Nucleic Acids Research

Articles:

Alex Pines, Lorena Perrone, Nicoletta Bivi, Milena Romanello, Giuseppe Damante, Massimo Gulisano, Mark R. Kelley, Franco Quadrifoglio, and Gianluca Tell

Activation of APE1/Ref-1 is dependent on reactive oxygen species generated after purinergic receptor stimulation by ATP
Nucl. Acids Res. 2005 33: 4379-4394; doi:10.1093/nar/gki751 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Besik I. Kankia, George Barany, and Karin Musier-Forsyth

Unfolding of DNA quadruplexes induced by HIV-1 nucleocapsid protein
Nucl. Acids Res. 2005 33: 4395-4403; doi:10.1093/nar/gki741 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Valeria Simonelli, Laura Narciso, Eugenia Dogliotti, and Paola Fortini

Base excision repair intermediates are mutagenic in mammalian cells
Nucl. Acids Res. 2005 33: 4404-4411; doi:10.1093/nar/gki749 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Alla Buzina, Mirit I. Aladjem, John L. Kolman, Geoffrey M. Wahl, and James Ellis

Initiation of DNA replication at the human ß-globin 3' enhancer
Nucl. Acids Res. 2005 33: 4412-4424; doi:10.1093/nar/gki747 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Earle Stellwagen, Yongjun Lu, and Nancy C. Stellwagen

Curved DNA molecules migrate anomalously slowly in free solution
Nucl. Acids Res. 2005 33: 4425-4432; doi:10.1093/nar/gki748 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Amy M. Hauth, Uwe G. Maier, B. Franz Lang, and Gertraud Burger

The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region
Nucl. Acids Res. 2005 33: 4433-4442; doi:10.1093/nar/gki757 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ramanjulu Sunkar, Thomas Girke, and Jian-Kang Zhu

Identification and characterization of endogenous small interfering RNAs from rice
Nucl. Acids Res. 2005 33: 4443-4454; doi:10.1093/nar/gki758 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jason E. Donald and Eugene I. Shakhnovich

Predicting specificity-determining residues in two large eukaryotic transcription factor families
Nucl. Acids Res. 2005 33: 4455-4465; doi:10.1093/nar/gki755 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Kangkan Halder and Shantanu Chowdhury

Kinetic resolution of bimolecular hybridization versus intramolecular folding in nucleic acids by surface plasmon resonance: application to G-quadruplex/duplex competition in human c-myc promoter
Nucl. Acids Res. 2005 33: 4466-4474; doi:10.1093/nar/gki750 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Thomas M. Williams, Melissa E. Williams, Joanne H. Heaton, Thomas D. Gelehrter, and Jeffrey W. Innis

Group 13 HOX proteins interact with the MH2 domain of R-Smads and modulate Smad transcriptional activation functions independent of HOX DNA-binding capability
Nucl. Acids Res. 2005 33: 4475-4484; doi:10.1093/nar/gki761 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Paul Piccinelli, Magnus Alm Rosenblad, and Tore Samuelsson

Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes
Nucl. Acids Res. 2005 33: 4485-4495; doi:10.1093/nar/gki756 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Erik Lindahl and Marc Delarue

Refinement of docked protein–ligand and protein–DNA structures using low frequency normal mode amplitude optimization
Nucl. Acids Res. 2005 33: 4496-4506; doi:10.1093/nar/gki730 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Esther A. Suswam, Yan Yan Li, Harry Mahtani, and Peter H. King

Novel DNA-binding properties of the RNA-binding protein TIAR
Nucl. Acids Res. 2005 33: 4507-4518; doi:10.1093/nar/gki763 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sarit Cohen, Neta Agmon, Keren Yacobi, Margarita Mislovati, and Daniel Segal

Evidence for rolling circle replication of tandem genes in Drosophila
Nucl. Acids Res. 2005 33: 4519-4526; doi:10.1093/nar/gki764 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Xiaoyu Lin, Xiaoan Ruan, Mark G. Anderson, Jeffrey A. McDowell, Paul E. Kroeger, Stephen W. Fesik, and Yu Shen

siRNA-mediated off-target gene silencing triggered by a 7 nt complementation
Nucl. Acids Res. 2005 33: 4527-4535; doi:10.1093/nar/gki762 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Oliver Dreesen, Bibo Li, and George A. M. Cross

Telomere structure and shortening in telomerase-deficient Trypanosoma brucei
Nucl. Acids Res. 2005 33: 4536-4543; doi:10.1093/nar/gki769 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yasukazu Yonetani, Helfrid Hochegger, Eiichiro Sonoda, Sayoko Shinya, Hideki Yoshikawa, Shunichi Takeda, and Mistuyoshi Yamazoe

Differential and collaborative actions of Rad51 paralog proteins in cellular response to DNA damage
Nucl. Acids Res. 2005 33: 4544-4552; doi:10.1093/nar/gki766 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Masanobu Nariai, Tomohisa Tanaka, Takafumi Okada, Chiharu Shirai, Chihiro Horigome, and Keiko Mizuta

