| | Articles NMR chemical shift and relaxation measurements provide evidence for the coupled folding and binding of the p53 transactivation domain Pamela D. Vise, Bharat Baral, Andrew J. Latos, and Gary W. Daughdrill PMCID: PMC1075921 Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities Shingo Nakahata and Sachiyo Kawamoto PMCID: PMC1075922 Human Ku70/80 interacts directly with hTR, the RNA component of human telomerase Nicholas S. Y. Ting, Yaping Yu, Brant Pohorelic, Susan P. Lees-Miller, and Tara L. Beattie PMCID: PMC1075923 Torque-limited RecA polymerization on dsDNA Thijn van der Heijden, John van Noort, Hendrikje van Leest, Roland Kanaar, Claire Wyman, Nynke Dekker, and Cees Dekker PMCID: PMC1075924 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 Teldja N. Azzouz, Andreas Gruber, and Daniel Schümperli PMCID: PMC1075925 Predicting the secondary structures and tertiary interactions of 211 group I introns in IE subgroup Zhijie Li and Yi Zhang PMCID: PMC1083426 Detecting DNA-binding helix–turn–helix structural motifs using sequence and structure information Marialuisa Pellegrini-Calace and Janet M. Thornton PMCID: PMC1079965 Ribonucleases J1 and J2: two novel endoribonucleases in B.subtilis with functional homology to E.coli RNase E Sergine Even, Olivier Pellegrini, Lena Zig, Valerie Labas, Joelle Vinh, Dominique Bréchemmier-Baey, and Harald Putzer PMCID: PMC1079966 DNA-binding specificity of rice mariner-like transposases and interactions with Stowaway MITEs Cédric Feschotte, Mark T. Osterlund, Ryan Peeler, and Susan R. Wessler PMCID: PMC1079968 Eukaryotic RNases H1 act processively by interactions through the duplex RNA-binding domain Sergei A. Gaidamakov, Inna I. Gorshkova, Peter Schuck, Peter J. Steinbach, Hirofumi Yamada, Robert J. Crouch, and Susana M. Cerritelli PMCID: PMC1079969 Masking repeats while clustering ESTs Korbinian Schneeberger, Ketil Malde, Eivind Coward, and Inge Jonassen PMCID: PMC1079970 Repair activity of base and nucleotide excision repair enzymes for guanine lesions induced by nitrosative stress Toshiaki Nakano, Atsushi Katafuchi, Ryoko Shimizu, Hiroaki Terato, Toshinori Suzuki, Hiroshi Tauchi, Keisuke Makino, Milan Skorvaga, Bennett Van Houten, and Hiroshi Ide PMCID: PMC1079971 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 Céline Douarre, Dennis Gomez, Hamid Morjani, Jean-Marie Zahm, Marie-Françoise O'Donohue, Lahcen Eddabra, Patrick Mailliet, Jean-François Riou, and Chantal Trentesaux PMCID: PMC1079972 APE1-dependent repair of DNA single-strand breaks containing 3′-end 8-oxoguanine Jason L. Parsons, Irina I. Dianova, and Grigory L. Dianov PMCID: PMC1079973 Asymmetry in RNA pseudoknots: observation and theory Daniel P. Aalberts and Nathan O. Hodas PMCID: PMC1079967 Pre-mRNA processing enhancer (PPE) elements from intronless genes play additional roles in mRNA biogenesis than do ones from intron-containing genes Shouhong Guang and Janet E. Mertz PMCID: PMC1083424 Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome? Kalin Taskov, Charles Chapple, Gregory V. Kryukov, Sergi Castellano, Alexey V. Lobanov, Konstantin V. Korotkov, Roderic Guigó, and Vadim N. Gladyshev PMCID: PMC1083425 Factors affecting translation at the programmed −1 ribosomal frameshifting site of Cocksfoot mottle virus RNA in vivo Katri Mäkeläinen and Kristiina Mäkinen PMCID: PMC1083427 Cryptic promoter activity in the DNA sequence corresponding to the pim-1 5′-UTR Zeping Wang, Matt Weaver, and Nancy