Nucleic Acids Research

Articles:

Jeong-Hoon Kim, Jaehoon Kim, Do-Hyung Kim, Gi-Hyuck Ryu, Sung-Ho Bae, and Yeon-Soo Seo

SCF^hFBH1 can act as helicase and E3 ubiquitin ligase
Nucl. Acids Res. 2004 32: 2287-2297; doi:10.1093/nar/gkh534 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Edward A. Carr, Janet Mead, and Andrew K. Vershon

1-induced DNA bending is required for transcriptional activation by the Mcm1–1 complex
Nucl. Acids Res. 2004 32: 2298-2305; doi:10.1093/nar/gkh560 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Víctor González-Huici, Margarita Salas, and José M. Hermoso

Genome wide, supercoiling-dependent in vivo binding of a viral protein involved in DNA replication and transcriptional control
Nucl. Acids Res. 2004 32: 2306-2314; doi:10.1093/nar/gkh565 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Roland P. Kuiper, Marga Schepens, José Thijssen, Eric F. P. M. Schoenmakers, and Ad Geurts van Kessel

Regulation of the MiTF/TFE bHLH-LZ transcription factors through restricted spatial expression and alternative splicing of functional domains
Nucl. Acids Res. 2004 32: 2315-2322; doi:10.1093/nar/gkh571 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Musa H. Asyali, Mohamed M. Shoukri, Omer Demirkaya, and Khalid S. A. Khabar

Assessment of reliability of microarray data and estimation of signal thresholds using mixture modeling
Nucl. Acids Res. 2004 32: 2323-2335; doi:10.1093/nar/gkh544 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Fei Chen, Ruijian Wang, Zhe Li, Bin Liu, Xiaoping Wang, Yanhong Sun, Dongyun Hao, and Jin Zhang

A novel replicating circular DNAzyme
Nucl. Acids Res. 2004 32: 2336-2341; doi:10.1093/nar/gkh547 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Peter S. Klosterman, Donna K. Hendrix, Makio Tamura, Stephen R. Holbrook, and Steven E. Brenner

Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns
Nucl. Acids Res. 2004 32: 2342-2352; doi:10.1093/nar/gkh537 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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

Identification and functional analysis of ‘hypothetical’ genes expressed in Haemophilus influenzae
Nucl. Acids Res. 2004 32: 2353-2361; doi:10.1093/nar/gkh555 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Gengxin Chen, Naoya Hata, and Michael Q. Zhang

Transcription factor binding element detection using functional clustering of mutant expression data
Nucl. Acids Res. 2004 32: 2362-2371; doi:10.1093/nar/gkh557 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Keiko Tawa and Wolfgang Knoll

Mismatching base-pair dependence of the kinetics of DNA–DNA hybridization studied by surface plasmon fluorescence spectroscopy
Nucl. Acids Res. 2004 32: 2372-2377; doi:10.1093/nar/gkh572 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

S. Anuradha and K. Muniyappa

Meiosis-specific yeast Hop1 protein promotes synapsis of double-stranded DNA helices via the formation of guanine quartets
Nucl. Acids Res. 2004 32: 2378-2385; doi:10.1093/nar/gkh559 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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

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
Nucl. Acids Res. 2004 32: 2386-2395; doi:10.1093/nar/gkh562 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Giuseppina M. Carbone, Eileen McGuffie, Sara Napoli, Courtney E. Flanagan, Chiara Dembech, Umberto Negri, Federico Arcamone, Massimo L. Capobianco, and Carlo V. Catapano

DNA binding and antigene activity of a daunomycin-conjugated triplex-forming oligonucleotide targeting the P2 promoter of the human c-myc gene
Nucl. Acids Res. 2004 32: 2396-2410; doi:10.1093/nar/gkh527 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Patricia Villacé, Rosa M. Marión, and Juan Ortín

The composition of Staufen-containing RNA granules from human cells indicates their role in the regulated transport and translation of messenger RNAs
Nucl. Acids Res. 2004 32: 2411-2420; doi:10.1093/nar/gkh552 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Rodolphe Suspène, Peter Sommer, Michel Henry, Stéphane Ferris, Denise Guétard, Sylvie Pochet, Ann Chester, Naveenan Navaratnam, Simon Wain-Hobson, and Jean-Pierre Vartanian