Synergistic defect in 60S ribosomal subunit assembly caused by a mutation of Rrs1p, a ribosomal protein L11-binding protein, and 3'-extension of 5S rRNA in Saccharomyces cerevisiae
Nucl. Acids Res. 2005 33: 4553-4562; doi:10.1093/nar/gki772 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jason Flannick and Serafim Batzoglou

Using multiple alignments to improve seeded local alignment algorithms
Nucl. Acids Res. 2005 33: 4563-4577; doi:10.1093/nar/gki767 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alexei Fedorov, Jesse Stombaugh, Michael W. Harr, Saihua Yu, Lorena Nasalean, and Valery Shepelev

Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database
Nucl. Acids Res. 2005 33: 4578-4583; doi:10.1093/nar/gki754 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Tanya Magazinnik, Monika Anand, Evelyn Sattlegger, Alan G. Hinnebusch, and Terri Goss Kinzy

Interplay between GCN2 and GCN4 expression, translation elongation factor 1 mutations and translational fidelity in yeast
Nucl. Acids Res. 2005 33: 4584-4592; doi:10.1093/nar/gki765 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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

GANA—a genetic algorithm for NMR backbone resonance assignment
Nucl. Acids Res. 2005 33: 4593-4601; doi:10.1093/nar/gki768 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mu Xiao, Tingting Li, Xiaoyan Yuan, Yuan Shang, Fu Wang, Shoudeng Chen, and Yi Zhang

A peripheral element assembles the compact core structure essential for group I intron self-splicing
Nucl. Acids Res. 2005 33: 4602-4611; doi:10.1093/nar/gki770 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Eli Eisenberg, Konstantin Adamsky, Lital Cohen, Ninette Amariglio, Abraham Hirshberg, Gideon Rechavi, and Erez Y. Levanon

Identification of RNA editing sites in the SNP database
Nucl. Acids Res. 2005 33: 4612-4617; doi:10.1093/nar/gki771 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Stephen Malin, Ylva Linderson, Jenny Almqvist, Ingemar Ernberg, Tiziano Tallone, and Sven Pettersson

DNA-dependent conversion of Oct-1 and Oct-2 into transcriptional repressors by Groucho/TLE
Nucl. Acids Res. 2005 33: 4618-4625; doi:10.1093/nar/gki744 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kira S. Makarova, Yuri I. Wolf, Sergey L. Mekhedov, Boris G. Mirkin, and Eugene V. Koonin

Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell
Nucl. Acids Res. 2005 33: 4626-4638; doi:10.1093/nar/gki775 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Cristina Di Primio, Alvaro Galli, Tiziana Cervelli, Monica Zoppè, and Giuseppe Rainaldi

Potentiation of gene targeting in human cells by expression of Saccharomyces cerevisiae Rad52
Nucl. Acids Res. 2005 33: 4639-4648; doi:10.1093/nar/gki778 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jing Li, John J. Correia, Lei Wang, John O. Trent, and Jonathan B. Chaires

Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal
Nucl. Acids Res. 2005 33: 4649-4659; doi:10.1093/nar/gki782 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jason F. Harrison, Scott B. Hollensworth, Douglas R. Spitz, William C. Copeland, Glenn L. Wilson, and Susan P. LeDoux

Oxidative stress-induced apoptosis in neurons correlates with mitochondrial DNA base excision repair pathway imbalance
Nucl. Acids Res. 2005 33: 4660-4671; doi:10.1093/nar/gki759 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

A. Bart, M. W. J. van Passel, K. van Amsterdam, and A. van der Ende

Direct detection of methylation in genomic DNA
Nucl. Acids Res. 2005 33: e124; doi:10.1093/nar/gni121 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ryan D. Egeland and Edwin M. Southern

Electrochemically directed synthesis of oligonucleotides for DNA microarray fabrication
Nucl. Acids Res. 2005 33: e125; doi:10.1093/nar/gni117 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yasushi Shigemori, Tsutomu Mikawa, Takehiko Shibata, and Michio Oishi

Multiplex PCR: use of heat-stable Thermus thermophilus RecA protein to minimize non-specific PCR products
Nucl. Acids Res. 2005 33: e126; doi:10.1093/nar/gni111 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Keith N. Rand, Thu Ho, Wenjia Qu, Susan M. Mitchell, Rose White, Susan J. Clark, and Peter L. Molloy

Headloop suppression PCR and its application to selective amplification of methylated DNA sequences
Nucl. Acids Res. 2005 33: e127; doi:10.1093/nar/gni120 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Anders O. H. Nygren, Najim Ameziane, Helena M. B. Duarte, Raymon N. C. P. Vijzelaar, Quinten Waisfisz, Corine J. Hess, Jan P. Schouten, and Abdellatif Errami

Methylation-Specific MLPA (MS-MLPA): simultaneous detection of CpG methylation and copy number changes of up to 40 sequences
Nucl. Acids Res. 2005 33: e128; doi:10.1093/nar/gni127 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

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