S. Magnuson PMCID: PMC1083428 Enzymatic processing of replication and recombination intermediates by the vaccinia virus DNA polymerase Michael D. Hamilton and David H. Evans PMCID: PMC1083429 The repressor DREAM acts as a transcriptional activator on Vitamin D and retinoic acid response elements Sona Scsucova, Daniela Palacios, Magali Savignac, Britt Mellström, Jose Ramon Naranjo, and Ana Aranda PMCID: PMC1084319 Influence of RNA structural stability on the RNA chaperone activity of the Escherichia coli protein StpA Rupert Grossberger, Oliver Mayer, Christina Waldsich, Katharina Semrad, Sandra Urschitz, and Renée Schroeder PMCID: PMC1084320 Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites Naum I. Gershenzon, Gary D. Stormo, and Ilya P. Ioshikhes PMCID: PMC1084321 TM-align: a protein structure alignment algorithm based on the TM-score Yang Zhang and Jeffrey Skolnick PMCID: PMC1084323 Inhibition of archaeal growth and DNA topoisomerase VI activities by the Hsp90 inhibitor radicicol D. Gadelle, C. Bocs, M. Graille, and P. Forterre PMCID: PMC1084324 COUP-TF interacting protein 2 represses the initial phase of HIV-1 gene transcription in human microglial cells Céline Marban, Laetitia Redel, Stella Suzanne, Carine Van Lint, Dominique Lecestre, Sylvette Chasserot-Golaz, Mark Leid, Dominique Aunis, Evelyne Schaeffer, and Olivier Rohr PMCID: PMC1084325 High frequency trans-splicing in a cell line producing spliced and polyadenylated RNA polymerase I transcripts from an rDNA-myc chimeric gene Célia Chen, Nicole Fossar, Dominique Weil, Marine Guillaud-Bataille, Gisèle Danglot, Brigitte Raynal, François Dautry, Alain Bernheim, and Olivier Brison PMCID: PMC1084326 Bacillus subtilis RecN binds and protects 3′-single-stranded DNA extensions in the presence of ATP Humberto Sanchez and Juan C. Alonso PMCID: PMC1084328 Methods Online A dual-light reporter system to determine the efficiency of protein–protein interactions in mammalian cells M. T. Nasim and R. C. Trembath PMCID: PMC1075926 Single copy shRNA configuration for ubiquitous gene knockdown in mice Jost Seibler, Birgit Küter-Luks, Heidrun Kern, Sandra Streu, Leona Plum, Jan Mauer, Ralf Kühn, Jens C. Brüning, and Frieder Schwenk PMCID: PMC1079974 Analysis of scanning force microscopy images of protein-induced DNA bending using simulations Remus T. Dame, Joost van Mameren, Martijn S. Luijsterburg, Monika E. Mysiak, Ana Janićijević, Grzegorz Pazdzior, Peter C. van der Vliet, Claire Wyman, and Gijs J.L. Wuite PMCID: PMC1083423 Surface plasmon field-enhanced fluorescence spectroscopy studies of primer extension reactions Gudrun Stengel and Wolfgang Knoll PMCID: PMC1084329 Corrigenda The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen Cheng-Hsun Chiu, Petrus Tang, Chishih ChuSongnian Hu, Qiyu Bao, Jun Yu, yun-Ying Chou, Hsin-Shih Wang, and Ying-Shiung Lee PMCID: PMC1084322 Corrects: Cheng-Hsun Chiu, et al. The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen. Nucleic Acids Res. 2005; 33(5): 1690–1698. Analysis of host response to bacterial infection using error model based gene expression microarray experiments Dov J. Stekel, Donatella Sarti, Victor Trevino, Lihong Zhang, Mike Salmon, Chris D. Buckley, Mark Stevens, Mark J. Pallen, Charles Penn, and Francesco Falciani PMCID: PMC1084327 Corrects: Dov J. Stekel, et al. Analysis of host response to bacterial infection using error model based gene expression microarray experiments. Nucleic Acids Res. 2005; 33(6): e53. |