APOBEC3G is a single-stranded DNA cytidine deaminase and functions independently of HIV reverse transcriptase
Nucl. Acids Res. 2004 32: 2421-2429; doi:10.1093/nar/gkh554 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Maarit Jokela, Anitta Eskelinen, Helmut Pospiech, Juha Rouvinen, and Juhani E. Syväoja

Characterization of the 3' exonuclease subunit DP1 of Methanococcus jannaschii replicative DNA polymerase D
Nucl. Acids Res. 2004 32: 2430-2440; doi:10.1093/nar/gkh558 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Doris Ursic, Karen Chinchilla, Jonathan S. Finkel, and Michael R. Culbertson

Multiple protein/protein and protein/RNA interactions suggest roles for yeast DNA/RNA helicase Sen1p in transcription, transcription-coupled DNA repair and RNA processing
Nucl. Acids Res. 2004 32: 2441-2452; doi:10.1093/nar/gkh561 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Janusz M. Bujnicki, Marcin Feder, Chastity L. Ayres, and Kent L. Redman

Sequence–structure–function studies of tRNA:m⁵C methyltransferase Trm4p and its relationship to DNA:m⁵C and RNA:m⁵U methyltransferases
Nucl. Acids Res. 2004 32: 2453-2463; doi:10.1093/nar/gkh564 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Jens Kleinjung, John Romein, Kuang Lin, and Jaap Heringa

Contact-based sequence alignment
Nucl. Acids Res. 2004 32: 2464-2473; doi:10.1093/nar/gkh566 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Joon-Hwa Lee, Chin-Ju Park, Jae-Sun Shin, Takahisa Ikegami, Hideo Akutsu, and Byong-Seok Choi

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
Nucl. Acids Res. 2004 32: 2474-2481; doi:10.1093/nar/gkh568 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

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

A DNA replication-related element downstream from the initiation site of Drosophila selenophosphate synthetase 2 gene is essential for its transcription
Nucl. Acids Res. 2004 32: 2482-2493; doi:10.1093/nar/gkh569 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mark M. Somoza, Daniele Andreatta, Catherine J. Murphy, Robert S. Coleman, and Mark A. Berg

Effect of lesions on the dynamics of DNA on the picosecond and nanosecond timescales using a polarity sensitive probe
Nucl. Acids Res. 2004 32: 2494-2507; doi:10.1093/nar/gkh577 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

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

Targeted transcriptional repression of Gfi1 by GFI1 and GFI1B in lymphoid cells
Nucl. Acids Res. 2004 32: 2508-2519; doi:10.1093/nar/gkh570 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Erica Friedrich-Heineken and Ulrich Hübscher

The Fen1 extrahelical 3'-flap pocket is conserved from archaea to human and regulates DNA substrate specificity
Nucl. Acids Res. 2004 32: 2520-2528; doi:10.1093/nar/gkh576 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Orna Dahan and Martin Kupiec

The Saccharomyces cerevisiae gene CDC40/PRP17 controls cell cycle progression through splicing of the ANC1 gene
Nucl. Acids Res. 2004 32: 2529-2540; doi:10.1093/nar/gkh574 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jiro Kondo, Wataru Adachi, Shun-ichi Umeda, Tomoko Sunami, and Akio Takénaka

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
Nucl. Acids Res. 2004 32: 2541-2549; doi:10.1093/nar/gkh575 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Irina I. Dianova, Kate M. Sleeth, Sarah L. Allinson, Jason L. Parsons, Claire Breslin, Keith W. Caldecott, and Grigory L. Dianov

XRCC1–DNA polymerase ß interaction is required for efficient base excision repair
Nucl. Acids Res. 2004 32: 2550-2555; doi:10.1093/nar/gkh567 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hiroshi Yokoyama, Naoyuki Sarai, Wataru Kagawa, Rima Enomoto, Takehiko Shibata, Hitoshi Kurumizaka, and Shigeyuki Yokoyama

