Nucleic Acids Research

Articles:

Helena Santos-Rosa, Ester Valls, Tony Kouzarides, and Marian Martínez-Balbás

Mechanisms of P/CAF auto-acetylation
Nucl. Acids Res. 2003 31: 4285-4292; doi:10.1093/nar/gkg655 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christoph Ufer, Astrid Borchert, and Hartmut Kuhn

Functional characterization of cis- and trans-regulatory elements involved in expression of phospholipid hydroperoxide glutathione peroxidase
Nucl. Acids Res. 2003 31: 4293-4303; doi:10.1093/nar/gkg650 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Kavitha Venkatesan, Heather R. McManus, Craig C. Mello, Temple F. Smith, and Ulla Hansen

Functional conservation between members of an ancient duplicated transcription factor family, LSF/Grainyhead
Nucl. Acids Res. 2003 31: 4304-4316; doi:10.1093/nar/gkg644 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Thomas J. Bollenbach and David B. Stern

Divalent metal-dependent catalysis and cleavage specificity of CSP41, a chloroplast endoribonuclease belonging to the short chain dehydrogenase/reductase superfamily
Nucl. Acids Res. 2003 31: 4317-4325; doi:10.1093/nar/gkg640 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

David W. Staple and Samuel E. Butcher

Solution structure of the HIV-1 frameshift inducing stem–loop RNA
Nucl. Acids Res. 2003 31: 4326-4331; doi:10.1093/nar/gkg654 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Benoit Pelletier, Jude Beaudoin, Caroline C. Philpott, and Simon Labbé

Fep1 represses expression of the fission yeast Schizosaccharomyces pombe siderophore-iron transport system
Nucl. Acids Res. 2003 31: 4332-4344; doi:10.1093/nar/gkg647 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Caroline Wilde, Frédéric Escartin, Susumu Kokeguchi, Patricia Latour-Lambert, Aude Lectard, and Jean-Marie Clément

Transposases are responsible for the target specificity of IS1397 and ISKpn1 for two different types of palindromic units (PUs)
Nucl. Acids Res. 2003 31: 4345-4353; doi:10.1093/nar/gkg494 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Masato Tamura, Chikako Nashimoto, Noriko Miyake, Yasushi Daikuhara, Kozo Ochi, and Masayuki Nashimoto

Intracellular mRNA cleavage by 3' tRNase under the direction of 2'-O-methyl RNA heptamers
Nucl. Acids Res. 2003 31: 4354-4360; doi:10.1093/nar/gkg641 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jaesung Lee and David L. Herrin

Mutagenesis of a light-regulated psbA intron reveals the importance of efficient splicing for photosynthetic growth
Nucl. Acids Res. 2003 31: 4361-4372; doi:10.1093/nar/gkg643 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Michelle Sabourin, John L. Nitiss, Karin C. Nitiss, Kazuo Tatebayashi, Hideo Ikeda, and Neil Osheroff

Yeast recombination pathways triggered by topoisomerase II-mediated DNA breaks
Nucl. Acids Res. 2003 31: 4373-4384; doi:10.1093/nar/gkg497 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Anton Buzdin, Elena Gogvadze, Elena Kovalskaya, Pavel Volchkov, Svetlana Ustyugova, Anna Illarionova, Alexey Fushan, Tatiana Vinogradova, and Eugene Sverdlov

The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination
Nucl. Acids Res. 2003 31: 4385-4390; doi:10.1093/nar/gkg496 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Hedije Meka, Gregoire Daoust, Kristine Bourke Arnvig, Finn Werner, Peter Brick, and Silvia Onesti

Structural and functional homology between the RNAP_I subunits A14/A43 and the archaeal RNAP subunits E/F
Nucl. Acids Res. 2003 31: 4391-4400; doi:10.1093/nar/gkg652 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Michiel Vandenbussche, Günter Theissen, Yves Van de Peer, and Tom Gerats

Structural diversification and neo-functionalization during floral MADS-box gene evolution by C-terminal frameshift mutations
Nucl. Acids Res. 2003 31: 4401-4409; doi:10.1093/nar/gkg642 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Derek J. Cashman, J. Neel Scarsdale, and Glen E. Kellogg

Hydropathic analysis of the free energy differences in anthracycline antibiotic binding to DNA
Nucl. Acids Res. 2003 31: 4410-4416; doi:10.1093/nar/gkg645 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Rosel Kretschmer-Kazemi Far and Georg Sczakiel

The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides
Nucl. Acids Res. 2003 31: 4417-4424; doi:10.1093/nar/gkg649 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Gábor Balázsi, Krin A. Kay, Albert-László Barabási, and Zoltán N. Oltvai

Spurious spatial periodicity of co-expression in microarray data due to printing design
Nucl. Acids Res. 2003 31: 4425-4433; doi:10.1093/nar/gkg485 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Gregor Witte, Claus Urbanke, and Ute Curth

DNA polymerase III subunit ties single-stranded DNA binding protein to the bacterial replication machinery
Nucl. Acids Res. 2003 31: 4434-4440; doi:10.1093/nar/gkg498 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

