| | Survey and Summary Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution Cameron Neylon PMCID: PMC390300 Articles In vivo interactions of the Acanthamoeba TBP gene promoter Li Chen, Zhihua Peng, and Erik Bateman PMCID: PMC390285 Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation Alissa Resch, Yi Xing, Alexander Alekseyenko, Barmak Modrek, and Christopher Lee PMCID: PMC390276 HIV-1 Tat directly binds to NFκB enhancer sequence: role in viral and cellular gene expression Dineshkumar H. Dandekar, Krishna N. Ganesh, and Debashis Mitra PMCID: PMC390279 Roles of AUF1 isoforms, HuR and BRF1 in ARE-dependent mRNA turnover studied by RNA interference Ines Raineri, Daniel Wegmueller, Brigitte Gross, Ulrich Certa, and Christoph Moroni PMCID: PMC390274 DNA elements important for CAG·CTG repeat thresholds in Saccharomyces cerevisiae Michael J. Dixon and Robert S. Lahue PMCID: PMC390281 LEON: multiple aLignment Evaluation Of Neighbours Julie D. Thompson, Véronique Prigent, and Olivier Poch PMCID: PMC390283 Identification of cellular proteins enhancing activities of internal ribosomal entry sites by competition with oligodeoxynucleotides Kobong Choi, Jong Heon Kim, Xiaoyu Li, Ki Young Paek, Sang Hoon Ha, Sung Ho Ryu, Eckard Wimmer, and Sung Key Jang PMCID: PMC390288 Transcriptional regulation of the Drosophila catalase gene by the DRE/DREF system So Young Park, Young-Shin Kim, Dong-Jin Yang, and Mi-Ae Yoo PMCID: PMC390290 The active form of Xp54 RNA helicase in translational repression is an RNA-mediated oligomer Nicola Minshall and Nancy Standart PMCID: PMC390291 The helix–turn–helix motif of bacterial insertion sequence IS911 transposase is required for DNA binding Philippe Rousseau, Erwan Gueguen, Guy Duval-Valentin, and Mick Chandler PMCID: PMC390272 The DNA-binding properties of the ARID-containing subunits of yeast and mammalian SWI/SNF complexes Deborah Wilsker, Antonia Patsialou, Steven D. Zumbrun, Suhkmann Kim, Yuan Chen, Peter B. Dallas, and Elizabeth Moran PMCID: PMC390273 CTCF-dependent enhancer blockers at the upstream region of the chicken α-globin gene domain Viviana Valadez-Graham, Sergey V. Razin, and Félix Recillas-Targa PMCID: PMC390289 ARB: a software environment for sequence data Wolfgang Ludwig, Oliver Strunk, Ralf Westram, Lothar Richter, Harald Meier, Yadhukumar, Arno Buchner, Tina Lai, Susanne Steppi, Gangolf Jobb, Wolfram Förster, Igor Brettske, Stefan Gerber, Anton W. Ginhart, Oliver Gross, Silke Grumann, Stefan Hermann, Ralf Jost, Andreas König, Thomas Liss, Ralph Lüßmann, Michael May, Björn Nonhoff, Boris Reichel, Robert Strehlow, Alexandros Stamatakis, Norbert Stuckmann, Alexander Vilbig, Michael Lenke, Thomas Ludwig, Arndt Bode, and Karl-Heinz Schleifer PMCID: PMC390282 Detection of functional DNA motifs via statistical over-representation Martin C. Frith, Yutao Fu, Liqun Yu, Jiang-Fan Chen, Ulla Hansen, and Zhiping Weng PMCID: PMC390287 5′-Untranslated regions with multiple upstream AUG codons can support low-level translation via leaky scanning and reinitiation Xue-Qing Wang and Joseph A. Rothnagel PMCID: PMC390293 Paradigms for computational nucleic acid design Robert M. Dirks, Milo Lin, Erik Winfree, and Niles A. Pierce PMCID: PMC390280 Two-hybrid Mpp10p interaction-defective Imp4 proteins are not interaction defective in vivo but do confer specific pre-rRNA processing defects in Saccharomyces cerevisiae Jennifer E. G. Gallagher and Susan J. Baserga PMCID: PMC390303 Identifying secretomes in people, pufferfish and pigs Eric W. Klee, Daniel F. Carlson, Scott C. Fahrenkrug, Stephen C. Ekker, and Lynda B. M. Ellis PMCID: PMC390277 Conformational change of pseudouridine 55 synthase upon its association with RNA substrate Kulwadee Phannachet and Raven H. Huang PMCID: PMC390278 UV-C response of the ribonucleotide reductase large subunit involves both E2F-mediated gene transcriptional regulation and protein subcellular relocalization in tobacco cells Frédéric Lincker, Gabriel Philipps, and Marie-Edith Chabouté PMCID: PMC390297 A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea F. Constantinesco, P. Forterre, E. V. Koonin, L. Aravind, and C. Elie PMCID: PMC390275 PKD1 intron 21: triplex DNA formation and effect on replication Hiren P. Patel, Lu Lu, Richard T. Blaszak, and John J. Bissler PMCID: PMC390299 Efficient RNA interference depends on global context of the target sequence: quantitative analysis of silencing efficiency using Eulerian graph representation of siRNA Petr Pancoska, Zdenek Moravek, and Ute M. Moll PMCID: PMC390352 The involvement of Srs2 in post-replication repair and homologous recombination in fission yeast Claudette L. Doe and Matthew C. Whitby PMCID: PMC390302 RING1 inhibits transactivation of RBP-J by Notch through interaction with LIM protein KyoT2 Hongyan Qin, Jishu Wang, Yingmin Liang, Yoshihito Taniguchi, Kenji Tanigaki, and