| | Articles SCFhFBH1 can act as helicase and E3 ubiquitin ligase Jeong-Hoon Kim, Jaehoon Kim, Do-Hyung Kim, Gi-Hyuck Ryu, Sung-Ho Bae, and Yeon-Soo Seo PMCID: PMC419438 α1-induced DNA bending is required for transcriptional activation by the Mcm1–α1 complex Edward A. Carr, Janet Mead, and Andrew K. Vershon PMCID: PMC419449 Genome wide, supercoiling-dependent in vivo binding of a viral protein involved in DNA replication and transcriptional control Víctor González-Huici, Margarita Salas, and José M. Hermoso PMCID: PMC419453 Regulation of the MiTF/TFE bHLH-LZ transcription factors through restricted spatial expression and alternative splicing of functional domains Roland P. Kuiper, Marga Schepens, José Thijssen, Eric F. P. M. Schoenmakers, and Ad Geurts van Kessel PMCID: PMC419459 Assessment of reliability of microarray data and estimation of signal thresholds using mixture modeling Musa H. Asyali, Mohamed M. Shoukri, Omer Demirkaya, and Khalid S. A. Khabar PMCID: PMC419441 A novel replicating circular DNAzyme Fei Chen, Ruijian Wang, Zhe Li, Bin Liu, Xiaoping Wang, Yanhong Sun, Dongyun Hao, and Jin Zhang PMCID: PMC419442 Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns Peter S. Klosterman, Donna K. Hendrix, Makio Tamura, Stephen R. Holbrook, and Steven E. Brenner PMCID: PMC419439 Identification and functional analysis of ‘hypothetical’ genes expressed in Haemophilus influenzae Eugene Kolker, Kira S. Makarova, Svetlana Shabalina, Alex F. Picone, Samuel Purvine, Ted Holzman, Tim Cherny, David Armbruster, Robert S. Munson, Jr, Grigory Kolesov, Dmitrij Frishman, and Michael Y. Galperin PMCID: PMC419445 Transcription factor binding element detection using functional clustering of mutant expression data Gengxin Chen, Naoya Hata, and Michael Q. Zhang PMCID: PMC419446 Mismatching base-pair dependence of the kinetics of DNA–DNA hybridization studied by surface plasmon fluorescence spectroscopy Keiko Tawa and Wolfgang Knoll PMCID: PMC419460 Meiosis-specific yeast Hop1 protein promotes synapsis of double-stranded DNA helices via the formation of guanine quartets S. Anuradha and K. Muniyappa PMCID: PMC419448 Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species Karen E. Nelson, Derrick E. Fouts, Emmanuel F. Mongodin, Jacques Ravel, Robert T. DeBoy, James F. Kolonay, David A. Rasko, Samuel V. Angiuoli, Steven R. Gill, Ian T. Paulsen, Jeremy Peterson, Owen White, William C. Nelson, William Nierman, Maureen J. Beanan, Lauren M. Brinkac, Sean C. Daugherty, Robert J. Dodson, A. Scott Durkin, Ramana Madupu, Daniel H. Haft, Jeremy Selengut, Susan Van Aken, Hoda Khouri, Nadia Fedorova, Heather Forberger, Bao Tran, Sophia Kathariou, Laura D. Wonderling, Gaylen A. Uhlich, Darrell O. Bayles, John B. Luchansky, and Claire M. Fraser PMCID: PMC419451 DNA binding and antigene activity of a daunomycin-conjugated triplex-forming oligonucleotide targeting the P2 promoter of the human c-myc gene Giuseppina M. Carbone, Eileen McGuffie, Sara Napoli, Courtney E. Flanagan, Chiara Dembech, Umberto Negri, Federico Arcamone, Massimo L. Capobianco, and Carlo V. Catapano PMCID: PMC419437 The composition of Staufen-containing RNA granules from human cells indicates their role in the regulated transport and translation of messenger RNAs Patricia Villacé, Rosa M. Marión, and Juan Ortín PMCID: PMC419443 APOBEC3G is a single-stranded DNA cytidine deaminase and functions independently of HIV reverse transcriptase Rodolphe Suspène, Peter Sommer, Michel Henry, Stéphane Ferris, Denise Guétard, Sylvie Pochet, Ann Chester, Naveenan Navaratnam, Simon Wain-Hobson, and Jean-Pierre Vartanian PMCID: PMC419444 Characterization of the 3′ exonuclease subunit DP1 of Methanococcus jannaschii replicative DNA polymerase D Maarit Jokela, Anitta Eskelinen, Helmut Pospiech, Juha Rouvinen, and Juhani E. Syväoja PMCID: PMC419447 Multiple protein/protein and protein/RNA interactions suggest roles for yeast DNA/RNA helicase Sen1p in transcription, transcription-coupled DNA repair and RNA processing Doris Ursic, Karen Chinchilla, Jonathan S. Finkel, and Michael R. Culbertson PMCID: PMC419450 Sequence–structure–function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases Janusz M. Bujnicki, Marcin Feder, Chastity L. Ayres, and Kent L. Redman PMCID: PMC419452 Contact-based sequence alignment Jens Kleinjung, John Romein, Kuang Lin, and Jaap Heringa PMCID: PMC419454 NMR structure of the DNA decamer duplex containing double T·G mismatches of cis–syn cyclobutane pyrimidine dimer: implications for DNA damage recognition by the XPC–hHR23B complex Joon-Hwa