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Previous 		Contents: Volume 36, Number 15, September 2008   [Index by Author] 

Down Editorial-Publication Charges
Down Computational Biology
Down Chemistry and Synthetic Biology
Down Gene Regulation, Chromatin and Epigenetics
Down Molecular Biology
Down Nucleic Acid Enzymes
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Down Structural Biology
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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.

Editorial-Publication Charges Back

Claire Bird, Keith Fox, and Rich Roberts
Editorial-Publication Charges
Nucleic Acids Research Advance Access published on August 12, 2008
Nucl. Acids Res. 2008 36: 4821-4822; doi:10.1093/nar/gkn521 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Computational Biology Back

Ana Rita Grosso, Anita Q. Gomes, Nuno L. Barbosa-Morais, Sandra Caldeira, Natalie P. Thorne, Godfrey Grech, Marieke von Lindern, and Maria Carmo-Fonseca
Tissue-specific splicing factor gene expression signatures
Nucleic Acids Research Advance Access published on July 24, 2008
Nucl. Acids Res. 2008 36: 4823-4832; doi:10.1093/nar/gkn463 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jiong-Tang Li, Yong Zhang, Lei Kong, Qing-Rong Liu, and Liping Wei
Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation
Nucleic Acids Research Advance Access published on July 24, 2008
Nucl. Acids Res. 2008 36: 4833-4844; doi:10.1093/nar/gkn470 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Yannis Burnier, Julien Dorier, and Andrzej Stasiak
DNA supercoiling inhibits DNA knotting
Nucleic Acids Research Advance Access published on July 25, 2008
Nucl. Acids Res. 2008 36: 4956-4963; doi:10.1093/nar/gkn467 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chemistry and Synthetic Biology Back

Natalia Borovok, Natalie Iram, Dragoslav Zikich, Jamal Ghabboun, Gideon I. Livshits, Danny Porath, and Alexander B. Kotlyar
Assembling of G-strands into novel tetra-molecular parallel G4-DNA nanostructures using avidin–biotin recognition
Nucleic Acids Research Advance Access published on July 28, 2008
Nucl. Acids Res. 2008 36: 5050-5060; doi:10.1093/nar/gkn459 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gene Regulation, Chromatin and Epigenetics Back

Jennifer M. Taylor, Kate Wicks, Claire Vandiedonck, and Julian C. Knight
Chromatin profiling across the human tumour necrosis factor gene locus reveals a complex, cell type-specific landscape with novel regulatory elements
Nucleic Acids Research Advance Access published on July 24, 2008
Nucl. Acids Res. 2008 36: 4845-4862; doi:10.1093/nar/gkn444 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Xiaohu Wang, Haichun Gao, Yufeng Shen, George M. Weinstock, Jizhong Zhou, and Timothy Palzkill
A high-throughput percentage-of-binding strategy to measure binding energies in DNA–protein interactions: application to genome-scale site discovery
Nucleic Acids Research Advance Access published on July 24, 2008
Nucl. Acids Res. 2008 36: 4863-4871; doi:10.1093/nar/gkn477 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Victor Y. Stefanovsky and Tom Moss
The splice variants of UBF differentially regulate RNA polymerase I transcription elongation in response to ERK phosphorylation
Nucleic Acids Research Advance Access published on August 1, 2008
Nucl. Acids Res. 2008 36: 5093-5101; doi:10.1093/nar/gkn484 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology Back

Svitlana Malyarchuk, Reneau Castore, and Lynn Harrison
DNA repair of clustered lesions in mammalian cells: involvement of non-homologous end-joining
Nucleic Acids Research Advance Access published on July 24, 2008
Nucl. Acids Res. 2008 36: 4872-4882; doi:10.1093/nar/gkn450 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Cyrille Le Breton, Pauline Dupaigne, Thomas Robert, Eric Le Cam, Serge Gangloff, Francis Fabre, and Xavier Veaute
Srs2 removes deadly recombination intermediates independently of its interaction with SUMO-modified PCNA
Nucleic Acids Research Advance Access published on July 25, 2008
Nucl. Acids Res. 2008 36: 4964-4974; doi:10.1093/nar/gkn441 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Zuzanna Bukowy, Jeanine A. Harrigan, Dale A. Ramsden, Barbara Tudek, Vilhelm A. Bohr, and Tinna Stevnsner
WRN Exonuclease activity is blocked by specific oxidatively induced base lesions positioned in either DNA strand
Nucleic Acids Research Advance Access published on July 25, 2008
Nucl. Acids Res. 2008 36: 4975-4987; doi:10.1093/nar/gkn468 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chao Lu, Jie-Qing Chen, Guo-Ping Zhou, Sheng-Hua Wu, Ya-Fei Guan, and Chuan-Shun Yuan
Multimolecular complex of Par-4 and E2F1 binding to Smac promoter contributes to glutamate-induced apoptosis in human- bone mesenchymal stem cells
Nucleic Acids Research Advance Access published on July 26, 2008
Nucl. Acids Res. 2008 36: 5021-5032; doi:10.1093/nar/gkn426 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Melda Tozluoglu, Ezgi Karaca, Turkan Haliloglu, and Ruth Nussinov
Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis
Nucleic Acids Research Advance Access published on July 26, 2008
Nucl. Acids Res. 2008 36: 5033-5049; doi:10.1093/nar/gkn481 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