José F. Ruiz, Raquel Juárez, Miguel García-Díaz, Gloria Terrados, Angel J. Picher, Sergio González-Barrera, Antonio R. Fernández de Henestrosa, and Luis Blanco

Lack of sugar discrimination by human Pol µ requires a single glycine residue
Nucl. Acids Res. 2003 31: 4441-4449; doi:10.1093/nar/gkg637 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

D. Rey Banatao, Russ B. Altman, and Teri E. Klein

Microenvironment analysis and identification of magnesium binding sites in RNA
Nucl. Acids Res. 2003 31: 4450-4460; doi:10.1093/nar/gkg471 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Elzbieta Kierzek and Ryszard Kierzek

The synthesis of oligoribonucleotides containing N⁶-alkyladenosines and 2-methylthio-N⁶-alkyladenosines via post-synthetic modification of precursor oligomers
Nucl. Acids Res. 2003 31: 4461-4471; doi:10.1093/nar/gkg632 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Elzbieta Kierzek and Ryszard Kierzek

The thermodynamic stability of RNA duplexes and hairpins containing N⁶-alkyladenosines and 2-methylthio-N⁶-alkyladenosines
Nucl. Acids Res. 2003 31: 4472-4480; doi:10.1093/nar/gkg633 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mitch Raponi and Greg M. Arndt

Double-stranded RNA-mediated gene silencing in fission yeast
Nucl. Acids Res. 2003 31: 4481-4489; doi:10.1093/nar/gkg484 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tomoki Matsuyama, Makoto T. Kimura, Kuniaki Koike, Tomoko Abe, Takeshi Nakano, Tadao Asami, Toshikazu Ebisuzaki, William A. Held, Shigeo Yoshida, and Hiroki Nagase

Global methylation screening in the Arabidopsis thaliana and Mus musculus genome: applications of virtual image restriction landmark genomic scanning (Vi-RLGS)
Nucl. Acids Res. 2003 31: 4490-4496; doi:10.1093/nar/gkg488 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Yoji Yamamoto, Wataru Tsuboi, and Makoto Komiyama

Oligoamine–acridine conjugates for promotion of gap-selective DNA hydrolysis by Ce(IV)/EDTA complex
Nucl. Acids Res. 2003 31: 4497-4502; doi:10.1093/nar/gkg634 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Andrew F. Neuwald

Evolutionary clues to DNA polymerase III ß clamp structural mechanisms
Nucl. Acids Res. 2003 31: 4503-4516; doi:10.1093/nar/gkg486 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Richard Ellis Hudson, Ulfar Bergthorsson, and Howard Ochman

Transcription increases multiple spontaneous point mutations in Salmonella enterica
Nucl. Acids Res. 2003 31: 4517-4522; doi:10.1093/nar/gkg651 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Takayuki Torigoe, Hiroto Izumi, Yoichiro Yoshida, Hiroshi Ishiguchi, Takashi Okamoto, Hideaki Itoh, and Kimitoshi Kohno

Low pH enhances Sp1 DNA binding activity and interaction with TBP
Nucl. Acids Res. 2003 31: 4523-4530; doi:10.1093/nar/gkg487 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Insuk Lee and Rasika M. Harshey

Patterns of sequence conservation at termini of long terminal repeat (LTR) retrotransposons and DNA transposons in the human genome: lessons from phage Mu
Nucl. Acids Res. 2003 31: 4531-4540; doi:10.1093/nar/gkg499 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Stanislav G. Kozmin, Youri I. Pavlov, Thomas A. Kunkel, and Evelyne Sage

Roles of Saccharomyces cerevisiae DNA polymerases Pol and Pol in response to irradiation by simulated sunlight
Nucl. Acids Res. 2003 31: 4541-4552; doi:10.1093/nar/gkg489 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Soumya Raychaudhuri, Jeffrey T. Chang, Farhad Imam, and Russ B. Altman

The computational analysis of scientific literature to define and recognize gene expression clusters
Nucl. Acids Res. 2003 31: 4553-4560; doi:10.1093/nar/gkg636 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Wei Zhu and Volker Brendel

Identification, characterization and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome
Nucl. Acids Res. 2003 31: 4561-4572; doi:10.1093/nar/gkg492 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Dwain I. D’souza and Lynn Harrison

Repair of clustered uracil DNA damages in Escherichia coli
Nucl. Acids Res. 2003 31: 4573-4581; doi:10.1093/nar/gkg493 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jianhua Ling, Wenhu Pi, Xiuping Yu, Chikh Bengra, Qiaoming Long, Huaqian Jin, Andreas Seyfang, and Dorothy Tuan

The ERV-9 LTR enhancer is not blocked by the HS5 insulator and synthesizes through the HS5 site non-coding, long RNAs that regulate LTR enhancer function
Nucl. Acids Res. 2003 31: 4582-4596; doi:10.1093/nar/gkg646 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ceri Van Slyke and Elizabeth J. Grayhack

The essential transcription factor Reb1p interacts with the CLB2 UAS outside of the G₂/M control region
Nucl. Acids Res. 2003 31: 4597-4607; doi:10.1093/nar/gkg638 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Swapan S. Jain, Matjaz Polak, and Nicholas V. Hud

