Nucleic Acids Research

Computational Biology

Get checked abstract Martin C. Frith, Yonil Park, Sergey L. Sheetlin, and John L. Spouge

The whole alignment and nothing but the alignment: the problem of spurious alignment flanks
Nucleic Acids Research Advance Access published on September 16, 2008
Nucl. Acids Res. 2008 36: 5863-5871; doi:10.1093/nar/gkn579 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Attilio Vittorio Vargiu, Paolo Ruggerone, Alessandra Magistrato, and Paolo Carloni

Dissociation of minor groove binders from DNA: insights from metadynamics simulations
Nucleic Acids Research Advance Access published on September 18, 2008
Nucl. Acids Res. 2008 36: 5910-5921; doi:10.1093/nar/gkn561 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Corinna Theis, Jens Reeder, and Robert Giegerich

KnotInFrame: prediction of –1 ribosomal frameshift events
Nucleic Acids Research Advance Access published on September 27, 2008
Nucl. Acids Res. 2008 36: 6013-6020; doi:10.1093/nar/gkn578 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gene regulation, Chromatin and Epigenetics

Get checked abstract Guisheng Song and Li Wang

Transcriptional mechanism for the paired miR-433 and miR-127 genes by nuclear receptors SHP and ERR
Nucleic Acids Research Advance Access published on September 6, 2008
Nucl. Acids Res. 2008 36: 5727-5735; doi:10.1093/nar/gkn567 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Huanyu Wang, Scott T. R. Walsh, and Mark R. Parthun

Expanded binding specificity of the human histone chaperone NASP
Nucleic Acids Research Advance Access published on September 9, 2008
Nucl. Acids Res. 2008 36: 5763-5772; doi:10.1093/nar/gkn574 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Padubidri V. Shivaprasad, Rajendran Rajeswaran, Todd Blevins, James Schoelz, Frederick Meins, Jr, Thomas Hohn, and Mikhail M. Pooggin

The CaMV transactivator/viroplasmin interferes with RDR6-dependent trans-acting and secondary siRNA pathways in Arabidopsis
Nucleic Acids Research Advance Access published on September 18, 2008
Nucl. Acids Res. 2008 36: 5896-5909; doi:10.1093/nar/gkn590 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Gaëlle André, Sergine Even, Harald Putzer, Pierre Burguière, Christian Croux, Antoine Danchin, Isabelle Martin-Verstraete, and Olga Soutourina

S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum
Nucleic Acids Research Advance Access published on September 23, 2008
Nucl. Acids Res. 2008 36: 5955-5969; doi:10.1093/nar/gkn601 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genome integrity, repair and replication

Get checked abstract Benito Baños, José M. Lázaro, Laurentino Villar, Margarita Salas, and Miguel de Vega

Editing of misaligned 3'-termini by an intrinsic 3'–5' exonuclease activity residing in the PHP domain of a family X DNA polymerase
Nucleic Acids Research Advance Access published on September 6, 2008
Nucl. Acids Res. 2008 36: 5736-5749; doi:10.1093/nar/gkn526 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sumithra Jayaram, Gary Ketner, Noritaka Adachi, and Les A. Hanakahi

Loss of DNA ligase IV prevents recognition of DNA by double-strand break repair proteins XRCC4 and XLF
Nucleic Acids Research Advance Access published on September 9, 2008
Nucl. Acids Res. 2008 36: 5773-5786; doi:10.1093/nar/gkn552 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Elizabeth A. Williamson, Kanwaldeep Kaur Rasila, Lori Kwan Corwin, Justin Wray, Brian D. Beck, Virginia Severns, Charlotte Mobarak, Suk-Hee Lee, Jac A. Nickoloff, and Robert Hromas

The SET and transposase domain protein Metnase enhances chromosome decatenation: regulation by automethylation
Nucleic Acids Research Advance Access published on September 12, 2008
Nucl. Acids Res. 2008 36: 5822-5831; doi:10.1093/nar/gkn560 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Evagelos Liapis, Keith I.E. McLuckie, Paul D. Lewis, Peter B. Farmer, and Karen Brown

Mutagenicity of tamoxifen DNA adducts in human endometrial cells and in silico prediction of p53 mutation hotspots
Nucleic Acids Research Advance Access published on September 19, 2008
Nucl. Acids Res. 2008 36: 5933-5945; doi:10.1093/nar/gkn586 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genomics

Get checked abstract Agnès Thierry, Christiane Bouchier, Bernard Dujon, and Guy-Franck Richard

Megasatellites: a peculiar class of giant minisatellites in genes involved in cell adhesion and pathogenicity in Candida glabrata
Nucleic Acids Research Advance Access published on September 23, 2008
Nucl. Acids Res. 2008 36: 5970-5982; doi:10.1093/nar/gkn594 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Molecular Biology

