Nucleic Acids Research

Articles:

Pernilla Bjerling, Karl Ekwall, Richard Egel, and Geneviève Thon

A novel type of silencing factor, Clr2, is necessary for transcriptional silencing at various chromosomal locations in the fission yeast Schizosaccharomyces pombe
Nucl. Acids Res. 2004 32: 4421-4428; doi:10.1093/nar/gkh780 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hiroaki Takaku, Asako Minagawa, Masamichi Takagi, and Masayuki Nashimoto

The N-terminal half-domain of the long form of tRNase Z is required for the RNase 65 activity
Nucl. Acids Res. 2004 32: 4429-4438; doi:10.1093/nar/gkh774 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sadie D. Osborne, Vicki E. C. Powers, David A. Rusling, Oliver Lack, Keith R. Fox, and Tom Brown

Selectivity and affinity of triplex-forming oligonucleotides containing 2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine for recognizing AT base pairs in duplex DNA
Nucl. Acids Res. 2004 32: 4439-4447; doi:10.1093/nar/gkh776 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Wenyi Gu, Mengrong Li, Wei Ming Zhao, Ning Xia Fang, Shurui Bu, Ian H. Frazer, and Kong-Nan Zhao

tRNA^Ser(CGA) differentially regulates expression of wild-type and codon-modified papillomavirus L1 genes
Nucl. Acids Res. 2004 32: 4448-4461; doi:10.1093/nar/gkh748 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Luis Rogelio Cruz-Vera, Marco Antonio Magos-Castro, Efraín Zamora-Romo, and Gabriel Guarneros

Ribosome stalling and peptidyl-tRNA drop-off during translational delay at AGA codons
Nucl. Acids Res. 2004 32: 4462-4468; doi:10.1093/nar/gkh784 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Liliana H. Mochmann and Robert D. Wells

Transcription influences the types of deletion and expansion products in an orientation-dependent manner from GAC•GTC repeats
Nucl. Acids Res. 2004 32: 4469-4479; doi:10.1093/nar/gkh787 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nelly Godefroy, Sylvina Bouleau, Gaëtan Gruel, Flore Renaud, Vincent Rincheval, Bernard Mignotte, Diana Tronik-Le Roux, and Jean-Luc Vayssière

Transcriptional repression by p53 promotes a Bcl-2-insensitive and mitochondria-independent pathway of apoptosis
Nucl. Acids Res. 2004 32: 4480-4490; doi:10.1093/nar/gkh773 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Deanna M. Janzen and Adam P. Geballe

The effect of eukaryotic release factor depletion on translation termination in human cell lines
Nucl. Acids Res. 2004 32: 4491-4502; doi:10.1093/nar/gkh791 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Pingfang Liu, Artur Burdzy, and Lawrence C. Sowers

DNA ligases ensure fidelity by interrogating minor groove contacts
Nucl. Acids Res. 2004 32: 4503-4511; doi:10.1093/nar/gkh781 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Y. V. Sun, D. R. Boverhof, L. D. Burgoon, M. R. Fielden, and T. R. Zacharewski

Comparative analysis of dioxin response elements in human, mouse and rat genomic sequences
Nucl. Acids Res. 2004 32: 4512-4523; doi:10.1093/nar/gkh782 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Laura A. Lindsey-Boltz, Eric M. Wauson, Lee M. Graves, and Aziz Sancar

The human Rad9 checkpoint protein stimulates the carbamoyl phosphate synthetase activity of the multifunctional protein CAD
Nucl. Acids Res. 2004 32: 4524-4530; doi:10.1093/nar/gkh789 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Stephen M. Sharkady and Kelly P. Williams

A third lineage with two-piece tmRNA
Nucl. Acids Res. 2004 32: 4531-4538; doi:10.1093/nar/gkh795 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Sadiqur R. Talukder, Darryll D. Dudley, Frederick W. Alt, Yousuke Takahama, and Yoshiko Akamatsu

Increased frequency of aberrant V(D)J recombination products in core RAG-expressing mice
Nucl. Acids Res. 2004 32: 4539-4549; doi:10.1093/nar/gkh778 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ingrid Pfeifer, Curtis Anderson, Rudolf Werner, and Elisa Oltra

Redefining the structure of the mouse connexin43 gene: selective promoter usage and alternative splicing mechanisms yield transcripts with different translational efficiencies
Nucl. Acids Res. 2004 32: 4550-4562; doi:10.1093/nar/gkh792 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kuanyu Li, Cécile Pasternak, Elisabeth Härtig, Kerstin Haberzettl, Anthony Maxwell, and Gabriele Klug

Thioredoxin can influence gene expression by affecting gyrase activity
Nucl. Acids Res. 2004 32: 4563-4575; doi:10.1093/nar/gkh794 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Paul E. Boehmer

RNA binding and R-loop formation by the herpes simplex virus type-1 single-stranded DNA-binding protein (ICP8)
Nucl. Acids Res. 2004 32: 4576-4584; doi:10.1093/nar/gkh797 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jean-Marc Lanchy, Quenna N. Szafran, and J. Stephen Lodmell

