| | Articles A novel type of silencing factor, Clr2, is necessary for transcriptional silencing at various chromosomal locations in the fission yeast Schizosaccharomyces pombe Pernilla Bjerling, Karl Ekwall, Richard Egel, and Geneviève Thon PMCID: PMC516054 The N-terminal half-domain of the long form of tRNase Z is required for the RNase 65 activity Hiroaki Takaku, Asako Minagawa, Masamichi Takagi, and Masayuki Nashimoto PMCID: PMC516050 Selectivity and affinity of triplex-forming oligonucleotides containing 2′-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine for recognizing AT base pairs in duplex DNA Sadie D. Osborne, Vicki E. C. Powers, David A. Rusling, Oliver Lack, Keith R. Fox, and Tom Brown PMCID: PMC516051 tRNASer(CGA) differentially regulates expression of wild-type and codon-modified papillomavirus L1 genes Wenyi Gu, Mengrong Li, Wei Ming Zhao, Ning Xia Fang, Shurui Bu, Ian H. Frazer, and Kong-Nan Zhao PMCID: PMC516046 Ribosome stalling and peptidyl-tRNA drop-off during translational delay at AGA codons Luis Rogelio Cruz-Vera, Marco Antonio Magos-Castro, Efraín Zamora-Romo, and Gabriel Guarneros PMCID: PMC516057 Transcription influences the types of deletion and expansion products in an orientation-dependent manner from GAC•GTC repeats Liliana H. Mochmann and Robert D. Wells PMCID: PMC516059 Transcriptional repression by p53 promotes a Bcl-2-insensitive and mitochondria-independent pathway of apoptosis Nelly Godefroy, Sylvina Bouleau, Gaëtan Gruel, Flore Renaud, Vincent Rincheval, Bernard Mignotte, Diana Tronik-Le Roux, and Jean-Luc Vayssière PMCID: PMC516049 The effect of eukaryotic release factor depletion on translation termination in human cell lines Deanna M. Janzen and Adam P. Geballe PMCID: PMC516063 DNA ligases ensure fidelity by interrogating minor groove contacts Pingfang Liu, Artur Burdzy, and Lawrence C. Sowers PMCID: PMC516055 Comparative analysis of dioxin response elements in human, mouse and rat genomic sequences Y. V. Sun, D. R. Boverhof, L. D. Burgoon, M. R. Fielden, and T. R. Zacharewski PMCID: PMC516056 The human Rad9 checkpoint protein stimulates the carbamoyl phosphate synthetase activity of the multifunctional protein CAD Laura A. Lindsey-Boltz, Eric M. Wauson, Lee M. Graves, and Aziz Sancar PMCID: PMC516061 A third lineage with two-piece tmRNA Stephen M. Sharkady and Kelly P. Williams PMCID: PMC516066 Increased frequency of aberrant V(D)J recombination products in core RAG-expressing mice Sadiqur R. Talukder, Darryll D. Dudley, Frederick W. Alt, Yousuke Takahama, and Yoshiko Akamatsu PMCID: PMC516053 Redefining the structure of the mouse connexin43 gene: selective promoter usage and alternative splicing mechanisms yield transcripts with different translational efficiencies Ingrid Pfeifer, Curtis Anderson, Rudolf Werner, and Elisa Oltra PMCID: PMC516064 Thioredoxin can influence gene expression by affecting gyrase activity Kuanyu Li, Cécile Pasternak, Elisabeth Härtig, Kerstin Haberzettl, Anthony Maxwell, and Gabriele Klug PMCID: PMC516065 RNA binding and R-loop formation by the herpes simplex virus type-1 single-stranded DNA-binding protein (ICP8) Paul E. Boehmer PMCID: PMC516068 Splicing affects presentation of RNA dimerization signals in HIV-2 in vitro Jean-Marc Lanchy, Quenna N. Szafran, and J. Stephen Lodmell PMCID: PMC516069 Nucleotide-dependent interactions between a fork junction–RNA polymerase complex and an AAA+ transcriptional activator protein W. V. Cannon, J. Schumacher, and M. Buck PMCID: PMC516047 Relative gene-silencing efficiencies of small interfering RNAs targeting sense and antisense transcripts from the same genetic locus