Nucleic Acids Research

Survey and Summary

Get checked abstract Steve Lefever, Jan Hellemans, Filip Pattyn, Daniel R. Przybylski, Chris Taylor, René Geurts, Andreas Untergasser, Jo Vandesompele, and on behalf of the RDML consortium

RDML: structured language and reporting guidelines for real-time quantitative PCR data
Nucleic Acids Research Advance Access published on February 17, 2009
Nucl. Acids Res. 2009 37: 2065-2069; doi:10.1093/nar/gkp056 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Computational Biology

Get checked abstract Jinhao Zhu, Bryan Wei, Yuan Yuan, and Yongli Mi

UNIQUIMER 3D, a software system for structural DNA nanotechnology design, analysis and evaluation
Nucleic Acids Research Advance Access published on February 18, 2009
Nucl. Acids Res. 2009 37: 2164-2175; doi:10.1093/nar/gkp005 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Boian S. Alexandrov, Vladimir Gelev, Yevgeniya Monisova, Ludmil B. Alexandrov, Alan R. Bishop, Kim Ø. Rasmussen, and Anny Usheva

A nonlinear dynamic model of DNA with a sequence-dependent stacking term
Nucleic Acids Research Advance Access published on March 5, 2009
Nucl. Acids Res. 2009 37: 2405-2410; doi:10.1093/nar/gkp016 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gene Regulation, Chromatin and Epigenetics

Get checked abstract Michal Stros, Eva Polanská, Sona Struncová, and Sárka Pospísilová

HMGB1 and HMGB2 proteins up-regulate cellular expression of human topoisomerase II
Nucleic Acids Research Advance Access published on February 17, 2009
Nucl. Acids Res. 2009 37: 2070-2086; doi:10.1093/nar/gkp067 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Keren Weidenfeld-Baranboim, Tal Hasin, Ilona Darlyuk, Ronit Heinrich, Ofer Elhanani, Jianzhi Pan, Kazunari K. Yokoyama, and Ami Aronheim

The ubiquitously expressed bZIP inhibitor, JDP2, suppresses the transcription of its homologue immediate early gene counterpart, ATF3
Nucleic Acids Research Advance Access published on February 20, 2009
Nucl. Acids Res. 2009 37: 2194-2203; doi:10.1093/nar/gkp083 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yahong Guo, Nataliya Nady, Chao Qi, Abdellah Allali-Hassani, Haizhong Zhu, Patricia Pan, Melanie A. Adams-Cioaba, Maria F. Amaya, Aiping Dong, Masoud Vedadi, Matthieu Schapira, Randy J. Read, Cheryl H. Arrowsmith, and Jinrong Min

Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2
Nucleic Acids Research Advance Access published on February 20, 2009
Nucl. Acids Res. 2009 37: 2204-2210; doi:10.1093/nar/gkp086 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Michael Backlund, Kirsi Paukku, Laurent Daviet, Rudolf A. De Boer, Erkka Valo, Sampsa Hautaniemi, Nisse Kalkkinen, Afshin Ehsan, Kimmo K. Kontula, and Jukka Y. A. Lehtonen

Posttranscriptional regulation of angiotensin II type 1 receptor expression by glyceraldehyde 3-phosphate dehydrogenase
Nucleic Acids Research Advance Access published on February 26, 2009
Nucl. Acids Res. 2009 37: 2346-2358; doi:10.1093/nar/gkp098 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genome Integrity, Repair and Replication

Get checked abstract Tomás Aparicio, Emmanuelle Guillou, Javier Coloma, Guillermo Montoya, and Juan Méndez

The human GINS complex associates with Cdc45 and MCM and is essential for DNA replication
Nucleic Acids Research Advance Access published on February 17, 2009
Nucl. Acids Res. 2009 37: 2087-2095; doi:10.1093/nar/gkp065 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Kenji Watanabe, Kuniyoshi Iwabuchi, Jinghua Sun, Yuri Tsuji, Tokio Tani, Kazuaki Tokunaga, Takayasu Date, Mitsumasa Hashimoto, Masaru Yamaizumi, and Satoshi Tateishi

