Nucleic Acids Research

Computational Biology

Get checked abstract Ryan K. Shultzaberger, Zehua Chen, Karen A. Lewis, and Thomas D. Schneider

Anatomy of Escherichia coli ⁷⁰ promoters
Nucleic Acids Research Advance Access published on December 22, 2006
Nucl. Acids Res. 2007 35: 771-788; doi:10.1093/nar/gkl956 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Molecular Biology

Get checked abstract Kohsuke Kato, Mary Miyaji-Yamaguchi, Mitsuru Okuwaki, and Kyosuke Nagata

Histone acetylation-independent transcription stimulation by a histone chaperone
Nucleic Acids Research Advance Access published on December 19, 2006
Nucl. Acids Res. 2007 35: 705-715; doi:10.1093/nar/gkl1077 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Mahajoub Bello-Roufaï, Olivier Lambert, and Bruno Pitard

Relationships between the physicochemical properties of an amphiphilic triblock copolymers/DNA complexes and their intramuscular transfection efficiency
Nucleic Acids Research Advance Access published on December 20, 2006
Nucl. Acids Res. 2007 35: 728-739; doi:10.1093/nar/gkl860 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Arie B. Brinkman, Sebastiaan W. C. Pennings, Georgia G. Braliou, Luc E. G. Rietveld, and Hendrik G. Stunnenberg

DNA methylation immediately adjacent to active histone marking does not silence transcription
Nucleic Acids Research Advance Access published on January 3, 2007
Nucl. Acids Res. 2007 35: 801-811; doi:10.1093/nar/gkl1014 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Geetu Mendiratta, Peter R. Eriksson, and David J. Clark

Cooperative binding of the yeast Spt10p activator to the histone upstream activating sequences is mediated through an N-terminal dimerization domain
Nucleic Acids Research Advance Access published on January 3, 2007
Nucl. Acids Res. 2007 35: 812-821; doi:10.1093/nar/gkl1079 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Nathalie Grandin and Michel Charbonneau

Control of the yeast telomeric senescence survival pathways of recombination by the Mec1 and Mec3 DNA damage sensors and RPA
Nucleic Acids Research Advance Access published on January 3, 2007
Nucl. Acids Res. 2007 35: 822-838; doi:10.1093/nar/gkl1081 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Kenji Fukui, Hiromichi Kosaka, Seiki Kuramitsu, and Ryoji Masui

Nuclease activity of the MutS homologue MutS2 from Thermus thermophilus is confined to the Smr domain
Nucleic Acids Research Advance Access published on January 10, 2007
Nucl. Acids Res. 2007 35: 850-860; doi:10.1093/nar/gkl735 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Ying Zhou, Haiping Kou, and Zhigang Wang

Tfb5 interacts with Tfb2 and facilitates nucleotide excision repair in yeast
Nucleic Acids Research Advance Access published on January 10, 2007
Nucl. Acids Res. 2007 35: 861-871; doi:10.1093/nar/gkl1085 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Lucy Glover, Sam Alsford, Caroline Beattie, and David Horn

Deletion of a trypanosome telomere leads to loss of silencing and progressive loss of terminal DNA in the absence of cell cycle arrest
Nucleic Acids Research Advance Access published on January 23, 2007
Nucl. Acids Res. 2007 35: 872-880; doi:10.1093/nar/gkl1100 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Timothy Grocott, Victoria Frost, Marjorie Maillard, Terje Johansen, Grant N. Wheeler, Lucy J. Dawes, I. Michael Wormstone, and Andrew Chantry

The MH1 domain of Smad3 interacts with Pax6 and represses autoregulation of the Pax6 P1 promoter
Nucleic Acids Research Advance Access published on January 23, 2007
Nucl. Acids Res. 2007 35: 890-901; doi:10.1093/nar/gkl1105 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Masahiro Hiratochi, Hisashi Nagase, Yu Kuramochi, Chang-Sung Koh, Takeshi Ohkawara, and Kohzo Nakayama

The Delta intracellular domain mediates TGF-ß/Activin signaling through binding to Smads and has an important bi-directional function in the Notch–Delta signaling pathway
Nucleic Acids Research Advance Access published on January 23, 2007
Nucl. Acids Res. 2007 35: 912-922; doi:10.1093/nar/gkl1128 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract J. Armando Casas-Mollano, Karin van Dijk, John Eisenhart, and Heriberto Cerutti

