| | Articles RNase H2 of Saccharomyces cerevisiae is a complex of three proteins Ho-Sang Jeong, Peter S. Backlund, Hao-Chia Chen, Alexander A. Karavanov, and Robert J. Crouch PMCID: PMC373335 The major 5′ determinant in stop codon read-through involves two adjacent adenines Sanaa Tork, Isabelle Hatin, Jean-Pierre Rousset, and Céline Fabret PMCID: PMC373328 Specific inhibitors of HCV polymerase identified using an NS5B with lower affinity for template/primer substrate Ginette McKercher, Pierre L. Beaulieu, Daniel Lamarre, Steven LaPlante, Sylvain Lefebvre, Charles Pellerin, Louise Thauvette, and George Kukolj PMCID: PMC373316 Formation of an intramolecular triple-stranded DNA structure monitored by fluorescence of 2-aminopurine or 6-methylisoxanthopterin Anna K. Shchyolkina, Dmitry N. Kaluzhny, Olga F. Borisova, Mary E. Hawkins, Robert L. Jernigan, Thomas M. Jovin, Donna J. Arndt-Jovin, and Victor B. Zhurkin PMCID: PMC373315 Exon repetition: a major pathway for processing mRNA of some genes is allele-specific Roberto Rigatti, Jian-Hua Jia, Nilesh J. Samani, and Ian C. Eperon PMCID: PMC373324 Statistical resynchronization and Bayesian detection of periodically expressed genes Xin Lu, Wen Zhang, Zhaohui S. Qin, Kurt E. Kwast, and Jun S. Liu PMCID: PMC373332 Crystal structure of the catalytic fragment of murine poly(ADP-ribose) polymerase-2 Antony W. Oliver, Jean-Christophe Amé, S. Mark Roe, Valerie Good, Gilbert de Murcia, and Laurence H. Pearl PMCID: PMC373339 A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase Martine Roovers, Johan Wouters, Janusz M. Bujnicki, Catherine Tricot, Victor Stalon, Henri Grosjean, and Louis Droogmans PMCID: PMC373318 Identification and characterization of two forms of mouse MUTYH proteins encoded by alternatively spliced transcripts Akimasa Ichinoe, Mehrdad Behmanesh, Yohei Tominaga, Yasuhiro Ushijima, Seiki Hirano, Yasunari Sakai, Daisuke Tsuchimoto, Kunihiko Sakumi, Norio Wake, and Yusaku Nakabeppu PMCID: PMC373338 Premature termination codons enhance mRNA decapping in human cells P. Couttet and T. Grange PMCID: PMC373342 Synthesis of phosphorothioamidites derived from 3′-thio-3′-deoxythymidine and 3′-thio-2′,3′-dideoxycytidine and the automated synthesis of oligodeoxynucleotides containing a 3′-S-phosphorothiolate linkage Ghalia Sabbagh, Kevin J. Fettes, Rajendra Gosain, Ian A. O'Neil, and Richard Cosstick PMCID: PMC373317 More active human L1 retrotransposons produce longer insertions Alexander H. Farley, Eline T. Luning Prak, and Haig H. Kazazian, Jr PMCID: PMC373329 Interaction of Saccharomyces Cdc13p with Pol1p, Imp4p, Sir4p and Zds2p is involved in telomere replication, telomere maintenance and cell growth control Chia-Ling Hsu, Ying-Shung Chen, Shih-Yin Tsai, Pei-Jung Tu, Mei-Jung Wang, and Jing-Jer Lin PMCID: PMC373330 Cassette-like variation of restriction enzyme genes in Escherichia coli C and relatives Marion H. Sibley and Elisabeth A. Raleigh PMCID: PMC373321 Design and synthesis of a photocleavable biotinylated nucleotide for DNA analysis by mass spectrometry Xiaopeng Bai, Sobin Kim, Zengmin Li, Nicholas J. Turro, and Jingyue Ju PMCID: PMC373325 Surprising features of plastid ndhD transcripts: addition of non-encoded nucleotides and polysome association