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Previous Next 		Contents: Volume 37, Number 9, May 2009   [Index by Author] 

Down Gene Regulation, Chromatin and Epigenetics
Down Genome Integrity, Repair and Replication
Down Genomics
Down Molecular Biology
Down Nucleic Acid Enzymes
Down RNA
Down Structural Biology
Down Methods Online
Down Corrigendum
Down Front-Matter/Back-Matter


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To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.

Gene Regulation, Chromatin and Epigenetics Back

Bessie W. Kebaara and Audrey L. Atkin
Long 3'-UTRs target wild-type mRNAs for nonsense-mediated mRNA decay in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on March 6, 2009
Nucl. Acids Res. 2009 37: 2771-2778; doi:10.1093/nar/gkp146 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Feng Cui and Victor B. Zhurkin
Distinctive sequence patterns in metazoan and yeast nucleosomes: Implications for linker histone binding to AT-rich and methylated DNA
Nucleic Acids Research Advance Access published on March 12, 2009
Nucl. Acids Res. 2009 37: 2818-2829; doi:10.1093/nar/gkp113 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Ian R. Logan, Hesta V. McNeill, Susan Cook, Xiaohong Lu, David W. Meek, Frances V. Fuller-Pace, John Lunec, and Craig N. Robson
Heat shock factor-1 modulates p53 activity in the transcriptional response to DNA damage
Nucleic Acids Research Advance Access published on March 18, 2009
Nucl. Acids Res. 2009 37: 2962-2973; doi:10.1093/nar/gkp180 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Peter G. Hawkins, Sharon Santoso, Christopher Adams, Vasiliki Anest, and Kevin V. Morris
Promoter targeted small RNAs induce long-term transcriptional gene silencing in human cells
Nucleic Acids Research Advance Access published on March 20, 2009
Nucl. Acids Res. 2009 37: 2984-2995; doi:10.1093/nar/gkp127 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Magnus L. Hansson, Anita E. Popko-Scibor, Mariana Saint Just Ribeiro, Beverley M. Dancy, Mikael J. Lindberg, Philip A. Cole, and Annika E. Wallberg
The transcriptional coactivator MAML1 regulates p300 autoacetylation and HAT activity
Nucleic Acids Research Advance Access published on March 20, 2009
Nucl. Acids Res. 2009 37: 2996-3006; doi:10.1093/nar/gkp163 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jan Lukas, Petr Mazna, Tomas Valenta, Lenka Doubravska, Vendula Pospichalova, Martina Vojtechova, Bohumil Fafilek, Robert Ivanek, Jiri Plachy, Jakub Novak, and Vladimir Korinek
Dazap2 modulates transcription driven by the Wnt effector TCF-4
Nucleic Acids Research Advance Access published on March 20, 2009
Nucl. Acids Res. 2009 37: 3007-3020; doi:10.1093/nar/gkp179 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genome Integrity, Repair and Replication Back

Sarah K. Scouten Ponticelli, Jill M. Duzen, and Mark D. Sutton
Contributions of the individual hydrophobic clefts of the Escherichia coli β sliding clamp to clamp loading, DNA replication and clamp recycling
Nucleic Acids Research Advance Access published on March 11, 2009
Nucl. Acids Res. 2009 37: 2796-2809; doi:10.1093/nar/gkp128 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Scott D. McCulloch, Robert J. Kokoska, Parie Garg, Peter M. Burgers, and Thomas A. Kunkel
The efficiency and fidelity of 8-oxo-guanine bypass by DNA polymerases {delta} and {eta}
Nucleic Acids Research Advance Access published on March 12, 2009
Nucl. Acids Res. 2009 37: 2830-2840; doi:10.1093/nar/gkp103 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genomics Back

Dwayne A. Elias, Aindrila Mukhopadhyay, Marcin P. Joachimiak, Elliott C. Drury, Alyssa M. Redding, Huei-Che B. Yen, Matthew W. Fields, Terry C. Hazen, Adam P. Arkin, Jay D. Keasling, and Judy D. Wall
Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation
Nucleic Acids Research Advance Access published on March 17, 2009
Nucl. Acids Res. 2009 37: 2926-2939; doi:10.1093/nar/gkp164 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Yoko Asakura and Ichizo Kobayashi
From damaged genome to cell surface: transcriptome changes during bacterial cell death triggered by loss of a restriction–modification gene complex
Nucleic Acids Research Advance Access published on March 20, 2009
Nucl. Acids Res. 2009 37: 3021-3031; doi:10.1093/nar/gkp148 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology Back

Amelia K. Linnemann and Stephen A. Krawetz
Silencing by nuclear matrix attachment distinguishes cell-type specificity: association with increased proliferation capacity
Nucleic Acids Research Advance Access published on March 10, 2009
Nucl. Acids Res. 2009 37: 2779-2788; doi:10.1093/nar/gkp135 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Manikandan Paramasivam, Alexandro Membrino, Susanna Cogoi, Hirokazu Fukuda, Hitoshi Nakagama, and Luigi E. Xodo
Protein hnRNP A1 and its derivative Up1 unfold quadruplex DNA in the human KRAS promoter: implications for transcription
Nucleic Acids Research Advance Access published on March 12, 2009
Nucl. Acids Res. 2009 37: 2841-2853; doi:10.1093/nar/gkp138 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Hana Kim, Keunsoo Kang, and Joomyeong Kim
AEBP2 as a potential targeting protein for Polycomb Repression Complex PRC2
Nucleic Acids Research Advance Access published on March 17, 2009
Nucl. Acids Res. 2009 37: 2940-2950; doi:10.1093/nar/gkp149 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

