Nucleic Acids Research

Articles:

Scott A. Irvine, Pelagia Foka, Sarah A. Rogers, James R. Mead, and Dipak P. Ramji

A critical role for the Sp1-binding sites in the transforming growth factor-ß-mediated inhibition of lipoprotein lipase gene expression in macrophages
Nucl. Acids Res. 2005 33: 1423-1434; doi:10.1093/nar/gki280 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alla I. Kalmykova, Dmitry I. Nurminsky, Dmirty V. Ryzhov, and Yuri Y. Shevelyov

Regulated chromatin domain comprising cluster of co-expressed genes in Drosophila melanogaster
Nucl. Acids Res. 2005 33: 1435-1444; doi:10.1093/nar/gki281 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Thomas A. Down and Tim J. P. Hubbard

NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence
Nucl. Acids Res. 2005 33: 1445-1453; doi:10.1093/nar/gki282 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Carla E. Hegeman, Christine P. Halter, Thomas G. Owens, and Maureen R. Hanson

Expression of complementary RNA from chloroplast transgenes affects editing efficiency of transgene and endogenous chloroplast transcripts
Nucl. Acids Res. 2005 33: 1454-1464; doi:10.1093/nar/gki286 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Antonio Ariza, Derek J. Richard, Malcolm F. White, and Charles S. Bond

Conformational flexibility revealed by the crystal structure of a crenarchaeal RadA
Nucl. Acids Res. 2005 33: 1465-1473; doi:10.1093/nar/gki288 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Martin Baril and Léa Brakier-Gingras

Translation of the F protein of hepatitis C virus is initiated at a non-AUG codon in a +1 reading frame relative to the polyprotein
Nucl. Acids Res. 2005 33: 1474-1486; doi:10.1093/nar/gki292 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Maria Piron, Nerea Beguiristain, Anna Nadal, Encarnación Martínez-Salas, and Jordi Gómez

Characterizing the function and structural organization of the 5' tRNA-like motif within the hepatitis C virus quasispecies
Nucl. Acids Res. 2005 33: 1487-1502; doi:10.1093/nar/gki290 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Helena Webb, Roisin Burns, Louise Ellis, Nicola Kimblin, and Mark Carrington

Developmentally regulated instability of the GPI-PLC mRNA is dependent on a short-lived protein factor
Nucl. Acids Res. 2005 33: 1503-1512; doi:10.1093/nar/gki298 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Robert Alazard, Magali Blaud, Shmouel Elbaz, Christine Vossen, Guillaume Icre, Gérard Joseph, Laurence Nieto, and Monique Erard

Identification of the ‘NORE’ (N-Oct-3 responsive element), a novel structural motif and composite element
Nucl. Acids Res. 2005 33: 1513-1523; doi:10.1093/nar/gki284 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sukhyun Kang, Joo Seok Han, Keun Pill Kim, Hye Yoon Yang, Kyung Yong Lee, Choo Bong Hong, and Deog Su Hwang

Dimeric configuration of SeqA protein bound to a pair of hemi-methylated GATC sequences
Nucl. Acids Res. 2005 33: 1524-1531; doi:10.1093/nar/gki289 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Caroline Crey-Desbiolles, Nathalie Berthet, Mitsuharu Kotera, and Pascal Dumy

Hybridization properties and enzymatic replication of oligonucleotides containing the photocleavable 7-nitroindole base analog
Nucl. Acids Res. 2005 33: 1532-1543; doi:10.1093/nar/gki293 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Nicki Tiffin, Janet F. Kelso, Alan R. Powell, Hong Pan, Vladimir B. Bajic, and Winston A. Hide

Integration of text- and data-mining using ontologies successfully selects disease gene candidates
Nucl. Acids Res. 2005 33: 1544-1552; doi:10.1093/nar/gki296 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Emily Manktelow, Kazuhiro Shigemoto, and Ian Brierley

Characterization of the frameshift signal of Edr, a mammalian example of programmed –1 ribosomal frameshifting
Nucl. Acids Res. 2005 33: 1553-1563; doi:10.1093/nar/gki299 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tony Nolan, Laura Braccini, Gianluca Azzalin, Arianna De Toni, Giuseppe Macino, and Carlo Cogoni