Preferential binding to branched DNA strands and strand-annealing activity of the human Rad51B, Rad51C, Rad51D and Xrcc2 protein complex
Nucl. Acids Res. 2004 32: 2556-2565; doi:10.1093/nar/gkh578 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Henry R. Bigelow, Donald S. Petrey, Jinfeng Liu, Dariusz Przybylski, and Burkhard Rost

Predicting transmembrane beta-barrels in proteomes
Nucl. Acids Res. 2004 32: 2566-2577; doi:10.1093/nar/gkh580 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Takemitsu Furuchi, Tsutomu Takahashi, Shogo Tanaka, Katsushi Nitta, and Akira Naganuma

Functions of yeast helicase Ssl2p that are essential for viability are also involved in protection from the toxicity of adriamycin
Nucl. Acids Res. 2004 32: 2578-2585; doi:10.1093/nar/gkh582 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

J. Eeckhoute, P. Formstecher, and B. Laine

Hepatocyte Nuclear Factor 4 enhances the Hepatocyte Nuclear Factor 1-mediated activation of transcription
Nucl. Acids Res. 2004 32: 2586-2593; doi:10.1093/nar/gkh581 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Maria M. Anokhina, Andrea Barta, Knud H. Nierhaus, Vera A. Spiridonova, and Alexei M. Kopylov

Mapping of the second tetracycline binding site on the ribosomal small subunit of E.coli
Nucl. Acids Res. 2004 32: 2594-2597; doi:10.1093/nar/gkh583 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Antonina Risitano and Keith R. Fox

Influence of loop size on the stability of intramolecular DNA quadruplexes
Nucl. Acids Res. 2004 32: 2598-2606; doi:10.1093/nar/gkh598 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Matthew C. A. Smith, Rob Till, Kevin Brady, Panos Soultanas, Helena Thorpe, and Margaret C. M. Smith

Synapsis and DNA cleavage in C31 integrase-mediated site-specific recombination
Nucl. Acids Res. 2004 32: 2607-2617; doi:10.1093/nar/gkh538 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Mark Halling-Brown, Clare Sansom, David S. Moss, Greg Elgar, and Yvonne J. K. Edwards

A Fugu–Human Genome Synteny Viewer: web software for graphical display and annotation reports of synteny between Fugu genomic sequence and human genes
Nucl. Acids Res. 2004 32: 2618-2622; doi:10.1093/nar/gkh573 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Gaël Cristofari, Roland Ivanyi-Nagy, Caroline Gabus, Steeve Boulant, Jean-Pierre Lavergne, François Penin, and Jean-Luc Darlix

The hepatitis C virus Core protein is a potent nucleic acid chaperone that directs dimerization of the viral (+) strand RNA in vitro
Nucl. Acids Res. 2004 32: 2623-2631; doi:10.1093/nar/gkh579 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Bradley J. Till, Chris Burtner, Luca Comai, and Steven Henikoff

Mismatch cleavage by single-strand specific nucleases
Nucl. Acids Res. 2004 32: 2632-2641; doi:10.1093/nar/gkh599 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Giulia Mearini, Peter E. Nielsen, and Frank O. Fackelmayer

Localization and dynamics of small circular DNA in live mammalian nuclei
Nucl. Acids Res. 2004 32: 2642-2651; doi:10.1093/nar/gkh587 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Elham S. Mohammadi, Elizabeth A. Ketner, David C. Johns, and Gary Ketner

Expression of the adenovirus E4 34k oncoprotein inhibits repair of double strand breaks in the cellular genome of a 293-based inducible cell line
Nucl. Acids Res. 2004 32: 2652-2659; doi:10.1093/nar/gkh593 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Michael Bordonaro, Darina L. Lazarova, and Alan C. Sartorelli

Pharmacological and genetic modulation of Wnt-targeted Cre-Lox-mediated gene expression in colorectal cancer cells
Nucl. Acids Res. 2004 32: 2660-2674; doi:10.1093/nar/gkh596 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Erratum:

Corrigendum
Nucl. Acids Res. 2004 32: 2675; doi:10.1093/nar/gkh602 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.