E. V. S. Raghu Ram, Rangeetha Naik, Munia Ganguli, and Saman Habib
DNA organization by the apicoplast-targeted bacterial histone-like protein of Plasmodium falciparum
Nucleic Acids Research Advance Access published on July 28, 2008
Nucl. Acids Res. 2008 36: 5061-5073; doi:10.1093/nar/gkn483 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Avanti Kulkarni, Daniel R. McNeill, Marc Gleichmann, Mark P. Mattson, and David M. Wilson, III
XRCC1 protects against the lethality of induced oxidative DNA damage in nondividing neural cells
Nucleic Acids Research Advance Access published on August 5, 2008
Nucl. Acids Res. 2008 36: 5111-5121; doi:10.1093/nar/gkn480 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes Back

Joseph E. Deweese, Alex B. Burgin, and Neil Osheroff
Human topoisomerase II{alpha} uses a two-metal-ion mechanism for DNA cleavage
Nucleic Acids Research Advance Access published on July 24, 2008
Nucl. Acids Res. 2008 36: 4883-4893; doi:10.1093/nar/gkn466 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tarmo Nuutinen, Helena Tossavainen, Kai Fredriksson, Päivi Pirilä, Perttu Permi, Helmut Pospiech, and Juhani E. Syvaoja
The solution structure of the amino-terminal domain of human DNA polymerase {varepsilon} subunit B is homologous to C-domains of AAA+ proteins
Nucleic Acids Research Advance Access published on August 2, 2008
Nucl. Acids Res. 2008 36: 5102-5110; doi:10.1093/nar/gkn497 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA Back

Pierre Barraud, Emmanuelle Schmitt, Yves Mechulam, Frédéric Dardel, and Carine Tisné
A unique conformation of the anticodon stem-loop is associated with the capacity of tRNAfMet to initiate protein synthesis
Nucleic Acids Research Advance Access published on July 24, 2008
Nucl. Acids Res. 2008 36: 4894-4901; doi:10.1093/nar/gkn462 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Marie-Cécile Didiot, Zhaoxia Tian, Céline Schaeffer, Murugan Subramanian, Jean-Louis Mandel, and Hervé Moine
The G-quartet containing FMRP binding site in FMR1 mRNA is a potent exonic splicing enhancer
Nucleic Acids Research Advance Access published on July 24, 2008
Nucl. Acids Res. 2008 36: 4902-4912; doi:10.1093/nar/gkn472 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Wei Wang, Zong-Qiang Cui, Han Han, Zhi-Ping Zhang, Hong-Ping Wei, Ya-Feng Zhou, Ze Chen, and Xian-En Zhang
Imaging and characterizing influenza A virus mRNA transport in living cells
Nucleic Acids Research Advance Access published on July 24, 2008
Nucl. Acids Res. 2008 36: 4913-4928; doi:10.1093/nar/gkn475 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alice Lebreton, Jean-Claude Rousselle, Pascal Lenormand, Abdelkader Namane, Alain Jacquier, Micheline Fromont-Racine, and Cosmin Saveanu
60S ribosomal subunit assembly dynamics defined by semi-quantitative mass spectrometry of purified complexes
Nucleic Acids Research Advance Access published on July 25, 2008
Nucl. Acids Res. 2008 36: 4988-4999; doi:10.1093/nar/gkn469 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology Back

