Nucleic Acids Research

Articles:

Stefania Petrucco

Sensing DNA damage by PARP-like fingers
Nucl. Acids Res. 2003 31: 6689-6699; doi:10.1093/nar/gkg890 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Stephen W. Santoro, J. Christopher Anderson, Vishva Lakshman, and Peter G. Schultz

An archaebacteria-derived glutamyl-tRNA synthetase and tRNA pair for unnatural amino acid mutagenesis of proteins in Escherichia coli
Nucl. Acids Res. 2003 31: 6700-6709; doi:10.1093/nar/gkg903 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Patrick J. Daniels and Glen K. Andrews

Dynamics of the metal-dependent transcription factor complex in vivo at the mouse metallothionein-I promoter
Nucl. Acids Res. 2003 31: 6710-6721; doi:10.1093/nar/gkg913 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Pelagia Foka, Scott A. Irvine, Feray Kockar, and Dipak P. Ramji

Interleukin-6 represses the transcription of the CCAAT/enhancer binding protein- gene in hepatoma cells by inhibiting its ability to autoactivate the proximal promoter region
Nucl. Acids Res. 2003 31: 6722-6732; doi:10.1093/nar/gkg861 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Elisabeth Piñeiro, Laura Fernàndez-López, Josep Gamez, Ricard Marcos, Jordi Surrallés, and Antonia Velázquez

Mutagenic stress modulates the dynamics of CTG repeat instability associated with myotonic dystrophy type 1
Nucl. Acids Res. 2003 31: 6733-6740; doi:10.1093/nar/gkg898 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Joshua Kim, Li Jia, Wayne D. Tilley, and Gerhard A. Coetzee

Dynamic methylation of histone H3 at lysine 4 in transcriptional regulation by the androgen receptor
Nucl. Acids Res. 2003 31: 6741-6747; doi:10.1093/nar/gkg909 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dmitry A. Rodionov, Alexey G. Vitreschak, Andrey A. Mironov, and Mikhail S. Gelfand

Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?
Nucl. Acids Res. 2003 31: 6748-6757; doi:10.1093/nar/gkg900 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Koen Nauwelaerts, Karen Vastmans, Matheus Froeyen, Veerle Kempeneers, Jef Rozenski, Helmut Rosemeyer, Arthur Van Aerschot, Roger Busson, Jeffrey C. Lacey, Ekaterina Efimtseva, Sergey Mikhailov, Eveline Lescrinier, and Piet Herdewijn

Cleavage of DNA without loss of genetic information by incorporation of a disaccharide nucleoside
Nucl. Acids Res. 2003 31: 6758-6769; doi:10.1093/nar/gkg911 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Ruy Jáuregui, Cei Abreu-Goodger, Gabriel Moreno-Hagelsieb, Julio Collado-Vides, and Enrique Merino

Conservation of DNA curvature signals in regulatory regions of prokaryotic genes
Nucl. Acids Res. 2003 31: 6770-6777; doi:10.1093/nar/gkg882 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Cédric Laguri, Mary K. Phillips-Jones, and Michael P. Williamson

Solution structure and DNA binding of the effector domain from the global regulator PrrA (RegA) from Rhodobacter sphaeroides: insights into DNA binding specificity
Nucl. Acids Res. 2003 31: 6778-6787; doi:10.1093/nar/gkg891 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Joanna Kufel, Christine Allmang, Loredana Verdone, Jean Beggs, and David Tollervey

A complex pathway for 3' processing of the yeast U3 snoRNA
Nucl. Acids Res. 2003 31: 6788-6797; doi:10.1093/nar/gkg904 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Amy Tabb-Massey, Jacqueline M. Caffrey, Paula Logsden, Stephen Taylor, John O. Trent, and Steven R. Ellis

Ribosomal proteins Rps0 and Rps21 of Saccharomyces cerevisiae have overlapping functions in the maturation of the 3' end of 18S rRNA
Nucl. Acids Res. 2003 31: 6798-6805; doi:10.1093/nar/gkg899 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Carl C. Correll, Jutta Beneken, Matthew J. Plantinga, Melissa Lubbers, and Yuen-Ling Chan

The common and the distinctive features of the bulged-G motif based on a 1.04 Å resolution RNA structure
Nucl. Acids Res. 2003 31: 6806-6818; doi:10.1093/nar/gkg908 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Eun-Jung Park, Doug W. Chan, Ji-Hye Park, Marjorie A. Oettinger, and Jongbum Kwon

DNA-PK is activated by nucleosomes and phosphorylates H2AX within the nucleosomes in an acetylation-dependent manner
Nucl. Acids Res. 2003 31: 6819-6827; doi:10.1093/nar/gkg921 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Rajesh K. Soni, Parul Mehra, Nirupam Roy Choudhury, Gauranga Mukhopadhyay, and Suman Kumar Dhar

