Nucleic Acids Research

Articles:

Attila Németh, Ralf Strohner, Ingrid Grummt, and Gernot Längst

The chromatin remodeling complex NoRC and TTF-I cooperate in the regulation of the mammalian rRNA genes in vivo
Nucl. Acids Res. 2004 32: 4091-4099; doi:10.1093/nar/gkh732 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Victoria Valinluck, Hsin-Hao Tsai, Daniel K. Rogstad, Artur Burdzy, Adrian Bird, and Lawrence C. Sowers

Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2)
Nucl. Acids Res. 2004 32: 4100-4108; doi:10.1093/nar/gkh739 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

R. Sathyapriya and Saraswathi Vishveshwara

Interaction of DNA with clusters of amino acids in proteins
Nucl. Acids Res. 2004 32: 4109-4118; doi:10.1093/nar/gkh733 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Takayuki Konno, Toshiharu Takahashi, Daisuke Kurita, Akira Muto, and Hyouta Himeno

A minimum structure of aminoglycosides that causes an initiation shift of trans-translation
Nucl. Acids Res. 2004 32: 4119-4126; doi:10.1093/nar/gkh750 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ilaria Chiodi, Margherita Corioni, Manuela Giordano, Rut Valgardsdottir, Claudia Ghigna, Fabio Cobianchi, Rui-Ming Xu, Silvano Riva, and Giuseppe Biamonti

RNA recognition motif 2 directs the recruitment of SF2/ASF to nuclear stress bodies
Nucl. Acids Res. 2004 32: 4127-4136; doi:10.1093/nar/gkh759 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Mizuki Takenaka, Julia Neuwirt, and Axel Brennicke

Complex cis-elements determine an RNA editing site in pea mitochondria
Nucl. Acids Res. 2004 32: 4137-4144; doi:10.1093/nar/gkh763 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Samer Khateb, Pnina Weisman-Shomer, Inbal Hershco, Lawrence A. Loeb, and Michael Fry

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
Nucl. Acids Res. 2004 32: 4145-4154; doi:10.1093/nar/gkh745 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Griet Vanpoucke, Steven Goossens, Bram De Craene, Barbara Gilbert, Frans van Roy, and Geert Berx

GATA-4 and MEF2C transcription factors control the tissue-specific expression of the T-catenin gene CTNNA3
Nucl. Acids Res. 2004 32: 4155-4165; doi:10.1093/nar/gkh727 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Luke J. Peakman and Mark D. Szczelkun

DNA communications by Type III restriction endonucleases—confirmation of 1D translocation over 3D looping
Nucl. Acids Res. 2004 32: 4166-4174; doi:10.1093/nar/gkh762 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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

BOD: a customizable bioinformatics on demand system accommodating multiple steps and parallel tasks
Nucl. Acids Res. 2004 32: 4175-4181; doi:10.1093/nar/gkh756 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

R. A. Saleem, S. Banerjee-Basu, T. C. Murphy, A. Baxevanis, and M. A. Walter

Essential structural and functional determinants within the forkhead domain of FOXC1
Nucl. Acids Res. 2004 32: 4182-4193; doi:10.1093/nar/gkh742 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Takeshi Nakajima, Sanae Fujino, Gen Nakanishi, Yong-Sik Kim, and Anton M. Jetten

TIP27: a novel repressor of the nuclear orphan receptor TAK1/TR4
Nucl. Acids Res. 2004 32: 4194-4204; doi:10.1093/nar/gkh741 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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

Genetic and biochemical analyses of Pfh1 DNA helicase function in fission yeast
Nucl. Acids Res. 2004 32: 4205-4216; doi:10.1093/nar/gkh720 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Atsushi Inoue, Yasuomi Takagi, and Kazunari Taira