The post-transcriptional gene silencing machinery functions independently of DNA methylation to repress a LINE1-like retrotransposon in Neurospora crassa
Nucl. Acids Res. 2005 33: 1564-1573; doi:10.1093/nar/gki300 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ezra Schildkraut, Cheryl A. Miller, and Jac A. Nickoloff

Gene conversion and deletion frequencies during double-strand break repair in human cells are controlled by the distance between direct repeats
Nucl. Acids Res. 2005 33: 1574-1580; doi:10.1093/nar/gki295 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Emily E. Bosco and Erik S. Knudsen

Differential role of RB in response to UV and IR damage
Nucl. Acids Res. 2005 33: 1581-1592; doi:10.1093/nar/gki283 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Qibin Zhang and Yinsheng Wang

Generation of 5-(2'-deoxycytidyl)methyl radical and the formation of intrastrand cross-link lesions in oligodeoxyribonucleotides
Nucl. Acids Res. 2005 33: 1593-1603; doi:10.1093/nar/gki301 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Lai Man Chi and Sik Lok Lam

Structural roles of CTG repeats in slippage expansion during DNA replication
Nucl. Acids Res. 2005 33: 1604-1617; doi:10.1093/nar/gki307 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Matthias D. Erlacher, Kathrin Lang, Nisha Shankaran, Brigitte Wotzel, Alexander Hüttenhofer, Ronald Micura, Alexander S. Mankin, and Norbert Polacek

Chemical engineering of the peptidyl transferase center reveals an important role of the 2'-hydroxyl group of A2451
Nucl. Acids Res. 2005 33: 1618-1627; doi:10.1093/nar/gki308 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shinya Oda, Yoshihiko Maehara, Yoichi Ikeda, Eiji Oki, Akinori Egashira, Yoshikazu Okamura, Ikuo Takahashi, Yoshihiro Kakeji, Yasushi Sumiyoshi, Kaname Miyashita, Yu Yamada, Yan Zhao, Hiroyoshi Hattori, Ken-ichi Taguchi, Tatsuro Ikeuchi, Teruhisa Tsuzuki, Mutsuo Sekiguchi, Peter Karran, and Mitsuaki A. Yoshida

Two modes of microsatellite instability in human cancer: differential connection of defective DNA mismatch repair to dinucleotide repeat instability
Nucl. Acids Res. 2005 33: 1628-1636; doi:10.1093/nar/gki303 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Natsuhisa Oka and Marc M. Greenberg

The effect of the 2-amino group of 7,8-dihydro-8-oxo-2'-deoxyguanosine on translesion synthesis and duplex stability
Nucl. Acids Res. 2005 33: 1637-1643; doi:10.1093/nar/gki305 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Lindsay R. Comstock and Scott R. Rajski

Conversion of DNA methyltransferases into azidonucleosidyl transferases via synthetic cofactors
Nucl. Acids Res. 2005 33: 1644-1652; doi:10.1093/nar/gki306 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Masayuki Sakurai, Takashi Ohtsuki, and Kimitsuna Watanabe

Modification at position 9 with 1-methyladenosine is crucial for structure and function of nematode mitochondrial tRNAs lacking the entire T-arm
Nucl. Acids Res. 2005 33: 1653-1661; doi:10.1093/nar/gki309 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Gregor Witte, Claus Urbanke, and Ute Curth

Single-stranded DNA-binding protein of Deinococcus radiodurans: a biophysical characterization
Nucl. Acids Res. 2005 33: 1662-1670; doi:10.1093/nar/gki310 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Quan Du, Håkan Thonberg, Jue Wang, Claes Wahlestedt, and Zicai Liang

A systematic analysis of the silencing effects of an active siRNA at all single-nucleotide mismatched target sites
Nucl. Acids Res. 2005 33: 1671-1677; doi:10.1093/nar/gki312 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Taras Afonyushkin, Branislav Vecerek, Isabella Moll, Udo Bläsi, and Vladimir R. Kaberdin

Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB
Nucl. Acids Res. 2005 33: 1678-1689; doi:10.1093/nar/gki313 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Cheng-Hsun Chiu, Petrus Tang, Chishih Chu, Songnian Hu, Qiyu Bao, Jun Yu, Yun-Ying Chou, Hsin-Shih Wang, and Ying-Shiung Lee