SET3p monomethylates histone H3 on lysine 9 and is required for the silencing of tandemly repeated transgenes in Chlamydomonas
Nucleic Acids Research Advance Access published on January 23, 2007
Nucl. Acids Res. 2007 35: 939-950; doi:10.1093/nar/gkl1149 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Tumpa Sarkar, Iulia Vitoc, Ishita Mukerji, and Nicholas V. Hud

Bacterial protein HU dictates the morphology of DNA condensates produced by crowding agents and polyamines
Nucleic Acids Research Advance Access published on January 26, 2007
Nucl. Acids Res. 2007 35: 951-961; doi:10.1093/nar/gkl1093 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Toshitsugu Fujita, Stephan Ryser, Silvia Tortola, Isabelle Piuz, and Werner Schlegel

Gene-specific recruitment of positive and negative elongation factors during stimulated transcription of the MKP-1 gene in neuroendocrine cells
Nucleic Acids Research Advance Access published on January 26, 2007
Nucl. Acids Res. 2007 35: 1007-1017; doi:10.1093/nar/gkl1138 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Nucleic Acid Enzymes

Get checked abstract Jeffrey L. Boldt, Kevin V. Kepple, Geoffrey D. Cassell, and Anca M. Segall

Spermidine biases the resolution of Holliday junctions by phage integrase
Nucleic Acids Research Advance Access published on December 19, 2006
Nucl. Acids Res. 2007 35: 716-727; doi:10.1093/nar/gkl1078 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Alexander E. Smith and Kevin G. Ford

Specific targeting of cytosine methylation to DNA sequences in vivo
Nucleic Acids Research Advance Access published on December 20, 2006
Nucl. Acids Res. 2007 35: 740-754; doi:10.1093/nar/gkl1053 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Dharmendra Kumar Singh, Mohammad Nurul Islam, Nirupam Roy Choudhury, Sumona Karjee, and Sunil Kumar Mukherjee

The 32 kDa subunit of replication protein A (RPA) participates in the DNA replication of Mung bean yellow mosaic India virus (MYMIV) by interacting with the viral Rep protein
Nucleic Acids Research Advance Access published on December 20, 2006
Nucl. Acids Res. 2007 35: 755-770; doi:10.1093/nar/gkl1088 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Amy Raymond and Stewart Shuman

Deinococcus radiodurans RNA ligase exemplifies a novel ligase clade with a distinctive N-terminal module that is important for 5'-PO₄ nick sealing and ligase adenylylation but dispensable for phosphodiester formation at an adenylylated nick
Nucleic Acids Research Advance Access published on January 4, 2007
Nucl. Acids Res. 2007 35: 839-849; doi:10.1093/nar/gkl1090 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Joanne L. Parker, Aleksandra B. Bielen, Ivan Dikic, and Helle D. Ulrich

Contributions of ubiquitin- and PCNA-binding domains to the activity of Polymerase in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on January 23, 2007
Nucl. Acids Res. 2007 35: 881-889; doi:10.1093/nar/gkl1102 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Géraldine Farge, Xuan Hoi Pham, Teresa Holmlund, Ivan Khorostov, and Maria Falkenberg

The accessory subunit B of DNA polymerase is required for mitochondrial replisome function
Nucleic Acids Research Advance Access published on January 23, 2007
Nucl. Acids Res. 2007 35: 902-911; doi:10.1093/nar/gkl1116 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sandra Wydau, Maria-Laura Ferri-Fioni, Sylvain Blanquet, and Pierre Plateau

GEK1, a gene product of Arabidopsis thaliana involved in ethanol tolerance, is a D-aminoacyl-tRNA deacylase
Nucleic Acids Research Advance Access published on January 23, 2007
Nucl. Acids Res. 2007 35: 930-938; doi:10.1093/nar/gkl1145 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Elizabeth R. Barry, Adam T. McGeoch, Zvi Kelman, and Stephen D. Bell

Archaeal MCM has separable processivity, substrate choice and helicase domains
Nucleic Acids Research Advance Access published on January 26, 2007
Nucl. Acids Res. 2007 35: 988-998; doi:10.1093/nar/gkl1117 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA

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

The BRCT domain of mammalian Pes1 is crucial for nucleolar localization and rRNA processing
Nucleic Acids Research Advance Access published on December 22, 2006
Nucl. Acids Res. 2007 35: 789-800; doi:10.1093/nar/gkl1058 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Michael P. Spiller, Kum-Loong Boon, Martin A. M. Reijns, and Jean D. Beggs