Importance in catalysis of a magnesium ion with very low affinity for a hammerhead ribozyme
Nucl. Acids Res. 2004 32: 4217-4223; doi:10.1093/nar/gkh753 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Emanuele Buratti, Marco Baralle, Laura De Conti, Diana Baralle, Maurizio Romano, Youhna M. Ayala, and Francisco E. Baralle

hnRNP H binding at the 5' splice site correlates with the pathological effect of two intronic mutations in the NF-1 and TSHß genes
Nucl. Acids Res. 2004 32: 4224-4236; doi:10.1093/nar/gkh752 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Agustin Chicas, Carlo Cogoni, and Giuseppe Macino

RNAi-dependent and RNAi-independent mechanisms contribute to the silencing of RIPed sequences in Neurospora crassa
Nucl. Acids Res. 2004 32: 4237-4243; doi:10.1093/nar/gkh764 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Katalin A. Hudak, Bijal A. Parikh, Rong Di, Marianne Baricevic, Maria Santana, Mirjana Seskar, and Nilgun E. Tumer

Generation of pokeweed antiviral protein mutations in Saccharomyces cerevisiae: evidence that ribosome depurination is not sufficient for cytotoxicity
Nucl. Acids Res. 2004 32: 4244-4256; doi:10.1093/nar/gkh757 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Edwin Haghnazari and Wolf-Dietrich Heyer

The DNA damage checkpoint pathways exert multiple controls on the efficiency and outcome of the repair of a double-stranded DNA gap
Nucl. Acids Res. 2004 32: 4257-4268; doi:10.1093/nar/gkh717 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Péter Várnai and Krystyna Zakrzewska

DNA and its counterions: a molecular dynamics study
Nucl. Acids Res. 2004 32: 4269-4280; doi:10.1093/nar/gkh765 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Peter Schattner, Wayne A. Decatur, Carrie A. Davis, Manuel Ares, Jr, Maurille J. Fournier, and Todd M. Lowe

Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome
Nucl. Acids Res. 2004 32: 4281-4296; doi:10.1093/nar/gkh768 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Michael W. Kaiser, Jing Chi, and David A. Brow

Position-dependent function of a B block promoter element implies a specialized chromatin structure on the S.cerevisiae U6 RNA gene, SNR6
Nucl. Acids Res. 2004 32: 4297-4305; doi:10.1093/nar/gkh769 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Stephan Watkins, Gertie van Pouderoyen, and Titia K. Sixma

Structural analysis of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA
Nucl. Acids Res. 2004 32: 4306-4312; doi:10.1093/nar/gkh770 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Joshua J. Smith, Eric S. Cole, and Daniel P. Romero

Transcriptional control of RAD51 expression in the ciliate Tetrahymena thermophila
Nucl. Acids Res. 2004 32: 4313-4321; doi:10.1093/nar/gkh771 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Colin S. Davey, Sari Pennings, Carmel Reilly, Richard R. Meehan, and James Allan

A determining influence for CpG dinucleotides on nucleosome positioning in vitro
Nucl. Acids Res. 2004 32: 4322-4331; doi:10.1093/nar/gkh749 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Huaxian Ma, Heung M. Lee, and Ella W. Englander

N-terminus of the rat adenine glycosylase MYH affects excision rates and processing of MYH-generated abasic sites
Nucl. Acids Res. 2004 32: 4332-4339; doi:10.1093/nar/gkh758 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sandra Laduron, Rachel Deplus, Sifang Zhou, Olga Kholmanskikh, Danièle Godelaine, Charles De Smet, S. Diane Hayward, François Fuks, Thierry Boon, and Etienne De Plaen

MAGE-A1 interacts with adaptor SKIP and the deacetylase HDAC1 to repress transcription
Nucl. Acids Res. 2004 32: 4340-4350; doi:10.1093/nar/gkh735 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Wesley D. Block, Yaping Yu, Dennis Merkle, Jessica L. Gifford, Qi Ding, Katheryn Meek, and Susan P. Lees-Miller

Autophosphorylation-dependent remodeling of the DNA-dependent protein kinase catalytic subunit regulates ligation of DNA ends
Nucl. Acids Res. 2004 32: 4351-4357; doi:10.1093/nar/gkh761 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Giuseppina M. Carbone, Sara Napoli, Alessandra Valentini, Franco Cavalli, Dennis K. Watson, and Carlo V. Catapano