Functional characterization of Helicobacter pylori DnaB helicase
Nucl. Acids Res. 2003 31: 6828-6840; doi:10.1093/nar/gkg895 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Lars Borrmann, Ralf Schwanbeck, Tomasz Heyduk, Birte Seebeck, Piere Rogalla, Jörn Bullerdiek, and Jacek R. Wisniewski

High mobility group A2 protein and its derivatives bind a specific region of the promoter of DNA repair gene ERCC1 and modulate its activity
Nucl. Acids Res. 2003 31: 6841-6851; doi:10.1093/nar/gkg884 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Klaus Klumpp, Julie Qi Hang, Surendran Rajendran, Yanli Yang, Andre Derosier, Philippe Wong Kai In, Hilary Overton, Kevin E. B. Parkes, Nick Cammack, and Joseph A. Martin

Two-metal ion mechanism of RNA cleavage by HIV RNase H and mechanism-based design of selective HIV RNase H inhibitors
Nucl. Acids Res. 2003 31: 6852-6859; doi:10.1093/nar/gkg881 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Han-Jong Kim, Joon-Young Kim, Yun-Yong Park, and Hueng-Sik Choi

Synergistic activation of the human orphan nuclear receptor SHP gene promoter by basic helix–loop–helix protein E2A and orphan nuclear receptor SF-1
Nucl. Acids Res. 2003 31: 6860-6872; doi:10.1093/nar/gkg906 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Csaba Miskey, Zsuzsanna Izsvák, Ronald H. Plasterk, and Zoltán Ivics

The Frog Prince: a reconstructed transposon from Rana pipiens with high transpositional activity in vertebrate cells
Nucl. Acids Res. 2003 31: 6873-6881; doi:10.1093/nar/gkg910 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Anne Rascle and Emma Lees

Chromatin acetylation and remodeling at the Cis promoter during STAT5-induced transcription
Nucl. Acids Res. 2003 31: 6882-6890; doi:10.1093/nar/gkg907 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jiajian Liu, Kai Tan, and Gary D. Stormo

Computational identification of the Spo0A-phosphate regulon that is essential for the cellular differentiation and development in Gram-positive spore-forming bacteria
Nucl. Acids Res. 2003 31: 6891-6903; doi:10.1093/nar/gkg879 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mahima Kaushik, Ritushree Kukreti, Deepak Grover, Samir K. Brahmachari, and Shrikant Kukreti

Hairpin–duplex equilibrium reflected in the AB transition in an undecamer quasi-palindrome present in the locus control region of the human ß-globin gene cluster
Nucl. Acids Res. 2003 31: 6904-6915; doi:10.1093/nar/gkg887 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Igor Shevelev, Giuseppina Blanca, Giuseppe Villani, Kristijan Ramadan, Silvio Spadari, Ulrich Hübscher, and Giovanni Maga

Mutagenesis of human DNA polymerase : essential roles of Tyr505 and Phe506 for both DNA polymerase and terminal transferase activities
Nucl. Acids Res. 2003 31: 6916-6925; doi:10.1093/nar/gkg896 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Marc Valls and Víctor de Lorenzo

Transient XylR binding to the UAS of the Pseudomonas putida ⁵⁴ promoter Pu revealed with high intensity UV footprinting in vivo
Nucl. Acids Res. 2003 31: 6926-6934; doi:10.1093/nar/gkg912 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Valer Gotea, Vamsi Veeramachaneni, and Wojciech Makalowski

Mastering seeds for genomic size nucleotide BLAST searches
Nucl. Acids Res. 2003 31: 6935-6941; doi:10.1093/nar/gkg886 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kamila Réblová, Nad’a Spacková, Judit E. Sponer, Jaroslav Koca, and Jirí Sponer

Molecular dynamics simulations of RNA kissing–loop motifs reveal structural dynamics and formation of cation-binding pockets
Nucl. Acids Res. 2003 31: 6942-6952; doi:10.1093/nar/gkg880 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Akinori Ikeuchi, Yoko Sasaki, Yasuaki Kawarasaki, and Tsuneo Yamane

Exhaustive identification of interaction domains using a high-throughput method based on two-hybrid screening and PCR-convergence: molecular dissection of a kinetochore subunit Spc34p
Nucl. Acids Res. 2003 31: 6953-6962; doi:10.1093/nar/gkg888 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Marcel Freund, Corinna Asang, Susanne Kammler, Carolin Konermann, Jörg Krummheuer, Marianne Hipp, Imke Meyer, Wolfram Gierling, Stephan Theiss, Thorsten Preuss, Detlev Schindler, Jørgen Kjems, and Heiner Schaal

A novel approach to describe a U1 snRNA binding site
Nucl. Acids Res. 2003 31: 6963-6975; doi:10.1093/nar/gkg901 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mario dos Reis, Lorenz Wernisch, and Renos Savva

Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome
Nucl. Acids Res. 2003 31: 6976-6985; doi:10.1093/nar/gkg897 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Ilham Cherrak, Olivier Mauffret, Fanny Santamaria, Alexandre Hocquet, Mahmoud Ghomi, Bernard Rayner, and Serge Fermandjian