Xiuyuan Hu, Sharlene Hipolito, Rebecca Lynn, Violet Abraham, Silvester Ramos, and Flossie Wong-Staal PMCID: PMC516062 Phosphorylation at 5′ end of guanosine stretches inhibits dimerization of G-quadruplexes and formation of a G-quadruplex interferes with the enzymatic activities of DNA enzymes M. Khabir Uddin, Yoshio Kato, Yasuomi Takagi, Toshiyasu Mikuma, and Kazunari Taira PMCID: PMC516048 Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs Petr Pancoska, Zdenek Moravek, and Ute M. Moll PMCID: PMC516071 Novel non-coding RNAs in Dictyostelium discoideum and their expression during development Anders Aspegren, Andrea Hinas, Pontus Larsson, Anders Larsson, and Fredrik Söderbom PMCID: PMC516072 Design and synthesis of fluorescent substrates for human tyrosyl-DNA phosphodiesterase I Marc C. Rideout, Amy C. Raymond, and Alex B. Burgin, Jr PMCID: PMC516067 Enzymatic switching for efficient and accurate translesion DNA replication Scott D. McCulloch, Robert J. Kokoska, Olga Chilkova, Carrie M. Welch, Erik Johansson, Peter M. J. Burgers, and Thomas A. Kunkel PMCID: PMC516052 Alternative splicing generates multiple SMRT transcripts encoding conserved repressor domains linked to variable transcription factor interaction domains Marianne Malartre, Stephen Short, and Colin Sharpe PMCID: PMC516058 Synthetic tRNALys,3 as the replication primer for the HIV-1HXB2 and HIV-1Mal genomes Jennifer T. Miller, Anastasia Khvorova, Stephen A. Scaringe, and Stuart F. J. Le Grice PMCID: PMC516074 Cooperative effects on the formation of intercalation sites Michael Trieb, Christine Rauch, Fajar R. Wibowo, Bernd Wellenzohn, and Klaus R. Liedl PMCID: PMC516060 Interaction of the Zα domain of human ADAR1 with a negatively supercoiled plasmid visualized by atomic force microscopy Alexander Y. Lushnikov, Bernard A. Brown, II, Elena A. Oussatcheva, Vladimir N. Potaman, Richard R. Sinden, and Yuri L. Lyubchenko PMCID: PMC516073 NAR Methods Online Semi-automated, single-band peak-fitting analysis of hydroxyl radical nucleic acid footprint autoradiograms for the quantitative analysis of transitions Keiji Takamoto, Mark R. Chance, and Michael Brenowitz PMCID: PMC516076 RNA expression microarrays (REMs), a high-throughput method to measure differences in gene expression in diverse biological samples Charles E. Rogler, Tatyana Tchaikovskaya, Raquel Norel, Aldo Massimi, Christopher Plescia, Eugeny Rubashevsky, Paul Siebert, and Leslie E. Rogler PMCID: PMC516075 Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments Torstein Tengs, Thomas LaFramboise, Robert B. Den, David N. Hayes, Jianhua Zhang, Saikat DebRoy, Robert C. Gentleman, Keith O'Neill, Bruce Birren, and Matthew Meyerson PMCID: PMC516078 A ‘one-pot’ assay for the accessibility of DNA in a nucleosome core particle Chenyi Wu and Andrew Travers PMCID: PMC516079 Quantitative assessment of a novel flow-through porous microarray for the rapid analysis of gene expression profiles Ying Wu, Peggy de Kievit, Lars Vahlkamp, Dirk Pijnenburg, Maarten Smit, Martijn Dankers, Diana Melchers, Martijn Stax, Piet J. Boender, Colin Ingham, Niek Bastiaensen, Rik de Wijn, Dirk van Alewijk, Henk van Damme, Anton K. Raap, Alan B. Chan, and Rinie van Beuningen PMCID: PMC516077 Comprehensive comparison of six microarray technologies Carole L. Yauk, M. Lynn Berndt, Andrew Williams, and George R. Douglas PMCID: PMC516080 Corrigendum Nucleic Acids Res. 2004; 32(15): 4713. Published online 2004 September 1. doi: 10.1093/nar/gkh801.PMCID: PMC516070 Corrects: John P. McCutcheon, et al. Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics. Nucleic Acids Res. 2003 July 15; 31(14): 4119–4128. |
