Nucleic Acids Research

Articles:

Jeff D. Ballin, Irina A. Shkel, and M. Thomas Record, Jr

Interactions of the KWK₆ cationic peptide with short nucleic acid oligomers: demonstration of large Coulombic end effects on binding at 0.1–0.2 M salt
Nucl. Acids Res. 2004 32: 3271-3281; doi:10.1093/nar/gkh646 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Dmitri Graifer, Maxim Molotkov, Valentina Styazhkina, Natalia Demeshkina, Konstantin Bulygin, Anna Eremina, Anton Ivanov, Elena Laletina, Aliya Ven'yaminova, and Galina Karpova

Variable and conserved elements of human ribosomes surrounding the mRNA at the decoding and upstream sites
Nucl. Acids Res. 2004 32: 3282-3293; doi:10.1093/nar/gkh657 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yong-Gang Zheng, Hui Wei, Chen Ling, Franck Martin, Gilbert Eriani, and En-Duo Wang

Two distinct domains of the ß subunit of Aquifex aeolicus leucyl-tRNA synthetase are involved in tRNA binding as revealed by a three-hybrid selection
Nucl. Acids Res. 2004 32: 3294-3303; doi:10.1093/nar/gkh665 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Marc Bühler, Alexandra Paillusson, and Oliver Mühlemann

Efficient downregulation of immunoglobulin µ mRNA with premature translation-termination codons requires the 5'-half of the VDJ exon
Nucl. Acids Res. 2004 32: 3304-3315; doi:10.1093/nar/gkh651 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Magali Toueille, Nazim El-Andaloussi, Isabelle Frouin, Raimundo Freire, Dorothee Funk, Igor Shevelev, Erica Friedrich-Heineken, Giuseppe Villani, Michael O. Hottiger, and Ulrich Hübscher

The human Rad9/Rad1/Hus1 damage sensor clamp interacts with DNA polymerase ß and increases its DNA substrate utilisation efficiency: implications for DNA repair
Nucl. Acids Res. 2004 32: 3316-3324; doi:10.1093/nar/gkh652 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Takamune T. Saito, Takahiro Tougan, Takashi Kasama, Daisuke Okuzaki, and Hiroshi Nojima

Mcp7, a meiosis-specific coiled-coil protein of fission yeast, associates with Meu13 and is required for meiotic recombination
Nucl. Acids Res. 2004 32: 3325-3339; doi:10.1093/nar/gkh654 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dmitry A. Rodionov, Alexey G. Vitreschak, Andrey A. Mironov, and Mikhail S. Gelfand

Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems
Nucl. Acids Res. 2004 32: 3340-3353; doi:10.1093/nar/gkh659 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Isabella Moll, Go Hirokawa, Michael C. Kiel, Akira Kaji, and Udo Bläsi

Translation initiation with 70S ribosomes: an alternative pathway for leaderless mRNAs
Nucl. Acids Res. 2004 32: 3354-3363; doi:10.1093/nar/gkh663 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christian G. Noble, Philip A. Walker, Lesley J. Calder, and Ian A. Taylor

Rna14–Rna15 assembly mediates the RNA-binding capability of Saccharomyces cerevisiae cleavage factor IA
Nucl. Acids Res. 2004 32: 3364-3375; doi:10.1093/nar/gkh664 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jason C. Y. Lau, Meredith L. Hanel, and Rachel Wevrick

Tissue-specific and imprinted epigenetic modifications of the human NDN gene
Nucl. Acids Res. 2004 32: 3376-3382; doi:10.1093/nar/gkh671 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Iris Cheung, Mike Schertzer, Agnes Baross, Ann M. Rose, Peter M. Lansdorp, and Duncan M. Baird

Strain-specific telomere length revealed by single telomere length analysis in Caenorhabditis elegans
Nucl. Acids Res. 2004 32: 3383-3391; doi:10.1093/nar/gkh661 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ashwin Hajarnavis, Ian Korf, and Richard Durbin

A probabilistic model of 3' end formation in Caenorhabditis elegans
Nucl. Acids Res. 2004 32: 3392-3399; doi:10.1093/nar/gkh656 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Matthew Sanders, Nausicaa Lannoo, Wendy Maddelein, Anna Depicker, Marc Van Montagu, Marc Cornelissen, and John Jacobs

The preferred route for the degradation of silencing target RNAs in transgenic plants depends on pre-established silencing conditions
Nucl. Acids Res. 2004 32: 3400-3409; doi:10.1093/nar/gkh662 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Peter L. James, Elena E. Merkina, Abedawn I. Khalaf, Colin J. Suckling, Roger D. Waigh, Tom Brown, and Keith R. Fox

DNA sequence recognition by an isopropyl substituted thiazole polyamide
Nucl. Acids Res. 2004 32: 3410-3417; doi:10.1093/nar/gkh666 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sébastien Rigali, Maximilian Schlicht, Paul Hoskisson, Harald Nothaft, Matthias Merzbacher, Bernard Joris, and Fritz Titgemeyer

Extending the classification of bacterial transcription factors beyond the helix–turn–helix motif as an alternative approach to discover new cis/trans relationships
Nucl. Acids Res. 2004 32: 3418-3426; doi:10.1093/nar/gkh673 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Kihoon Kim, Phong Trang, Sean Umamoto, Rong Hai, and Fenyong Liu

RNase P ribozyme inhibits cytomegalovirus replication by blocking the expression of viral capsid proteins
Nucl. Acids Res. 2004 32: 3427-3434; doi:10.1093/nar/gkh660 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christopher D. Deppmann, Asha Acharya, Vikas Rishi, Barry Wobbes, Sjef Smeekens, Elizabeth J. Taparowsky, and Charles Vinson

