Nucleic Acids Research

Articles:

Nidhanapati K. Raghavendra and Desirazu N. Rao

Unidirectional translocation from recognition site and a necessary interaction with DNA end for cleavage by Type III restriction enzyme
Nucl. Acids Res. 2004 32: 5703-5711; doi:10.1093/nar/gkh899 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christoph S. Janssen, R. Stephen Phillips, C. Michael R. Turner, and Michael P. Barrett

Plasmodium interspersed repeats: the major multigene superfamily of malaria parasites
Nucl. Acids Res. 2004 32: 5712-5720; doi:10.1093/nar/gkh907 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Svitlana Malyarchuk, Katherine L. Brame, Reneau Youngblood, Runhua Shi, and Lynn Harrison

Two clustered 8-oxo-7,8-dihydroguanine (8-oxodG) lesions increase the point mutation frequency of 8-oxodG, but do not result in double strand breaks or deletions in Escherichia coli
Nucl. Acids Res. 2004 32: 5721-5731; doi:10.1093/nar/gkh911 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Koji Kasai, Takuya Kanno, Yaeta Endo, Kyo Wakasa, and Yuzuru Tozawa

Guanosine tetra- and pentaphosphate synthase activity in chloroplasts of a higher plant: association with 70S ribosomes and inhibition by tetracycline
Nucl. Acids Res. 2004 32: 5732-5741; doi:10.1093/nar/gkh916 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Myungjin Kim, Binh N. Trinh, Tiffany I. Long, Shirley Oghamian, and Peter W. Laird

Dnmt1 deficiency leads to enhanced microsatellite instability in mouse embryonic stem cells
Nucl. Acids Res. 2004 32: 5742-5749; doi:10.1093/nar/gkh912 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Michael O'Connor, Steven T. Gregory, and Albert E. Dahlberg

Multiple defects in translation associated with altered ribosomal protein L4
Nucl. Acids Res. 2004 32: 5750-5756; doi:10.1093/nar/gkh913 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kathrin S. Schmidt, Sandra Borkowski, Jens Kurreck, Andrew W. Stephens, Rolf Bald, Maren Hecht, Matthias Friebe, Ludger Dinkelborg, and Volker A. Erdmann

Application of locked nucleic acids to improve aptamer in vivo stability and targeting function
Nucl. Acids Res. 2004 32: 5757-5765; doi:10.1093/nar/gkh862 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Valérie Barbe, David Vallenet, Nuria Fonknechten, Annett Kreimeyer, Sophie Oztas, Laurent Labarre, Stéphane Cruveiller, Catherine Robert, Simone Duprat, Patrick Wincker, L. Nicholas Ornston, Jean Weissenbach, Philippe Marlière, Georges N. Cohen, and Claudine Médigue

Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium
Nucl. Acids Res. 2004 32: 5766-5779; doi:10.1093/nar/gkh910 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

David Metzgar, Jamie M. Bacher, Valérie Pezo, John Reader, Volker Döring, Paul Schimmel, Philippe Marlière, and Valérie de Crécy-Lagard

Acinetobacter sp. ADP1: an ideal model organism for genetic analysis and genome engineering
Nucl. Acids Res. 2004 32: 5780-5790; doi:10.1093/nar/gkh881 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

J. B. Opalinska, A. Kalota, Lida K. Gifford, Ponzy Lu, Kuang-Yu Jen, P. I. Pradeepkumar, J. Barman, T. K. Kim, C. R. Swider, J. Chattopadhyaya, and A. M. Gewirtz

Oxetane modified, conformationally constrained, antisense oligodeoxyribonucleotides function efficiently as gene silencing molecules
Nucl. Acids Res. 2004 32: 5791-5799; doi:10.1093/nar/gkh893 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Riki Druker, Timothy James Bruxner, Nicolas John Lehrbach, and Emma Whitelaw

Complex patterns of transcription at the insertion site of a retrotransposon in the mouse
Nucl. Acids Res. 2004 32: 5800-5808; doi:10.1093/nar/gkh914 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Naoto Ohtani, Hiroshi Yanagawa, Masaru Tomita, and Mitsuhiro Itaya

Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7
Nucl. Acids Res. 2004 32: 5809-5819; doi:10.1093/nar/gkh917 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Suparna Mukhopadhyay, Denise R. Clark, Nicholas B. Watson, Wolfgang Zacharias, and W. Glenn McGregor

REV1 accumulates in DNA damage-induced nuclear foci in human cells and is implicated in mutagenesis by benzo[a]pyrenediolepoxide
Nucl. Acids Res. 2004 32: 5820-5826; doi:10.1093/nar/gkh903 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Harmjan R. Vos, Ralph Bax, Alex W. Faber, Jan C. Vos, and Hendrik A. Raué

