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Previous Next 		Contents: Volume 36, Number 9, May 2008   [Index by Author] 

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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.

Survey and Summary Back

Karin Hoelzer, Laura A. Shackelton, and Colin R. Parrish
Presence and role of cytosine methylation in DNA viruses of animals
Nucleic Acids Research Advance Access published on March 26, 2008
Nucl. Acids Res. 2008 36: 2825-2837; doi:10.1093/nar/gkn121 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chemistry Back

Masafumi Minoshima, Toshikazu Bando, Shunta Sasaki, Jun Fujimoto, and Hiroshi Sugiyama
Pyrrole-imidazole hairpin polyamides with high affinity at 5'–CGCG–3' DNA sequence; influence of cytosine methylation on binding
Nucleic Acids Research Advance Access published on April 1, 2008
Nucl. Acids Res. 2008 36: 2889-2894; doi:10.1093/nar/gkn116 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Mehrdad Majlessi and Michael M. Becker
Formation of the double helix: a mutational study
Nucleic Acids Research Advance Access published on April 3, 2008
Nucl. Acids Res. 2008 36: 2981-2989; doi:10.1093/nar/gkn134 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology Back

Hairong Wei, Pei Fen Kuan, Shulan Tian, Chuhu Yang, Jeff Nie, Srikumar Sengupta, Victor Ruotti, Gudrun A. Jonsdottir, Sunduz Keles, James A. Thomson, and Ron Stewart
A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets
Nucleic Acids Research Advance Access published on April 1, 2008
Nucl. Acids Res. 2008 36: 2926-2938; doi:10.1093/nar/gkn133 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Marcela Dávila López, Magnus Alm Rosenblad, and Tore Samuelsson
Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components
Nucleic Acids Research Advance Access published on April 4, 2008
Nucl. Acids Res. 2008 36: 3001-3010; doi:10.1093/nar/gkn142 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Yanzhi Guo, Lezheng Yu, Zhining Wen, and Menglong Li
Using support vector machine combined with auto covariance to predict protein–protein interactions from protein sequences
Nucleic Acids Research Advance Access published on April 4, 2008
Nucl. Acids Res. 2008 36: 3025-3030; doi:10.1093/nar/gkn159 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

A. C. Ziesel, M. A. Chrenek, and P. W. Wong
MultiPriDe: automated batch development of quantitative real-time PCR primers
Nucleic Acids Research Advance Access published on April 8, 2008
Nucl. Acids Res. 2008 36: 3095-3100; doi:10.1093/nar/gkn165 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yingjia Shen, Guoli Ji, Brian J. Haas, Xiaohui Wu, Jianti Zheng, Greg J. Reese, and Qingshun Quinn Li
Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation
Nucleic Acids Research Advance Access published on April 13, 2008
Nucl. Acids Res. 2008 36: 3150-3161; doi:10.1093/nar/gkn158 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics Back

Hameed Khan and John M. Archibald
Lateral transfer of introns in the cryptophyte plastid genome
Nucleic Acids Research Advance Access published on April 8, 2008
Nucl. Acids Res. 2008 36: 3043-3053; doi:10.1093/nar/gkn095 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology Back

