Nucleic Acids Research

Articles:

Olga Amosova, Steven L. Broitman, and Jacques R. Fresco

Repairing the Sickle Cell mutation. II. Effect of psoralen linker length on specificity of formation and yield of third strand-directed photoproducts with the mutant target sequence
Nucl. Acids Res. 2003 31: 4673-4681; doi:10.1093/nar/gkg659 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Steven L. Broitman, Olga Amosova, and Jacques R. Fresco

Repairing the Sickle Cell mutation. III. Effect of irradiation wavelength on the specificity and type of photoproduct formed by a 3'-terminal psoralen on a third strand directed to the mutant base pair
Nucl. Acids Res. 2003 31: 4682-4688; doi:10.1093/nar/gkg658 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jennie E. Mitchell, Dongling Zheng, Stephen J. W. Busby, and Stephen D. Minchin

Identification and analysis of ‘extended –10’ promoters in Escherichia coli
Nucl. Acids Res. 2003 31: 4689-4695; doi:10.1093/nar/gkg694 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hiroshi Mitsuzawa, Emi Kanda, and Akira Ishihama

Rpb7 subunit of RNA polymerase II interacts with an RNA-binding protein involved in processing of transcripts
Nucl. Acids Res. 2003 31: 4696-4701; doi:10.1093/nar/gkg688 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

John F. Davidson, Richard Fox, Dawn D. Harris, Sally Lyons-Abbott, and Lawrence A. Loeb

Insertion of the T3 DNA polymerase thioredoxin binding domain enhances the processivity and fidelity of Taq DNA polymerase
Nucl. Acids Res. 2003 31: 4702-4709; doi:10.1093/nar/gkg667 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Vladimir R. Kaberdin

Probing the substrate specificity of Escherichia coli RNase E using a novel oligonucleotide-based assay
Nucl. Acids Res. 2003 31: 4710-4716; doi:10.1093/nar/gkg690 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Julie Stinson, Toshiaki Inoue, Paula Yates, Anne Clancy, John D. Norton, and Andrew D. Sharrocks

Regulation of TCF ETS-domain transcription factors by helix–loop–helix motifs
Nucl. Acids Res. 2003 31: 4717-4728; doi:10.1093/nar/gkg689 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Renaud Geslain, Franck Martin, Alain Camasses, and Gilbert Eriani

A yeast knockout strain to discriminate between active and inactive tRNA molecules
Nucl. Acids Res. 2003 31: 4729-4737; doi:10.1093/nar/gkg685 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christian Toft Madsen, Jonas Mengel-Jørgensen, Finn Kirpekar, and Stephen Douthwaite

Identifying the methyltransferases for m⁵U747 and m⁵U1939 in 23S rRNA using MALDI mass spectrometry
Nucl. Acids Res. 2003 31: 4738-4746; doi:10.1093/nar/gkg657 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Joon-Hwa Lee, Chin-Ju Park, Alphonse I. Arunkumar, Walter J. Chazin, and Byong-Seok Choi

NMR study on the interaction between RPA and DNA decamer containing cis-syn cyclobutane pyrimidine dimer in the presence of XPA: implication for damage verification and strand-specific dual incision in nucleotide excision repair
Nucl. Acids Res. 2003 31: 4747-4754; doi:10.1093/nar/gkg683 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Carlos M. Duarte, Leven M. Wadley, and Anna Marie Pyle

RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space
Nucl. Acids Res. 2003 31: 4755-4761; doi:10.1093/nar/gkg682 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Xiaolin Zhang, Shuyu Zhang, and Richard J. Meyer

Molecular handcuffing of the relaxosome at the origin of conjugative transfer of the plasmid R1162
Nucl. Acids Res. 2003 31: 4762-4768; doi:10.1093/nar/gkg687 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Patrick J. Finn, Matthew G. Bull, Haiguang Xiao, Paula D. Phillips, John R. Nelson, Greg Grossmann, Satyam Nampalli, Bernard F. McArdle, J. Anthony Mamone, Parke K. Flick, Carl W. Fuller, and Shiv Kumar

