Nucleic Acids Research

Survey and Summary:

Steve L. Reichow, Tomoko Hamma, Adrian R. Ferré-D'Amaré, and Gabriele Varani

The structure and function of small nucleolar ribonucleoproteins
Nucleic Acids Research Advance Access published on February 6, 2007
Nucl. Acids Res. 2007 35: 1452-1464; doi:10.1093/nar/gkl1172 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chemistry:

Jonathan K. Watts, Niloufar Choubdar, Kashinath Sadalapure, Francis Robert, Alexander S. Wahba, Jerry Pelletier, B. Mario Pinto, and Masad J. Damha

2'-Fluoro-4'-thioarabino-modified oligonucleotides: conformational switches linked to siRNA activity
Nucleic Acids Research Advance Access published on February 6, 2007
Nucl. Acids Res. 2007 35: 1441-1451; doi:10.1093/nar/gkl1153 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Computational Biology:

Harianto Tjong and Huan-Xiang Zhou

DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces
Nucleic Acids Research Advance Access published on February 6, 2007
Nucl. Acids Res. 2007 35: 1465-1477; doi:10.1093/nar/gkm008 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Giacomo Finocchiaro, Maria Stella Carro, Stephanie Francois, Paola Parise, Valentina DiNinni, and Heiko Muller

Localizing hotspots of antisense transcription
Nucleic Acids Research Advance Access published on February 6, 2007
Nucl. Acids Res. 2007 35: 1488-1500; doi:10.1093/nar/gkm027 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Genomics:

Alexander Boyko, Palak Kathiria, Franz J. Zemp, Youli Yao, Igor Pogribny, and Igor Kovalchuk

Transgenerational changes in the genome stability and methylation in pathogen-infected plants: (Virus-induced plant genome instability)
Nucleic Acids Research Advance Access published on February 20, 2007
Nucl. Acids Res. 2007 35: 1714-1725; doi:10.1093/nar/gkm029 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Molecular Biology:

Alain N. S. Newo, Martin Lützelberger, Claudia A. Bottner, Jürgen Wehland, Josef Wissing, Lothar Jänsch, and Norbert F. Käufer

Proteomic analysis of the U1 snRNP of Schizosaccharomyces pombe reveals three essential organism-specific proteins
Nucleic Acids Research Advance Access published on January 30, 2007
Nucl. Acids Res. 2007 35: 1391-1401; doi:10.1093/nar/gkl1144 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

S. Semprini, T.J. Troup, N. Kotelevtseva, K. King, J.R.E. Davis, L.J. Mullins, K.E. Chapman, D.R. Dunbar, and J.J. Mullins

Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques
Nucleic Acids Research Advance Access published on February 6, 2007
Nucl. Acids Res. 2007 35: 1402-1410; doi:10.1093/nar/gkl1108 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Xian-Jun Mao, Yi-Xin Huo, Martin Buck, Annie Kolb, and Yi-Ping Wang

Interplay between CRP-cAMP and PII-Ntr systems forms novel regulatory network between carbon metabolism and nitrogen assimilation in Escherichia coli
Nucleic Acids Research Advance Access published on February 6, 2007
Nucl. Acids Res. 2007 35: 1432-1440; doi:10.1093/nar/gkl1142 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kyu Young Song, Cheol Kyu Hwang, Chun Sung Kim, Hack Sun Choi, Ping-Yee Law, Li-Na Wei, and Horace H. Loh

Translational repression of mouse mu opioid receptor expression via leaky scanning
Nucleic Acids Research Advance Access published on February 6, 2007
Nucl. Acids Res. 2007 35: 1501-1513; doi:10.1093/nar/gkm034 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Anastassia V. Komarova, Eléonore Real, Andrew M. Borman, Michèle Brocard, Patrick England, Noël Tordo, John W.B. Hershey, Katherine M. Kean, and Yves Jacob