Controlling nucleic acid secondary structure by intercalation: effects of DNA strand length on coralyne-driven duplex disproportionation
Nucl. Acids Res. 2003 31: 4608-4615; doi:10.1093/nar/gkg648 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Zifan Lu, Youyi Zhang, Li Ku, Houping Wang, Amir Ahmadian, and Yue Feng

The quakingviable mutation affects qkI mRNA expression specifically in myelin-producing cells of the nervous system
Nucl. Acids Res. 2003 31: 4616-4624; doi:10.1093/nar/gkg635 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Isidore Rigoutsos, Peter Riek, Robert M. Graham, and Jiri Novotny

Structural details (kinks and non- conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors
Nucl. Acids Res. 2003 31: 4625-4631; doi:10.1093/nar/gkg639 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Anton J. Enright, Victor Kunin, and Christos A. Ouzounis

Protein families and TRIBES in genome sequence space
Nucl. Acids Res. 2003 31: 4632-4638; doi:10.1093/nar/gkg495 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Flavio Mignone, Giorgio Grillo, Sabino Liuni, and Graziano Pesole

Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis
Nucl. Acids Res. 2003 31: 4639-4645; doi:10.1093/nar/gkg483 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yoshitaka Yamamoto, Yuhki Fujimoto, Ryota Arai, Makoto Fujie, Shoji Usami, and Takashi Yamada

Retrotransposon-mediated restoration of Chlorella telomeres: accumulation of Zepp retrotransposons at termini of newly formed minichromosomes
Nucl. Acids Res. 2003 31: 4646-4653; doi:10.1093/nar/gkg490 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jae-Ryeon Ryu and David N. Arnosti

Functional similarity of Knirps CtBP-dependent and CtBP-independent transcriptional repressor activities
Nucl. Acids Res. 2003 31: 4654-4662; doi:10.1093/nar/gkg491 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Martti T. Tammi, Erik Arner, Ellen Kindlund, and Björn Andersson

Correcting errors in shotgun sequences
Nucl. Acids Res. 2003 31: 4663-4672; doi:10.1093/nar/gkg653; [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

NAR Methods Online:

Shiro Matsukura, Peter A. Jones, and Daiya Takai

Establishment of conditional vectors for hairpin siRNA knockdowns
Nucl. Acids Res. 2003 31: e77; doi:10.1093/nar/gng077 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Etsuko Miyamoto-Sato, Hideaki Takashima, Shinichiro Fuse, Kaori Sue, Masamichi Ishizaka, Seiji Tateyama, Kenichi Horisawa, Tatsuya Sawasaki, Yaeta Endo, and Hiroshi Yanagawa

Highly stable and efficient mRNA templates for mRNA–protein fusions and C-terminally labeled proteins
Nucl. Acids Res. 2003 31: e78; doi:10.1093/nar/gng078 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Angelika Gabler, Stefan Krebs, Doris Seichter, and Martin Förster

Fast and accurate determination of sites along the FUT2 in vitro transcript that are accessible to antisense oligonucleotides by application of secondary structure predictions and RNase H in combination with MALDI-TOF mass spectrometry
Nucl. Acids Res. 2003 31: e79; doi:10.1093/nar/gng079 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yongping Yang and Shyam K. Sharan

A simple two-step, ‘hit and fix’ method to generate subtle mutations in BACs using short denatured PCR fragments
Nucl. Acids Res. 2003 31: e80; doi:10.1093/nar/gng080 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Xin-Mei Zhang and Jian-Dong Huang

Combination of overlapping bacterial artificial chromosomes by a two-step recombinogenic engineering method
Nucl. Acids Res. 2003 31: e81; doi:10.1093/nar/gng081 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Scott C. Walker, Johanna M. Avis, and Graeme L. Conn

General plasmids for producing RNA in vitro transcripts with homogeneous ends
Nucl. Acids Res. 2003 31: e82; doi:10.1093/nar/gng082 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christine P. Diggle, Johanne Bentley, and Anne E. Kiltie

Development of a rapid, small-scale DNA repair assay for use on clinical samples
Nucl. Acids Res. 2003 31: e83; doi:10.1093/nar/gng083 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Joshua Merritt, Jason R. DiTonno, Robi D. Mitra, George M. Church, and Jeremy S. Edwards

Parallel competition analysis of Saccharomyces cerevisiae strains differing by a single base using polymerase colonies
Nucl. Acids Res. 2003 31: e84; doi:10.1093/nar/gng084 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Anthony E. Brown, Laurence Bugeon, Andrea Crisanti, and Flaminia Catteruccia

Stable and heritable gene silencing in the malaria vector Anopheles stephensi
Nucl. Acids Res. 2003 31: e85; doi:10.1093/nar/gng085 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Stanislaw J. Kaczmarczyk and Jeffrey E. Green

Induction of cre recombinase activity using modified androgen receptor ligand binding domains: a sensitive assay for ligand-receptor interactions
Nucl. Acids Res. 2003 31: e86; doi:10.1093/nar/gng087 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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