristiina Mäkinen

Factors affecting translation at the programmed –1 ribosomal frameshifting site of Cocksfoot mottle virus RNA in vivo
Nucl. Acids Res. 2005 33: 2239-2247; doi:10.1093/nar/gki521 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zeping Wang, Matt Weaver, and Nancy S. Magnuson

Cryptic promoter activity in the DNA sequence corresponding to the pim-1 5'-UTR
Nucl. Acids Res. 2005 33: 2248-2258; doi:10.1093/nar/gki523 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Michael D. Hamilton and David H. Evans

Enzymatic processing of replication and recombination intermediates by the vaccinia virus DNA polymerase
Nucl. Acids Res. 2005 33: 2259-2268; doi:10.1093/nar/gki525 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sona Scsucova, Daniela Palacios, Magali Savignac, Britt Mellström, Jose Ramon Naranjo, and Ana Aranda

The repressor DREAM acts as a transcriptional activator on Vitamin D and retinoic acid response elements
Nucl. Acids Res. 2005 33: 2269-2279; doi:10.1093/nar/gki503 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Rupert Grossberger, Oliver Mayer, Christina Waldsich, Katharina Semrad, Sandra Urschitz, and Renée Schroeder

Influence of RNA structural stability on the RNA chaperone activity of the Escherichia coli protein StpA
Nucl. Acids Res. 2005 33: 2280-2289; doi:10.1093/nar/gki515 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Naum I. Gershenzon, Gary D. Stormo, and Ilya P. Ioshikhes

Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites
Nucl. Acids Res. 2005 33: 2290-2301; doi:10.1093/nar/gki519 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Yang Zhang and Jeffrey Skolnick

TM-align: a protein structure alignment algorithm based on the TM-score
Nucl. Acids Res. 2005 33: 2302-2309; doi:10.1093/nar/gki524 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

D. Gadelle, C. Bocs, M. Graille, and P. Forterre

Inhibition of archaeal growth and DNA topoisomerase VI activities by the Hsp90 inhibitor radicicol
Nucl. Acids Res. 2005 33: 2310-2317; doi:10.1093/nar/gki526 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Céline Marban, Laetitia Redel, Stella Suzanne, Carine Van Lint, Dominique Lecestre, Sylvette Chasserot-Golaz, Mark Leid, Dominique Aunis, Evelyne Schaeffer, and Olivier Rohr

COUP-TF interacting protein 2 represses the initial phase of HIV-1 gene transcription in human microglial cells
Nucl. Acids Res. 2005 33: 2318-2331; doi:10.1093/nar/gki529 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Célia Chen, Nicole Fossar, Dominique Weil, Marine Guillaud-Bataille, Gisèle Danglot, Brigitte Raynal, François Dautry, Alain Bernheim, and Olivier Brison

High frequency trans-splicing in a cell line producing spliced and polyadenylated RNA polymerase I transcripts from an rDNA-myc chimeric gene
Nucl. Acids Res. 2005 33: 2332-2342; doi:10.1093/nar/gki530 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Humberto Sanchez and Juan C. Alonso

Bacillus subtilis RecN binds and protects 3'-single-stranded DNA extensions in the presence of ATP
Nucl. Acids Res. 2005 33: 2343-2350; doi:10.1093/nar/gki533 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Corrigendum:

Cheng-Hsun Chiu, Petrus Tang, Chishih ChuSongnian Hu, Qiyu Bao, Jun Yu, yun-Ying Chou, Hsin-Shih Wang, and Ying-Shiung Lee

The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen
Nucl. Acids Res. 2005 33: 2351; doi:10.1093/nar/gki522 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Dov J. Stekel, Donatella Sarti, Victor Trevino, Lihong Zhang, Mike Salmon, Chris D. Buckley, Mark Stevens, Mark J. Pallen, Charles Penn, and Francesco Falciani

Analysis of host response to bacterial infection using error model based gene expression microarray experiments
Nucl. Acids Res. 2005 33: 2352-2353; doi:10.1093/nar/gki532 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

M. T. Nasim and R. C. Trembath

A dual-light reporter system to determine the efficiency of protein–protein interactions in mammalian cells
Nucl. Acids Res. 2005 33: e66; doi:10.1093/nar/gni066 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jost Seibler, Birgit Küter-Luks, Heidrun Kern, Sandra Streu, Leona Plum, Jan Mauer, Ralf Kühn, Jens C. Brüning, and Frieder Schwenk

Single copy shRNA configuration for ubiquitous gene knockdown in mice
Nucl. Acids Res. 2005 33: e67; doi:10.1093/nar/gni065 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Remus T. Dame, Joost van Mameren, Martijn S. Luijsterburg, Monika E. Mysiak, Ana Janicijevic, Grzegorz Pazdzior, Peter C. van der Vliet, Claire Wyman, and Gijs J.L. Wuite

Analysis of scanning force microscopy images of protein-induced DNA bending using simulations
Nucl. Acids Res. 2005 33: e68; doi:10.1093/nar/gni073 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gudrun Stengel and Wolfgang Knoll

Surface plasmon field-enhanced fluorescence spectroscopy studies of primer extension reactions
Nucl. Acids Res. 2005 33: e69; doi:10.1093/nar/gni067 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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