of mRNAs with an unedited start codon Aitor Zandueta-Criado and Ralph Bock PMCID: PMC373341 Protein structure prediction using sparse dipolar coupling data Youxing Qu, Jun-tao Guo, Victor Olman, and Ying Xu PMCID: PMC373331 Automated correction of genome sequence errors Pawel Gajer, Michael Schatz, and Steven L. Salzberg PMCID: PMC373340 Catalytic and DNA-binding properties of the human Ogg1 DNA N-glycosylase/AP lyase: biochemical exploration of H270, Q315 and F319, three amino acids of the 8-oxoguanine-binding pocket Patricia Auffret van der Kemp, Jean-Baptiste Charbonnier, Marc Audebert, and Serge Boiteux PMCID: PMC373348 On the interpretation of Raman spectra of 1-aminooxy-spermine/DNA complexes A. J. Ruiz-Chica, M. A. Medina, F. Sánchez-Jiménez, and F. J. Ramírez PMCID: PMC373354 Sequence-specific transcriptional repression by an MBD2-interacting zinc finger protein MIZF Masayuki Sekimata and Yoshimi Homma PMCID: PMC373363 Modification of de novo DNA methyltransferase 3a (Dnmt3a) by SUMO-1 modulates its interaction with histone deacetylases (HDACs) and its capacity to repress transcription Yan Ling, Umesh T. Sankpal, Andrea K. Robertson, James G. McNally, Tatiana Karpova, and Keith D. Robertson PMCID: PMC373322 Characterization of the 5′-untranslated region of YB-1 mRNA and autoregulation of translation by YB-1 protein Takao Fukuda, Megumi Ashizuka, Takanori Nakamura, Kotaro Shibahara, Katsumasa Maeda, Hiroto Izumi, Kimitoshi Kohno, Michihiko Kuwano, and Takeshi Uchiumi PMCID: PMC373347 Linker phosphoramidite reagents for the attachment of the first nucleoside to underivatized solid-phase supports Richard T. Pon and Shuyuan Yu PMCID: PMC373346 Functional analysis of subcellular localization and protein–protein interaction sequences in the essential DNA ligase I protein of fission yeast Ina V. Martin and Stuart A. MacNeill PMCID: PMC373326 Nuclear MxA proteins form a complex with influenza virus NP and inhibit the transcription of the engineered influenza virus genome Kadir Turan, Masaki Mibayashi, Kenji Sugiyama, Shoko Saito, Akiko Numajiri, and Kyosuke Nagata PMCID: PMC373319 Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase Jennifer H. Eastberg, John Pelletier, and Barry L. Stoddard PMCID: PMC373337 Targeting Alzheimer's disease genes with RNA interference: an efficient strategy for silencing mutant alleles Victor M. Miller, Cynthia M. Gouvion, Beverly L. Davidson, and Henry L. Paulson PMCID: PMC373334 Poly(ADP-ribose) polymerase (PARP-1) and p53 independently function in regulating double-strand break repair in primate cells Silke Süsse, Claus-Jürgen Scholz, Alexander Bürkle, and Lisa Wiesmüller PMCID: PMC373350 Guidelines for incorporating non-perfectly matched oligonucleotides into target-specific hybridization probes for a DNA microarray Inhan Lee, Alan A. Dombkowski, and Brian D. Athey PMCID: PMC373323 Effects on RNAi of the tight structure, sequence and position of the targeted region Koichi Yoshinari, Makoto Miyagishi, and Kazunari Taira PMCID: PMC373345 The Trypanosoma brucei spliced leader RNA and rRNA gene promoters have interchangeable TbSNAP50-binding elements Bernd Schimanski, Gabriele Laufer, Lilia Gontcharova, and Arthur Günzl PMCID: PMC373353 A novel concept for ligand