Nucleic Acids Research

Survey and Summary:

Robert D. Wells, Ruhee Dere, Micheal L. Hebert, Marek Napierala, and Leslie S. Son

Advances in mechanisms of genetic instability related to hereditary neurological diseases
Nucl. Acids Res. 2005 33: 3785-3798; doi:10.1093/nar/gki697 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Articles:

Aristotelis Tsirigos and Isidore Rigoutsos

A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes
Nucl. Acids Res. 2005 33: 3699-3707; doi:10.1093/nar/gki660 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Vassiliki Prokova, Sofia Mavridou, Paraskevi Papakosta, and Dimitris Kardassis

Characterization of a novel transcriptionally active domain in the transforming growth factor ß-regulated Smad3 protein
Nucl. Acids Res. 2005 33: 3708-3721; doi:10.1093/nar/gki679 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

J. A. Stuart, S. Mayard, K. Hashiguchi, N. C. Souza-Pinto, and V. A. Bohr

Localization of mitochondrial DNA base excision repair to an inner membrane-associated particulate fraction
Nucl. Acids Res. 2005 33: 3722-3732; doi:10.1093/nar/gki683 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Charlotte Andrieu-Soler, Mariana Casas, Anne-Marie Faussat, Christelle Gandolphe, Marc Doat, Denis Tempé, Carine Giovannangeli, Francine Behar-Cohen, and Jean-Paul Concordet

Stable transmission of targeted gene modification using single-stranded oligonucleotides with flanking LNAs
Nucl. Acids Res. 2005 33: 3733-3742; doi:10.1093/nar/gki686 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Michael Petrascheck, Dominik Escher, Tokameh Mahmoudi, C. Peter Verrijzer, Walter Schaffner, and Alcide Barberis

DNA looping induced by a transcriptional enhancer in vivo
Nucl. Acids Res. 2005 33: 3743-3750; doi:10.1093/nar/gki689 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ji-Young Ahn, Hyung Choi, Yang-Hoon Kim, Kyung-Yeon Han, Jin-Seung Park, Sung-Sik Han, and Jeewon Lee

Heterologous gene expression using self-assembled supra-molecules with high affinity for HSP70 chaperone
Nucl. Acids Res. 2005 33: 3751-3762; doi:10.1093/nar/gki692 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zhaoqian Liu, Zizheng Dong, Baoguang Han, Youyun Yang, Yang Liu, and Jian-Ting Zhang

Regulation of expression by promoters versus internal ribosome entry site in the 5'-untranslated sequence of the human cyclin-dependent kinase inhibitor p27^kip1
Nucl. Acids Res. 2005 33: 3763-3771; doi:10.1093/nar/gki680 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Catrióna R. Johnston and Denis C. Shields

A sequence sub-sampling algorithm increases the power to detect distant homologues
Nucl. Acids Res. 2005 33: 3772-3778; doi:10.1093/nar/gki687 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Toru Ishibashi, Hiroshi Hayakawa, Riyoko Ito, Masayuki Miyazawa, Yuriko Yamagata, and Mutsuo Sekiguchi

Mammalian enzymes for preventing transcriptional errors caused by oxidative damage
Nucl. Acids Res. 2005 33: 3779-3784; doi:10.1093/nar/gki682 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Cecilia Lundin, Matthew North, Klaus Erixon, Kevin Walters, Dag Jenssen, Alastair S. H. Goldman, and Thomas Helleday

Methyl methanesulfonate (MMS) produces heat-labile DNA damage but no detectable in vivo DNA double-strand breaks
Nucl. Acids Res. 2005 33: 3799-3811; doi:10.1093/nar/gki681 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Paola Loguercio Polosa, Stefania Deceglie, Marina Roberti, Maria Nicola Gadaleta, and Palmiro Cantatore

Contrahelicase activity of the mitochondrial transcription termination factor mtDBP
Nucl. Acids Res. 2005 33: 3812-3820; doi:10.1093/nar/gki693 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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

A highly distinctive mechanical property found in the majority of human promoters and its transcriptional relevance
Nucl. Acids Res. 2005 33: 3821-3827; doi:10.1093/nar/gki700 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Veerle Kempeneers, Marleen Renders, Matheus Froeyen, and Piet Herdewijn

Investigation of the DNA-dependent cyclohexenyl nucleic acid polymerization and the cyclohexenyl nucleic acid-dependent DNA polymerization
Nucl. Acids Res. 2005 33: 3828-3836; doi:10.1093/nar/gki695 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Steven J. Pearson, Jennifer Ferguson, Mauro Santibanez-Koref, and Geoffrey P. Margison

Inhibition of O⁶-methylguanine-DNA methyltransferase by an alkyltransferase-like protein from Escherichia coli
Nucl. Acids Res. 2005 33: 3837-3844; doi:10.1093/nar/gki696 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jonathan H. Esensten, Alla V. Tsytsykova, Cristina Lopez-Rodriguez, Filipa A. Ligeiro, Anjana Rao, and Anne E. Goldfeld