Efficient incorporation of positively charged 2', 3'-dideoxynucleoside-5'-triphosphates by DNA polymerases and their application in ‘direct-load’ DNA sequencing
Nucl. Acids Res. 2003 31: 4769-4778; doi:10.1093/nar/gkg669 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Massimiliano Gentile, Leena Latonen, and Marikki Laiho

Cell cycle arrest and apoptosis provoked by UV radiation-induced DNA damage are transcriptionally highly divergent responses
Nucl. Acids Res. 2003 31: 4779-4790; doi:10.1093/nar/gkg675 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Dierk Ingelfinger, Sven F. Göthel, Mohamed A. Marahiel, Ulrich Reidt, Ralf Ficner, Reinhard Lührmann, and Tilmann Achsel

Two protein–protein interaction sites on the spliceosome-associated human cyclophilin CypH
Nucl. Acids Res. 2003 31: 4791-4796; doi:10.1093/nar/gkg660 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mizue Hisano, Hiroshi Ohta, Yoshitake Nishimune, and Masami Nozaki

Methylation of CpG dinucleotides in the open reading frame of a testicular germ cell-specific intronless gene, Tact1/Actl7b, represses its expression in somatic cells
Nucl. Acids Res. 2003 31: 4797-4804; doi:10.1093/nar/gkg670 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sirik R. Leliveld, Remus T. Dame, Mieke A. Mommaas, Henk K. Koerten, Claire Wyman, Astrid A. A. M. Danen-van Oorschot, Jennifer L. Rohn, Mathieu H. M. Noteborn, and Jan Pieter Abrahams

Apoptin protein multimers form distinct higher-order nucleoprotein complexes with DNA
Nucl. Acids Res. 2003 31: 4805-4813; doi:10.1093/nar/gkg661 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ganesh Natrajan, Meindert H. Lamers, Jacqueline H. Enzlin, Herrie H. K. Winterwerp, Anastassis Perrakis, and Titia K. Sixma

Structures of Escherichia coli DNA mismatch repair enzyme MutS in complex with different mismatches: a common recognition mode for diverse substrates
Nucl. Acids Res. 2003 31: 4814-4821; doi:10.1093/nar/gkg677 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Clive Lo, Kiichi Adachi, Jeffrey R. Shuster, John E. Hamer, and Lisbeth Hamer

The bacterial transposon Tn7 causes premature polyadenylation of mRNA in eukaryotic organisms: TAGKO mutagenesis in filamentous fungi
Nucl. Acids Res. 2003 31: 4822-4827; doi:10.1093/nar/gkg676 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Shuo Liu and Russ B. Altman

Large scale study of protein domain distribution in the context of alternative splicing
Nucl. Acids Res. 2003 31: 4828-4835; doi:10.1093/nar/gkg668 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Amit Cohen, Robert Reiner, and Nayef Jarrous

Alterations in the intracellular level of a protein subunit of human RNase P affect processing of tRNA precursors
Nucl. Acids Res. 2003 31: 4836-4846; doi:10.1093/nar/gkg691 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nick Lee, Robert J. Gorelick, and Karin Musier-Forsyth

Zinc finger-dependent HIV-1 nucleocapsid protein–TAR RNA interactions
Nucl. Acids Res. 2003 31: 4847-4855; doi:10.1093/nar/gkg679 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Najib M. A. El-Sayed, Elodie Ghedin, Jinming Song, Annette MacLeod, Frederic Bringaud, Christopher Larkin, David Wanless, Jeremy Peterson, Lihua Hou, Sonya Taylor, Alison Tweedie, Nicolas Biteau, Hanif G. Khalak, Xiaoying Lin, Tanya Mason, Linda Hannick, Elisabet Caler, Gaëlle Blandin, Daniella Bartholomeu, Anjana J. Simpson, Samir Kaul, Hong Zhao, Grace Pai, Susan Van Aken, Teresa Utterback, Brian Haas, Hean L. Koo, Lowell Umayam, Bernard Suh, Caroline Gerrard, Vanessa Leech, Rong Qi, Shiguo Zhou, David Schwartz, Tamara Feldblyum, Steven Salzberg, Andrew Tait, C. Michael R. Turner, Elisabetta Ullu, Owen White, Sara Melville, Mark D. Adams, Claire M. Fraser, and John E. Donelson

