Nucleic Acids Research

Articles:

Ran Elkon, Karen I. Zeller, Chaim Linhart, Chi V. Dang, Ron Shamir, and Yosef Shiloh

In silico identification of transcriptional regulators associated with c-Myc
Nucl. Acids Res. 2004 32: 4955-4961; doi:10.1093/nar/gkh816 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Kristiane A. Schmidt, Christiaan V. Henkel, Grzegorz Rozenberg, and Herman P. Spaink

DNA computing using single-molecule hybridization detection
Nucl. Acids Res. 2004 32: 4962-4968; doi:10.1093/nar/gkh817 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Marie Touchon, Alain Arneodo, Yves d'Aubenton-Carafa, and Claude Thermes

Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes
Nucl. Acids Res. 2004 32: 4969-4978; doi:10.1093/nar/gkh823 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Chengpeng Bi and Peter K. Rogan

Bipartite pattern discovery by entropy minimization-based multiple local alignment
Nucl. Acids Res. 2004 32: 4979-4991; doi:10.1093/nar/gkh825 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Corrado Guarnaccia, Bakthisaran Raman, Sotir Zahariev, András Simoncsits, and Sándor Pongor

DNA-mediated assembly of weakly interacting DNA-binding protein subunits: in vitro recruitment of phage 434 repressor and yeast GCN4 DNA-binding domains
Nucl. Acids Res. 2004 32: 4992-5002; doi:10.1093/nar/gkh827 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Marcelo de Padula, Guenaelle Slezak, Patricia Auffret van Der Kemp, and Serge Boiteux

The post-replication repair RAD18 and RAD6 genes are involved in the prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine in Saccharomyces cerevisiae
Nucl. Acids Res. 2004 32: 5003-5010; doi:10.1093/nar/gkh831 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kathryn E. Richmond, Mo-Huang Li, Matthew J. Rodesch, Madhusudan Patel, Aaron M. Lowe, Changhan Kim, Larry L. Chu, Narasimhar Venkataramaian, Shane F. Flickinger, James Kaysen, Peter J. Belshaw, Michael R. Sussman, and Franco Cerrina

Amplification and assembly of chip-eluted DNA (AACED): a method for high-throughput gene synthesis
Nucl. Acids Res. 2004 32: 5011-5018; doi:10.1093/nar/gkh793 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jiaqiang Huang, Tao Fan, Qingsheng Yan, Heming Zhu, Stephen Fox, Haleem J. Issaq, Lionel Best, Lisa Gangi, David Munroe, and Kathrin Muegge

Lsh, an epigenetic guardian of repetitive elements
Nucl. Acids Res. 2004 32: 5019-5028; doi:10.1093/nar/gkh821 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Vladimir N. Babenko and Dmitri M. Krylov

Comparative analysis of complete genomes reveals gene loss, acquisition and acceleration of evolutionary rates in Metazoa, suggests a prevalence of evolution via gene acquisition and indicates that the evolutionary rates in animals tend to be conserved
Nucl. Acids Res. 2004 32: 5029-5035; doi:10.1093/nar/gkh833 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mario dos Reis, Renos Savva, and Lorenz Wernisch

Solving the riddle of codon usage preferences: a test for translational selection
Nucl. Acids Res. 2004 32: 5036-5044; doi:10.1093/nar/gkh834 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Laure Weill, Dominique Louis, and Bruno Sargueil

Selection and evolution of NTP-specific aptamers
Nucl. Acids Res. 2004 32: 5045-5058; doi:10.1093/nar/gkh835 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kuen-Pin Wu, Hsin-Nan Lin, Jia-Ming Chang, Ting-Yi Sung, and Wen-Lian Hsu

HYPROSP: a hybrid protein secondary structure prediction algorithm—a knowledge-based approach
Nucl. Acids Res. 2004 32: 5059-5065; doi:10.1093/nar/gkh836 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yu Zhu and Wei Xiao

Pdr3 is required for DNA damage induction of MAG1 and DDI1 via a bi-directional promoter element
Nucl. Acids Res. 2004 32: 5066-5075; doi:10.1093/nar/gkh838 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Aurélie Fender, Renaud Geslain, Gilbert Eriani, Richard Giegé, Marie Sissler, and Catherine Florentz

A yeast arginine specific tRNA is a remnant aspartate acceptor
Nucl. Acids Res. 2004 32: 5076-5086; doi:10.1093/nar/gkh843 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

K. Cecilia Engman, Peter Sandin, Sadie Osborne, Tom Brown, Martin Billeter, Per Lincoln, Bengt Nordén, Bo Albinsson, and L. Marcus Wilhelmsson