Lee, Chin-Ju Park, Jae-Sun Shin, Takahisa Ikegami, Hideo Akutsu, and Byong-Seok Choi PMCID: PMC419456 A DNA replication-related element downstream from the initiation site of Drosophila selenophosphate synthetase 2 gene is essential for its transcription Jing Shun Jin, Seunghee Baek, Hyesin Lee, Mi Young Oh, Yong Eui Koo, Myoung Sup Shim, So Yeon Kwon, Iksoo Jeon, So Young Park, Kwanghee Baek, Mi Ae Yoo, Dolph Lee Hatfield, and Byeong Jae Lee PMCID: PMC419457 Effect of lesions on the dynamics of DNA on the picosecond and nanosecond timescales using a polarity sensitive probe Mark M. Somoza, Daniele Andreatta, Catherine J. Murphy, Robert S. Coleman, and Mark A. Berg PMCID: PMC419465 Targeted transcriptional repression of Gfi1 by GFI1 and GFI1B in lymphoid cells Loretta L. Doan, Susan D. Porter, Zhijun Duan, Marcella M. Flubacher, Diego Montoya, Philip N. Tsichlis, Marshall Horwitz, C. Blake Gilks, and H. Leighton Grimes PMCID: PMC419458 The Fen1 extrahelical 3′-flap pocket is conserved from archaea to human and regulates DNA substrate specificity Erica Friedrich-Heineken and Ulrich Hübscher PMCID: PMC419464 The Saccharomyces cerevisiae gene CDC40/PRP17 controls cell cycle progression through splicing of the ANC1 gene Orna Dahan and Martin Kupiec PMCID: PMC419462 Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats Jiro Kondo, Wataru Adachi, Shun-ichi Umeda, Tomoko Sunami, and Akio Takénaka PMCID: PMC419463 XRCC1–DNA polymerase β interaction is required for efficient base excision repair Irina I. Dianova, Kate M. Sleeth, Sarah L. Allinson, Jason L. Parsons, Claire Breslin, Keith W. Caldecott, and Grigory L. Dianov PMCID: PMC419455 Preferential binding to branched DNA strands and strand-annealing activity of the human Rad51B, Rad51C, Rad51D and Xrcc2 protein complex Hiroshi Yokoyama, Naoyuki Sarai, Wataru Kagawa, Rima Enomoto, Takehiko Shibata, Hitoshi Kurumizaka, and Shigeyuki Yokoyama PMCID: PMC419466 Predicting transmembrane beta-barrels in proteomes Henry R. Bigelow, Donald S. Petrey, Jinfeng Liu, Dariusz Przybylski, and Burkhard Rost PMCID: PMC419468 Functions of yeast helicase Ssl2p that are essential for viability are also involved in protection from the toxicity of adriamycin Takemitsu Furuchi, Tsutomu Takahashi, Shogo Tanaka, Katsushi Nitta, and Akira Naganuma PMCID: PMC419470 Hepatocyte Nuclear Factor 4α enhances the Hepatocyte Nuclear Factor 1α-mediated activation of transcription J. Eeckhoute, P. Formstecher, and B. Laine PMCID: PMC419469 Mapping of the second tetracycline binding site on the ribosomal small subunit of E.coli Maria M. Anokhina, Andrea Barta, Knud H. Nierhaus, Vera A. Spiridonova, and Alexei M. Kopylov PMCID: PMC419471 Influence of loop size on the stability of intramolecular DNA quadruplexes Antonina Risitano and Keith R. Fox PMCID: PMC419475 Synapsis and DNA cleavage in ![[var phi]](corehtml/pmc/pmcents/x03C6.gif) C31 integrase-mediated site-specific recombination Matthew C. A. Smith, Rob Till, Kevin Brady, Panos Soultanas, Helena Thorpe, and Margaret C. M. Smith PMCID: PMC419440 A Fugu–Human Genome Synteny Viewer: web software for graphical display and annotation reports of synteny between Fugu genomic sequence and human genes Mark Halling-Brown, Clare Sansom, David S. Moss, Greg Elgar, and Yvonne J. K. Edwards PMCID: PMC419461 The hepatitis C virus Core protein is a potent nucleic acid chaperone that directs dimerization of the viral (+) strand RNA in vitro Gaël Cristofari, Roland Ivanyi-Nagy, Caroline Gabus, Steeve Boulant, Jean-Pierre Lavergne, François Penin, and Jean-Luc Darlix PMCID: PMC419467 Mismatch cleavage by single-strand specific nucleases Bradley J. Till, Chris Burtner, Luca Comai, and Steven Henikoff PMCID: PMC419476 Localization and dynamics of small circular DNA in live mammalian nuclei Giulia Mearini, Peter E. Nielsen, and Frank O. Fackelmayer PMCID: PMC419472 Expression of the adenovirus E4 34k oncoprotein inhibits repair of double strand breaks in the cellular genome of a 293-based inducible cell line Elham S. Mohammadi, Elizabeth A. Ketner, David C. Johns, and Gary Ketner PMCID: PMC419473 Pharmacological and genetic modulation of Wnt-targeted Cre-Lox-mediated gene expression in colorectal cancer cells Michael Bordonaro, Darina L. Lazarova, and Alan C. Sartorelli PMCID: PMC419474 Corrigendum Nucleic Acids Res. 2004; 32(8): 2675. Published online 2004 May 11. doi: 10.1093/nar/gkh602.PMCID: PMC419477 Corrects: Jiashun Zheng, et al. An approach to identify over-represented cis-elements in related sequences. Nucleic Acids Res. 2003 April 1; 31(7): 1995–2005. |