Jun Gao, Mari K. Davidson, and Wayne P. Wahls
Distinct regions of ATF/CREB proteins Atf1 and Pcr1 control recombination hotspot ade6–M26 and the osmotic stress response
Nucleic Acids Research Advance Access published on March 29, 2008
Nucl. Acids Res. 2008 36: 2838-2851; doi:10.1093/nar/gkn037 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Marta Lloret-Llinares, Clément Carré, Alejandro Vaquero, Natalia de Olano, and Fernando Azorín
Characterization of Drosophila melanogaster JmjC+N histone demethylases
Nucleic Acids Research Advance Access published on March 29, 2008
Nucl. Acids Res. 2008 36: 2852-2863; doi:10.1093/nar/gkn098 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gudrun Bjornsdottir and Lawrence C. Myers
Minimal components of the RNA polymerase II transcription apparatus determine the consensus TATA box
Nucleic Acids Research Advance Access published on April 1, 2008
Nucl. Acids Res. 2008 36: 2906-2916; doi:10.1093/nar/gkn130 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Zehui Hong, Jie Jiang, Li Lan, Satoshi Nakajima, Shin-ichiro Kanno, Haruhiko Koseki, and Akira Yasui
A polycomb group protein, PHF1, is involved in the response to DNA double-strand breaks in human cell
Nucleic Acids Research Advance Access published on April 1, 2008
Nucl. Acids Res. 2008 36: 2939-2947; doi:10.1093/nar/gkn146 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Ralf D. Kirschner, Katja Sänger, Gerd A. Müller, and Kurt Engeland
Transcriptional activation of the tumor suppressor and differentiation gene S100A2 by a novel p63-binding site
Nucleic Acids Research Advance Access published on April 3, 2008
Nucl. Acids Res. 2008 36: 2969-2980; doi:10.1093/nar/gkn132 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Takako Hattori, Francoise Coustry, Shelley Stephens, Heidi Eberspaecher, Masaharu Takigawa, Hideyo Yasuda, and Benoit de Crombrugghe
Transcriptional regulation of chondrogenesis by coactivator Tip60 via chromatin association with Sox9 and Sox5
Nucleic Acids Research Advance Access published on April 4, 2008
Nucl. Acids Res. 2008 36: 3011-3024; doi:10.1093/nar/gkn150 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Qiuhe Lu, Jing Han, Ligang Zhou, James A. Coker, Priya DasSarma, Shiladitya DasSarma, and Hua Xiang
Dissection of the regulatory mechanism of a heat-shock responsive promoter in Haloarchaea: a new paradigm for general transcription factor directed archaeal gene regulation
Nucleic Acids Research Advance Access published on April 5, 2008
Nucl. Acids Res. 2008 36: 3031-3042; doi:10.1093/nar/gkn152 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Marie Wolf, Maria Dimitrova, Thomas F. Baumert, and Catherine Schuster
The major form of hepatitis C virus alternate reading frame protein is suppressed by core protein expression
Nucleic Acids Research Advance Access published on April 8, 2008
Nucl. Acids Res. 2008 36: 3054-3064; doi:10.1093/nar/gkn111 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Joanna Rorbach, Abdul Aziz Yusoff, Helen Tuppen, Dyg P. Abg-Kamaludin, Zofia M.A. Chrzanowska-Lightowlers, Robert W. Taylor, Douglass M. Turnbull, Robert McFarland, and Robert N. Lightowlers
Overexpression of human mitochondrial valyl tRNA synthetase can partially restore levels of cognate mt-tRNAVal carrying the pathogenic C25U mutation
Nucleic Acids Research Advance Access published on April 8, 2008
Nucl. Acids Res. 2008 36: 3065-3074; doi:10.1093/nar/gkn147 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Peter Dy, Alfredo Penzo-Méndez, Hongzhe Wang, Carlos E. Pedraza, Wendy B. Macklin, and Véronique Lefebvre
The three SoxC proteins—Sox4, Sox11 and Sox12—exhibit overlapping expression patterns and molecular properties
Nucleic Acids Research Advance Access published on April 10, 2008
Nucl. Acids Res. 2008 36: 3101-3117; doi:10.1093/nar/gkn162 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes Back

Catherine P. Lu, Jennifer E. Posey, and David B. Roth
Understanding how the V(D)J recombinase catalyzes transesterification: distinctions between DNA cleavage and transposition
Nucleic Acids Research Advance Access published on March 29, 2008
Nucl. Acids Res. 2008 36: 2864-2873; doi:10.1093/nar/gkn128 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Rui-Zhe Zhou, Luis Blanco, Miguel Garcia-Diaz, Katarzyna Bebenek, Thomas A. Kunkel, and Lawrence F. Povirk
Tolerance for 8-oxoguanine but not thymine glycol in alignment-based gap filling of partially complementary double-strand break ends by DNA polymerase {lambda} in human nuclear extracts
Nucleic Acids Research Advance Access published on April 1, 2008
Nucl. Acids Res. 2008 36: 2895-2905; doi:10.1093/nar/gkn126 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Ben Youngblood, Eleanor Bonnist, David T.F. Dryden, Anita C. Jones, and Norbert O. Reich
Differential stabilization of reaction intermediates: specificity checkpoints for M.EcoRI revealed by transient fluorescence and fluorescence lifetime studies
Nucleic Acids Research Advance Access published on April 1, 2008
Nucl. Acids Res. 2008 36: 2917-2925; doi:10.1093/nar/gkn131 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Bryan J. Davis, Jody M. Havener, and Dale A. Ramsden
End-bridging is required for pol µ to efficiently promote repair of noncomplementary ends by nonhomologous end joining
Nucleic Acids Research Advance Access published on April 8, 2008
Nucl. Acids Res. 2008 36: 3085-3094; doi:10.1093/nar/gkn164 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA Back