L-nucleotides and 8-methylguanine of d(C₁^m8G₂C₃G₄C_5LG_6LC₇G₈C₉G₁₀)₂ act cooperatively to promote a left-handed helix under physiological salt conditions
Nucl. Acids Res. 2003 31: 6986-6995; doi:10.1093/nar/gkg893 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Ludmila S. Tchufistova, Anastassia V. Komarova, and Irina V. Boni

A key role for the mRNA leader structure in translational control of ribosomal protein S1 synthesis in -proteobacteria
Nucl. Acids Res. 2003 31: 6996-7002; doi:10.1093/nar/gkg883 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tanja Waldmann, Martina Baack, Nicole Richter, and Claudia Gruss

Structure-specific binding of the proto-oncogene protein DEK to DNA
Nucl. Acids Res. 2003 31: 7003-7010; doi:10.1093/nar/gkg864 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Zdenko Herceg, Hai Li, Cyrille Cuenin, Vivek Shukla, Martin Radolf, Peter Steinlein, and Zhao-Qi Wang

Genome-wide analysis of gene expression regulated by the HAT cofactor Trrap in conditional knockout cells
Nucl. Acids Res. 2003 31: 7011-7023; doi:10.1093/nar/gkg902 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nilanjana Banerjee and Michael Q. Zhang

Identifying cooperativity among transcription factors controlling the cell cycle in yeast
Nucl. Acids Res. 2003 31: 7024-7031; doi:10.1093/nar/gkg894 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Erick L. Y. Ho and Masahiko S. Satoh

Repair of single-strand DNA interruptions by redundant pathways and its implication in cellular sensitivity to DNA-damaging agents
Nucl. Acids Res. 2003 31: 7032-7040; doi:10.1093/nar/gkg892 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ryan Mills, Michael Rozanov, Alexandre Lomsadze, Tatiana Tatusova, and Mark Borodovsky

Improving gene annotation of complete viral genomes
Nucl. Acids Res. 2003 31: 7041-7055; doi:10.1093/nar/gkg878 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

NAR Methods Online:

Zhiwen Tang, Kemin Wang, Weihong Tan, Jun Li, Lingfeng Liu, Qiuping Guo, Xiangxian Meng, Changbei Ma, and Shasheng Huang

Real-time monitoring of nucleic acid ligation in homogenous solutions using molecular beacons
Nucl. Acids Res. 2003 31: e148; doi:10.1093/nar/gng146 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Chiara Romualdi, Silvia Trevisan, Barbara Celegato, Germano Costa, and Gerolamo Lanfranchi

Improved detection of differentially expressed genes in microarray experiments through multiple scanning and image integration
Nucl. Acids Res. 2003 31: e149; doi:10.1093/nar/gng149 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Rita Meunier-Prest, Suzanne Raveau, Eric Finot, Guillaume Legay, Mustapha Cherkaoui-Malki, and Norbert Latruffe

Direct measurement of the melting temperature of supported DNA by electrochemical method
Nucl. Acids Res. 2003 31: e150; doi:10.1093/nar/gng150 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Michael Baum, Simone Bielau, Nicole Rittner, Kathrin Schmid, Kathrin Eggelbusch, Michael Dahms, Andrea Schlauersbach, Harald Tahedl, Markus Beier, Ramon Güimil, Matthias Scheffler, Carsten Hermann, Jörg-Michael Funk, Anke Wixmerten, Hans Rebscher, Matthias Hönig, Claas Andreae, Daniel Büchner, Erich Moschel, Andreas Glathe, Evelyn Jäger, Marc Thom, Andreas Greil, Felix Bestvater, Frank Obermeier, Josef Burgmaier, Klaus Thome, Sigrid Weichert, Silke Hein, Tim Binnewies, Volker Foitzik, Manfred Müller, Cord Friedrich Stähler, and Peer Friedrich Stähler

Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling
Nucl. Acids Res. 2003 31: e151; doi:10.1093/nar/gng151 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Alison Mortlock, Walter Low, and Andrea Crisanti

Suppression of gene expression by a cell-permeable Tet repressor
Nucl. Acids Res. 2003 31: e152; doi:10.1093/nar/gng152 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Eric Eldering, C. Arnold Spek, Hella L. Aberson, Annette Grummels, Ingrid A. Derks, Alex F. de Vos, Cathal J. McElgunn, and Jan P. Schouten

Expression profiling via novel multiplex assay allows rapid assessment of gene regulation in defined signalling pathways
Nucl. Acids Res. 2003 31: e153; doi:10.1093/nar/gng153 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Corrigenda:

Corrigenda
Nucl. Acids Res. 2003 31: 7056; doi:10.1093/nar/gkg939 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Corrigenda
Nucl. Acids Res. 2003 31: 7057; doi:10.1093/nar/gkg940 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

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