The sequence and analysis of Trypanosoma brucei chromosome II
Nucl. Acids Res. 2003 31: 4856-4863; doi:10.1093/nar/gkg673 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Neil Hall, Matthew Berriman, Nicola J. Lennard, Barbara R. Harris, Christiane Hertz-Fowler, Emmanuelle N. Bart-Delabesse, Caroline S. Gerrard, Rebecca J. Atkin, Andrew J. Barron, Sharen Bowman, Sarah P. Bray-Allen, Frédéric Bringaud, Louise N. Clark, Craig H. Corton, Ann Cronin, Robert Davies, Jonathon Doggett, Audrey Fraser, Eric Grüter, Sarah Hall, A. David Harper, Mike P. Kay, Vanessa Leech, Rebecca Mayes, Claire Price, Michael A. Quail, Ester Rabbinowitsch, Christopher Reitter, Kim Rutherford, Jürgen Sasse, Sarah Sharp, Ratna Shownkeen, Annette MacLeod, Sonya Taylor, Alison Tweedie, C. Michael R. Turner, Andrew Tait, Keith Gull, Bart Barrell, and Sara E. Melville

The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism
Nucl. Acids Res. 2003 31: 4864-4873; doi:10.1093/nar/gkg674 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Annika M. Källman, Margareta Sahlin, and Marie Öhman

ADAR2 AI editing: site selectivity and editing efficiency are separate events
Nucl. Acids Res. 2003 31: 4874-4881; doi:10.1093/nar/gkg681 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Xiukun Lin, Jun Liu, Frank Maley, and Edward Chu

Role of cysteine amino acid residues on the RNA binding activity of human thymidylate synthase
Nucl. Acids Res. 2003 31: 4882-4887; doi:10.1093/nar/gkg678 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ian Grainge, Sarah Scaife, and Dale B. Wigley

Biochemical analysis of components of the pre-replication complex of Archaeoglobus fulgidus
Nucl. Acids Res. 2003 31: 4888-4898; doi:10.1093/nar/gkg662 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

John Mouaikel, Janusz M. Bujnicki, Jamal Tazi, and Rémy Bordonné

Sequence–structure–function relationships of Tgs1, the yeast snRNA/snoRNA cap hypermethylase
Nucl. Acids Res. 2003 31: 4899-4909; doi:10.1093/nar/gkg656 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Circe Tsui, Laura E. Coleman, Jacqulyn L. Griffith, E. Andrew Bennett, Summer G. Goodson, Jason D. Scott, W. Stephen Pittard, and Scott E. Devine

Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map
Nucl. Acids Res. 2003 31: 4910-4916; doi:10.1093/nar/gkg664 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tobias Hanke, María J. Ramiro, Sonia Trigueros, Joaquim Roca, and Vicente Larraga

Cloning, functional analysis and post-transcriptional regulation of a type II DNA topoisomerase from Leishmania infantum. A new potential target for anti-parasite drugs
Nucl. Acids Res. 2003 31: 4917-4928; doi:10.1093/nar/gkg671 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nuo Yang, Lin Zhang, Yue Zhang, and Haig H. Kazazian, Jr

An important role for RUNX3 in human L1 transcription and retrotransposition
Nucl. Acids Res. 2003 31: 4929-4940; doi:10.1093/nar/gkg663 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Gordana Maravic, Janusz M. Bujnicki, Marcin Feder, Sándor Pongor, and Mirna Flögel

Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein–RNA interactions
Nucl. Acids Res. 2003 31: 4941-4949; doi:10.1093/nar/gkg666 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Natale Scaramozzino, Guenhael Sanz, Jean Marc Crance, Murat Saparbaev, Robert Drillien, Jacques Laval, Bodil Kavli, and Daniel Garin

Characterisation of the substrate specificity of homogeneous vaccinia virus uracil-DNA glycosylase
Nucl. Acids Res. 2003 31: 4950-4957; doi:10.1093/nar/gkg672 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

NAR Methods Online:

Scott Taylor, Stephanie Smith, Brad Windle, and Anthony Guiseppi-Elie

Impact of surface chemistry and blocking strategies on DNA microarrays
Nucl. Acids Res. 2003 31: e87; doi:10.1093/nar/gng086 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Véronique Le Berre, Emmanuelle Trévisiol, Adilia Dagkessamanskaia, Serguei Sokol, Anne-Marie Caminade, Jean Pierre Majoral, Bernard Meunier, and Jean François