DNA adopts normal B-form upon incorporation of highly fluorescent DNA base analogue tC: NMR structure and UV-Vis spectroscopy characterization
Nucl. Acids Res. 2004 32: 5087-5095; doi:10.1093/nar/gkh844 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Kei Iida, Motoaki Seki, Tetsuya Sakurai, Masakazu Satou, Kenji Akiyama, Tetsuro Toyoda, Akihiko Konagaya, and Kazuo Shinozaki

Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences
Nucl. Acids Res. 2004 32: 5096-5103; doi:10.1093/nar/gkh845 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yvan Canitrot, Jean-Pascal Capp, Nadine Puget, Anne Bieth, Bernard Lopez, Jean-Sébastien Hoffmann, and Christophe Cazaux

DNA polymerase ß overexpression stimulates the Rad51-dependent homologous recombination in mammalian cells
Nucl. Acids Res. 2004 32: 5104-5112; doi:10.1093/nar/gkh848 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hidetsugu Sotoya, Akimasa Matsugami, Tetsuro Ikeda, Kiyoshi Ouhashi, Seiichi Uesugi, and Masato Katahira

Method for direct discrimination of intra- and intermolecular hydrogen bonds, and characterization of the G(:A):G(:A):G(:A):G heptad, with scalar couplings across hydrogen bonds
Nucl. Acids Res. 2004 32: 5113-5118; doi:10.1093/nar/gkh849 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ingrun Alseth, Hanne Korvald, Fekret Osman, Erling Seeberg, and Magnar Bjørås

A general role of the DNA glycosylase Nth1 in the abasic sites cleavage step of base excision repair in Schizosaccharomyces pombe
Nucl. Acids Res. 2004 32: 5119-5125; doi:10.1093/nar/gkh851 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Albert Weixlbaumer, Andreas Werner, Christoph Flamm, Eric Westhof, and Renée Schroeder

Determination of thermodynamic parameters for HIV DIS type loop–loop kissing complexes
Nucl. Acids Res. 2004 32: 5126-5133; doi:10.1093/nar/gkh841 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Natalia G. Beloglazova, Oleg O. Kirpota, Konstantin V. Starostin, Alexander A. Ishchenko, Vitaly I. Yamkovoy, Dmitry O. Zharkov, Kenneth T. Douglas, and Georgy A. Nevinsky

Thermodynamic, kinetic and structural basis for recognition and repair of abasic sites in DNA by apurinic/apyrimidinic endonuclease from human placenta
Nucl. Acids Res. 2004 32: 5134-5146; doi:10.1093/nar/gkh846 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yu Chen, Tanja Kortemme, Tim Robertson, David Baker, and Gabriele Varani

A new hydrogen-bonding potential for the design of protein–RNA interactions predicts specific contacts and discriminates decoys
Nucl. Acids Res. 2004 32: 5147-5162; doi:10.1093/nar/gkh785 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Smitha Antony, Paola B. Arimondo, Jian-Sheng Sun, and Yves Pommier

Position- and orientation-specific enhancement of topoisomerase I cleavage complexes by triplex DNA structures
Nucl. Acids Res. 2004 32: 5163-5173; doi:10.1093/nar/gkh847 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Romary Perrin, Heike Lange, Jean-Michel Grienenberger, and Dominique Gagliardi

AtmtPNPase is required for multiple aspects of the 18S rRNA metabolism in Arabidopsis thaliana mitochondria
Nucl. Acids Res. 2004 32: 5174-5182; doi:10.1093/nar/gkh852 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ming Li, Magnus Nordborg, and Lei M. Li

Adjust quality scores from alignment and improve sequencing accuracy
Nucl. Acids Res. 2004 32: 5183-5191; doi:10.1093/nar/gkh850 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Anatoly I. Dragan, Yingyun Liu, Elena N. Makeyeva, and Peter L. Privalov

DNA-binding domain of GCN4 induces bending of both the ATF/CREB and AP-1 binding sites of DNA
Nucl. Acids Res. 2004 32: 5192-5197; doi:10.1093/nar/gkh854 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ernesto I. Gonzalez de Valdivia and Leif A. Isaksson

A codon window in mRNA downstream of the initiation codon where NGG codons give strongly reduced gene expression in Escherichia coli
Nucl. Acids Res. 2004 32: 5198-5205; doi:10.1093/nar/gkh857 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tiffany A. Simms, Elsy C. Miller, Nicolas P. Buisson, Nithya Jambunathan, and David Donze

