| | Articles The chromatin remodeling complex NoRC and TTF-I cooperate in the regulation of the mammalian rRNA genes in vivo Attila Németh, Ralf Strohner, Ingrid Grummt, and Gernot Längst PMCID: PMC514363 Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2) Victoria Valinluck, Hsin-Hao Tsai, Daniel K. Rogstad, Artur Burdzy, Adrian Bird, and Lawrence C. Sowers PMCID: PMC514367 Interaction of DNA with clusters of amino acids in proteins R. Sathyapriya and Saraswathi Vishveshwara PMCID: PMC514364 A minimum structure of aminoglycosides that causes an initiation shift of trans-translation Takayuki Konno, Toshiharu Takahashi, Daisuke Kurita, Akira Muto, and Hyouta Himeno PMCID: PMC514373 RNA recognition motif 2 directs the recruitment of SF2/ASF to nuclear stress bodies Ilaria Chiodi, Margherita Corioni, Manuela Giordano, Rut Valgardsdottir, Claudia Ghigna, Fabio Cobianchi, Rui-Ming Xu, Silvano Riva, and Giuseppe Biamonti PMCID: PMC514380 Complex cis-elements determine an RNA editing site in pea mitochondria Mizuki Takenaka, Julia Neuwirt, and Axel Brennicke PMCID: PMC514384 Destabilization of tetraplex structures of the fragile X repeat sequence (CGG)n is mediated by homolog-conserved domains in three members of the hnRNP family Samer Khateb, Pnina Weisman-Shomer, Inbal Hershco, Lawrence A. Loeb, and Michael Fry PMCID: PMC514371 GATA-4 and MEF2C transcription factors control the tissue-specific expression of the αT-catenin gene CTNNA3 Griet Vanpoucke, Steven Goossens, Bram De Craene, Barbara Gilbert, Frans van Roy, and Geert Berx PMCID: PMC514362 DNA communications by Type III restriction endonucleases—confirmation of 1D translocation over 3D looping Luke J. Peakman and Mark D. Szczelkun PMCID: PMC514383 BOD: a customizable bioinformatics on demand system accommodating multiple steps and parallel tasks Li-An Qiao, Jing Zhu, Qingyan Liu, Tao Zhu, Chi Song, Wei Lin, Guozhu Wei, Lisen Mu, Jiang Tao, Nanming Zhao, Guangwen Yang, and Xiangjun Liu PMCID: PMC514377 Essential structural and functional determinants within the forkhead domain of FOXC1 R. A. Saleem, S. Banerjee-Basu, T. C. Murphy, A. Baxevanis, and M. A. Walter PMCID: PMC514369 TIP27: a novel repressor of the nuclear orphan receptor TAK1/TR4 Takeshi Nakajima, Sanae Fujino, Gen Nakanishi, Yong-Sik Kim, and Anton M. Jetten PMCID: PMC514368 Genetic and biochemical analyses of Pfh1 DNA helicase function in fission yeast Gi-Hyuck Ryu, Hiroyuki Tanaka, Do-Hyung Kim, Jeong-Hoon Kim, Sung-Ho Bae, Young-Nam Kwon, Joon Shick Rhee, Stuart A. MacNeill, and Yeon-Soo Seo PMCID: PMC514361 Importance in catalysis of a magnesium ion with very low affinity for a hammerhead ribozyme Atsushi Inoue, Yasuomi Takagi, and Kazunari Taira PMCID: PMC514375 hnRNP H binding at the 5′ splice site correlates with the pathological effect of two intronic mutations in the NF-1 and TSHβ genes Emanuele Buratti, Marco Baralle, Laura De Conti, Diana Baralle, Maurizio Romano, Youhna M. Ayala, and Francisco E. Baralle PMCID: PMC514374 RNAi-dependent and RNAi-independent mechanisms contribute to the silencing of RIPed sequences in Neurospora crassa Agustin Chicas, Carlo Cogoni, and Giuseppe Macino PMCID: PMC514385 Generation of pokeweed antiviral protein mutations in Saccharomyces cerevisiae: evidence that ribosome depurination is not sufficient for cytotoxicity Katalin A. Hudak, Bijal A. Parikh, Rong Di, Marianne Baricevic, Maria Santana, Mirjana Seskar, and Nilgun E. Tumer PMCID: PMC514378 The DNA damage checkpoint pathways exert multiple controls on the efficiency and outcome of the repair of a double-stranded DNA gap Edwin Haghnazari and Wolf-Dietrich Heyer PMCID: PMC514360 DNA and its counterions: a molecular dynamics study Péter Várnai and Krystyna Zakrzewska PMCID: PMC514386 Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome Peter Schattner, Wayne A. Decatur, Carrie A. Davis, Manuel Ares, Jr, Maurille J. Fournier, and Todd M. Lowe PMCID: PMC514388 Position-dependent function of a B block promoter element implies a specialized chromatin structure on the S.cerevisiae U6 RNA gene, SNR6 Michael W. Kaiser, Jing Chi, and David A. Brow PMCID: PMC514389 Structural