Hélène Walbott, Nicolas Leulliot, Henri Grosjean, and Béatrice Golinelli-Pimpaneau
The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity
Nucleic Acids Research Advance Access published on July 24, 2008
Nucl. Acids Res. 2008 36: 4929-4940; doi:10.1093/nar/gkn437 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Cameron Mura and J. Andrew McCammon
Molecular dynamics of a {kappa}B DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation
Nucleic Acids Research Advance Access published on July 24, 2008
Nucl. Acids Res. 2008 36: 4941-4955; doi:10.1093/nar/gkn473 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Matthias Bahr, Valérie Gabelica, Anton Granzhan, Marie-Paule Teulade-Fichou, and Elmar Weinhold
Selective recognition of pyrimidine–pyrimidine DNA mismatches by distance-constrained macrocyclic bis-intercalators
Nucleic Acids Research Advance Access published on July 25, 2008
Nucl. Acids Res. 2008 36: 5000-5012; doi:10.1093/nar/gkn392 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Masayoshi Honda, Tetsuro Fujisawa, Takehiko Shibata, and Tsutomu Mikawa
RecR forms a ring-like tetramer that encircles dsDNA by forming a complex with RecF
Nucleic Acids Research Advance Access published on July 25, 2008
Nucl. Acids Res. 2008 36: 5013-5020; doi:10.1093/nar/gkn471 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Kiyoshi Ozawa, Slobodan Jergic, Ah Young Park, Nicholas E. Dixon, and Gottfried Otting
The proofreading exonuclease subunit {varepsilon} of Escherichia coli DNA polymerase III is tethered to the polymerase subunit {alpha} via a flexible linker
Nucleic Acids Research Advance Access published on July 28, 2008
Nucl. Acids Res. 2008 36: 5074-5082; doi:10.1093/nar/gkn489 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Joseph D. Bauman, Kalyan Das, William C. Ho, Mukta Baweja, Daniel M. Himmel, Arthur D. Clark, Jr, Deena A. Oren, Paul L. Boyer, Stephen H. Hughes, Aaron J. Shatkin, and Eddy Arnold
Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design
Nucleic Acids Research Advance Access published on August 1, 2008
Nucl. Acids Res. 2008 36: 5083-5092; doi:10.1093/nar/gkn464 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Erratum Back

Lucy E. Catto, Stuart R. W. Bellamy, Susan E. Retter, and Stephen E. Halford
Dynamics and consequences of DNA looping by the FokI restriction endonuclease
Nucl. Acids Res. 2008 36: 5122; doi:10.1093/nar/gkn565 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online Back

Takahiro Tougan, Daisuke Okuzaki, and Hiroshi Nojima
Chum-RNA allows preparation of a high-quality cDNA library from a single-cell quantity of mRNA without PCR amplification
Nucleic Acids Research Advance Access published on July 4, 2008
Nucl. Acids Res. 2008 36: e92; doi:10.1093/nar/gkn420 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gouse M. Shaik, Lubica Dráberová, Peter Dráber, Michael Boubelík, and Petr Dráber
Tetraalkylammonium derivatives as real-time PCR enhancers and stabilizers of the qPCR mixtures containing SYBR Green I
Nucleic Acids Research Advance Access published on July 7, 2008
Nucl. Acids Res. 2008 36: e93; doi:10.1093/nar/gkn421 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Johannes Dapprich, Deborah Ferriola, Eleni E. Magira, Mark Kunkel, and Dimitri Monos
SNP-specific extraction of haplotype-resolved targeted genomic regions
Nucleic Acids Research Advance Access published on July 8, 2008
Nucl. Acids Res. 2008 36: e94; doi:10.1093/nar/gkn345 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Loic Jaffrelo, Sandrine Chabas, Sandrine Reigadas, Aude Pflieger, Czeslaw Wychowski, Julie Rumi, Michel Ventura, Jean-Jacques Toulmé, and Cathy Staedel
A functional selection of viral genetic elements in cultured cells to identify hepatitis C virus RNA translation inhibitors
Nucleic Acids Research Advance Access published on July 9, 2008
Nucl. Acids Res. 2008 36: e95; doi:10.1093/nar/gkn427 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gaurav Backliwal, Markus Hildinger, Sebastien Chenuet, Sarah Wulhfard, Maria De Jesus, and Florian M. Wurm
Rational vector design and multi-pathway modulation of HEK 293E cells yield recombinant antibody titers exceeding 1 g/l by transient transfection under serum-free conditions
Nucleic Acids Research Advance Access published on July 10, 2008
Nucl. Acids Res. 2008 36: e96; doi:10.1093/nar/gkn423 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Christina Sæten Fjeldbo, Kristine Misund, Clara-Cecilie Günther, Mette Langaas, Tonje Strømmen Steigedal, Liv Thommesen, Astrid Lægreid, and Torunn Bruland
Functional studies on transfected cell microarray analysed by linear regression modelling
Nucleic Acids Research Advance Access published on July 15, 2008
Nucl. Acids Res. 2008 36: e97; doi:10.1093/nar/gkn428 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Greg P. Brewood, Yaswanth Rangineni, Daniel J. Fish, Ashwini S. Bhandiwad, David R. Evans, Raj Solanki, and Albert S. Benight
Electrical detection of the temperature induced melting transition of a DNA hairpin covalently attached to gold interdigitated microelectrodes
Nucleic Acids Research Advance Access published on July 15, 2008
Nucl. Acids Res. 2008 36: e98; doi:10.1093/nar/gkn436 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

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.