RAD18 promotes DNA double-strand break repair during G1 phase through chromatin retention of 53BP1
Nucleic Acids Research Advance Access published on February 19, 2009
Nucl. Acids Res. 2009 37: 2176-2193; doi:10.1093/nar/gkp082 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Liliana Krasinska and Daniel Fisher

Replication initiation complex formation in the absence of nuclear function in Xenopus
Nucleic Acids Research Advance Access published on February 22, 2009
Nucl. Acids Res. 2009 37: 2238-2248; doi:10.1093/nar/gkp081 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Lars Schomacher, James P. J. Chong, Paul McDermott, Wilfried Kramer, and Hans-Joachim Fritz

DNA uracil repair initiated by the archaeal ExoIII homologue Mth212 via direct strand incision
Nucleic Acids Research Advance Access published on February 24, 2009
Nucl. Acids Res. 2009 37: 2283-2293; doi:10.1093/nar/gkp102 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Anne M. Dickson, Yulia Krasikova, Pavel Pestryakov, Olga Lavrik, and Marc S. Wold

Essential functions of the 32 kDa subunit of yeast replication protein A
Nucleic Acids Research Advance Access published on February 25, 2009
Nucl. Acids Res. 2009 37: 2313-2326; doi:10.1093/nar/gkp090 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Laura J. Bailey, Tricia J. Cluett, Aurelio Reyes, Tom A. Prolla, Joanna Poulton, Christiaan Leeuwenburgh, and Ian J. Holt

Mice expressing an error-prone DNA polymerase in mitochondria display elevated replication pausing and chromosomal breakage at fragile sites of mitochondrial DNA
Nucleic Acids Research Advance Access published on February 25, 2009
Nucl. Acids Res. 2009 37: 2327-2335; doi:10.1093/nar/gkp091 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics

Get checked abstract Sean D. Hooper, Iain J. Anderson, Amrita Pati, Daniel Dalevi, Konstantinos Mavromatis, and Nikos C. Kyrpides

Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach
Nucleic Acids Research Advance Access published on February 17, 2009
Nucl. Acids Res. 2009 37: 2096-2104; doi:10.1093/nar/gkp075 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Katsuya Tsuchihara, Yutaka Suzuki, Hiroyuki Wakaguri, Takuma Irie, Kousuke Tanimoto, Shin-ichi Hashimoto, Kouji Matsushima, Junko Mizushima-Sugano, Riu Yamashita, Kenta Nakai, David Bentley, Hiroyasu Esumi, and Sumio Sugano

Massive transcriptional start site analysis of human genes in hypoxia cells
Nucleic Acids Research Advance Access published on February 22, 2009
Nucl. Acids Res. 2009 37: 2249-2263; doi:10.1093/nar/gkp066 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract María Méndez-Lago, Jadwiga Wild, Siobhan L. Whitehead, Alan Tracey, Beatriz de Pablos, Jane Rogers, Waclaw Szybalski, and Alfredo Villasante

Novel sequencing strategy for repetitive DNA in a Drosophila BAC clone reveals that the centromeric region of the Y chromosome evolved from a telomere
Nucleic Acids Research Advance Access published on February 23, 2009
Nucl. Acids Res. 2009 37: 2264-2273; doi:10.1093/nar/gkp085 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract Sushil Kumar Tomar, Neha Dhimole, Moon Chatterjee, and Balaji Prakash

Distinct GDP/GTP bound states of the tandem G-domains of EngA regulate ribosome binding
Nucleic Acids Research Advance Access published on February 26, 2009
Nucl. Acids Res. 2009 37: 2359-2370; doi:10.1093/nar/gkp107 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes

Get checked abstract Kelly L. Sanders, Lucy E. Catto, Stuart R. W. Bellamy, and Stephen E. Halford

Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands
Nucleic Acids Research Advance Access published on February 17, 2009
Nucl. Acids Res. 2009 37: 2105-2115; doi:10.1093/nar/gkp046 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Qiu-Mei Zhang-Akiyama, Hironobu Morinaga, Masahiro Kikuchi, Shin-Ichiro Yonekura, Hiroshi Sugiyama, Kazuo Yamamoto, and Shuji Yonei