analysis of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA Stephan Watkins, Gertie van Pouderoyen, and Titia K. Sixma PMCID: PMC514390 Transcriptional control of RAD51 expression in the ciliate Tetrahymena thermophila Joshua J. Smith, Eric S. Cole, and Daniel P. Romero PMCID: PMC514391 A determining influence for CpG dinucleotides on nucleosome positioning in vitro Colin S. Davey, Sari Pennings, Carmel Reilly, Richard R. Meehan, and James Allan PMCID: PMC514372 N-terminus of the rat adenine glycosylase MYH affects excision rates and processing of MYH-generated abasic sites Huaxian Ma, Heung M. Lee, and Ella W. Englander PMCID: PMC514379 MAGE-A1 interacts with adaptor SKIP and the deacetylase HDAC1 to repress transcription Sandra Laduron, Rachel Deplus, Sifang Zhou, Olga Kholmanskikh, Danièle Godelaine, Charles De Smet, S. Diane Hayward, François Fuks, Thierry Boon, and Etienne De Plaen PMCID: PMC514365 Autophosphorylation-dependent remodeling of the DNA-dependent protein kinase catalytic subunit regulates ligation of DNA ends Wesley D. Block, Yaping Yu, Dennis Merkle, Jessica L. Gifford, Qi Ding, Katheryn Meek, and Susan P. Lees-Miller PMCID: PMC514382 Triplex DNA-mediated downregulation of Ets2 expression results in growth inhibition and apoptosis in human prostate cancer cells Giuseppina M. Carbone, Sara Napoli, Alessandra Valentini, Franco Cavalli, Dennis K. Watson, and Carlo V. Catapano PMCID: PMC514370 Sequential dimerization of human zipcode-binding protein IMP1 on RNA: a cooperative mechanism providing RNP stability Jacob Nielsen, Mette Ahm Kristensen, Martin Willemoës, Finn Cilius Nielsen, and Jan Christiansen PMCID: PMC514376 SELEX-derived aptamers of the duck hepatitis B virus RNA encapsidation signal distinguish critical and non-critical residues for productive initiation of reverse transcription Kanghong Hu, Jürgen Beck, and Michael Nassal PMCID: PMC514392 Transcription factor YY1 associates with pericentromeric γ-satellite DNA in cycling but not in quiescent (G0) cells Elena A. Shestakova, Zeyni Mansuroglu, Houda Mokrani, Nicolae Ghinea, and Eliette Bonnefoy PMCID: PMC514366 Meiotic chromosome segregation mutants identified by insertional mutagenesis of fission yeast Schizosaccharomyces pombe; tandem-repeat, single-site integrations Mari K. Davidson, Nathan P. Young, Gloria G. Glick, and Wayne P. Wahls PMCID: PMC514387 Inhibition of MDR1 gene expression by chimeric HNA antisense oligonucleotides Hyunmin Kang, Michael H. Fisher, Dong Xu, Yuko J. Miyamoto, Arnaud Marchand, Arthur Van Aerschot, Piet Herdewijn, and Rudolph L. Juliano PMCID: PMC514393 NAR Methods Online Transposon Express, a software application to report the identity of insertions obtained by comprehensive transposon mutagenesis of sequenced genomes: analysis of the preference for in vitro Tn5 transposition into GC-rich DNA Paul R. Herron, Gareth Hughes, Govind Chandra, Susan Fielding, and Paul J. Dyson PMCID: PMC514396 An in vitro strategy for the selective isolation of anomalous DNA from prokaryotic genomes M. W. J. van Passel, A. Bart, R. J. A. Waaijer, A. C. M. Luyf, A. H. C. van Kampen, and A. van der Ende PMCID: PMC514399 An efficient one-step site-directed and site-saturation mutagenesis protocol Lei Zheng, Ulrich Baumann, and Jean-Louis Reymond PMCID: PMC514394 Induction and characterization of taxol-resistance phenotypes with a transiently expressed artificial transcriptional activator library Dong-ki Lee, Yong Ha Kim, Jin-Soo Kim, and Wongi Seol PMCID: PMC514398 Mos as a tool for genome-wide insertional mutagenesis in Caenorhabditis elegans: results of a pilot study Laure Granger, Edwige Martin, and Laurent Ségalat PMCID: PMC514395 Submicron patterning of DNA oligonucleotides on silicon H. B. Yin, T. Brown, J. S. Wilkinson, R. W. Eason, and T. Melvin PMCID: PMC514397 Erratum Nucleic Acids Res. 2004; 32(14): 4420. Published online 2004 August 17. doi: 10.1093/nar/gkh760.PMCID: PMC514381 Corrects: Christopher D. Deppmann, et al. Dimerization specificity of all 67 B-ZIP motifs in Arabidopsis thaliana: a comparison to Homo sapiens B-ZIP motifs. Nucleic Acids Res. 2004; 32(11): 3435–3445. |
