Nucleic Acids Research

Survey and Summary:

Nicki Tiffin, Euan Adie, Frances Turner, Han G. Brunner, Marc A. van Driel, Martin Oti, Nuria Lopez-Bigas, Christos Ouzounis, Carolina Perez-Iratxeta, Miguel A. Andrade-Navarro, Adebowale Adeyemo, Mary Elizabeth Patti, Colin A. M. Semple, and Winston Hide

Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes
Nucl. Acids Res. 2006 34: 3067-3081; doi:10.1093/nar/gkl381 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Andrew Weston and John Sommerville

Xp54 and related (DDX6-like) RNA helicases: roles in messenger RNP assembly, translation regulation and RNA degradation
Nucl. Acids Res. 2006 34: 3082-3094; doi:10.1093/nar/gkl409 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Articles:

Erica M. Seitz and Stephen C. Kowalczykowski

Human Rad51 protein displays enhanced homologous pairing of DNA sequences resembling those at genetically unstable loci
Nucl. Acids Res. 2006 34: 2847-2852; doi:10.1093/nar/gkl355 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Dibyakanti Mandal, Chandravanu Dash, Stuart F. J. Le Grice, and Vinayaka R. Prasad

Analysis of HIV-1 replication block due to substitutions at F61 residue of reverse transcriptase reveals additional defects involving the RNase H function
Nucl. Acids Res. 2006 34: 2853-2863; doi:10.1093/nar/gkl360 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gregory J. Gemmen, Rachel Millin, and Douglas E. Smith

DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force
Nucl. Acids Res. 2006 34: 2864-2877; doi:10.1093/nar/gkl382 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Eveline Lescrinier, Koen Nauwelaerts, Katia Zanier, Koen Poesen, Michael Sattler, and Piet Herdewijn

The naturally occurring N6-threonyl adenine in anticodon loop of Schizosaccharomyces pombe tRNA_i causes formation of a unique U-turn motif
Nucl. Acids Res. 2006 34: 2878-2886; doi:10.1093/nar/gkl081 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Andrew Flaus, David M. A. Martin, Geoffrey J. Barton, and Tom Owen-Hughes

Identification of multiple distinct Snf2 subfamilies with conserved structural motifs
Nucl. Acids Res. 2006 34: 2887-2905; doi:10.1093/nar/gkl295 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Nicoletta Potenza, Vincenzo Salvatore, Annalucia Migliozzi, Valentina Martone, Valentina Nobile, and Aniello Russo

Hybridase activity of human ribonuclease-1 revealed by a real-time fluorometric assay
Nucl. Acids Res. 2006 34: 2906-2913; doi:10.1093/nar/gkl368 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yeon-Hee Kim, Daisuke Ishikawa, Ho Phu Ha, Minetaka Sugiyama, Yoshinobu Kaneko, and Satoshi Harashima

Chromosome XII context is important for rDNA function in yeast
Nucl. Acids Res. 2006 34: 2914-2924; doi:10.1093/nar/gkl293 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Cyrille Girard, Henry Neel, Edouard Bertrand, and Rémy Bordonné

Depletion of SMN by RNA interference in HeLa cells induces defects in Cajal body formation
Nucl. Acids Res. 2006 34: 2925-2932; doi:10.1093/nar/gkl374 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Vandana Payal and Paul Gollnick

Substitutions of Thr30 provide mechanistic insight into tryptophan-mediated activation of TRAP binding to RNA
Nucl. Acids Res. 2006 34: 2933-2942; doi:10.1093/nar/gkl383 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fred P. Davis, Hannes Braberg, Min-Yi Shen, Ursula Pieper, Andrej Sali, and M.S. Madhusudhan

Protein complex compositions predicted by structural similarity
Nucl. Acids Res. 2006 34: 2943-2952; doi:10.1093/nar/gkl353 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mark J. M. van Ooij, Charlotta Polacek, Dirk H. R. F. Glaudemans, Judith Kuijpers, Frank J. M. van Kuppeveld, Raul Andino, Vadim I. Agol, and Willem J. G. Melchers

