Nucleic Acids Research

Chemistry

Get checked abstract William Chiuman and Yingfu Li

Efficient signaling platforms built from a small catalytic DNA and doubly labeled fluorogenic substrates
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 401-405; doi:10.1093/nar/gkl1056 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Eric E. Swayze, Andrew M. Siwkowski, Edward V. Wancewicz, Michael T. Migawa, Tadeusz K. Wyrzykiewicz, Gene Hung, Brett P. Monia, and and C. Frank Bennett

Antisense oligonucleotides containing locked nucleic acid improve potency but cause significant hepatotoxicity in animals
Nucleic Acids Research Advance Access published on December 19, 2006
Nucl. Acids Res. 2007 35: 687-700; doi:10.1093/nar/gkl1071 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology

Get checked abstract Istvan Ladunga

More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 433-440; doi:10.1093/nar/gkl1065 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Xiaolu Huang and Hesham Ali

High sensitivity RNA pseudoknot prediction
Nucleic Acids Research Advance Access published on December 19, 2006
Nucl. Acids Res. 2007 35: 656-663; doi:10.1093/nar/gkl943 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Xiaoqiu Huang and Douglas L. Brutlag

Dynamic use of multiple parameter sets in sequence alignment
Nucleic Acids Research Advance Access published on December 19, 2006
Nucl. Acids Res. 2007 35: 678-686; doi:10.1093/nar/gkl1063 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genomics

Get checked abstract Julian L. Huppert and Shankar Balasubramanian

G-quadruplexes in promoters throughout the human genome
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 406-413; doi:10.1093/nar/gkl1057 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Lutz Krause, Alice C. McHardy, Tim W. Nattkemper, Alfred Pühler, Jens Stoye, and Folker Meyer

GISMO—gene identification using a support vector machine for ORF classification
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 540-549; doi:10.1093/nar/gkl1083 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yuping Luo and Siguang Li

Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 559-571; doi:10.1093/nar/gkl1086 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Molecular Biology

Get checked abstract Hideaki Ogiwara, Ayako Ui, Takemi Enomoto, and Masayuki Seki

Role of Elg1 protein in double strand break repair
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 353-362; doi:10.1093/nar/gkl1027 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Nicholas G. Nickols, Claire S. Jacobs, Michelle E. Farkas, and Peter B. Dervan

Improved nuclear localization of DNA-binding polyamides
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 363-370; doi:10.1093/nar/gkl1042 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Heiko Mix, Alexey V. Lobanov, and Vadim N. Gladyshev

SECIS elements in the coding regions of selenoprotein transcripts are functional in higher eukaryotes
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 414-423; doi:10.1093/nar/gkl1060 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jen-Wen Lin, Min-Pey Ding, Yau-Heiu Hsu, and Ching-Hsiu Tsai

Chloroplast phosphoglycerate kinase, a gluconeogenetic enzyme, is required for efficient accumulation of Bamboo mosaic virus
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 424-432; doi:10.1093/nar/gkl1061 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Mindy Reynolds, Lauren Stoddard, Ivan Bespalov, and Anatoly Zhitkovich

Ascorbate acts as a highly potent inducer of chromate mutagenesis and clastogenesis: linkage to DNA breaks in G₂ phase by mismatch repair
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 465-476; doi:10.1093/nar/gkl1069 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Barbara Di Marco, Michela Massetti, Stefano Bruscoli, Antonio Macchiarulo, Rosa Di Virgilio, Enrico Velardi, Valerio Donato, Graziella Migliorati, and Carlo Riccardi

Glucocorticoid-induced leucine zipper (GILZ)/NF-B interaction: role of GILZ homo-dimerization and C-terminal domain
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 517-528; doi:10.1093/nar/gkl1080 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Tasneem Khanam, Timofey S. Rozhdestvensky, Marsha Bundman, Chenna R. Galiveti, Sergej Handel, Valentina Sukonina, Ursula Jordan, Jürgen Brosius, and Boris V. Skryabin

Two primate-specific small non-protein-coding RNAs in transgenic mice: neuronal expression, subcellular localization and binding partners
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 529-539; doi:10.1093/nar/gkl1082 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Michal Krawczyk, Elisa Leimgruber, Queralt Seguín-Estévez, Isabelle Dunand-Sauthier, Emmanuèle Barras, and Walter Reith

Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes
Nucleic Acids Research Advance Access published on December 15, 2006
Nucl. Acids Res. 2007 35: 595-605; doi:10.1093/nar/gkl980 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Eveline Peeters, Carine Wartel, Dominique Maes, and Daniel Charlier

Analysis of the DNA-binding sequence specificity of the archaeal transcriptional regulator Ss-LrpB from Sulfolobus solfataricus by systematic mutagenesis and high resolution contact probing
Nucleic Acids Research Advance Access published on December 18, 2006
Nucl. Acids Res. 2007 35: 623-633; doi:10.1093/nar/gkl1095 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Tomoya Ohno, Yoshiaki Onishi, and Norio Ishida

A novel E4BP4 element drives circadian expression of mPeriod2
Nucleic Acids Research Advance Access published on December 19, 2006
Nucl. Acids Res. 2007 35: 648-655; doi:10.1093/nar/gkl868 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Ernesto Zanotto, Zahid H. Shah, and Howard T. Jacobs