Ying Poi Liu, Joost Haasnoot, Olivier ter Brake, Ben Berkhout, and Pavlina Konstantinova
Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron
Nucleic Acids Research Advance Access published on March 16, 2008
Nucl. Acids Res. 2008 36: 2811-2824; doi:10.1093/nar/gkn109 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Seweryn Mroczek and Joanna Kufel
Apoptotic signals induce specific degradation of ribosomal RNA in yeast
Nucleic Acids Research Advance Access published on April 1, 2008
Nucl. Acids Res. 2008 36: 2874-2888; doi:10.1093/nar/gkm1100 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Benjamin J. Kaspar, Abby L. Bifano, and Mark G. Caprara
A shared RNA-binding site in the Pet54 protein is required for translational activation and group I intron splicing in yeast mitochondria
Nucleic Acids Research Advance Access published on April 3, 2008
Nucl. Acids Res. 2008 36: 2958-2968; doi:10.1093/nar/gkn045 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Abigail L. Brown, Anne T. Perrotta, Timothy S. Wadkins, and Michael D. Been
The poly(A) site sequence in HDV RNA alters both extent and rate of self-cleavage of the antigenomic ribozyme
Nucleic Acids Research Advance Access published on April 3, 2008
Nucl. Acids Res. 2008 36: 2990-3000; doi:10.1093/nar/gkn156 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Delphine Ciais, Markus T. Bohnsack, and David Tollervey
The mRNA encoding the yeast ARE-binding protein Cth2 is generated by a novel 3' processing pathway
Nucleic Acids Research Advance Access published on April 8, 2008
Nucl. Acids Res. 2008 36: 3075-3084; doi:10.1093/nar/gkn160 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Aarti Sevilimedu, Hua Shi, and John T. Lis
TFIIB aptamers inhibit transcription by perturbing PIC formation at distinct stages
Nucleic Acids Research Advance Access published on April 10, 2008
Nucl. Acids Res. 2008 36: 3118-3127; doi:10.1093/nar/gkn163 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology Back

Kuo-Hsiang Tang, Marc Niebuhr, Chang-Shung Tung, Hsiu-chien Chan, Chia-Cheng Chou, and Ming-Daw Tsai
Mismatched dNTP incorporation by DNA polymerase β does not proceed via globally different conformational pathways
Nucleic Acids Research Advance Access published on April 2, 2008
Nucl. Acids Res. 2008 36: 2948-2957; doi:10.1093/nar/gkn138 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Xiaohua Chen, Haiqing Hua, Kuppusamy Balamurugan, Xiangming Kong, Limei Zhang, Graham N. George, Oleg Georgiev, Walter Schaffner, and David P. Giedroc
Copper sensing function of Drosophila metal-responsive transcription factor-1 is mediated by a tetranuclear Cu(I) cluster
Nucleic Acids Research Advance Access published on April 13, 2008
Nucl. Acids Res. 2008 36: 3128-3138; doi:10.1093/nar/gkn103 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Michael P. Killoran and James L. Keck
Structure and function of the regulatory C-terminal HRDC domain from Deinococcus radiodurans RecQ
Nucleic Acids Research Advance Access published on April 13, 2008
Nucl. Acids Res. 2008 36: 3139-3149; doi:10.1093/nar/gkn143 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online Back

Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, and Kazuyuki Aihara
Uncovering signal transduction networks from high-throughput data by integer linear programming
Nucleic Acids Research Advance Access published on April 13, 2008
Nucl. Acids Res. 2008 36: e48; doi:10.1093/nar/gkn145 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gary P. Wang, Alexandrine Garrigue, Angela Ciuffi, Keshet Ronen, Jeremy Leipzig, Charles Berry, Chantal Lagresle-Peyrou, Fatine Benjelloun, Salima Hacein-Bey-Abina, Alain Fischer, Marina Cavazzana-Calvo, and Frederic D. Bushman
DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer
Nucleic Acids Research Advance Access published on April 14, 2008
Nucl. Acids Res. 2008 36: e49; doi:10.1093/nar/gkn125 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Hua Wei, Caitlin Therrien, Aine Blanchard, Shengxi Guan, and Zhenyu Zhu
The Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases
Nucleic Acids Research Advance Access published on April 15, 2008
Nucl. Acids Res. 2008 36: e50; doi:10.1093/nar/gkn182 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Michael R. Dyson, Rajika L. Perera, S. Paul Shadbolt, Lynn Biderman, Krystyna Bromek, Natalia V. Murzina, and John McCafferty
Identification of soluble protein fragments by gene fragmentation and genetic selection
Nucleic Acids Research Advance Access published on April 17, 2008
Nucl. Acids Res. 2008 36: e51; doi:10.1093/nar/gkn151 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Andreas Wilm, Desmond G. Higgins, and Cédric Notredame
R-Coffee: a method for multiple alignment of non-coding RNA
Nucleic Acids Research Advance Access published on April 17, 2008
Nucl. Acids Res. 2008 36: e52; doi:10.1093/nar/gkn174 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Cecilia Dahlgren, Hong-Yan Zhang, Quan Du, Maria Grahn, Gunnar Norstedt, Claes Wahlestedt, and Zicai Liang
Analysis of siRNA specificity on targets with double-nucleotide mismatches
Nucleic Acids Research Advance Access published on April 17, 2008
Nucl. Acids Res. 2008 36: e53; doi:10.1093/nar/gkn190 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Changlin Fu, Daniel R. Wehr, Janice Edwards, and Brian Hauge
Rapid one-step recombinational cloning
Nucleic Acids Research Advance Access published on April 19, 2008
Nucl. Acids Res. 2008 36: e54; doi:10.1093/nar/gkn167 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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.