Polyadenylation of genomic RNA and initiation of antigenomic RNA in a positive-strand RNA virus are controlled by the same cis-element
Nucl. Acids Res. 2006 34: 2953-2965; doi:10.1093/nar/gkl349 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shimyn Slomovic, David Laufer, Dan Geiger, and Gadi Schuster

Polyadenylation of ribosomal RNA in human cells
Nucl. Acids Res. 2006 34: 2966-2975; doi:10.1093/nar/gkl357 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Housheng He, Lun Cai, Geir Skogerbø, Wei Deng, Tao Liu, Xiaopeng Zhu, Yudong Wang, Dong Jia, Zhihua Zhang, Yong Tao, Haipan Zeng, Muhammad Nauman Aftab, Yan Cui, Guozhen Liu, and Runsheng Chen

Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray
Nucl. Acids Res. 2006 34: 2976-2983; doi:10.1093/nar/gkl371 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Katarzyna Pachulska-Wieczorek, Katarzyna J. Purzycka, and Ryszard W. Adamiak

New, extended hairpin form of the TAR-2 RNA domain points to the structural polymorphism at the 5' end of the HIV-2 leader RNA
Nucl. Acids Res. 2006 34: 2984-2997; doi:10.1093/nar/gkl373 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jean-Pascal Capp, François Boudsocq, Pascale Bertrand, Audrey Laroche-Clary, Philippe Pourquier, Bernard S. Lopez, Christophe Cazaux, Jean-Sébastien Hoffmann, and Yvan Canitrot

The DNA polymerase is required for the repair of non-compatible DNA double strand breaks by NHEJ in mammalian cells
Nucl. Acids Res. 2006 34: 2998-3007; doi:10.1093/nar/gkl380 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sandrine Castella, Gregg Bingham, and Cyril M. Sanders

Common determinants in DNA melting and helicase-catalysed DNA unwinding by papillomavirus replication protein E1
Nucl. Acids Res. 2006 34: 3008-3019; doi:10.1093/nar/gkl384 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alicia K. Byrd and Kevin D. Raney

Displacement of a DNA binding protein by Dda helicase
Nucl. Acids Res. 2006 34: 3020-3029; doi:10.1093/nar/gkl369 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Thomas Grimm, Michael Hölzel, Michaela Rohrmoser, Thomas Harasim, Anastassia Malamoussi, Anita Gruber-Eber, Elisabeth Kremmer, and Dirk Eick

Dominant-negative Pes1 mutants inhibit ribosomal RNA processing and cell proliferation via incorporation into the PeBoW-complex
Nucl. Acids Res. 2006 34: 3030-3043; doi:10.1093/nar/gkl378 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shuibang Wang, Jianhua Zhang, Stephanie Theel, Jennifer J. Barb, Peter J. Munson, and Robert L. Danner

Nitric oxide activation of Erk1/2 regulates the stability and translation of mRNA transcripts containing CU-rich elements
Nucl. Acids Res. 2006 34: 3044-3056; doi:10.1093/nar/gkl386 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fernando Moreno-Herrero, Ralf Seidel, Steven M. Johnson, Andrew Fire, and Nynke H. Dekker

Structural analysis of hyperperiodic DNA from Caenorhabditis elegans
Nucl. Acids Res. 2006 34: 3057-3066; doi:10.1093/nar/gkl397 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Juqiang Han, Lihua Ding, Bin Yuan, Xiao Yang, Xiaohui Wang, Jiezhi Li, Qiujun Lu, Cuifen Huang, and Qinong Ye

Hepatitis B virus X protein and the estrogen receptor variant lacking exon 5 inhibit estrogen receptor signaling in hepatoma cells
Nucl. Acids Res. 2006 34: 3095-3106; doi:10.1093/nar/gkl389 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Patricia Pérez-Arnaiz, José M. Lázaro, Margarita Salas, and Miguel de Vega