U3 snoRNP and Rrp5p associate independently with Saccharomyces cerevisiae 35S pre-rRNA, but Rrp5p is essential for association of Rok1p
Nucl. Acids Res. 2004 32: 5827-5833; doi:10.1093/nar/gkh904 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yoshiro Fukue, Noriyuki Sumida, Jun-ichi Nishikawa, and Takashi Ohyama

Core promoter elements of eukaryotic genes have a highly distinctive mechanical property
Nucl. Acids Res. 2004 32: 5834-5840; doi:10.1093/nar/gkh905 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Steven A. Keatch, Tsueu-Ju Su, and David T. F. Dryden

Alleviation of restriction by DNA condensation and non-specific DNA binding ligands
Nucl. Acids Res. 2004 32: 5841-5850; doi:10.1093/nar/gkh918 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Céline Bouchoux, Guillaume Hautbergue, Sabrina Grenetier, Christophe Carles, Michel Riva, and Valérie Goguel

CTD kinase I is involved in RNA polymerase I transcription
Nucl. Acids Res. 2004 32: 5851-5860; doi:10.1093/nar/gkh927 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

José F. Ruiz, Daniel Lucas, Esther García-Palomero, Ana I. Saez, Manuel A. González, Miguel A. Piris, Antonio Bernad, and Luis Blanco

Overexpression of human DNA polymerase µ (Pol µ) in a Burkitt's lymphoma cell line affects the somatic hypermutation rate
Nucl. Acids Res. 2004 32: 5861-5873; doi:10.1093/nar/gkh929 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dongling Zheng, Chrystala Constantinidou, Jon L. Hobman, and Stephen D. Minchin

Identification of the CRP regulon using in vitro and in vivo transcriptional profiling
Nucl. Acids Res. 2004 32: 5874-5893; doi:10.1093/nar/gkh908 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Allyson F. O'Donnell, Neil K. Brewster, Joelius Kurniawan, Laura V. Minard, Gerald C. Johnston, and Richard A. Singer

Domain organization of the yeast histone chaperone FACT: the conserved N-terminal domain of FACT subunit Spt16 mediates recovery from replication stress
Nucl. Acids Res. 2004 32: 5894-5906; doi:10.1093/nar/gkh922 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christian Hoischen, Alexander Bolshoy, Kenn Gerdes, and Stephan Diekmann

Centromere parC of plasmid R1 is curved
Nucl. Acids Res. 2004 32: 5907-5915; doi:10.1093/nar/gkh920 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Steven J. Raynard and Mark D. Baker

Cis-acting regulatory sequences promote high-frequency gene conversion between repeated sequences in mammalian cells
Nucl. Acids Res. 2004 32: 5916-5927; doi:10.1093/nar/gkh926 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Keiji Hashimoto, Yohei Tominaga, Yusaku Nakabeppu, and Masaaki Moriya

Futile short-patch DNA base excision repair of adenine:8-oxoguanine mispair
Nucl. Acids Res. 2004 32: 5928-5934; doi:10.1093/nar/gkh909 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Pierpaolo Ceci, Sara Cellai, Elisabetta Falvo, Claudio Rivetti, Gian Luigi Rossi, and Emilia Chiancone

DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus
Nucl. Acids Res. 2004 32: 5935-5944; doi:10.1093/nar/gkh915 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

S. Thiyagarajan, S. S. Rajan, and N. Gautham

Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA).d(TGCGCG) in two crystal forms
Nucl. Acids Res. 2004 32: 5945-5953; doi:10.1093/nar/gkh919 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jill Thompson and Albert E. Dahlberg

Testing the conservation of the translational machinery over evolution in diverse environments: assaying Thermus thermophilus ribosomes and initiation factors in a coupled transcription–translation system from Escherichia coli
Nucl. Acids Res. 2004 32: 5954-5961; doi:10.1093/nar/gkh925 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Laura M. Pollard, Rajesh Sharma, Mariluz Gómez, Sonali Shah, Martin B. Delatycki, Luigi Pianese, Antonella Monticelli, Bronya J.B. Keats, and Sanjay I. Bidichandani

Replication-mediated instability of the GAA triplet repeat mutation in Friedreich ataxia
Nucl. Acids Res. 2004 32: 5962-5971; doi:10.1093/nar/gkh933 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Corrigenda:

Li-Xuan Qin, and Kathleen F. Kerr Contributing Members of the Toxicogenomics Research Consortium

Empirical evaluation of data transformations and ranking statistics for microarray analysis
Nucl. Acids Res. 2004 32: 5972; doi:10.1093/nar/gkh928 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dilip K. Nag, Manisha Suri, and Erin K. Stenson

Both CAG repeats and inverted DNA repeats stimulate spontaneous unequal sister-chromatid exchange in Saccharomyces cerevisiae
Nucl. Acids Res. 2004 32: 5972; doi:10.1093/nar/gkh930 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Leonardo Mariño-Ramírez, John L. Spuge, Gavin C. Kanga, and David Landsman

