Nucleic Acids Research

Editorial: Topoisomerase Special Issue

Tony Maxwell and Andy Bates

Topo2008: DNA Topoisomerases in Biology and Medicine
Nucl. Acids Res. 2009 37: 659-660; doi:10.1093/nar/gkp072 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Survey and Summary

Get checked abstract Zhirong Liu, Richard W. Deibler, Hue Sun Chan, and Lynn Zechiedrich

The why and how of DNA unlinking
Nucl. Acids Res. 2009 37: 661-671; doi:10.1093/nar/gkp041 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Charles J. Dorman and Colin P. Corcoran

Bacterial DNA topology and infectious disease
Nucleic Acids Research Advance Access published on December 10, 2008
Nucl. Acids Res. 2009 37: 672-678; doi:10.1093/nar/gkn996 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Patrick Forterre and Danièle Gadelle

Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms
Nucleic Acids Research Advance Access published on February 9, 2009
Nucl. Acids Res. 2009 37: 679-692; doi:10.1093/nar/gkp032 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Nicole M. Baker, Rakhi Rajan, and Alfonso Mondragón

Structural studies of type I topoisomerases
Nucleic Acids Research Advance Access published on December 23, 2008
Nucl. Acids Res. 2009 37: 693-701; doi:10.1093/nar/gkn1009 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Claudia Sissi and Manlio Palumbo

Effects of magnesium and related divalent metal ions in topoisomerase structure and function
Nucleic Acids Research Advance Access published on February 2, 2009
Nucl. Acids Res. 2009 37: 702-711; doi:10.1093/nar/gkp024 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Tammy R. L. Collins, Gordon G. Hammes, and Tao-shih Hsieh

Analysis of the eukaryotic topoisomerase II DNA gate: a single-molecule FRET and structural perspective
Nucleic Acids Research Advance Access published on January 20, 2009
Nucl. Acids Res. 2009 37: 712-720; doi:10.1093/nar/gkn1059 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Joaquim Roca

Topoisomerase II: a fitted mechanism for the chromatin landscape
Nucleic Acids Research Advance Access published on December 5, 2008
Nucl. Acids Res. 2009 37: 721-730; doi:10.1093/nar/gkn994 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yuk-Ching Tse-Dinh

Bacterial topoisomerase I as a target for discovery of antibacterial compounds
Nucleic Acids Research Advance Access published on November 28, 2008
Nucl. Acids Res. 2009 37: 731-737; doi:10.1093/nar/gkn936 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Joseph E. Deweese and Neil Osheroff

The DNA cleavage reaction of topoisomerase II: wolf in sheep's clothing
Nucleic Acids Research Advance Access published on November 28, 2008
Nucl. Acids Res. 2009 37: 738-748; doi:10.1093/nar/gkn937 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chemistry and Synthetic Biology

Get checked abstract Regis Marty, Christophe N. N'soukpoé-Kossi, David Charbonneau, Carl Maximilian Weinert, Laurent Kreplak, and Heidar-Ali Tajmir-Riahi

Structural analysis of DNA complexation with cationic lipids
Nucleic Acids Research Advance Access published on December 22, 2008
Nucl. Acids Res. 2009 37: 849-857; doi:10.1093/nar/gkn1003 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Computational Biology

Get checked abstract Raul Rodriguez-Esteban, Phoebe M. Roberts, and Matthew E. Crawford

Identifying and classifying biomedical perturbations in text
Nucleic Acids Research Advance Access published on December 12, 2008
Nucl. Acids Res. 2009 37: 771-777; doi:10.1093/nar/gkn986 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Stephen F. Altschul, E. Michael Gertz, Richa Agarwala, Alejandro A. Schäffer, and Yi-Kuo Yu

PSI-BLAST pseudocounts and the minimum description length principle
Nucleic Acids Research Advance Access published on December 16, 2008
Nucl. Acids Res. 2009 37: 815-824; doi:10.1093/nar/gkn981 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Shuye Pu, Jessica Wong, Brian Turner, Emerson Cho, and Shoshana J. Wodak

Up-to-date catalogues of yeast protein complexes
Nucleic Acids Research Advance Access published on December 18, 2008
Nucl. Acids Res. 2009 37: 825-831; doi:10.1093/nar/gkn1005 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Timo Lassmann, Oliver Frings, and Erik L. L. Sonnhammer

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features
Nucleic Acids Research Advance Access published on December 22, 2008
Nucl. Acids Res. 2009 37: 858-865; doi:10.1093/nar/gkn1006 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Keishin Nishida, Martin C. Frith, and Kenta Nakai

