Nucleic Acids Research

Survey and Summary

Get checked abstract Alexander Vologodskii

Theoretical models of DNA topology simplification by type IIA DNA topoisomerases
Nucleic Acids Research Advance Access published on April 21, 2009
Nucl. Acids Res. 2009 37: 3125-3133; doi:10.1093/nar/gkp250 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology

Get checked abstract Anastasis Oulas, Alexandra Boutla, Katerina Gkirtzou, Martin Reczko, Kriton Kalantidis, and Panayiota Poirazi

Prediction of novel microRNA genes in cancer-associated genomic regions—a combined computational and experimental approach
Nucleic Acids Research Advance Access published on March 25, 2009
Nucl. Acids Res. 2009 37: 3276-3287; doi:10.1093/nar/gkp120 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gene Regulation, Chromatin and Epigenetics

Get checked abstract Abdenour Soufi, Peter Noy, Malcolm Buckle, Anyaporn Sawasdichai, Kevin Gaston, and Padma-Sheela Jayaraman

CK2 phosphorylation of the PRH/Hex homeodomain functions as a reversible switch for DNA binding
Nucleic Acids Research Advance Access published on March 25, 2009
Nucl. Acids Res. 2009 37: 3288-3300; doi:10.1093/nar/gkp197 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Ekaterina Bogdanova, Marina Zakharova, Simon Streeter, James Taylor, Tomasz Heyduk, Geoff Kneale, and Konstantin Severinov

Transcription regulation of restriction-modification system Esp1396I
Nucleic Acids Research Advance Access published on March 30, 2009
Nucl. Acids Res. 2009 37: 3354-3366; doi:10.1093/nar/gkp210 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract S. Orthaus, K. Klement, N. Happel, C. Hoischen, and S. Diekmann

Linker histone H1 is present in centromeric chromatin of living human cells next to inner kinetochore proteins
Nucleic Acids Research Advance Access published on March 31, 2009
Nucl. Acids Res. 2009 37: 3391-3406; doi:10.1093/nar/gkp199 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genome Integrity, Repair and Replication

Get checked abstract Nicolas Lévy, Maren Oehlmann, François Delalande, Heinz Peter Nasheuer, Alain Van Dorsselaer, Valérie Schreiber, Gilbert de Murcia, Josiane Ménissier-de Murcia, Domenico Maiorano, and Anne Bresson

XRCC1 interacts with the p58 subunit of DNA Pol -primase and may coordinate DNA repair and replication during S phase
Nucleic Acids Research Advance Access published on March 21, 2009
Nucl. Acids Res. 2009 37: 3177-3188; doi:10.1093/nar/gkp144 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Takako Ishida, Yoshimasa Takizawa, Takashi Kainuma, Jin Inoue, Tsutomu Mikawa, Takehiko Shibata, Hidekazu Suzuki, Satoshi Tashiro, and Hitoshi Kurumizaka

DIDS, a chemical compound that inhibits RAD51-mediated homologous pairing and strand exchange
Nucleic Acids Research Advance Access published on March 30, 2009
Nucl. Acids Res. 2009 37: 3367-3376; doi:10.1093/nar/gkp200 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Emma Bolderson, Derek J. Richard, Winfried Edelmann, and Kum Kum Khanna

Involvement of Exo1b in DNA damage-induced apoptosis
Nucleic Acids Research Advance Access published on April 1, 2009
Nucl. Acids Res. 2009 37: 3452-3463; doi:10.1093/nar/gkp194 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics

Get checked abstract Piotr A. Ziolkowski, Grzegorz Koczyk, Lukasz Galganski, and Jan Sadowski

Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes
Nucleic Acids Research Advance Access published on March 21, 2009
Nucl. Acids Res. 2009 37: 3189-3201; doi:10.1093/nar/gkp183 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Daniella C. Bartholomeu, Gustavo C. Cerqueira, Ana Carolina A. Leão, Wanderson D. daRocha, Fabiano S. Pais, Camila Macedo, Appolinaire Djikeng, Santuza M. R. Teixeira, and Najib M. El-Sayed

Genomic organization and expression profile of the mucin-associated surface protein (masp) family of the human pathogen Trypanosoma cruzi
Nucleic Acids Research Advance Access published on March 31, 2009
Nucl. Acids Res. 2009 37: 3407-3417; doi:10.1093/nar/gkp172 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract Carsten Schwarz, Regis Debruyne, Melanie Kuch, Elizabeth McNally, Henry Schwarcz, Andrew D. Aubrey, Jeffrey Bada, and Hendrik Poinar

New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains
Nucleic Acids Research Advance Access published on March 24, 2009
Nucl. Acids Res. 2009 37: 3215-3229; doi:10.1093/nar/gkp159 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Antonio Rodríguez-García, Alberto Sola-Landa, Kristian Apel, Fernando Santos-Beneit, and Juan F. Martín