Rabies virus matrix protein interplay with eIF3, new insights into rabies virus pathogenesis
Nucleic Acids Research Advance Access published on February 7, 2007
Nucl. Acids Res. 2007 35: 1522-1532; doi:10.1093/nar/gkl1127 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Susumu Hama, Hidetaka Akita, Shinya Iida, Hiroyuki Mizuguchi, and Hideyoshi Harashima

Quantitative and mechanism-based investigation of post-nuclear delivery events between adenovirus and lipoplex
Nucleic Acids Research Advance Access published on February 7, 2007
Nucl. Acids Res. 2007 35: 1533-1543; doi:10.1093/nar/gkl1165 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Eleonora Parlanti, Giada Locatelli, Giovanni Maga, and Eugenia Dogliotti

Human base excision repair complex is physically associated to DNA replication and cell cycle regulatory proteins
Nucleic Acids Research Advance Access published on February 8, 2007
Nucl. Acids Res. 2007 35: 1569-1577; doi:10.1093/nar/gkl1159 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Denise S.B. Chan, Lai-On Chu, Ka-Ming Lee, Priscilla H.M. Too, Kit-Wan Ma, Kong-Hung Sze, Guang Zhu, Pang-Chui Shaw, and Kam-Bo Wong

Interaction between trichosanthin, a ribosome-inactivating protein, and the ribosomal stalk protein P2 by chemical shift perturbation and mutagenesis analyses
Nucleic Acids Research Advance Access published on February 18, 2007
Nucl. Acids Res. 2007 35: 1660-1672; doi:10.1093/nar/gkm065 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jun Yan, Yong-Sik Kim, Xiao-Ping Yang, Michael Albers, Manfred Koegl, and Anton M. Jetten

Ubiquitin-interaction motifs of RAP80 are critical in its regulation of estrogen receptor
Nucleic Acids Research Advance Access published on February 20, 2007
Nucl. Acids Res. 2007 35: 1673-1686; doi:10.1093/nar/gkl1112 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Mahalakshmi Nair, Virginia Bilanchone, Kori Ortt, Satrajit Sinha, and Xing Dai

Ovol1 represses its own transcription by competing with transcription activator c-Myb and by recruiting histone deacetylase activity
Nucleic Acids Research Advance Access published on February 20, 2007
Nucl. Acids Res. 2007 35: 1687-1697; doi:10.1093/nar/gkl1141 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acid Enzymes:

Stéphane Hausmann, Alejandro Ramirez, Susanne Schneider, Beate Schwer, and Stewart Shuman

Biochemical and genetic analysis of RNA cap guanine-N2 methyltransferases from Giardia lamblia and Schizosaccharomyces pombe
Nucleic Acids Research Advance Access published on February 6, 2007
Nucl. Acids Res. 2007 35: 1411-1420; doi:10.1093/nar/gkl1150 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Stuart R.W. Bellamy, Kuakarun Krusong, and Geoff S. Baldwin

A rapid reaction analysis of uracil DNA glycosylase indicates an active mechanism of base flipping
Nucleic Acids Research Advance Access published on February 6, 2007
Nucl. Acids Res. 2007 35: 1478-1487; doi:10.1093/nar/gkm018 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Justin B. Robbins, Michelle Stapleton, Matthew J. Stanger, Dorie Smith, John T. Dansereau, Victoria Derbyshire, and Marlene Belfort

Homing endonuclease I-TevIII: dimerization as a means to a double-strand break
Nucleic Acids Research Advance Access published on February 8, 2007
Nucl. Acids Res. 2007 35: 1589-1600; doi:10.1093/nar/gkl1170 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jeffrey O. Blaisdell and Susan S. Wallace

Rapid determination of the active fraction of DNA repair glycosylases: a novel fluorescence assay for trapped intermediates
Nucleic Acids Research Advance Access published on February 8, 2007
Nucl. Acids Res. 2007 35: 1601-1611; doi:10.1093/nar/gkm021 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sangeetha Vijayakumar, Brian R. Chapados, Kristina H. Schmidt, Richard D. Kolodner, John A. Tainer, and Alan E. Tomkinson

