| | Articles Sensing DNA damage by PARP-like fingers Stefania Petrucco PMCID: PMC290258 An archaebacteria-derived glutamyl-tRNA synthetase and tRNA pair for unnatural amino acid mutagenesis of proteins in Escherichia coli Stephen W. Santoro, J. Christopher Anderson, Vishva Lakshman, and Peter G. Schultz PMCID: PMC290271 Dynamics of the metal-dependent transcription factor complex in vivo at the mouse metallothionein-I promoter Patrick J. Daniels and Glen K. Andrews PMCID: PMC290280 Interleukin-6 represses the transcription of the CCAAT/enhancer binding protein-α gene in hepatoma cells by inhibiting its ability to autoactivate the proximal promoter region Pelagia Foka, Scott A. Irvine, Feray Kockar, and Dipak P. Ramji PMCID: PMC290246 Mutagenic stress modulates the dynamics of CTG repeat instability associated with myotonic dystrophy type 1 Elisabeth Piñeiro, Laura Fernàndez-López, Josep Gamez, Ricard Marcos, Jordi Surrallés, and Antonia Velázquez PMCID: PMC290266 Dynamic methylation of histone H3 at lysine 4 in transcriptional regulation by the androgen receptor Joshua Kim, Li Jia, Wayne D. Tilley, and Gerhard A. Coetzee PMCID: PMC290276 Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Dmitry A. Rodionov, Alexey G. Vitreschak, Andrey A. Mironov, and Mikhail S. Gelfand PMCID: PMC290268 Cleavage of DNA without loss of genetic information by incorporation of a disaccharide nucleoside 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 PMCID: PMC290278 Conservation of DNA curvature signals in regulatory regions of prokaryotic genes Ruy Jáuregui, Cei Abreu-Goodger, Gabriel Moreno-Hagelsieb, Julio Collado-Vides, and Enrique Merino PMCID: PMC290252 Solution structure and DNA binding of the effector domain from the global regulator PrrA (RegA) from Rhodobacter sphaeroides: insights into DNA binding specificity Cédric Laguri, Mary K. Phillips-Jones, and Michael P. Williamson PMCID: PMC290259 A complex pathway for 3′ processing of the yeast U3 snoRNA Joanna Kufel, Christine Allmang, Loredana Verdone, Jean Beggs, and David Tollervey PMCID: PMC290272 Ribosomal proteins Rps0 and Rps21 of Saccharomyces cerevisiae have overlapping functions in the maturation of the 3′ end of 18S rRNA Amy Tabb-Massey, Jacqueline M. Caffrey, Paula Logsden, Stephen Taylor, John O. Trent, and Steven R. Ellis PMCID: PMC290267 The common and the distinctive features of the bulged-G motif based on a 1.04 Å resolution RNA structure Carl C. Correll, Jutta Beneken, Matthew J. Plantinga, Melissa Lubbers, and Yuen-Ling Chan PMCID: PMC290275 DNA-PK is activated by nucleosomes and phosphorylates H2AX within the nucleosomes in an acetylation-dependent manner Eun-Jung Park, Doug W. Chan, Ji-Hye Park, Marjorie A. Oettinger, and Jongbum Kwon PMCID: PMC290281 Functional characterization of Helicobacter pylori DnaB helicase Rajesh K. Soni, Parul Mehra, Nirupam Roy Choudhury, Gauranga Mukhopadhyay, and Suman Kumar Dhar PMCID: PMC290263 High mobility group A2 protein and its derivatives bind a specific region of the promoter of DNA repair gene ERCC1 and modulate its activity Lars Borrmann, Ralf Schwanbeck, Tomasz Heyduk, Birte Seebeck, Piere Rogalla, Jörn Bullerdiek, and Jacek R. Wiśniewski PMCID: PMC290254 Two-metal ion mechanism of RNA cleavage by HIV RNase H and mechanism-based design of selective HIV RNase H inhibitors 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 PMCID: PMC290251 Synergistic activation of the human orphan nuclear receptor SHP gene promoter by basic helix–loop–helix protein E2A and orphan nuclear receptor SF-1 Han-Jong Kim, Joon-Young Kim, Yun-Yong Park, and Hueng-Sik Choi PMCID: PMC290273 The Frog Prince: a reconstructed transposon from Rana pipiens with high transpositional activity in vertebrate cells Csaba Miskey, Zsuzsanna Izsvák, Ronald H. Plasterk, and Zoltán Ivics PMCID: PMC290277 Chromatin acetylation and remodeling at the Cis promoter during STAT5-induced transcription Anne Rascle and Emma Lees PMCID: PMC290274 Computational identification of the Spo0A-phosphate regulon that is essential for the cellular differentiation and development in Gram-positive spore-forming bacteria Jiajian Liu, Kai Tan, and Gary D. Stormo PMCID: PMC290249 Hairpin–duplex equilibrium reflected in the A→B transition in an undecamer quasi-palindrome present in the locus control region of the human β-globin gene cluster Mahima Kaushik, Ritushree Kukreti, Deepak Grover, Samir K. Brahmachari, and