Splicing affects presentation of RNA dimerization signals in HIV-2 in vitro
Nucl. Acids Res. 2004 32: 4585-4595; doi:10.1093/nar/gkh800 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

W. V. Cannon, J. Schumacher, and M. Buck

Nucleotide-dependent interactions between a fork junction–RNA polymerase complex and an AAA+ transcriptional activator protein
Nucl. Acids Res. 2004 32: 4596-4608; doi:10.1093/nar/gkh755 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Xiuyuan Hu, Sharlene Hipolito, Rebecca Lynn, Violet Abraham, Silvester Ramos, and Flossie Wong-Staal

Relative gene-silencing efficiencies of small interfering RNAs targeting sense and antisense transcripts from the same genetic locus
Nucl. Acids Res. 2004 32: 4609-4617; doi:10.1093/nar/gkh790 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

M. Khabir Uddin, Yoshio Kato, Yasuomi Takagi, Toshiyasu Mikuma, and Kazunari Taira

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
Nucl. Acids Res. 2004 32: 4618-4629; doi:10.1093/nar/gkh766 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Petr Pancoska, Zdenek Moravek, and Ute M. Moll

Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs
Nucl. Acids Res. 2004 32: 4630-4645; doi:10.1093/nar/gkh802 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Anders Aspegren, Andrea Hinas, Pontus Larsson, Anders Larsson, and Fredrik Söderbom

Novel non-coding RNAs in Dictyostelium discoideum and their expression during development
Nucl. Acids Res. 2004 32: 4646-4656; doi:10.1093/nar/gkh804 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Marc C. Rideout, Amy C. Raymond, and Alex B. Burgin, Jr

Design and synthesis of fluorescent substrates for human tyrosyl-DNA phosphodiesterase I
Nucl. Acids Res. 2004 32: 4657-4664; doi:10.1093/nar/gkh796 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Scott D. McCulloch, Robert J. Kokoska, Olga Chilkova, Carrie M. Welch, Erik Johansson, Peter M. J. Burgers, and Thomas A. Kunkel

Enzymatic switching for efficient and accurate translesion DNA replication
Nucl. Acids Res. 2004 32: 4665-4675; doi:10.1093/nar/gkh777 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Marianne Malartre, Stephen Short, and Colin Sharpe

Alternative splicing generates multiple SMRT transcripts encoding conserved repressor domains linked to variable transcription factor interaction domains
Nucl. Acids Res. 2004 32: 4676-4686; doi:10.1093/nar/gkh786 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jennifer T. Miller, Anastasia Khvorova, Stephen A. Scaringe, and Stuart F. J. Le Grice

Synthetic tRNA^Lys,3 as the replication primer for the HIV-1_HXB2 and HIV-1_Mal genomes
Nucl. Acids Res. 2004 32: 4687-4695; doi:10.1093/nar/gkh813 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Michael Trieb, Christine Rauch, Fajar R. Wibowo, Bernd Wellenzohn, and Klaus R. Liedl

Cooperative effects on the formation of intercalation sites
Nucl. Acids Res. 2004 32: 4696-4703; doi:10.1093/nar/gkh788 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Alexander Y. Lushnikov, Bernard A. Brown, II, Elena A. Oussatcheva, Vladimir N. Potaman, Richard R. Sinden, and Yuri L. Lyubchenko

Interaction of the Z domain of human ADAR1 with a negatively supercoiled plasmid visualized by atomic force microscopy
Nucl. Acids Res. 2004 32: 4704-4712; doi:10.1093/nar/gkh810 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Corrigenda:

John P. McCutcheon and Sean R. Eddy

Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics
Nucl. Acids Res. 2004 32: 4713; doi:10.1093/nar/gkh801 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Methods Online:

Keiji Takamoto, Mark R. Chance, and Michael Brenowitz

Semi-automated, single-band peak-fitting analysis of hydroxyl radical nucleic acid footprint autoradiograms for the quantitative analysis of transitions
Nucl. Acids Res. 2004 32: e119; doi:10.1093/nar/gnh117 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Charles E. Rogler, Tatyana Tchaikovskaya, Raquel Norel, Aldo Massimi, Christopher Plescia, Eugeny Rubashevsky, Paul Siebert, and Leslie E. Rogler

RNA expression microarrays (REMs), a high-throughput method to measure differences in gene expression in diverse biological samples
Nucl. Acids Res. 2004 32: e120; doi:10.1093/nar/gnh116 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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

Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments
Nucl. Acids Res. 2004 32: e121; doi:10.1093/nar/gnh120 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Chenyi Wu and Andrew Travers

A ‘one-pot’ assay for the accessibility of DNA in a nucleosome core particle
Nucl. Acids Res. 2004 32: e122; doi:10.1093/nar/gnh121 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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

Quantitative assessment of a novel flow-through porous microarray for the rapid analysis of gene expression profiles
Nucl. Acids Res. 2004 32: e123; doi:10.1093/nar/gnh118 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Carole L. Yauk, M. Lynn Berndt, Andrew Williams, and George R. Douglas

Comprehensive comparison of six microarray technologies
Nucl. Acids Res. 2004 32: e124; doi:10.1093/nar/gnh123 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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