| | Articles Activation of APE1/Ref-1 is dependent on reactive oxygen species generated after purinergic receptor stimulation by ATP Alex Pines, Lorena Perrone, Nicoletta Bivi, Milena Romanello, Giuseppe Damante, Massimo Gulisano, Mark R. Kelley, Franco Quadrifoglio, and Gianluca Tell PMCID: PMC1182699 Unfolding of DNA quadruplexes induced by HIV-1 nucleocapsid protein Besik I. Kankia, George Barany, and Karin Musier-Forsyth PMCID: PMC1182697 Base excision repair intermediates are mutagenic in mammalian cells Valeria Simonelli, Laura Narciso, Eugenia Dogliotti, and Paola Fortini PMCID: PMC1182698 Initiation of DNA replication at the human β-globin 3′ enhancer Alla Buzina, Mirit I. Aladjem, John L. Kolman, Geoffrey M. Wahl, and James Ellis PMCID: PMC1183104 Curved DNA molecules migrate anomalously slowly in free solution Earle Stellwagen, Yongjun Lu, and Nancy C. Stellwagen PMCID: PMC1183105 The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region Amy M. Hauth, Uwe G. Maier, B. Franz Lang, and Gertraud Burger PMCID: PMC1183108 Identification and characterization of endogenous small interfering RNAs from rice Ramanjulu Sunkar, Thomas Girke, and Jian-Kang Zhu PMCID: PMC1182700 Predicting specificity-determining residues in two large eukaryotic transcription factor families Jason E. Donald and Eugene I. Shakhnovich PMCID: PMC1183107 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 Kangkan Halder and Shantanu Chowdhury PMCID: PMC1183106 Group 13 HOX proteins interact with the MH2 domain of R-Smads and modulate Smad transcriptional activation functions independent of HOX DNA-binding capability Thomas M. Williams, Melissa E. Williams, Joanne H. Heaton, Thomas D. Gelehrter, and Jeffrey W. Innis PMCID: PMC1183491 Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes Paul Piccinelli, Magnus Alm Rosenblad, and Tore Samuelsson PMCID: PMC1183490 Refinement of docked protein–ligand and protein–DNA structures using low frequency normal mode amplitude optimization Erik Lindahl and Marc Delarue PMCID: PMC1183489 Novel DNA-binding properties of the RNA-binding protein TIAR Esther A. Suswam, Yan Yan Li, Harry Mahtani, and Peter H. King PMCID: PMC1184220 Evidence for rolling circle replication of tandem genes in Drosophila Sarit Cohen, Neta Agmon, Keren Yacobi, Margarita Mislovati, and Daniel Segal PMCID: PMC1184221 siRNA-mediated off-target gene silencing triggered by a 7 nt complementation Xiaoyu Lin, Xiaoan Ruan, Mark G. Anderson, Jeffrey A. McDowell, Paul E. Kroeger, Stephen W. Fesik, and Yu Shen PMCID: PMC1184219 Telomere structure and shortening in telomerase-deficient Trypanosoma brucei Oliver Dreesen, Bibo Li, and George A. M. Cross PMCID: PMC1184224 Differential and collaborative actions of Rad51 paralog proteins in cellular response to DNA damage Yasukazu Yonetani, Helfrid Hochegger, Eiichiro Sonoda, Sayoko Shinya, Hideki Yoshikawa, Shunichi Takeda, and Mistuyoshi Yamazoe PMCID: PMC1184222 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 Masanobu Nariai, Tomohisa Tanaka, Takafumi Okada, Chiharu Shirai, Chihiro Horigome, and Keiko Mizuta PMCID: PMC1185577 Using multiple alignments to improve seeded local alignment algorithms Jason Flannick and Serafim Batzoglou PMCID: PMC1185574 Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database Alexei Fedorov, Jesse Stombaugh, Michael W. Harr, Saihua Yu, Lorena Nasalean, and Valery Shepelev PMCID: PMC1184218 Interplay between GCN2 and GCN4 expression, translation elongation factor 1 mutations and translational fidelity in yeast Tanya Magazinnik, Monika Anand, Evelyn Sattlegger, Alan G. Hinnebusch, and Terri Goss Kinzy PMCID: PMC1185573 GANA—a genetic algorithm for NMR backbone resonance assignment Hsin-Nan Lin, Kun-Pin Wu, Jia-Ming Chang, Ting-Yi Sung, and Wen-Lian Hsu PMCID: PMC1184223 A peripheral element assembles the compact core structure essential for group I intron self-splicing Mu Xiao, Tingting Li, Xiaoyan Yuan, Yuan Shang, Fu Wang, Shoudeng Chen, and Yi Zhang PMCID: PMC1185575 Identification of RNA editing sites in the SNP database Eli Eisenberg, Konstantin Adamsky, Lital Cohen, Ninette Amariglio, Abraham Hirshberg, Gideon Rechavi, and Erez Y. Levanon PMCID: PMC1185576 DNA-dependent conversion of Oct-1 and Oct-2 into transcriptional repressors by Groucho/TLE Stephen Malin, Ylva Linderson, Jenny Almqvist, Ingemar Ernberg, Tiziano Tallone, and Sven Pettersson PMCID: PMC1187819 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Kira S. Makarova, Yuri I. Wolf, Sergey L. Mekhedov, Boris G. Mirkin, and Eugene V. Koonin PMCID: PMC1187821 Potentiation of gene targeting in human cells by expression of Saccharomyces cerevisiae Rad52 Cristina Di Primio, Alvaro Galli, Tiziana Cervelli, Monica Zoppè, and Giuseppe Rainaldi PMCID: PMC1187822 Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal Jing Li, John J. Correia, Lei Wang, John O. Trent, and Jonathan B. Chaires PMCID: PMC1187823 Oxidative stress-induced apoptosis in neurons correlates with mitochondrial DNA base excision repair pathway imbalance Jason F. Harrison, Scott B. Hollensworth, Douglas R. Spitz, William C. Copeland, Glenn L. Wilson, and Susan P. LeDoux PMCID: PMC1187820 Methods Online Direct detection of methylation in genomic DNA A. Bart, M. W. J. van Passel, K. van Amsterdam, and A. van der Ende PMCID: PMC1184226 Electrochemically directed synthesis of oligonucleotides for DNA microarray fabrication Ryan D. Egeland and Edwin M. Southern PMCID: PMC1183109 Multiplex PCR: use of heat-stable Thermus thermophilus RecA protein to minimize non-specific PCR products Yasushi Shigemori, Tsutomu Mikawa, Takehiko Shibata, and Michio Oishi PMCID: PMC1183492 Headloop suppression PCR and its application to selective amplification of methylated DNA sequences Keith N. Rand, Thu Ho, Wenjia Qu, Susan M. Mitchell, Rose White, Susan J. Clark, and Peter L. Molloy PMCID: PMC1184225 Methylation-Specific MLPA (MS-MLPA): simultaneous detection of CpG methylation and copy number changes of up to 40 sequences 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 PMCID: PMC1187824 |