NFAT5 binds to the TNF promoter distinctly from NFATp, c, 3 and 4, and activates TNF transcription during hypertonic stress alone
Nucl. Acids Res. 2005 33: 3845-3854; doi:10.1093/nar/gki701 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Wei Tan, Andrei S. Zolotukhin, Irina Tretyakova, Jenifer Bear, Susan Lindtner, Sergey V. Smulevitch, and Barbara K. Felber

Identification and characterization of the mouse nuclear export factor (Nxf) family members
Nucl. Acids Res. 2005 33: 3855-3865; doi:10.1093/nar/gki706 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Dong-Ho Kim, Marc-Andre Langlois, Kwang-Back Lee, Arthur D. Riggs, Jack Puymirat, and John J. Rossi

HnRNP H inhibits nuclear export of mRNA containing expanded CUG repeats and a distal branch point sequence
Nucl. Acids Res. 2005 33: 3866-3874; doi:10.1093/nar/gki698 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Lakshminarayan M. Iyer, Eugene V. Koonin, Detlef D. Leipe, and L. Aravind

Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members
Nucl. Acids Res. 2005 33: 3875-3896; doi:10.1093/nar/gki702 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Haixin Lei, Ian N. M. Day, and Igor Vorechovsky

Exonization of AluYa5 in the human ACE gene requires mutations in both 3' and 5' splice sites and is facilitated by a conserved splicing enhancer
Nucl. Acids Res. 2005 33: 3897-3906; doi:10.1093/nar/gki707 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Michael Y. Tolstorukov, Konstantin M. Virnik, Sankar Adhya, and Victor B. Zhurkin

A-tract clusters may facilitate DNA packaging in bacterial nucleoid
Nucl. Acids Res. 2005 33: 3907-3918; doi:10.1093/nar/gki699 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nikita A. Kuznetsov, Vladimir V. Koval, Dmitry O. Zharkov, Georgy A. Nevinsky, Kenneth T. Douglas, and Olga S. Fedorova

Kinetics of substrate recognition and cleavage by human 8-oxoguanine-DNA glycosylase
Nucl. Acids Res. 2005 33: 3919-3931; doi:10.1093/nar/gki694 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Chit Fang Cheok, Leonard Wu, Patrick L. Garcia, Pavel Janscak, and Ian D. Hickson

The Bloom's syndrome helicase promotes the annealing of complementary single-stranded DNA
Nucl. Acids Res. 2005 33: 3932-3941; doi:10.1093/nar/gki712 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Begoña Carrasco, Silvia Ayora, Rudi Lurz, and Juan C. Alonso

Bacillus subtilis RecU Holliday-junction resolvase modulates RecA activities
Nucl. Acids Res. 2005 33: 3942-3952; doi:10.1093/nar/gki713 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Corrigendum:

Jiang Qian, Noriko Esumi, Yangjian Chen, Qingliang Wang, Itay Chowers, and Donald J. Zack

Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation
Nucl. Acids Res. 2005 33: 3953; doi:10.1093/nar/gki719 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Daniel S. Yuan, Xuewen Pan, Siew Loon Ooi, Brian D. Peyser, Forrest A. Spencer, Rafael A. Irizarry, and Jef D. Boeke

Improved microarray methods for profiling the yeast knockout strain collection
Nucl. Acids Res. 2005 33: e103; doi:10.1093/nar/gni105 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Eini Poussu, Jussi Jäntti, and Harri Savilahti

A gene truncation strategy generating N- and C-terminal deletion variants of proteins for functional studies: mapping of the Sec1p binding domain in yeast Mso1p by a Mu in vitro transposition-based approach
Nucl. Acids Res. 2005 33: e104; doi:10.1093/nar/gni102 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Magdalena Alejska, Magdalena Figlerowicz, Nelli Malinowska, Anna Urbanowicz, and Marek Figlerowicz

A universal BMV-based RNA recombination system—how to search for general rules in RNA recombination
Nucl. Acids Res. 2005 33: e105; doi:10.1093/nar/gni106 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Bong Jin Hong, Vijaya Sunkara, and Joon Won Park

DNA microarrays on nanoscale-controlled surface
Nucl. Acids Res. 2005 33: e106; doi:10.1093/nar/gni109 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Laetitia Malphettes, Cornelia C. Weber, Marie Daoud El-Baba, Ronald G. Schoenmakers, Dominique Aubel, Wilfried Weber, and Martin Fussenegger

A novel mammalian expression system derived from components coordinating nicotine degradation in arthrobacter nicotinovorans pAO1
Nucl. Acids Res. 2005 33: e107; doi:10.1093/nar/gni107 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kazunori Ikebukuro, Yuji Okumura, Koichi Sumikura, and Isao Karube

A novel method of screening thrombin-inhibiting DNA aptamers using an evolution-mimicking algorithm
Nucl. Acids Res. 2005 33: e108; doi:10.1093/nar/gni108 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yasuhiro Suzuki, Naoko Kagawa, Toru Fujino, Tsuyoshi Sumiya, Taichi Andoh, Kumiko Ishikawa, Rie Kimura, Kiyokazu Kemmochi, Tsutomu Ohta, and Shigeo Tanaka

A novel high-throughput (HTP) cloning strategy for site-directed designed chimeragenesis and mutation using the Gateway cloning system
Nucl. Acids Res. 2005 33: e109; doi:10.1093/nar/gni103 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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