The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase
Nucleic Acids Research Advance Access published on February 18, 2007
Nucl. Acids Res. 2007 35: 1624-1637; doi:10.1093/nar/gkm006 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material][Supplementary Material] [Request Permissions]  

RNA:

Takashi Nishiyama, Hiroshi Yamamoto, Toshio Uchiumi, and Nobuhiko Nakashima

Eukaryotic ribosomal protein RPS25 interacts with the conserved loop region in a dicistroviral intergenic internal ribosome entry site
Nucleic Acids Research Advance Access published on February 7, 2007
Nucl. Acids Res. 2007 35: 1514-1521; doi:10.1093/nar/gkl1121 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Monika J. Madej, Juan D. Alfonzo, and Alexander Hüttenhofer

Small ncRNA transcriptome analysis from kinetoplast mitochondria of Leishmania tarentolae
Nucleic Acids Research Advance Access published on February 7, 2007
Nucl. Acids Res. 2007 35: 1544-1554; doi:10.1093/nar/gkm004 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Nasslie Choonee, Sergine Even, Lena Zig, and Harald Putzer

Ribosomal protein L20 controls expression of the Bacillus subtilis infC operon via a transcription attenuation mechanism
Nucleic Acids Research Advance Access published on February 8, 2007
Nucl. Acids Res. 2007 35: 1578-1588; doi:10.1093/nar/gkm011 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fredrik B. Stabell, Nicolas J. Tourasse, Solveig Ravnum, and Anne-Brit Kolstø

Group II intron in Bacillus cereus has an unusual 3' extension and splices 56 nucleotides downstream of the predicted site
Nucleic Acids Research Advance Access published on February 14, 2007
Nucl. Acids Res. 2007 35: 1612-1623; doi:10.1093/nar/gkm031 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Marcel Ooms, Daniel Cupac, Truus E. M. Abbink, Hendrik Huthoff, and Ben Berkhout

The availability of the primer activation signal (PAS) affects the efficiency of HIV-1 reverse transcription initiation
Nucleic Acids Research Advance Access published on February 18, 2007
Nucl. Acids Res. 2007 35: 1649-1659; doi:10.1093/nar/gkm046 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Structural Biology:

Marzanna Deniziak, Claude Sauter, Hubert Dominique Becker, Caroline Alexandra Paulus, Richard Giegé, and Daniel Kern

Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation
Nucleic Acids Research Advance Access published on February 6, 2007
Nucl. Acids Res. 2007 35: 1421-1431; doi:10.1093/nar/gkl1164 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fabián A. Rodríguez, Yuqin Cai, Chin Lin, Yijin Tang, Alexander Kolbanovskiy, Shantu Amin, Dinshaw J. Patel, Suse Broyde, and Nicholas E. Geacintov

Exocyclic amino groups of flanking guanines govern sequence-dependent adduct conformations and local structural distortions for minor groove-aligned benzo[a]pyrenyl-guanine lesions in a GG mutation hotspot context
Nucleic Acids Research Advance Access published on February 7, 2007
Nucl. Acids Res. 2007 35: 1555-1568; doi:10.1093/nar/gkm022 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ravi K. Nookala, Shobbir Hussain, and Luca Pellegrini

Insights into Fanconi Anaemia from the structure of human FANCE
Nucleic Acids Research Advance Access published on February 18, 2007
Nucl. Acids Res. 2007 35: 1638-1648; doi:10.1093/nar/gkm033 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Xiaoyan Sun, Qi Zhang, and Hashim M. Al-Hashimi

Resolving fast and slow motions in the internal loop containing stem-loop 1 of HIV-1 that are modulated by Mg²⁺ binding: role in the kissing–duplex structural transition
Nucleic Acids Research Advance Access published on February 20, 2007
Nucl. Acids Res. 2007 35: 1698-1713; doi:10.1093/nar/gkm020 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Karine St-Onge, Philippe Thibault, Sylvie Hamel, and François Major