KsgA, a 16S rRNA adenine methyltransferase, has a novel DNA glycosylase/AP lyase activity to prevent mutations in Escherichia coli
Nucleic Acids Research Advance Access published on February 17, 2009
Nucl. Acids Res. 2009 37: 2116-2125; doi:10.1093/nar/gkp057 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sushil Kumar and Patrick C. Swanson

Full-length RAG1 promotes contact with coding and intersignal sequences in RAG protein complexes bound to recombination signals paired in cis
Nucleic Acids Research Advance Access published on February 20, 2009
Nucl. Acids Res. 2009 37: 2211-2226; doi:10.1093/nar/gkp047 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Joshua N. Farb and Scott W. Morrical

Functional complementation of UvsX and UvsY mutations in the mediation of T4 homologous recombination
Nucleic Acids Research Advance Access published on February 25, 2009
Nucl. Acids Res. 2009 37: 2336-2345; doi:10.1093/nar/gkp096 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Laetitia Bonné, Sarah Bigot, Fabien Chevalier, Jean-François Allemand, and François-Xavier Barre

Asymmetric DNA requirements in Xer recombination activation by FtsK
Nucleic Acids Research Advance Access published on February 26, 2009
Nucl. Acids Res. 2009 37: 2371-2380; doi:10.1093/nar/gkp104 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Udesh de Silva, Fred W. Perrino, and Thomas Hollis

DNA binding induces active site conformational change in the human TREX2 3'-exonuclease
Nucleic Acids Research Advance Access published on March 24, 2009
Nucl. Acids Res. 2009 37: 2411-2417; doi:10.1093/nar/gkp025 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA

Get checked abstract Akiko Takeuchi, David Schmitt, Charles Chapple, Elena Babaylova, Galina Karpova, Roderic Guigo, Alain Krol, and Christine Allmang

A short motif in Drosophila SECIS Binding Protein 2 provides differential binding affinity to SECIS RNA hairpins
Nucleic Acids Research Advance Access published on February 17, 2009
Nucl. Acids Res. 2009 37: 2126-2141; doi:10.1093/nar/gkp078 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract You Li, Eric S. Ho, Samuel I. Gunderson, and Megerditch Kiledjian

Mutational analysis of a Dcp2-binding element reveals general enhancement of decapping by 5'-end stem-loop structures
Nucleic Acids Research Advance Access published on February 20, 2009
Nucl. Acids Res. 2009 37: 2227-2237; doi:10.1093/nar/gkp087 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Mark Carlile, Daniel Swan, Kelly Jackson, Keziah Preston-Fayers, Benoit Ballester, Paul Flicek, and Andreas Werner

Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues
Nucleic Acids Research Advance Access published on February 23, 2009
Nucl. Acids Res. 2009 37: 2274-2282; doi:10.1093/nar/gkp088 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jesse Stombaugh, Craig L. Zirbel, Eric Westhof, and Neocles B. Leontis

Frequency and isostericity of RNA base pairs
Nucleic Acids Research Advance Access published on February 24, 2009
Nucl. Acids Res. 2009 37: 2294-2312; doi:10.1093/nar/gkp011 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Yuan He, Rebecca Imhoff, Anirban Sahu, and Ishwar Radhakrishnan

Solution structure of a novel zinc finger motif in the SAP30 polypeptide of the Sin3 corepressor complex and its potential role in nucleic acid recognition
Nucleic Acids Research Advance Access published on February 17, 2009
Nucl. Acids Res. 2009 37: 2142-2152; doi:10.1093/nar/gkp051 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Tanya Zaliznyak, Rahda Bonala, Sivaprasad Attaluri, Francis Johnson, and Carlos de los Santos