Statistical analysis of over-represented words in human promoter sequences
Nucl. Acids Res. 2004 32: 5972; doi:10.1093/nar/gkh938 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Methods Online:

Anca Bene, Richard C. Kurten, and Timothy C. Chambers

Subcellular localization as a limiting factor for utilization of decoy oligonucleotides
Nucl. Acids Res. 2004 32: e142; doi:10.1093/nar/gnh139 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Jan Faix, Lisa Kreppel, Gad Shaulsky, Michael Schleicher, and Alan R. Kimmel

A rapid and efficient method to generate multiple gene disruptions in Dictyostelium discoideum using a single selectable marker and the Cre-loxP system
Nucl. Acids Res. 2004 32: e143; doi:10.1093/nar/gnh136 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Youdong Mao, Chunxiong Luo, Wei Deng, Guangyin Jin, Xiaomei Yu, Zhaohui Zhang, Qi Ouyang, Runsheng Chen, and Dapeng Yu

Reversibly switchable DNA nanocompartment on surfaces
Nucl. Acids Res. 2004 32: e144; doi:10.1093/nar/gnh145 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Ryota Fujii, Motomitsu Kitaoka, and Kiyoshi Hayashi

One-step random mutagenesis by error-prone rolling circle amplification
Nucl. Acids Res. 2004 32: e145; doi:10.1093/nar/gnh147 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Joana Cardoso, Lia Molenaar, Renée X. de Menezes, Carla Rosenberg, Hans Morreau, Gabriela Möslein, Riccardo Fodde, and Judith M. Boer

Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH
Nucl. Acids Res. 2004 32: e146; doi:10.1093/nar/gnh142 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Igor Dozmorov, Nicholas Knowlton, Yuhong Tang, Alan Shields, Parima Pathipvanich, James N. Jarvis, and Michael Centola

Hypervariable genes—experimental error or hidden dynamics
Nucl. Acids Res. 2004 32: e147; doi:10.1093/nar/gnh146 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hanna Pincas, Maneesh R. Pingle, Jianmin Huang, Kaiqin Lao, Philip B. Paty, Alan M. Friedman, and Francis Barany

High sensitivity EndoV mutation scanning through real-time ligase proofreading
Nucl. Acids Res. 2004 32: e148; doi:10.1093/nar/gnh150 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Raymond M. Schiffelers, Aslam Ansari, Jun Xu, Qin Zhou, Qingquan Tang, Gert Storm, Grietje Molema, Patrick Y. Lu, Puthupparampil V. Scaria, and Martin C. Woodle

Cancer siRNA therapy by tumor selective delivery with ligand-targeted sterically stabilized nanoparticle
Nucl. Acids Res. 2004 32: e149; doi:10.1093/nar/gnh140 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Heike Thomas, Sabine Senkel, Silke Erdmann, Tanja Arndt, Gülüzar Turan, Ludger Klein-Hitpass, and Gerhart U. Ryffel

Pattern of genes influenced by conditional expression of the transcription factors HNF6, HNF4 and HNF1ß in a pancreatic ß-cell line
Nucl. Acids Res. 2004 32: e150; doi:10.1093/nar/gnh144 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Joseph V. Geisberg and Kevin Struhl

Quantitative sequential chromatin immunoprecipitation, a method for analyzing co-occupancy of proteins at genomic regions in vivo
Nucl. Acids Res. 2004 32: e151; doi:10.1093/nar/gnh148 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jörg S. Hartig and Eric T. Kool

Small circular DNAs for synthesis of the human telomere repeat: varied sizes, structures and telomere-encoding activities
Nucl. Acids Res. 2004 32: e152; doi:10.1093/nar/gnh149 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Yoji Yamamoto, Akihiko Uehara, Takafumi Tomita, and Makoto Komiyama

Site-selective and hydrolytic two-strand scission of double-stranded DNA using Ce(IV)/EDTA and pseudo-complementary PNA
Nucl. Acids Res. 2004 32: e153; doi:10.1093/nar/gnh151 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Besik I. Kankia

Optical absorption assay for strand-exchange reactions in unlabeled nucleic acids
Nucl. Acids Res. 2004 32: e154; doi:10.1093/nar/gnh152 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Alison J. Rattray

A method for cloning and sequencing long palindromic DNA junctions
Nucl. Acids Res. 2004 32: e155; doi:10.1093/nar/gnh143 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kyoko Takatsu, Toyokazu Yokomaku, Shinya Kurata, and Takahiro Kanagawa

A FRET-based analysis of SNPs without fluorescent probes
Nucl. Acids Res. 2004 32: e156; doi:10.1093/nar/gnh155 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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