Hua Han PMCID: PMC390284 Solid phase synthesis and binding affinity of peptidyl transferase transition state mimics containing 2′-OH at P-site position A76 Joshua S. Weinger, David Kitchen, Stephen A. Scaringe, Scott A. Strobel, and Gregory W. Muth PMCID: PMC390298 Modified U1 snRNA suppresses expression of a targeted endogenous RNA by inhibiting polyadenylation of the transcript Peng Liu, Mark Kronenberg, Xi Jiang, and David Rowe PMCID: PMC390301 Efficiency and pattern of UV pulse laser-induced RNA–RNA cross-linking in the ribosome Tatjana Shapkina, Simon Lappi, Stefan Franzen, and Paul Wollenzien PMCID: PMC390305 Biochemical and random mutagenesis analysis of the region carrying the catalytic E152 amino acid of HIV-1 integrase C. Calmels, V. Richard de Soultrait, A. Caumont, C. Desjobert, A. Faure, M. Fournier, L. Tarrago-Litvak, and V. Parissi PMCID: PMC390286 Using pyrrolo-deoxycytosine to probe RNA/DNA hybrids containing the human immunodeficiency virus type-1 3′ polypurine tract Chandravanu Dash, Jason W. Rausch, and Stuart F. J. Le Grice PMCID: PMC390295 Interaction of human and bacterial AlkB proteins with DNA as probed through chemical cross-linking studies Yukiko Mishina, Chih-Hui J. Lee, and Chuan He PMCID: PMC390304 Integration of the 5′ end of the retrotransposon, R2Bm, can be complemented by homologous recombination Hirofumi Fujimoto, Yukiko Hirukawa, Hideki Tani, Yoshiharu Matsuura, Kazuo Hashido, Kozo Tsuchida, Naoko Takada, Masahiko Kobayashi, and Hideaki Maekawa PMCID: PMC390292 Influence of in vitro manipulation on the stability of methylation patterns in the Snurf/Snrpn-imprinting region in mouse embryonic stem cells Axel Schumacher and Walter Doerfler PMCID: PMC390307 Myosin light chain 1 atrial isoform (MLC1A) is expressed in pre-B cells under control of the BOB.1/OBF.1 coactivator Helmut Laumen, Cornelia Brunner, Axel Greiner, and Thomas Wirth PMCID: PMC390310 DNA dynamically directs its own transcription initiation Chu H. Choi, George Kalosakas, Kim Ø. Rasmussen, Makoto Hiromura, Alan R. Bishop, and Anny Usheva PMCID: PMC390311 Sequence-specific cleavage of RNA in the absence of divalent metal ions by a DNAzyme incorporating imidazolyl and amino functionalities Alexander V. Sidorov, Jane A. Grasby, and David M. Williams PMCID: PMC390309 Processing of clustered DNA damage generates additional double-strand breaks in mammalian cells post-irradiation Melanie Gulston, Catherine de Lara, Terry Jenner, Emma Davis, and Peter O'Neill PMCID: PMC390294 A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo Beatrix Suess, Barbara Fink, Christian Berens, Régis Stentz, and Wolfgang Hillen PMCID: PMC390306 NAR Methods Online Homologous gene targeting in Caenorhabditis elegans by biolistic transformation Eugene Berezikov, Cornelia I. Bargmann, and Ronald H. A. Plasterk PMCID: PMC390312 Intensity-based analysis of two-colour microarrays enables efficient and flexible hybridization designs Peter A. C. 't Hoen, Rolf Turk, Judith M. Boer, Ellen Sterrenburg, Renée X. de Menezes, Gert-Jan B. van Ommen, and Johan T. den Dunnen PMCID: PMC390313 Straightforward detection of SNPs in double-stranded DNA by using exonuclease III/nuclease S1/PNA system Binzhi Ren, Jing-Min Zhou, and Makoto Komiyama PMCID: PMC390314 A high-throughput method to monitor the expression of microRNA precursors Thomas D. Schmittgen, Jinmai Jiang, Qian Liu, and Liuqing Yang PMCID: PMC390315 Quantitative high-throughput analysis of transcription factor binding specificities Jane Linnell, Richard Mott, Simon Field, Dominic P. Kwiatkowski, Jiannis Ragoussis, and Irina A. Udalova PMCID: PMC390317 A novel method for screening species-specific gDNA probes for species identification Tong Xiang Li, JinKe Wang, YunFei Bai, XiangDong Sun, and ZuHong Lu PMCID: PMC390316 Identification and handling of artifactual gene expression profiles emerging in microarray hybridization experiments Leonid Brodsky, Andrei Leontovich, Michael Shtutman, and Elena Feinstein PMCID: PMC390318 SNPWaveTM: a flexible multiplexed SNP genotyping technology Michiel J. T. van Eijk, José L. N. Broekhof, Hein J. A. van der Poel, René C. J. Hogers, Harrie Schneiders, Judith Kamerbeek, Esther Verstege, Joris W. van Aart, Henk Geerlings, Jaap B. Buntjer, A. Jan van Oeveren, and Pieter Vos PMCID: PMC390319 Corrigendum Nucleic Acids Res. 2004; 32(4): 1615. Published online 2004 March 5. doi: 10.1093/nar/gkh308.PMCID: PMC390296 Corrects: Longchuan Bai, et al. Transcription factor ZBP-89 is required for STAT1 constitutive expression. Nucleic Acids Res. 2003 December 15; 31(24): 7264–7270. Erratum Nucleic Acids Res. 2004; 32(4): 1616. Published online 2004 March 5. doi: 10.1093/nar/gkh323.PMCID: PMC390308 Corrects: Ho-Sang Jeong, et al. RNase H2 of Saccharomyces cerevisiae is a complex of three proteins. Nucleic Acids Res. 2004; 32(2): 407–414. |