Pseudocounts for transcription factor binding sites
Nucleic Acids Research Advance Access published on December 23, 2008
Nucl. Acids Res. 2009 37: 939-944; doi:10.1093/nar/gkn1019 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Kensuke Morita, Yutaka Saito, Kengo Sato, Kotaro Oka, Kohji Hotta, and Yasubumi Sakakibara

Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 999-1009; doi:10.1093/nar/gkn1054 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gene regulation, Chromatin and Epigenetics

Get checked abstract Hisashi Miura, Yasuhiro Tomaru, Misato Nakanishi, Shinji Kondo, Yoshihide Hayashizaki, and Masanori Suzuki

Identification of DNA regions and a set of transcriptional regulatory factors involved in transcriptional regulation of several human liver-enriched transcription factor genes
Nucleic Acids Research Advance Access published on December 15, 2008
Nucl. Acids Res. 2009 37: 778-792; doi:10.1093/nar/gkn978 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yinming Chen, Amrita Dhupelia, and Christopher J. Schoenherr

The Igf2/H19 imprinting control region exhibits sequence-specific and cell-type-dependent DNA methylation-mediated repression
Nucleic Acids Research Advance Access published on December 15, 2008
Nucl. Acids Res. 2009 37: 793-803; doi:10.1093/nar/gkn985 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Na-zi Lei, Xiao-yan Zhang, Hang-zi Chen, Yuan Wang, Yan-yan Zhan, Zhong-hui Zheng, Yue-mao Shen, and Qiao Wu

A feedback regulatory loop between methyltransferase PRMT1 and orphan receptor TR3
Nucleic Acids Research Advance Access published on December 18, 2008
Nucl. Acids Res. 2009 37: 832-848; doi:10.1093/nar/gkn941 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Iwona Mruk and Robert M. Blumenthal

Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system
Nucleic Acids Research Advance Access published on January 6, 2009
Nucl. Acids Res. 2009 37: 983-998; doi:10.1093/nar/gkn1010 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genome integrity, repair and replication

Get checked abstract Akiko Hori, Minoru Yoshida, Takehiko Shibata, and Feng Ling

Reactive oxygen species regulate DNA copy number in isolated yeast mitochondria by triggering recombination-mediated replication
Nucleic Acids Research Advance Access published on December 11, 2008
Nucl. Acids Res. 2009 37: 749-761; doi:10.1093/nar/gkn993 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Supplementary Data]  

Molecular Biology

Get checked abstract Cátia S. M. Ferreira, Melissa C. Cheung, Sotiris Missailidis, Stuart Bisland, and Jean Gariépy

Phototoxic aptamers selectively enter and kill epithelial cancer cells
Nucleic Acids Research Advance Access published on December 22, 2008
Nucl. Acids Res. 2009 37: 866-876; doi:10.1093/nar/gkn967 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes

Get checked abstract Ryo Takeuchi, Michael Certo, Mark G. Caprara, Andrew M. Scharenberg, and Barry L. Stoddard

Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation
Nucleic Acids Research Advance Access published on December 22, 2008
Nucl. Acids Res. 2009 37: 877-890; doi:10.1093/nar/gkn1007 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA

Get checked abstract Rei Yoshimoto, Naoyuki Kataoka, Katsuya Okawa, and Mutsuhito Ohno

Isolation and characterization of post-splicing lariat–intron complexes
Nucleic Acids Research Advance Access published on December 22, 2008
Nucl. Acids Res. 2009 37: 891-902; doi:10.1093/nar/gkn1002 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Gersende Lepère, Mariusz Nowacki, Vincent Serrano, Jean-François Gout, Gérard Guglielmi, Sandra Duharcourt, and Eric Meyer

Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia
Nucleic Acids Research Advance Access published on December 22, 2008
Nucl. Acids Res. 2009 37: 903-915; doi:10.1093/nar/gkn1018 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Liang-Jiao Xue, Jing-Jing Zhang, and Hong-Wei Xue

Characterization and expression profiles of miRNAs in rice seeds
Nucleic Acids Research Advance Access published on December 22, 2008
Nucl. Acids Res. 2009 37: 916-930; doi:10.1093/nar/gkn998 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Cameron P. Keating, Melissa K. Hill, David J. Hawkes, Redmond P. Smyth, Catherine Isel, Shu-Yun Le, Ann C. Palmenberg, John A. Marshall, Roland Marquet, Gary J. Nabel, and Johnson Mak

The A-rich RNA sequences of HIV-1 pol are important for the synthesis of viral cDNA
Nucleic Acids Research Advance Access published on December 23, 2008
Nucl. Acids Res. 2009 37: 945-956; doi:10.1093/nar/gkn1015 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract María Inés Barría, Angel González, Jorge Vera-Otarola, Ursula León, Valeska Vollrath, Delphine Marsac, Octavio Monasterio, Tomás Pérez-Acle, Alejandro Soza, and Marcelo López-Lastra