Dendrimeric coating of glass slides for sensitive DNA microarrays analysis
Nucl. Acids Res. 2003 31: e88; doi:10.1093/nar/gng088 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kerstin Korn, Paola Gardellin, Bohao Liao, Mario Amacker, Åsa Bergström, Henrik Björkman, Agnès Camacho, Sabine Dörhöfer, Klaus Dörre, Johanna Enström, Thomas Ericson, Tatiana Favez, Michael Gösch, Adrian Honegger, Sandra Jaccoud, Markus Lapczyna, Erik Litborn, Per Thyberg, Holger Winter, and Rudolf Rigler

Gene expression analysis using single molecule detection
Nucl. Acids Res. 2003 31: e89; doi:10.1093/nar/gng089 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christof M. Niemeyer, Ron Wacker, and Michael Adler

Combination of DNA-directed immobilization and immuno-PCR: very sensitive antigen detection by means of self-assembled DNA–protein conjugates
Nucl. Acids Res. 2003 31: e90; doi:10.1093/nar/gng090 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Daisuke Umeno, Kaori Hiraga, and Frances H. Arnold

Method to protect a targeted amino acid residue during random mutagenesis
Nucl. Acids Res. 2003 31: e91; doi:10.1093/nar/gng091 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Peng Hou, Meiju Ji, Cunwang Ge, Jiayao Shen, Song Li, Nongyue He, and Zuhong Lu

Detection of methylation of human p16^Ink4a gene 5'-CpG islands by electrochemical method coupled with linker-PCR
Nucl. Acids Res. 2003 31: e92; doi:10.1093/nar/gng092 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

R. G. Rutledge and C. Côté

Mathematics of quantitative kinetic PCR and the application of standard curves
Nucl. Acids Res. 2003 31: e93; doi:10.1093/nar/gng093 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Ryutaro Fukumura, Hirokazu Takahashi, Toshiyuki Saito, Yoko Tsutsumi, Akira Fujimori, Shinji Sato, Kouichi Tatsumi, Ryoko Araki, and Masumi Abe

A sensitive transcriptome analysis method that can detect unknown transcripts
Nucl. Acids Res. 2003 31: e94; doi:10.1093/nar/gng094 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Eugene R. Zabarovsky, Lev Petrenko, Alexei Protopopov, Olga Vorontsova, Alexey S. Kutsenko, Yanyan Zhao, Gelena Kilosanidze, Veronika Zabarovska, Elian Rakhmanaliev, Bertil Pettersson, Vladimir I. Kashuba, Olle Ljungqvist, Elisabeth Norin, Tore Midtvedt, Roland Möllby, Gösta Winberg, and Ingemar Ernberg

Restriction site tagged (RST) microarrays: a novel technique to study the species composition of complex microbial systems
Nucl. Acids Res. 2003 31: e95; doi:10.1093/nar/gng096 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yongxiang Fang, Andrew Brass, David C. Hoyle, Andrew Hayes, Abdulla Bashein, Stephen G. Oliver, David Waddington, and Magnus Rattray

A model-based analysis of microarray experimental error and normalisation
Nucl. Acids Res. 2003 31: e96; doi:10.1093/nar/gng097 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Andrea S. Kim and William G. Thilly

Ligation of high-melting-temperature ‘clamp’ sequence extends the scanning range of rare point-mutational analysis by constant denaturant capillary electrophoresis (CDCE) to most of the human genome
Nucl. Acids Res. 2003 31: e97; doi:10.1093/nar/gng099 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Maria Pilar Bayona-Bafaluy, Giovanni Manfredi, and Carlos T. Moraes

A chemical enucleation method for the transfer of mitochondrial DNA to ° cells
Nucl. Acids Res. 2003 31: e98; doi:10.1093/nar/gng100 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yair Benita, Ronald S. Oosting, Martin C. Lok, Michael J. Wise, and Ian Humphery-Smith

Regionalized GC content of template DNA as a predictor of PCR success
Nucl. Acids Res. 2003 31: e99; doi:10.1093/nar/gng101 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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