Phosphate control over nitrogen metabolism in Streptomyces coelicolor: direct and indirect negative control of glnR, glnA, glnII and amtB expression by the response regulator PhoP
Nucleic Acids Research Advance Access published on March 24, 2009
Nucl. Acids Res. 2009 37: 3230-3242; doi:10.1093/nar/gkp162 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yael Yoffe, Mélissa Léger, Alexandra Zinoviev, Joanna Zuberek, Edward Darzynkiewicz, Gerhard Wagner, and Michal Shapira

Evolutionary changes in the Leishmania eIF4F complex involve variations in the eIF4E–eIF4G interactions
Nucleic Acids Research Advance Access published on March 24, 2009
Nucl. Acids Res. 2009 37: 3243-3253; doi:10.1093/nar/gkp190 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Radhashree Maitra and Moshe J. Sadofsky

A WW-like module in the RAG1 N-terminal domain contributes to previously unidentified protein–protein interactions
Nucleic Acids Research Advance Access published on March 25, 2009
Nucl. Acids Res. 2009 37: 3301-3309; doi:10.1093/nar/gkp192 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Niti Kumar, Richa Basundra, and Souvik Maiti

Elevated polyamines induce c-MYC overexpression by perturbing quadruplex–WC duplex equilibrium
Nucleic Acids Research Advance Access published on March 26, 2009
Nucl. Acids Res. 2009 37: 3321-3331; doi:10.1093/nar/gkp196 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Caroline Lemieux and François Bachand

Cotranscriptional recruitment of the nuclear poly(A)-binding protein Pab2 to nascent transcripts and association with translating mRNPs
Nucleic Acids Research Advance Access published on March 31, 2009
Nucl. Acids Res. 2009 37: 3418-3430; doi:10.1093/nar/gkp207 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nucleic Acid Enzymes

Get checked abstract Macmillan Nongkhlaw, Popy Dutta, Joel W. Hockensmith, Sneha Sudha Komath, and Rohini Muthuswami

Elucidating the mechanism of DNA-dependent ATP hydrolysis mediated by DNA-dependent ATPase A, a member of the SWI2/SNF2 protein family
Nucleic Acids Research Advance Access published on March 26, 2009
Nucl. Acids Res. 2009 37: 3332-3341; doi:10.1093/nar/gkp178 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Piero R. Bianco, Cuiling Xu, and Min Chi

Type I restriction endonucleases are true catalytic enzymes
Nucleic Acids Research Advance Access published on March 30, 2009
Nucl. Acids Res. 2009 37: 3377-3390; doi:10.1093/nar/gkp195 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Zhigang Guo, Li Zheng, Huifang Dai, Mian Zhou, Hong Xu, and Binghui Shen

Human DNA polymerase β polymorphism, Arg137Gln, impairs its polymerase activity and interaction with PCNA and the cellular base excision repair capacity
Nucleic Acids Research Advance Access published on March 31, 2009
Nucl. Acids Res. 2009 37: 3431-3441; doi:10.1093/nar/gkp201 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA

Get checked abstract Chiaolong Hsiao and Loren Dean Williams

A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center
Nucleic Acids Research Advance Access published on March 11, 2009
Nucl. Acids Res. 2009 37: 3134-3142; doi:10.1093/nar/gkp119 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Fredrik B. Stabell, Nicolas J. Tourasse, and Anne-Brit Kolstø

A conserved 3' extension in unusual group II introns is important for efficient second-step splicing
Nucleic Acids Research Advance Access published on March 21, 2009
Nucl. Acids Res. 2009 37: 3202-3214; doi:10.1093/nar/gkp186 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Roman N. Kotelnikov, Mikhail S. Klenov, Yakov M. Rozovsky, Ludmila V. Olenina, Mikhail V. Kibanov, and Vladimir A. Gvozdev

Peculiarities of piRNA-mediated post-transcriptional silencing of Stellate repeats in testes of Drosophila melanogaster
Nucleic Acids Research Advance Access published on March 24, 2009
Nucl. Acids Res. 2009 37: 3254-3263; doi:10.1093/nar/gkp167 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Marie-Line Bortolin-Cavaillé, Marie Dance, Michel Weber, and Jérôme Cavaillé

C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts
Nucleic Acids Research Advance Access published on April 1, 2009
Nucl. Acids Res. 2009 37: 3464-3473; doi:10.1093/nar/gkp205 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Structural Biology

Get checked abstract Yu Seon Chung, Therese Brendler, Stuart Austin, and Alba Guarné

Structural insights into the cooperative binding of SeqA to a tandem GATC repeat
Nucleic Acids Research Advance Access published on March 20, 2009
Nucl. Acids Res. 2009 37: 3143-3152; doi:10.1093/nar/gkp151 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Todd A. Gangelhoff, Purnima S. Mungalachetty, Jay C. Nix, and Mair E. A. Churchill