Triplex DNA-mediated downregulation of Ets2 expression results in growth inhibition and apoptosis in human prostate cancer cells
Nucl. Acids Res. 2004 32: 4358-4367; doi:10.1093/nar/gkh744 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jacob Nielsen, Mette Ahm Kristensen, Martin Willemoës, Finn Cilius Nielsen, and Jan Christiansen

Sequential dimerization of human zipcode-binding protein IMP1 on RNA: a cooperative mechanism providing RNP stability
Nucl. Acids Res. 2004 32: 4368-4376; doi:10.1093/nar/gkh754 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Kanghong Hu, Jürgen Beck, and Michael Nassal

SELEX-derived aptamers of the duck hepatitis B virus RNA encapsidation signal distinguish critical and non-critical residues for productive initiation of reverse transcription
Nucl. Acids Res. 2004 32: 4377-4389; doi:10.1093/nar/gkh772 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Elena A. Shestakova, Zeyni Mansuroglu, Houda Mokrani, Nicolae Ghinea, and Eliette Bonnefoy

Transcription factor YY1 associates with pericentromeric -satellite DNA in cycling but not in quiescent (G₀) cells
Nucl. Acids Res. 2004 32: 4390-4399; doi:10.1093/nar/gkh737 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mari K. Davidson, Nathan P. Young, Gloria G. Glick, and Wayne P. Wahls

Meiotic chromosome segregation mutants identified by insertional mutagenesis of fission yeast Schizosaccharomyces pombe; tandem-repeat, single-site integrations
Nucl. Acids Res. 2004 32: 4400-4410; doi:10.1093/nar/gkh767 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hyunmin Kang, Michael H. Fisher, Dong Xu, Yuko J. Miyamoto, Arnaud Marchand, Arthur Van Aerschot, Piet Herdewijn, and Rudolph L. Juliano

Inhibition of MDR1 gene expression by chimeric HNA antisense oligonucleotides
Nucl. Acids Res. 2004 32: 4411-4419; doi:10.1093/nar/gkh775 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Errata:

Christopher D. Deppmann, Asha Acharya, Vikas Rishi, Barry Wobbes, Sjef Smeekens, Elizabeth J. Taparowsky, and Charles Vinson

Dimerization specificity of all 67 B-ZIP motifs in Arabidopsis thaliana: a comparison to Homo sapiens B-ZIP motifs
Nucl. Acids Res. 2004 32: 4420; doi:10.1093/nar/gkh760 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Methods Online:

Paul R. Herron, Gareth Hughes, Govind Chandra, Susan Fielding, and Paul J. Dyson

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
Nucl. Acids Res. 2004 32: e113; doi:10.1093/nar/gnh112 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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

An in vitro strategy for the selective isolation of anomalous DNA from prokaryotic genomes
Nucl. Acids Res. 2004 32: e114; doi:10.1093/nar/gnh115 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Lei Zheng, Ulrich Baumann, and Jean-Louis Reymond

An efficient one-step site-directed and site-saturation mutagenesis protocol
Nucl. Acids Res. 2004 32: e115; doi:10.1093/nar/gnh110 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dong-ki Lee, Yong Ha Kim, Jin-Soo Kim, and Wongi Seol

Induction and characterization of taxol-resistance phenotypes with a transiently expressed artificial transcriptional activator library
Nucl. Acids Res. 2004 32: e116; doi:10.1093/nar/gnh114 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Laure Granger, Edwige Martin, and Laurent Ségalat

Mos as a tool for genome-wide insertional mutagenesis in Caenorhabditis elegans: results of a pilot study
Nucl. Acids Res. 2004 32: e117; doi:10.1093/nar/gnh111 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

H. B. Yin, T. Brown, J. S. Wilkinson, R. W. Eason, and T. Melvin

Submicron patterning of DNA oligonucleotides on silicon
Nucl. Acids Res. 2004 32: e118; doi:10.1093/nar/gnh113 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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