Get checked abstract John D. Curry and Mark S. Schlissel

RAG2's non-core domain contributes to the ordered regulation of V(D)J recombination
Nucleic Acids Research Advance Access published on September 6, 2008
Nucl. Acids Res. 2008 36: 5750-5762; doi:10.1093/nar/gkn553 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Joanna Rorbach, Ricarda Richter, Hans J. Wessels, Mateusz Wydro, Marcin Pekalski, Murtada Farhoud, Inge Kühl, Mauricette Gaisne, Nathalie Bonnefoy, Jan A. Smeitink, Robert N. Lightowlers, and Zofia M.A. Chrzanowska-Lightowlers

The human mitochondrial ribosome recycling factor is essential for cell viability
Nucleic Acids Research Advance Access published on September 9, 2008
Nucl. Acids Res. 2008 36: 5787-5799; doi:10.1093/nar/gkn576 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Joël Acker, Christophe Ozanne, Rym Kachouri-Lafond, Claude Gaillardin, Cécile Neuvéglise, and Christian Marck

Dicistronic tRNA–5S rRNA genes in Yarrowia lipolytica: an alternative TFIIIA-independent way for expression of 5S rRNA genes
Nucleic Acids Research Advance Access published on September 12, 2008
Nucl. Acids Res. 2008 36: 5832-5844; doi:10.1093/nar/gkn549 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Sandra L. Martin, Diane Bushman, Fei Wang, Patrick Wai-Lun Li, Ann Walker, Jessica Cummiskey, Dan Branciforte, and Mark C. Williams

A single amino acid substitution in ORF1 dramatically decreases L1 retrotransposition and provides insight into nucleic acid chaperone activity
Nucleic Acids Research Advance Access published on September 12, 2008
Nucl. Acids Res. 2008 36: 5845-5854; doi:10.1093/nar/gkn554 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Vadim A. Klenchin, Agata Czyz, Igor Y. Goryshin, Richard Gradman, Scott Lovell, Ivan Rayment, and William S. Reznikoff

Phosphate coordination and movement of DNA in the Tn5 synaptic complex: role of the (R)YREK motif
Nucleic Acids Research Advance Access published on September 12, 2008
Nucl. Acids Res. 2008 36: 5855-5862; doi:10.1093/nar/gkn577 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Peter Seibel, Chiara Di Nunno, Christian Kukat, Ingo Schäfer, Roberto Del Bo, Andreina Bordoni, Giacomo P. Comi, Astrid Schön, Ferdinando Capuano, Dominga Latorre, and Gaetano Villani

Cosegregation of novel mitochondrial 16S rRNA gene mutations with the age-associated T414G variant in human cybrids
Nucleic Acids Research Advance Access published on September 16, 2008
Nucl. Acids Res. 2008 36: 5872-5881; doi:10.1093/nar/gkn592 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Sridharan Rajagopalan, Agnes M. Jaulent, Mark Wells, Dmitry B. Veprintsev, and Alan R. Fersht

14-3-3 activation of DNA binding of p53 by enhancing its association into tetramers
Nucleic Acids Research Advance Access published on September 23, 2008
Nucl. Acids Res. 2008 36: 5983-5991; doi:10.1093/nar/gkn598 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Melissa J. Taylor and Brenda A. Peculis

Evolutionary conservation supports ancient origin for Nudt16, a nuclear-localized, RNA-binding, RNA-decapping enzyme
Nucleic Acids Research Advance Access published on September 27, 2008
Nucl. Acids Res. 2008 36: 6021-6034; doi:10.1093/nar/gkn605 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes

Get checked abstract Martin H. Linden, Roland K. Hartmann, and Dagmar Klostermeier

The putative RNase P motif in the DEAD box helicase Hera is dispensable for efficient interaction with RNA and helicase activity
Nucleic Acids Research Advance Access published on September 9, 2008
Nucl. Acids Res. 2008 36: 5800-5811; doi:10.1093/nar/gkn581 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yoandris del Toro Duany, Stefan P. Jungblut, Andreas S. Schmidt, and Dagmar Klostermeier

The reverse gyrase helicase-like domain is a nucleotide-dependent switch that is attenuated by the topoisomerase domain
Nucleic Acids Research Advance Access published on September 16, 2008
Nucl. Acids Res. 2008 36: 5882-5895; doi:10.1093/nar/gkn587 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Andres A. Larrea, Ilene M. Pedroso, Arun Malhotra, and Richard S. Myers

Identification of two conserved aspartic acid residues required for DNA digestion by a novel thermophilic Exonuclease VII in Thermotoga maritima
Nucleic Acids Research Advance Access published on September 23, 2008
Nucl. Acids Res. 2008 36: 5992-6003; doi:10.1093/nar/gkn588 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Huafeng Fang and John-Stephen Taylor