The Lsm2-8 complex determines nuclear localization of the spliceosomal U6 snRNA
Nucleic Acids Research Advance Access published on January 23, 2007
Nucl. Acids Res. 2007 35: 923-929; doi:10.1093/nar/gkl1130 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Pierre Mandin, Francis Repoila, Massimo Vergassola, Thomas Geissmann, and Pascale Cossart

Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets
Nucleic Acids Research Advance Access published on January 26, 2007
Nucl. Acids Res. 2007 35: 962-974; doi:10.1093/nar/gkl1096 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Véronique Arluison, Sungchul Hohng, Rahul Roy, Olivier Pellegrini, Philippe Régnier, and Taekjip Ha

Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA
Nucleic Acids Research Advance Access published on January 26, 2007
Nucl. Acids Res. 2007 35: 999-1006; doi:10.1093/nar/gkl1124 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Johannes H. Urban and Jörg Vogel

Translational control and target recognition by Escherichia coli small RNAs in vivo
Nucleic Acids Research Advance Access published on January 30, 2007
Nucl. Acids Res. 2007 35: 1018-1037; doi:10.1093/nar/gkl1040 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Structural Biology

Get checked abstract Svetlana Baranova, Fedor V. Tuzikov, Olga D. Zakharova, Natalia A. Tuzikova, Christina Calmels, Simon Litvak, Laura Tarrago-Litvak, Vincent Parissi, and Georgy A. Nevinsky

Small-angle X-ray characterization of the nucleoprotein complexes resulting from DNA-induced oligomerization of HIV-1 integrase
Nucleic Acids Research Advance Access published on January 26, 2007
Nucl. Acids Res. 2007 35: 975-987; doi:10.1093/nar/gkl1111 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online

Get checked abstract Pierre Taberlet, Eric Coissac, François Pompanon, Ludovic Gielly, Christian Miquel, Alice Valentini, Thierry Vermat, Gérard Corthier, Christian Brochmann, and Eske Willerslev

Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: e14; doi:10.1093/nar/gkl938 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Heike Fiegler, Jochen B. Geigl, Sabine Langer, Diane Rigler, Keith Porter, Kristian Unger, Nigel P. Carter, and Michael R. Speicher

High resolution array-CGH analysis of single cells
Nucleic Acids Research Advance Access published on December 18, 2006
Nucl. Acids Res. 2007 35: e15; doi:10.1093/nar/gkl1030 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Ming Xiao, Angie Phong, Connie Ha, Ting-Fung Chan, Dongmei Cai, Lucinda Leung, Eunice Wan, Amy L. Kistler, Joseph L. DeRisi, Paul R. Selvin, and Pui-Yan Kwok

Rapid DNA mapping by fluorescent single molecule detection
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: e16; doi:10.1093/nar/gkl1044 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Michael Hölzel, Michaela Rohrmoser, Mathias Orban, Cornelia Hömig, Thomas Harasim, Anastassia Malamoussi, Anita Gruber-Eber, Vigo Heissmeyer, Georg Bornkamm, and Dirk Eick

Rapid conditional knock-down–knock-in system for mammalian cells
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: e17; doi:10.1093/nar/gkl1055 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Li Zhang, Chunlei Wu, Roberto Carta, and Haitao Zhao

Free energy of DNA duplex formation on short oligonucleotide microarrays
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: e18; doi:10.1093/nar/gkl1064 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract John A. L. Armour, Raquel Palla, Patrick L. J. M. Zeeuwen, Martin den Heijer, Joost Schalkwijk, and Edward J. Hollox

Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: e19; doi:10.1093/nar/gkl1089 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Timothy E. Reddy, Boris E. Shakhnovich, Daniel S. Roberts, Shelley J. Russek, and Charles DeLisi

Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABA_A receptor subunit genes
Nucleic Acids Research Advance Access published on January 3, 2007
Nucl. Acids Res. 2007 35: e20; doi:10.1093/nar/gkl1062 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Corrigendum

Raphaël Kiekens, Annelies Vercauteren, Beatrijs Moerkerke, Els Goetghebeur, Hilde Van Den Daele, Roel Sterken, Martin Kuiper, Fred van Eeuwijk, and Marnik Vuylsteke

Genome-wide screening for cis-regulatory variation using a classical diallel crossing scheme
Nucleic Acids Research Advance Access published on January 23, 2007
Nucl. Acids Res. 2007 35: 1038; doi:10.1093/nar/gkm007 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

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