C. Benjamin Lai, Ying Zhang, Sally L. Rogers, and Dixie L. Mager
Creation of the two isoforms of rodent NKG2D was driven by a B1 retrotransposon insertion
Nucleic Acids Research Advance Access published on March 20, 2009
Nucl. Acids Res. 2009 37: 3032-3043; doi:10.1093/nar/gkp174 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Emily Towers, Jonathan Gilley, Rebecca Randall, Rosie Hughes, Mark Kristiansen, and Jonathan Ham
The proapoptotic dp5 gene is a direct target of the MLK-JNK-c-Jun pathway in sympathetic neurons
Nucleic Acids Research Advance Access published on March 20, 2009
Nucl. Acids Res. 2009 37: 3044-3060; doi:10.1093/nar/gkp175 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Georgios Giamas, Leandro Castellano, Qin Feng, Uwe Knippschild, Jimmy Jacob, Ross S. Thomas, R. Charles Coombes, Carolyn L. Smith, Long R. Jiao, and Justin Stebbing
CK1{delta} modulates the transcriptional activity of ER{alpha} via AIB1 in an estrogen-dependent manner and regulates ER{alpha}–AIB1 interactions
Nucleic Acids Research Advance Access published on April 1, 2009
Nucl. Acids Res. 2009 37: 3110-3123; doi:10.1093/nar/gkp136 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes Back

Ruzaliya Fazlieva, Cynthia S. Spittle, Darlene Morrissey, Harutoshi Hayashi, Hong Yan, and Yoshihiro Matsumoto
Proofreading exonuclease activity of human DNA polymerase {delta} and its effects on lesion-bypass DNA synthesis
Nucleic Acids Research Advance Access published on March 12, 2009
Nucl. Acids Res. 2009 37: 2854-2866; doi:10.1093/nar/gkp155 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Shaun M. Lippow, Patti M. Aha, Matthew H. Parker, William J. Blake, Brian M. Baynes, and Dasa Lipovsek
Creation of a type IIS restriction endonuclease with a long recognition sequence
Nucleic Acids Research Advance Access published on March 20, 2009
Nucl. Acids Res. 2009 37: 3061-3073; doi:10.1093/nar/gkp182 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA Back

Jesper B. Bramsen, Maria B. Laursen, Anne F. Nielsen, Thomas B. Hansen, Claus Bus, Niels Langkjær, B. Ravindra Babu, Torben Højland, Mikhail Abramov, Arthur Van Aerschot, Dalibor Odadzic, Romualdas Smicius, Jens Haas, Cordula Andree, Jharna Barman, Malgorzata Wenska, Puneet Srivastava, Chuanzheng Zhou, Dmytro Honcharenko, Simone Hess, Elke Müller, Georgii V. Bobkov, Sergey N. Mikhailov, Eugenio Fava, Thomas F. Meyer, Jyoti Chattopadhyaya, Marino Zerial, Joachim W. Engels, Piet Herdewijn, Jesper Wengel, and Jørgen Kjems
A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity
Nucleic Acids Research Advance Access published on March 12, 2009
Nucl. Acids Res. 2009 37: 2867-2881; doi:10.1093/nar/gkp106 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Basma El Yacoubi, Benjamin Lyons, Yulien Cruz, Robert Reddy, Brian Nordin, Fabio Agnelli, James R. Williamson, Paul Schimmel, Manal A. Swairjo, and Valérie de Crécy-Lagard
The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA
Nucleic Acids Research Advance Access published on March 13, 2009
Nucl. Acids Res. 2009 37: 2894-2909; doi:10.1093/nar/gkp152 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Keith T. Gagnon, Show-Yi Ju, Michael B. Goshe, E. Stuart Maxwell, and Stefan Franzen
A role for hydrophobicity in a Diels–Alder reaction catalyzed by pyridyl-modified RNA
Nucleic Acids Research Advance Access published on March 20, 2009
Nucl. Acids Res. 2009 37: 3074-3082; doi:10.1093/nar/gkp177 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Bogna Szarzynska, Lukasz Sobkowiak, Bikram Datt Pant, Salma Balazadeh, Wolf-Rüdiger Scheible, Bernd Mueller-Roeber, Artur Jarmolowski, and Zofia Szweykowska-Kulinska
Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs
Nucleic Acids Research Advance Access published on March 20, 2009
Nucl. Acids Res. 2009 37: 3083-3093; doi:10.1093/nar/gkp189 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jiehua Zhou, Piotr Swiderski, Haitang Li, Jane Zhang, C. Preston Neff, Ramesh Akkina, and John J. Rossi
Selection, characterization and application of new RNA HIV gp 120 aptamers for facile delivery of Dicer substrate siRNAs into HIV infected cells
Nucleic Acids Research Advance Access published on March 21, 2009
Nucl. Acids Res. 2009 37: 3094-3109; doi:10.1093/nar/gkp185 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology Back