Dimerization specificity of all 67 B-ZIP motifs in Arabidopsis thaliana: a comparison to Homo sapiens B-ZIP motifs
Nucl. Acids Res. 2004 32: 3435-3445; doi:10.1093/nar/gkh653 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

John W. Pham, Ishwar Radhakrishnan, and Erik J. Sontheimer

Thermodynamic and structural characterization of 2'-nitrogen-modified RNA duplexes
Nucl. Acids Res. 2004 32: 3446-3455; doi:10.1093/nar/gkh658 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Pål Ø. Falnes, Magnar Bjørås, Per Arne Aas, Ottar Sundheim, and Erling Seeberg

Substrate specificities of bacterial and human AlkB proteins
Nucl. Acids Res. 2004 32: 3456-3461; doi:10.1093/nar/gkh655 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Daniel Y. L. Mao, Dalia Barsyte-Lovejoy, Cynthia S. W. Ho, John D. Watson, Angelina Stojanova, and Linda Z. Penn

Promoter-binding and repression of PDGFRB by c-Myc are separable activities
Nucl. Acids Res. 2004 32: 3462-3468; doi:10.1093/nar/gkh669 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Darren M. Gowers, Stuart R.W. Bellamy, and Stephen E. Halford

One recognition sequence, seven restriction enzymes, five reaction mechanisms
Nucl. Acids Res. 2004 32: 3469-3479; doi:10.1093/nar/gkh685 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Miguel Landers, Daria L. Bancescu, Elodie Le Meur, Claire Rougeulle, Heather Glatt-Deeley, Camilynn Brannan, Françoise Muscatelli, and Marc Lalande

Regulation of the large (1000 kb) imprinted murine Ube3a antisense transcript by alternative exons upstream of Snurf/Snrpn
Nucl. Acids Res. 2004 32: 3480-3492; doi:10.1093/nar/gkh670 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Víctor González-Huici, Martín Alcorlo, Margarita Salas, and José M. Hermoso

Binding of phage 29 architectural protein p6 to the viral genome: evidence for topological restriction of the phage linear DNA
Nucl. Acids Res. 2004 32: 3493-3502; doi:10.1093/nar/gkh668 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tetsuro Hirose and Masahiro Sugiura

Multiple elements required for translation of plastid atpB mRNA lacking the Shine-Dalgarno sequence
Nucl. Acids Res. 2004 32: 3503-3510; doi:10.1093/nar/gkh682 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Corrigenda:

Taku Tanaka, Yasuhiro Tomaru, Yuki Nomura, Hisashi Miura, Masanori Suzuki, and Yoshihide Hayashizaki

Comprehensive search for HNF-1ß-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi
Nucl. Acids Res. 2004 32: 3511; doi:10.1093/nar/gkh679 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Errata:

Fabien Darfeuille, Jens Bo Hansen, Henrik Orum, Carmelo Di Primo, and Jean-Jacques Toulmé

LNA/DNA chimeric oligomers mimic RNA aptamers targeted to the TAR RNA element of HIV-1
Nucl. Acids Res. 2004 32: 3512; doi:10.1093/nar/gkh678 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Methods Online:

Kyle Cole, Vivi Truong, Dale Barone, and Glenn McGall

Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes
Nucl. Acids Res. 2004 32: e86; doi:10.1093/nar/gnh085 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Pawel Jaruga, Jacob Theruvathu, Miral Dizdaroglu, and Philip J. Brooks

Complete release of (5'S)-8,5'-cyclo-2'-deoxyadenosine from dinucleotides, oligodeoxynucleotides and DNA, and direct comparison of its levels in cellular DNA with other oxidatively induced DNA lesions
Nucl. Acids Res. 2004 32: e87; doi:10.1093/nar/gnh087 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Juan Sandoval, José L. Rodríguez, Gema Tur, Gaetano Serviddio, Javier Pereda, Abdelhalim Boukaba, Juan Sastre, Luis Torres, Luis Franco, and Gerardo López-Rodas

RNAPol-ChIP: a novel application of chromatin immunoprecipitation to the analysis of real-time gene transcription
Nucl. Acids Res. 2004 32: e88; doi:10.1093/nar/gnh091 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Don Benjamin, Marco Colombi, and Christoph Moroni

A GFP-based assay for rapid screening of compounds affecting ARE-dependent mRNA turnover
Nucl. Acids Res. 2004 32: e89; doi:10.1093/nar/gnh086 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

María Martell, Carlos Briones, Aránzazu de Vicente, María Piron, Juan I. Esteban, Rafael Esteban, Jaime Guardia, and Jordi Gómez

Structural analysis of hepatitis C RNA genome using DNA microarrays
Nucl. Acids Res. 2004 32: e90; doi:10.1093/nar/gnh088 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

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

A novel 4-base-recognizing RNA cutter that can remove the single 3' terminal nucleotides from RNA molecules
Nucl. Acids Res. 2004 32: e91; doi:10.1093/nar/gnh092 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Richard Kemp, Heather Ireland, Elizabeth Clayton, Carol Houghton, Louise Howard, and Douglas J. Winton

Elimination of background recombination: somatic induction of Cre by combined transcriptional regulation and hormone binding affinity
Nucl. Acids Res. 2004 32: e92; doi:10.1093/nar/gnh090 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Wan Ji, Wenli Zhou, Keqin Gregg, Nan Yu, Scott Davis, and Sara Davis

A method for cross-species gene expression analysis with high-density oligonucleotide arrays
Nucl. Acids Res. 2004 32: e93; doi:10.1093/nar/gnh084 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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