Solution structure of DNA containing -OH-PdG: the mutagenic adduct produced by acrolein
Nucleic Acids Research Advance Access published on February 17, 2009
Nucl. Acids Res. 2009 37: 2153-2163; doi:10.1093/nar/gkp076 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yuan-Chao Lou, Shu-Yi Wei, M. Rajasekaran, Chun-Chi Chou, Hong-Ming Hsu, Jung-Hsiang Tai, and Chinpan Chen

NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalis
Nucleic Acids Research Advance Access published on February 26, 2009
Nucl. Acids Res. 2009 37: 2381-2394; doi:10.1093/nar/gkp097 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Karin V. Loscha, Kristaps Jaudzems, Charikleia Ioannou, Xun-Cheng Su, Flynn R. Hill, Gottfried Otting, Nicholas E. Dixon, and Edvards Liepinsh

A novel zinc-binding fold in the helicase interaction domain of the Bacillus subtilis DnaI helicase loader
Nucleic Acids Research Advance Access published on March 2, 2009
Nucl. Acids Res. 2009 37: 2395-2404; doi:10.1093/nar/gkp092 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online

Get checked abstract Bogdan Tokovenko, Rostyslav Golda, Oleksiy Protas, Maria Obolenskaya, and Anna El'skaya

COTRASIF: conservation-aided transcription-factor-binding site finder
Nucleic Acids Research Advance Access published on March 5, 2009
Nucl. Acids Res. 2009 37: e49; doi:10.1093/nar/gkp084 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Ina Weidenfeld, Manfred Gossen, Rainer Löw, David Kentner, Stefan Berger, Dirk Görlich, Dusan Bartsch, Hermann Bujard, and Kai Schönig

Inducible expression of coding and inhibitory RNAs from retargetable genomic loci
Nucleic Acids Research Advance Access published on March 5, 2009
Nucl. Acids Res. 2009 37: e50; doi:10.1093/nar/gkp108 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Hongye Ye, Mo Chao Huang, Mo-Huang Li, and Jackie Y. Ying

Experimental analysis of gene assembly with TopDown one-step real-time gene synthesis
Nucleic Acids Research Advance Access published on March 5, 2009
Nucl. Acids Res. 2009 37: e51; doi:10.1093/nar/gkp118 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Brona Brejová, Tomás Vinar, Yangyi Chen, Shengyue Wang, Guoping Zhao, Daniel G. Brown, Ming Li, and Yan Zhou

Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence
Nucleic Acids Research Advance Access published on March 5, 2009
Nucl. Acids Res. 2009 37: e52; doi:10.1093/nar/gkp052 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract J. Hooyberghs, P. Van Hummelen, and E. Carlon

The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters
Nucleic Acids Research Advance Access published on March 6, 2009
Nucl. Acids Res. 2009 37: e53; doi:10.1093/nar/gkp109 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Gregory R. Stuart, William C. Copeland, and Micheline K. Strand

Construction and application of a protein and genetic interaction network (yeast interactome)
Nucleic Acids Research Advance Access published on March 9, 2009
Nucl. Acids Res. 2009 37: e54; doi:10.1093/nar/gkp140 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Omar Nyabi, Michael Naessens, Katharina Haigh, Agnieszka Gembarska, Steven Goossens, Marion Maetens, Sarah De Clercq, Benjamin Drogat, Lieven Haenebalcke, Sonia Bartunkova, Ilse De Vos, Bram De Craene, Mansour Karimi, Geert Berx, Andras Nagy, Pierre Hilson, Jean-Christophe Marine, and Jody J. Haigh

Efficient mouse transgenesis using Gateway-compatible ROSA26 locus targeting vectors and F1 hybrid ES cells
Nucleic Acids Research Advance Access published on March 11, 2009
Nucl. Acids Res. 2009 37: e55; doi:10.1093/nar/gkp112 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Takashi Abe, Kazuhito Goda, Kazunobu Futami, and Yasuhiro Furuichi

Detection of siRNA administered to cells and animals by using a fluorescence intensity distribution analysis polarization system
Nucleic Acids Research Advance Access published on March 12, 2009
Nucl. Acids Res. 2009 37: e56; doi:10.1093/nar/gkp131 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 37 ISSUE 7 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkp344 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkp343 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkp345 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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