attachment to oligonucleotides via a 2′-succinyl linker Johannes Winkler, Ernst Urban, Doris Losert, Volker Wacheck, Hubert Pehamberger, and Christian R. Noe PMCID: PMC373351 A new γ-interferon-inducible promoter and splice variants of an anti-angiogenic human tRNA synthetase Jianming Liu, Eveline Shue, Karla L. Ewalt, and Paul Schimmel PMCID: PMC373357 PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1 A. Michael Sismour, Stefan Lutz, Jeong-Ho Park, Michael J. Lutz, Paul L. Boyer, Stephen H. Hughes, and Steven A. Benner PMCID: PMC373358 Fission yeast Arp6 is required for telomere silencing, but functions independently of Swi6 Masaru Ueno, Tadashi Murase, Tatsuya Kibe, Noriyuki Ohashi, Kazunori Tomita, Yota Murakami, Masahiro Uritani, Takashi Ushimaru, and Masahiko Harata PMCID: PMC373355 High-throughput protein analysis integrating bioinformatics and experimental assays Coral del Val, Alexander Mehrle, Mechthild Falkenhahn, Markus Seiler, Karl-Heinz Glatting, Annemarie Poustka, Sandor Suhai, and Stefan Wiemann PMCID: PMC373366 Structure of a palindromic amplicon junction implicates microhomology-mediated end joining as a mechanism of sister chromatid fusion during gene amplification Yukiko Okuno, Peter J. Hahn, and David M. Gilbert PMCID: PMC373360 Transcription regulation of TNF-α-early response genes by poly(ADP-ribose) polymerase-1 in murine heart endothelial cells Ana Carrillo, Yolanda Monreal, Pablo Ramírez, Luis Marin, Pascual Parrilla, Francisco Javier Oliver, and José Yélamos PMCID: PMC373356 Involvement of Hus1 in the chain elongation step of DNA replication after exposure to camptothecin or ionizing radiation Xiang Wang, Jun Guan, Baocheng Hu, Robert S. Weiss, George Iliakis, and Ya Wang PMCID: PMC373359 Gene structure conservation aids similarity based gene prediction Irmtraud M. Meyer and Richard Durbin PMCID: PMC373336 A programmed –1 ribosomal frameshift signal can function as a cis-acting mRNA destabilizing element Ewan P. Plant, Pinger Wang, Jonathan L. Jacobs, and Jonathan D. Dinman PMCID: PMC373365 VITO-1 is an essential cofactor of TEF1-dependent muscle-specific gene regulation Stefan Günther, Michal Mielcarek, Marcus Krüger, and Thomas Braun PMCID: PMC373362 Recent horizontal intron transfer to a chloroplast genome Elena V. Sheveleva and Richard B. Hallick PMCID: PMC373349 The sea urchin stem–loop-binding protein: a maternally expressed protein that probably functions in expression of multiple classes of histone mRNA Anthony J. Robertson, Jason T. Howard, Zbigniew Dominski, Bradley J. Schnackenberg, Jan L. Sumerel, John J. McCarthy, James A. Coffman, and William F. Marzluff PMCID: PMC373320 Probing alternative foldings of the HIV-1 leader RNA by antisense oligonucleotide scanning arrays Marcel Ooms, Koen Verhoef, Edwin Southern, Hendrik Huthoff, and Ben Berkhout PMCID: PMC373333 2′-O-[2-[(N,N-dimethylamino)oxy]ethyl]-modified oligonucleotides inhibit expression of mRNA in vitro and in vivo Thazha P. Prakash, Joseph F. Johnston, Mark J. Graham, Thomas P. Condon, and Muthiah Manoharan PMCID: PMC373344 Role of the RNA polymerase α subunits in CII-dependent activation of the bacteriophage λ pE promoter: identification of important residues and positioning of the α C-terminal domains