Modeling RNA tertiary structure motifs by graph-grammars
Nucleic Acids Research Advance Access published on February 21, 2007
Nucl. Acids Res. 2007 35: 1726-1736; doi:10.1093/nar/gkm069 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Maria C. Monti, Ana M. Hernández-Arriaga, Monique B. Kamphuis, Juan López-Villarejo, Albert J. R. Heck, Rolf Boelens, Ramón Díaz-Orejas, and Robert H. H. van den Heuvel

Interactions of Kid–Kis toxin–antitoxin complexes with the parD operator-promoter region of plasmid R1 are piloted by the Kis antitoxin and tuned by the stoichiometry of Kid–Kis oligomers
Nucleic Acids Research Advance Access published on February 21, 2007
Nucl. Acids Res. 2007 35: 1737-1749; doi:10.1093/nar/gkm073 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Methods Online:

Mathias Ehrich, Scott Zoll, Sudipto Sur, and Dirk van den Boom

A new method for accurate assessment of DNA quality after bisulfite treatment
Nucleic Acids Research Advance Access published on January 26, 2007
Nucl. Acids Res. 2007 35: e29; doi:10.1093/nar/gkl1134 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material][Supplementary Material] [Request Permissions]  

Eugeny A. Lukhtanov, Sergey G. Lokhov, Vladimir V. Gorn, Mikhail A. Podyminogin, and Walt Mahoney

Novel DNA probes with low background and high hybridization-triggered fluorescence
Nucleic Acids Research Advance Access published on January 26, 2007
Nucl. Acids Res. 2007 35: e30; doi:10.1093/nar/gkl1136 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zhongfa Liu, Shujun Liu, Zhiliang Xie, William Blum, Danilo Perrotti, Peter Paschka, Rebecca Klisovic, John Byrd, Kenneth K. Chan, and Guido Marcucci

Characterization of in vitro and in vivo hypomethylating effects of decitabine in acute myeloid leukemia by a rapid, specific and sensitive LC-MS/MS method
Nucleic Acids Research Advance Access published on January 30, 2007
Nucl. Acids Res. 2007 35: e31; doi:10.1093/nar/gkl1156 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nina Bandmann and Per-Åke Nygren

Combinatorial expression vector engineering for tuning of recombinant protein production in Escherichia coli
Nucleic Acids Research Advance Access published on January 30, 2007
Nucl. Acids Res. 2007 35: e32; doi:10.1093/nar/gkl1171 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Youdong Mao, Dongsheng Liu, Shutao Wang, Songnian Luo, Wenxing Wang, Yanlian Yang, Qi Ouyang, and Lei Jiang

Alternating-electric-field-enhanced reversible switching of DNA nanocontainers with pH
Nucleic Acids Research Advance Access published on January 30, 2007
Nucl. Acids Res. 2007 35: e33; doi:10.1093/nar/gkl1161 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Lili Milani, Manu Gupta, Malin Andersen, Sumeer Dhar, Mårten Fryknäs, Anders Isaksson, Rolf Larsson, and Ann-Christine Syvänen

Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells
Nucleic Acids Research Advance Access published on January 31, 2007
Nucl. Acids Res. 2007 35: e34; doi:10.1093/nar/gkl1152 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jing Hu, Jian-Bo Gao, Yinhe Cao, Erwin Bottinger, and Weijia Zhang

Exploiting noise in array CGH data to improve detection of DNA copy number change
Nucleic Acids Research Advance Access published on February 1, 2007
Nucl. Acids Res. 2007 35: e35; doi:10.1093/nar/gkl730 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ismail Hassan Ismail, Tabasum Imran Wadhra, and Ola Hammarsten

An optimized method for detecting gamma-H2AX in blood cells reveals a significant interindividual variation in the gamma-H2AX response among humans
Nucleic Acids Research Advance Access published on February 6, 2007
Nucl. Acids Res. 2007 35: e36; doi:10.1093/nar/gkl1169 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material][Supplementary Material] [Request Permissions]  

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