Serial analysis of mutation spectra (SAMS): a new approach for the determination of mutation spectra of site-specific DNA damage and their sequence dependence
Nucleic Acids Research Advance Access published on September 23, 2008
Nucl. Acids Res. 2008 36: 6004-6012; doi:10.1093/nar/gkn595 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA

Get checked abstract Masayuki Sano, Malgorzata Sierant, Makoto Miyagishi, Mahito Nakanishi, Yasuomi Takagi, and Shizuyo Sutou

Effect of asymmetric terminal structures of short RNA duplexes on the RNA interference activity and strand selection
Nucleic Acids Research Advance Access published on September 9, 2008
Nucl. Acids Res. 2008 36: 5812-5821; doi:10.1093/nar/gkn584 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Shandar Ahmad, Ozlem Keskin, Akinori Sarai, and Ruth Nussinov

Protein–DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins
Nucleic Acids Research Advance Access published on September 18, 2008
Nucl. Acids Res. 2008 36: 5922-5932; doi:10.1093/nar/gkn573 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Pavol Cekan, Alyssa L. Smith, Nivrutti Barhate, Bruce H. Robinson, and Snorri Th. Sigurdsson

Rigid spin-labeled nucleoside Ç: a nonperturbing EPR probe of nucleic acid conformation
Nucleic Acids Research Advance Access published on September 19, 2008
Nucl. Acids Res. 2008 36: 5946-5954; doi:10.1093/nar/gkn562 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online

Get checked abstract Koen J. T. Venken, Jaroslaw Kasprowicz, Sabine Kuenen, Jiekun Yan, Bassem A. Hassan, and Patrik Verstreken

Recombineering-mediated tagging of Drosophila genomic constructs for in vivo localization and acute protein inactivation
Nucleic Acids Research Advance Access published on August 1, 2008
Nucl. Acids Res. 2008 36: e114; doi:10.1093/nar/gkn486 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Simon J. Furney, Borja Calvo, Pedro Larrañaga, Jose A. Lozano, and Nuria Lopez-Bigas

Prioritization of candidate cancer genes—an aid to oncogenomic studies
Nucleic Acids Research Advance Access published on August 18, 2008
Nucl. Acids Res. 2008 36: e115; doi:10.1093/nar/gkn482 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jian Qin, Robert C. Jones, and Ramesh Ramakrishnan

Studying copy number variations using a nanofluidic platform
Nucleic Acids Research Advance Access published on August 18, 2008
Nucl. Acids Res. 2008 36: e116; doi:10.1093/nar/gkn518 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Julio Gómez-Rodríguez, Valance Washington, Jun Cheng, Amalia Dutra, Evgenia Pak, Pentao Liu, Daniel W. McVicar, and Pamela L. Schwartzberg

Advantages of q-PCR as a method of screening for gene targeting in mammalian cells using conventional and whole BAC-based constructs
Nucleic Acids Research Advance Access published on August 18, 2008
Nucl. Acids Res. 2008 36: e117; doi:10.1093/nar/gkn523 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Dany Morisset, David Dobnik, Sandrine Hamels, Jana Zel, and Kristina Gruden

NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs
Nucleic Acids Research Advance Access published on August 18, 2008
Nucl. Acids Res. 2008 36: e118; doi:10.1093/nar/gkn524 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Eoin P. Quinlivan and Jesse F. Gregory, III

DNA methylation determination by liquid chromatography–tandem mass spectrometry using novel biosynthetic [U-¹⁵N]deoxycytidine and [U-¹⁵N]methyldeoxycytidine internal standards
Nucleic Acids Research Advance Access published on August 20, 2008
Nucl. Acids Res. 2008 36: e119; doi:10.1093/nar/gkn534 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Zongzhi Liu, Todd Z. DeSantis, Gary L. Andersen, and Rob Knight

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
Nucleic Acids Research Advance Access published on August 22, 2008
Nucl. Acids Res. 2008 36: e120; doi:10.1093/nar/gkn491 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract John G. K. Williams, David L. Steffens, Jon P. Anderson, Teresa M. Urlacher, Donald T. Lamb, Daniel L. Grone, and Jolene C. Egelhoff

An artificial processivity clamp made with streptavidin facilitates oriented attachment of polymerase–DNA complexes to surfaces
Nucleic Acids Research Advance Access published on August 22, 2008
Nucl. Acids Res. 2008 36: e121; doi:10.1093/nar/gkn531 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 36 ISSUE 18 2008
Nucl. Acids Res. 2008 36: i; doi:10.1093/nar/gkn779 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2008 36: ii; doi:10.1093/nar/gkn789 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2008 36: iii; doi:10.1093/nar/gkn780 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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