Barbara Kedzierska, David J. Lee, Grzegorz Węgrzyn, Stephen J. W. Busby, and Mark S. Thomas PMCID: PMC373352 Two mutations in the tetracycline repressor change the inducer anhydrotetracycline to a corepressor Annette Kamionka, Joanna Bogdanska-Urbaniak, Oliver Scholz, and Wolfgang Hillen PMCID: PMC373327 Disruption of type III secretion in Salmonella enterica serovar Typhimurium by external guide sequences Jeffrey S. McKinney, Haifeng Zhang, Tomoko Kubori, Jorge E. Galán, and Sidney Altman PMCID: PMC373343 Fission yeast global repressors regulate the specificity of chromatin alteration in response to distinct environmental stresses Kouji Hirota, Tomoko Hasemi, Takatomi Yamada, Ken-ich Mizuno, Charles S. Hoffman, Takehiko Shibata, and Kunihiro Ohta PMCID: PMC373364 NAR Methods Online Highly sensitive amperometric detection of genomic DNA in animal tissues Hong Xie, Yuan Hong Yu, Pei-Lin Mao, and Zhiqiang Gao PMCID: PMC373372 Rapid and accurate characterisation of short tandem repeats by MALDI-TOF analysis of endonuclease cleaved RNA transcripts Doris Seichter, Stefan Krebs, and Martin Förster PMCID: PMC373373 A novel approach for evaluating the efficiency of siRNAs on protein levels in cultured cells Weilin Wu, Emily Hodges, Jenny Redelius, and Christer Höög PMCID: PMC373369 Rapid detection of single nucleotide polymorphisms associated with spinal muscular atrophy by use of a reusable fibre-optic biosensor James H. Watterson, Sandeep Raha, Christopher C. Kotoris, Christopher C. Wust, Farhad Gharabaghi, Sarah C. Jantzi, Nicole K. Haynes, Nathalie H. Gendron, Ulrich J. Krull, Alex E. Mackenzie, and Paul A. E. Piunno PMCID: PMC373370 Construction of long DNA molecules using long PCR-based fusion of several fragments simultaneously Nikolai A. Shevchuk, Anton V. Bryksin, Yevgeniya A. Nusinovich, Felipe C. Cabello, Margaret Sutherland, and Stephan Ladisch PMCID: PMC373371 Impedance-based detection of DNA sequences using a silicon transducer with PNA as the probe layer A. Macanovic, C. Marquette, C. Polychronakos, and M. F. Lawrence PMCID: PMC373368 Selective DNA amplification from complex genomes using universal double-sided adapters Matthew J. Callow, Snezana Drmanac, and Radoje Drmanac PMCID: PMC373375 Oligonucleotide-directed site-specific integration of high complexity libraries into ssDNA templates M. B. Hale, G. P. Nolan, and R. Wolkowicz PMCID: PMC373376 Two-dimensional conformation-dependent electrophoresis (2D-CDE) to separate DNA fragments containing unmatched bulge from complex DNA samples Gudmundur H. Gunnarsson, Hans G. Thormar, Bjarki Gudmundsson, Lina Akesson, and Jon J. Jonsson PMCID: PMC373374 Corrigenda Nucleic Acids Res. 2004; 32(2): 863–864. Published online 2004 February 4. doi: 10.1093/nar/gkh245.PMCID: PMC373361 Corrects: Eveline Lescrinier, et al. SURVEY AND SUMMARY: Difference in conformational diversity between nucleic acids with a six-membered ‘sugar’ unit and natural ‘furanose’ nucleic acids. Nucleic Acids Res. 2003 June 15; 31(12): 2975–2989. Nucleic Acids Res. 2004; 32(2): 865. Published online 2004 February 4. doi: 10.1093/nar/gkh270.PMCID: PMC373367 Corrects: Norie Fujikawa, et al. Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein. Nucleic Acids Res. 2004; 32(1): 82–92. |