Shrikant Kukreti PMCID: PMC290256 Mutagenesis of human DNA polymerase λ: essential roles of Tyr505 and Phe506 for both DNA polymerase and terminal transferase activities Igor Shevelev, Giuseppina Blanca, Giuseppe Villani, Kristijan Ramadan, Silvio Spadari, Ulrich Hübscher, and Giovanni Maga PMCID: PMC290264 Transient XylR binding to the UAS of the Pseudomonas putida σ54 promoter Pu revealed with high intensity UV footprinting in vivo Marc Valls and Víctor de Lorenzo PMCID: PMC290279 Mastering seeds for genomic size nucleotide BLAST searches Valer Gotea, Vamsi Veeramachaneni, and Wojciech Makałowski PMCID: PMC290255 Molecular dynamics simulations of RNA kissing–loop motifs reveal structural dynamics and formation of cation-binding pockets Kamila Réblová, Nad'a Špačková, Judit E. Šponer, Jaroslav Koča, and Jiří Šponer PMCID: PMC290250 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 Akinori Ikeuchi, Yoko Sasaki, Yasuaki Kawarasaki, and Tsuneo Yamane PMCID: PMC290257 A novel approach to describe a U1 snRNA binding site 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 PMCID: PMC290269 Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome Mario dos Reis, Lorenz Wernisch, and Renos Savva PMCID: PMC290265 L-nucleotides and 8-methylguanine of d(C1m8G2C3G4C5LG6LC7G8C9G10)2 act cooperatively to promote a left-handed helix under physiological salt conditions Ilham Cherrak, Olivier Mauffret, Fanny Santamaria, Alexandre Hocquet, Mahmoud Ghomi, Bernard Rayner, and Serge Fermandjian PMCID: PMC290261 A key role for the mRNA leader structure in translational control of ribosomal protein S1 synthesis in γ-proteobacteria Ludmila S. Tchufistova, Anastassia V. Komarova, and Irina V. Boni PMCID: PMC290253 Structure-specific binding of the proto-oncogene protein DEK to DNA Tanja Waldmann, Martina Baack, Nicole Richter, and Claudia Gruss PMCID: PMC290247 Genome-wide analysis of gene expression regulated by the HAT cofactor Trrap in conditional knockout cells Zdenko Herceg, Hai Li, Cyrille Cuenin, Vivek Shukla, Martin Radolf, Peter Steinlein, and Zhao-Qi Wang PMCID: PMC290270 Identifying cooperativity among transcription factors controlling the cell cycle in yeast Nilanjana Banerjee and Michael Q. Zhang PMCID: PMC290262 Repair of single-strand DNA interruptions by redundant pathways and its implication in cellular sensitivity to DNA-damaging agents Erick L. Y. Ho and Masahiko S. Satoh PMCID: PMC290260 Improving gene annotation of complete viral genomes Ryan Mills, Michael Rozanov, Alexandre Lomsadze, Tatiana Tatusova, and Mark Borodovsky PMCID: PMC290248 NAR Methods Online Real-time monitoring of nucleic acid ligation in homogenous solutions using molecular beacons Zhiwen Tang, Kemin Wang, Weihong Tan, Jun Li, Lingfeng Liu, Qiuping Guo, Xiangxian Meng, Changbei Ma, and Shasheng Huang PMCID: PMC290283 Improved detection of differentially expressed genes in microarray experiments through multiple scanning and image integration Chiara Romualdi, Silvia Trevisan, Barbara Celegato, Germano Costa, and Gerolamo Lanfranchi PMCID: PMC290284 Direct measurement of the melting temperature of supported DNA by electrochemical method Rita Meunier-Prest, Suzanne Raveau, Eric Finot, Guillaume Legay, Mustapha Cherkaoui-Malki, and Norbert Latruffe PMCID: PMC290285 Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling 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 PMCID: PMC290286 Suppression of gene expression by a cell-permeable Tet repressor Alison Mortlock, Walter Low, and Andrea Crisanti PMCID: PMC290287 Expression profiling via novel multiplex assay allows rapid assessment of gene regulation in defined signalling pathways Eric Eldering, C. Arnold Spek, Hella L. Aberson, Annette Grummels, Ingrid A. Derks, Alex F. de Vos, Cathal J. McElgunn, and Jan P. Schouten PMCID: PMC290288 Corrigenda Nucleic Acids Res. 2003 December 1; 31(23): 7056. doi: 10.1093/nar/gkg939.PMCID: PMC300890 Corrects: Isabelle Salles-Passador, et al. Phosphorylation of the PCNA binding domain of the large subunit of replication factor C on Thr506 by cyclin-dependent kinases regulates binding to PCNA. Nucleic Acids Res. 2003 September 1; 31(17): 5202–5211. Nucleic Acids Res. 2003 December 1; 31(23): 7057. doi: 10.1093/nar/gkg940.PMCID: PMC290282 Corrects: Gunnar Wrobel, et al. Optimization of high-density cDNA-microarray protocols by ‘design of experiments’. Nucleic Acids Res. 2003 June 15; 31(12): e67. |