Chiara Zurla, Carlo Manzo, David Dunlap, Dale E. A. Lewis, Sankar Adhya, and Laura Finzi
Direct demonstration and quantification of long-range DNA looping by the {lambda} bacteriophage repressor
Nucleic Acids Research Advance Access published on March 10, 2009
Nucl. Acids Res. 2009 37: 2789-2795; doi:10.1093/nar/gkp134 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Saikat Chakraborty, Suruchi Sharma, Prabal K. Maiti, and Yamuna Krishnan
The poly dA helix: a new structural motif for high performance DNA-based molecular switches
Nucleic Acids Research Advance Access published on March 11, 2009
Nucl. Acids Res. 2009 37: 2810-2817; doi:10.1093/nar/gkp133 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Davide Demurtas, Arnaud Amzallag, Eric J. Rawdon, John H. Maddocks, Jacques Dubochet, and Andrzej Stasiak
Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles
Nucleic Acids Research Advance Access published on March 12, 2009
Nucl. Acids Res. 2009 37: 2882-2893; doi:10.1093/nar/gkp137 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Yoko Suzuki, Akiko Noma, Tsutomu Suzuki, Ryuichiro Ishitani, and Osamu Nureki
Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4
Nucleic Acids Research Advance Access published on March 14, 2009
Nucl. Acids Res. 2009 37: 2910-2925; doi:10.1093/nar/gkp158 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Francesca Chignola, Massimiliano Gaetani, Ana Rebane, Tõnis Org, Luca Mollica, Chiara Zucchelli, Andrea Spitaleri, Valeria Mannella, Pärt Peterson, and Giovanna Musco
The solution structure of the first PHD finger of autoimmune regulator in complex with non-modified histone H3 tail reveals the antagonistic role of H3R2 methylation
Nucleic Acids Research Advance Access published on March 17, 2009
Nucl. Acids Res. 2009 37: 2951-2961; doi:10.1093/nar/gkp166 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Ana Eulalio, Felix Tritschler, Regina Büttner, Oliver Weichenrieder, Elisa Izaurralde, and Vincent Truffault
The RRM domain in GW182 proteins contributes to miRNA-mediated gene silencing
Nucleic Acids Research Advance Access published on March 18, 2009
Nucl. Acids Res. 2009 37: 2974-2983; doi:10.1093/nar/gkp173 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online Back

Liam Childs, Zoran Nikoloski, Patrick May, and Dirk Walther
Identification and classification of ncRNA molecules using graph properties
Nucleic Acids Research Advance Access published on April 1, 2009
Nucl. Acids Res. 2009 37: e66; doi:10.1093/nar/gkp206 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

François-Olivier Desmet, Dalil Hamroun, Marine Lalande, Gwenaëlle Collod-Béroud, Mireille Claustres, and Christophe Béroud
Human Splicing Finder: an online bioinformatics tool to predict splicing signals
Nucleic Acids Research Advance Access published on April 1, 2009
Nucl. Acids Res. 2009 37: e67; doi:10.1093/nar/gkp215 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Xiangduo Kong, Samarendra K. Mohanty, Jared Stephens, Jason T. Heale, Veronica Gomez-Godinez, Linda Z. Shi, Jong-Soo Kim, Kyoko Yokomori, and Michael W. Berns
Comparative analysis of different laser systems to study cellular responses to DNA damage in mammalian cells
Nucleic Acids Research Advance Access published on April 7, 2009
Nucl. Acids Res. 2009 37: e68; doi:10.1093/nar/gkp221 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Ho-Ming Chen and Shu-Hsing Wu
Mining small RNA sequencing data: a new approach to identify small nucleolar RNAs in Arabidopsis
Nucleic Acids Research Advance Access published on April 8, 2009
Nucl. Acids Res. 2009 37: e69; doi:10.1093/nar/gkp225 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jose Luis Ortega-Roldan, Malene Ringkjøbing Jensen, Bernhard Brutscher, Ana I. Azuaga, Martin Blackledge, and Nico A. J. van Nuland
Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex
Nucleic Acids Research Advance Access published on April 9, 2009
Nucl. Acids Res. 2009 37: e70; doi:10.1093/nar/gkp211 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Daiying Xu and Hua Shi
Composite RNA aptamers as functional mimics of proteins
Nucleic Acids Research Advance Access published on April 20, 2009
Nucl. Acids Res. 2009 37: e71; doi:10.1093/nar/gkp243 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Corrigendum Back

Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, Vadim Miller, Ilene Mizrachi, James Ostell, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko, and Jian Ye
Database resources of the National Center for Biotechnology Information
Nucl. Acids Res. 2009 37: 3124; doi:10.1093/nar/gkp382 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Front-Matter/Back-Matter Back

Nucleic Acids Research: VOLUME 37 ISSUE 9 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkp459 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkp458 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkp472 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.