Analysis of natural variants of the hepatitis C virus internal ribosome entry site reveals that primary sequence plays a key role in cap-independent translation
Nucleic Acids Research Advance Access published on December 23, 2008
Nucl. Acids Res. 2009 37: 957-971; doi:10.1093/nar/gkn1022 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Structural Biology

Get checked abstract Christopher K. Kennaway, Agnieszka Obarska-Kosinska, John H. White, Irina Tuszynska, Laurie P. Cooper, Janusz M. Bujnicki, John Trinick, and David T. F. Dryden

The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein
Nucleic Acids Research Advance Access published on December 11, 2008
Nucl. Acids Res. 2009 37: 762-770; doi:10.1093/nar/gkn988 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yu-Hua Lo, Kuang-Lei Tsai, Yuh-Ju Sun, Wei-Ti Chen, Cheng-Yang Huang, and Chwan-Deng Hsiao

The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA
Nucleic Acids Research Advance Access published on December 15, 2008
Nucl. Acids Res. 2009 37: 804-814; doi:10.1093/nar/gkn999 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Samir Amrane, Rita Wan Lin Ang, Zhong Ming Tan, Chun Li, Joefina Kim Cheow Lim, Jocelyn Mei Wen Lim, Kah Wai Lim, and Anh Tuân Phan

A novel chair-type G-quadruplex formed by a Bombyx mori telomeric sequence
Nucleic Acids Research Advance Access published on December 22, 2008
Nucl. Acids Res. 2009 37: 931-938; doi:10.1093/nar/gkn990 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Ji Wook Shim, Qiulin Tan, and Li-Qun Gu

Single-molecule detection of folding and unfolding of the G-quadruplex aptamer in a nanopore nanocavity
Nucleic Acids Research Advance Access published on December 26, 2008
Nucl. Acids Res. 2009 37: 972-982; doi:10.1093/nar/gkn968 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online

Get checked abstract Germán Gastón Leparc, Thomas Tüchler, Gerald Striedner, Karl Bayer, Peter Sykacek, Ivo L. Hofacker, and David P. Kreil

Model-based probe set optimization for high-performance microarrays
Nucleic Acids Research Advance Access published on December 22, 2008
Nucl. Acids Res. 2009 37: e18; doi:10.1093/nar/gkn1001 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Taku Murakami, Jun Sumaoka, and Makoto Komiyama

Sensitive isothermal detection of nucleic-acid sequence by primer generation–rolling circle amplification
Nucleic Acids Research Advance Access published on December 23, 2008
Nucl. Acids Res. 2009 37: e19; doi:10.1093/nar/gkn1014 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Qiuping Guo, Xiaohai Yang, Kemin Wang, Weihong Tan, Wei Li, Hongxing Tang, and Huimin Li

Sensitive fluorescence detection of nucleic acids based on isothermal circular strand-displacement polymerization reaction
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: e20; doi:10.1093/nar/gkn1024 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Richard M. Cawthon

Telomere length measurement by a novel monochrome multiplex quantitative PCR method
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: e21; doi:10.1093/nar/gkn1027 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Carina Frauer and Heinrich Leonhardt

A versatile non-radioactive assay for DNA methyltransferase activity and DNA binding
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: e22; doi:10.1093/nar/gkn1029 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Tomoaki Shiohara, Hirohide Saito, and Tan Inoue

A designed RNA selection: establishment of a stable complex between a target and selectant RNA via two coordinated interactions
Nucleic Acids Research Advance Access published on January 9, 2009
Nucl. Acids Res. 2009 37: e23; doi:10.1093/nar/gkn1012 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yanjie Lu, Jiening Xiao, Huixian Lin, Yunlong Bai, Xiaobin Luo, Zhiguo Wang, and Baofeng Yang

A single anti-microRNA antisense oligodeoxyribonucleotide (AMO) targeting multiple microRNAs offers an improved approach for microRNA interference
Nucleic Acids Research Advance Access published on January 9, 2009
Nucl. Acids Res. 2009 37: e24; doi:10.1093/nar/gkn1053 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Volodymyr V. Shvadchak, Andrey S. Klymchenko, Hugues de Rocquigny, and Yves Mély

Sensing peptide–oligonucleotide interactions by a two-color fluorescence label: application to the HIV-1 nucleocapsid protein
Nucleic Acids Research Advance Access published on January 16, 2009
Nucl. Acids Res. 2009 37: e25; doi:10.1093/nar/gkn1083 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 37 ISSUE 3 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkp142 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkp141 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkp143 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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