The Saccharomyces cerevisiae TRT2 tRNA^Thr gene upstream of STE6 is a barrier to repression in MAT cells and exerts a potential tRNA position effect in MATa cells
Nucl. Acids Res. 2004 32: 5206-5213; doi:10.1093/nar/gkh858 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Denise P. Muñoz and Kathleen Collins

Biochemical properties of Trypanosoma cruzi telomerase
Nucl. Acids Res. 2004 32: 5214-5222; doi:10.1093/nar/gkh864 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mariarosaria De Falco, Alessandra Fusco, Mariarita De Felice, Mosè Rossi, and Francesca M. Pisani

The DNA primase of Sulfolobus solfataricus is activated by substrates containing a thymine-rich bubble and has a 3'-terminal nucleotidyl-transferase activity
Nucl. Acids Res. 2004 32: 5223-5230; doi:10.1093/nar/gkh865 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tancred Frickey and Andrei N. Lupas

PhyloGenie: automated phylome generation and analysis
Nucl. Acids Res. 2004 32: 5231-5238; doi:10.1093/nar/gkh867 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Luciana Ferrara and Eric B. Kmiec

Camptothecin enhances the frequency of oligonucleotide-directed gene repair in mammalian cells by inducing DNA damage and activating homologous recombination
Nucl. Acids Res. 2004 32: 5239-5248; doi:10.1093/nar/gkh822 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Johanne Bentley, Christine P. Diggle, Patricia Harnden, Margaret A. Knowles, and Anne E. Kiltie

DNA double strand break repair in human bladder cancer is error prone and involves microhomology-associated end-joining
Nucl. Acids Res. 2004 32: 5249-5259; doi:10.1093/nar/gkh842 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Lakshminarayan M. Iyer, Kira S. Makarova, Eugene V. Koonin, and L. Aravind

Comparative genomics of the FtsK–HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging
Nucl. Acids Res. 2004 32: 5260-5279; doi:10.1093/nar/gkh828 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Hanna Harant and Ivan J. D. Lindley

Negative cross-talk between the human orphan nuclear receptor Nur77/NAK-1/TR3 and nuclear factor-B
Nucl. Acids Res. 2004 32: 5280-5290; doi:10.1093/nar/gkh856 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mayumi Matsubara, Tamon Tanaka, Hiroaki Terato, Eiji Ohmae, Shunsuke Izumi, Katsuo Katayanagi, and Hiroshi Ide

Mutational analysis of the damage-recognition and catalytic mechanism of human SMUG1 DNA glycosylase
Nucl. Acids Res. 2004 32: 5291-5302; doi:10.1093/nar/gkh859 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Hyouta Himeno, Kyoko Hanawa-Suetsugu, Takatsugu Kimura, Kuniaki Takagi, Wakana Sugiyama, Shinobu Shirata, Tomoyuki Mikami, Fujiko Odagiri, Yukiko Osanai, Daisuke Watanabe, Simon Goto, Liliya Kalachnyuk, Chisato Ushida, and Akira Muto

A novel GTPase activated by the small subunit of ribosome
Nucl. Acids Res. 2004 32: 5303-5309; doi:10.1093/nar/gkh861 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Aude-Emmanuelle Navarro, Nicolas Spinelli, Corinne Moustrou, Carole Chaix, Bernard Mandrand, and Hugues Brisset

Automated synthesis of new ferrocenyl-modified oligonucleotides: study of their properties in solution
Nucl. Acids Res. 2004 32: 5310-5319; doi:10.1093/nar/gkh874 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Corrigenda:

Chengpeng Bi and Peter K. Rogan

Bipartite pattern discovery by entropy minimization-based multiple local alignment
Nucl. Acids Res. 2004 32: 5320; doi:10.1093/nar/gkh890 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Methods Online:

Paul M. K. Gordon and Christoph W. Sensen

Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays
Nucl. Acids Res. 2004 32: e133; doi:10.1093/nar/gnh127 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Deming Gou, Telugu Narasaraju, Narendranath Reddy Chintagari, Nili Jin, Pengcheng Wang, and Lin Liu

Gene silencing in alveolar type II cells using cell-specific promoter in vitro and in vivo
Nucl. Acids Res. 2004 32: e134; doi:10.1093/nar/gnh129 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Brooks E. Miner, Reinhard J. Stöger, Alice F. Burden, Charles D. Laird, and R. Scott Hansen

Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR
Nucl. Acids Res. 2004 32: e135; doi:10.1093/nar/gnh132 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Joel Osuna, Jorge Yáñez, Xavier Soberón, and Paul Gaytán

Protein evolution by codon-based random deletions
Nucl. Acids Res. 2004 32: e136; doi:10.1093/nar/gnh135 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

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