Involvement of 29 DNA polymerase thumb subdomain in the proper coordination of synthesis and degradation during DNA replication
Nucl. Acids Res. 2006 34: 3107-3115; doi:10.1093/nar/gkl402 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Giacomo Donati, Carol Imbriano, and Roberto Mantovani

Dynamic recruitment of transcription factors and epigenetic changes on the ER stress response gene promoters
Nucl. Acids Res. 2006 34: 3116-3127; doi:10.1093/nar/gkl304 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ya-Han Hsu, Meng-Wen Chung, and Tsai-Kun Li

Distribution of gyrase and topoisomerase IV on bacterial nucleoid: implications for nucleoid organization
Nucl. Acids Res. 2006 34: 3128-3138; doi:10.1093/nar/gkl392 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Anna-Helena Saariaho and Harri Savilahti

Characteristics of MuA transposase-catalyzed processing of model transposon end DNA hairpin substrates
Nucl. Acids Res. 2006 34: 3139-3149; doi:10.1093/nar/gkl405 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yi Xing, Tianwei Yu, Ying Nian Wu, Meenakshi Roy, Joseph Kim, and Christopher Lee

An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs
Nucl. Acids Res. 2006 34: 3150-3160; doi:10.1093/nar/gkl396 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Angel A. Martí, Xiaoxu Li, Steffen Jockusch, Zengmin Li, Bindu Raveendra, Sergey Kalachikov, James J. Russo, Irina Morozova, Sathyanarayanan V. Puthanveettil, Jingyue Ju, and Nicholas J. Turro

Pyrene binary probes for unambiguous detection of mRNA using time-resolved fluorescence spectroscopy
Nucl. Acids Res. 2006 34: 3161-3168; doi:10.1093/nar/gkl406 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Robert Ahrends, Jan Kosinski, Dieter Kirsch, Laura Manelyte, Luis Giron-Monzon, Lars Hummerich, Oliver Schulz, Bernhard Spengler, and Peter Friedhoff

Identifying an interaction site between MutH and the C-terminal domain of MutL by crosslinking, affinity purification, chemical coding and mass spectrometry
Nucl. Acids Res. 2006 34: 3169-3180; doi:10.1093/nar/gkl407 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jun-ichi Fukunaga, Satoshi Ohno, Kazuya Nishikawa, and Takashi Yokogawa

A base pair at the bottom of the anticodon stem is reciprocally preferred for discrimination of cognate tRNAs by Escherichia coli lysyl- and glutaminyl-tRNA synthetases
Nucl. Acids Res. 2006 34: 3181-3188; doi:10.1093/nar/gkl414 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sander Granneman, ChieYu Lin, Erica A. Champion, Madhusudan R. Nandineni, Cornelia Zorca, and Susan J. Baserga

The nucleolar protein Esf2 interacts directly with the DExD/H box RNA helicase, Dbp8, to stimulate ATP hydrolysis
Nucl. Acids Res. 2006 34: 3189-3199; doi:10.1093/nar/gkl419 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Ted C. Chu, Karen Y. Twu, Andrew D. Ellington, and Matthew Levy

Aptamer mediated siRNA delivery
Nucl. Acids Res. 2006 34: e73; doi:10.1093/nar/gkl388 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Malgorzata A. Witek, Shawn D. Llopis, Abigail Wheatley, Robin L. McCarley, and Steven A. Soper

Purification and preconcentration of genomic DNA from whole cell lysates using photoactivated polycarbonate (PPC) microfluidic chips
Nucl. Acids Res. 2006 34: e74; doi:10.1093/nar/gkl146 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Minseon Cho, Sohyun Lee, Se-Young Han, Jin-Young Park, Md Aminur Rahman, Yoon-Bo Shim, and Changill Ban

Electrochemical detection of mismatched DNA using a MutS probe
Nucl. Acids Res. 2006 34: e75; doi:10.1093/nar/gkl364 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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