The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen
Nucl. Acids Res. 2005 33: 1690-1698; doi:10.1093/nar/gki297 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Paul-André Genest, Bas ter Riet, Carole Dumas, Barbara Papadopoulou, Henri G. A. M. van Luenen, and Piet Borst

Formation of linear inverted repeat amplicons following targeting of an essential gene in Leishmania
Nucl. Acids Res. 2005 33: 1699-1709; doi:10.1093/nar/gki304 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Suganthi Balasubramanian, Yu Xia, Elizaveta Freinkman, and Mark Gerstein

Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms
Nucl. Acids Res. 2005 33: 1710-1721; doi:10.1093/nar/gki311 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Michael K. Kibe, Alexandra Coppin, Najoua Dendouga, Gabrielle Oria, Edwige Meurice, Marlène Mortuaire, Edwige Madec, and Stanislas Tomavo

Transcriptional regulation of two stage-specifically expressed genes in the protozoan parasite Toxoplasma gondii
Nucl. Acids Res. 2005 33: 1722-1736; doi:10.1093/nar/gki314 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Corrigendum:

Alistair M. Chalk, Richard E. Warfinge, Patrick Georgii-Hemming, and Erik L. L. Sonnhammer

siRNAdb: a database of siRNA sequences
Nucl. Acids Res. 2005 33: 1737; doi:10.1093/nar/gki294 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sreeparna Banerjee and Hernan Flores-Rozas

Cadmium inhibits mismatch repair by blocking the ATPase activity of the MSH2–MSH6 complex
Nucl. Acids Res. 2005 33: 1738; doi:10.1093/nar/gki330 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Erratum:

Rajeev Gangal, Pankaj Sharma, Rajeev Gangal, and Pankaj Sharma

Human pol II promoter prediction: time series descriptors and machine learning
Nucl. Acids Res. 2005 33: 1739; doi:10.1093/nar/gki320 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Naoki Kimura, Takeshi Nagasaka, Jun Murakami, Hiromi Sasamoto, Masahiro Murakami, Noriaki Tanaka, and Nagahide Matsubara

Methylation profiles of genes utilizing newly developed CpG island methylation microarray on colorectal cancer patients
Nucl. Acids Res. 2005 33: e46; doi:10.1093/nar/gni046 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Pascale Fehlbaum, Caroline Guihal, Laurent Bracco, and Olivier Cochet

A microarray configuration to quantify expression levels and relative abundance of splice variants
Nucl. Acids Res. 2005 33: e47; doi:10.1093/nar/gni047 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Emilie Hultin, Max Käller, Afshin Ahmadian, and Joakim Lundeberg

Competitive enzymatic reaction to control allele-specific extensions
Nucl. Acids Res. 2005 33: e48; doi:10.1093/nar/gni048 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Juno Choe, Haiwei H. Guo, and Ger van den Engh

A dual-fluorescence reporter system for high-throughput clone characterization and selection by cell sorting
Nucl. Acids Res. 2005 33: e49; doi:10.1093/nar/gni049 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zhanyou Xu, Marco A. van den Berg, Chantel Scheuring, Lina Covaleda, Hong Lu, Felipe A. Santos, Taesik Uhm, Mi-Kyung Lee, Chengcang Wu, Steve Liu, and Hong-Bin Zhang

Genome physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis: a robust physical map of Penicillium chrysogenum
Nucl. Acids Res. 2005 33: e50; doi:10.1093/nar/gni037 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Gusztav Belteki, Jody Haigh, Nikolett Kabacs, Katharina Haigh, Karen Sison, Frank Costantini, Jeff Whitsett, Susan E. Quaggin, and Andras Nagy

Conditional and inducible transgene expression in mice through the combinatorial use of Cre-mediated recombination and tetracycline induction
Nucl. Acids Res. 2005 33: e51; doi:10.1093/nar/gni051 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Minako Aoyama, Kazuko Agari, Ge-Hong Sun-Wada, Masamitsu Futai, and Yoh Wada

Simple and straightforward construction of a mouse gene targeting vector using in vitro transposition reactions
Nucl. Acids Res. 2005 33: e52; doi:10.1093/nar/gni055 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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