Structural analysis and DNA binding of the HMG domains of the human mitochondrial transcription factor A
Nucleic Acids Research Advance Access published on March 20, 2009
Nucl. Acids Res. 2009 37: 3153-3164; doi:10.1093/nar/gkp157 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Giuseppe Sicoli, Gérald Mathis, Samia Aci-Sèche, Christine Saint-Pierre, Yves Boulard, Didier Gasparutto, and Serge Gambarelli

Lesion-induced DNA weak structural changes detected by pulsed EPR spectroscopy combined with site-directed spin labelling
Nucleic Acids Research Advance Access published on March 20, 2009
Nucl. Acids Res. 2009 37: 3165-3176; doi:10.1093/nar/gkp165 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Júlia Viladoms, Núria Escaja, Miriam Frieden, Irene Gómez-Pinto, Enrique Pedroso, and Carlos González

Self-association of short DNA loops through minor groove C:G:G:C tetrads
Nucleic Acids Research Advance Access published on March 24, 2009
Nucl. Acids Res. 2009 37: 3264-3275; doi:10.1093/nar/gkp191 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Joseph D. Schonhoft, Rabindra Bajracharya, Soma Dhakal, Zhongbo Yu, Hanbin Mao, and Soumitra Basu

Direct experimental evidence for quadruplex–quadruplex interaction within the human ILPR
Nucleic Acids Research Advance Access published on March 25, 2009
Nucl. Acids Res. 2009 37: 3310-3320; doi:10.1093/nar/gkp181 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yann Bilbille, Franck A. P. Vendeix, Richard Guenther, Andrzej Malkiewicz, Xavier Ariza, Jaume Vilarrasa, and Paul F. Agris

The structure of the human tRNA^Lys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs
Nucleic Acids Research Advance Access published on March 26, 2009
Nucl. Acids Res. 2009 37: 3342-3353; doi:10.1093/nar/gkp187 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Young Jun An, Bo-Eun Ahn, A-Reum Han, Hae-Mi Kim, Kyung Min Chung, Jung-Ho Shin, Yoo-Bok Cho, Jung-Hye Roe, and Sun-Shin Cha

Structural basis for the specialization of Nur, a nickel-specific Fur homolog, in metal sensing and DNA recognition
Nucleic Acids Research Advance Access published on March 31, 2009
Nucl. Acids Res. 2009 37: 3442-3451; doi:10.1093/nar/gkp198 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online

Get checked abstract Shaoqiang Zhang, Minli Xu, Shan Li, and Zhengchang Su

Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes
Nucleic Acids Research Advance Access published on April 21, 2009
Nucl. Acids Res. 2009 37: e72; doi:10.1093/nar/gkp248 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Justin Ashworth and David Baker

Assessment of the optimization of affinity and specificity at protein–DNA interfaces
Nucleic Acids Research Advance Access published on April 23, 2009
Nucl. Acids Res. 2009 37: e73; doi:10.1093/nar/gkp242 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Ping Qiu, Vincent Sanfiorenzo, Stephanie Curry, Zhuyan Guo, Shaotang Liu, Angela Skelton, Ellen Xia, Constance Cullen, Robert Ralston, Jonathan Greene, and Xiao Tong

Identification of HCV protease inhibitor resistance mutations by selection pressure-based method
Nucleic Acids Research Advance Access published on April 24, 2009
Nucl. Acids Res. 2009 37: e74; doi:10.1093/nar/gkp251 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sika Zheng and Liang Chen

A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level
Nucleic Acids Research Advance Access published on May 5, 2009
Nucl. Acids Res. 2009 37: e75; doi:10.1093/nar/gkp282 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yijun Sun, Yunpeng Cai, Li Liu, Fahong Yu, Michael L. Farrell, William McKendree, and William Farmerie

ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences
Nucleic Acids Research Advance Access published on May 5, 2009
Nucl. Acids Res. 2009 37: e76; doi:10.1093/nar/gkp285 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Ren-Jun Hsu, Hsin-Jung Yang, and Huai-Jen Tsai

Labeled microRNA pull-down assay system: an experimental approach for high-throughput identification of microRNA-target mRNAs
Nucleic Acids Research Advance Access published on May 6, 2009
Nucl. Acids Res. 2009 37: e77; doi:10.1093/nar/gkp274 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Retraction

Yoke W. Kow, Barry Imhoff, Bernard Weiss, David C. I. Hung, Antreas A. Hindoyan, Randall M. Story, and Steven D. Goodman

Escherichia coli HU protein has a role in the repair of abasic sites in DNA
Nucleic Acids Research Advance Access published on May 19, 2009
Nucl. Acids Res. 2009 37: 3474; doi:10.1093/nar/gkp454 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 37 ISSUE 10 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkp523 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkp521 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkp522 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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