The bidirectional promoter of two genes for the mitochondrial translational apparatus in mouse is regulated by an array of CCAAT boxes interacting with the transcription factor NF-Y
Nucleic Acids Research Advance Access published on December 19, 2006
Nucl. Acids Res. 2007 35: 664-677; doi:10.1093/nar/gkl1037 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Nucleic Acid Enzymes

Get checked abstract Ya-Qiang Li, Ping-Zhu Zhou, Xiu-Dan Zheng, Colum P. Walsh, and Guo-Liang Xu

Association of Dnmt3a and thymine DNA glycosylase links DNA methylation with base-excision repair
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 390-400; doi:10.1093/nar/gkl1052 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Wafa Zghidi, Livia Merendino, Annick Cottet, Régis Mache, and Silva Lerbs-Mache

Nucleus-encoded plastid sigma factor SIG3 transcribes specifically the psbN gene in plastids
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 455-464; doi:10.1093/nar/gkl1067 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Veronika Németh-Pongrácz, Orsolya Barabás, Mónika Fuxreiter, István Simon, Iva Pichová, Michalea Rumlová, Helena Zábranská, Dmitri Svergun, Maxim Petoukhov, Veronika Harmat, Éva Klement, Éva Hunyadi-Gulyás, Katalin F. Medzihradszky, Emese Kónya, and Beáta G. Vértessy

Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 495-505; doi:10.1093/nar/gkl1074 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Cécile Zaros, Jean-François Briand, Yves Boulard, Sylvie Labarre-Mariotte, M. Carmen Garcia-Lopez, Pierre Thuriaux, and Francisco Navarro

Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases
Nucleic Acids Research Advance Access published on December 19, 2006
Nucl. Acids Res. 2007 35: 634-647; doi:10.1093/nar/gkl686 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Retraction

Non-random, individual-specific methylation profiles are present at the sixth CTCF binding site in the human H19/IGF2 imprinting control region.
Nucleic Acids Research Advance Access published on December 18, 2006
Nucl. Acids Res. 2007 35: 701; doi:10.1093/nar/gkl1107 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA

Get checked abstract Jin Sun Kim, Su Jung Park, Kyung Jin Kwak, Yeon Ok Kim, Joo Yeol Kim, Jinkyung Song, Boseung Jang, Che-Hun Jung, and Hunseung Kang

Cold shock domain proteins and glycine-rich RNA-binding proteins from Arabidopsis thaliana can promote the cold adaptation process in Escherichia coli
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 506-516; doi:10.1093/nar/gkl1076 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Xinliang Zhao and Yi-Tao Yu

Incorporation of 5-fluorouracil into U2 snRNA blocks pseudouridylation and pre-mRNA splicing in vivo
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 550-558; doi:10.1093/nar/gkl1084 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jonas Noeske, Janina Buck, Boris Fürtig, Hamid R. Nasiri, Harald Schwalbe, and Jens Wöhnert

Interplay of ‘induced fit’ and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 572-583; doi:10.1093/nar/gkl1094 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Michela Raponi, Francisco E. Baralle, and Franco Pagani

Reduced splicing efficiency induced by synonymous substitutions may generate a substrate for natural selection of new splicing isoforms: the case of CFTR exon 12
Nucleic Acids Research Advance Access published on December 15, 2006
Nucl. Acids Res. 2007 35: 606-613; doi:10.1093/nar/gkl1087 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract A. Xayaphoummine, V. Viasnoff, S. Harlepp, and H. Isambert

Encoding folding paths of RNA switches
Nucleic Acids Research Advance Access published on December 18, 2006
Nucl. Acids Res. 2007 35: 614-622; doi:10.1093/nar/gkl1036 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Structural Biology

Get checked abstract Natalia N. Singh, Ravindra N. Singh, and Elliot J. Androphy

Modulating role of RNA structure in alternative splicing of a critical exon in the spinal muscular atrophy genes
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 371-389; doi:10.1093/nar/gkl1050 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Hendrik R. A. Jonker, Serge Ilin, S. Kaspar Grimm, Jens Wöhnert, and Harald Schwalbe

L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 441-454; doi:10.1093/nar/gkl1066 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jiansheng Jiang, Jia Sheng, Nicolas Carrasco, and Zhen Huang

Selenium derivatization of nucleic acids for crystallography
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 477-485; doi:10.1093/nar/gkl1070 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Shu-ichi Nakano, Toshimasa Kirihata, Satoshi Fujii, Hiroshi Sakai, Masayasu Kuwahara, Hiroaki Sawai, and Naoki Sugimoto

Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 486-494; doi:10.1093/nar/gkl1073 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Yi-Ting Wang, Wei-Jen Yang, Chia-Lung Li, Lyudmila G. Doudeva, and Hanna S. Yuan

Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases
Nucleic Acids Research Advance Access published on December 15, 2006
Nucl. Acids Res. 2007 35: 584-594; doi:10.1093/nar/gkl621 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online

Get checked abstract Haiyuan Yu, Katherine Nguyen, Tom Royce, Jiang Qian, Kenneth Nelson, Michael Snyder, and Mark Gerstein

Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: e8; doi:10.1093/nar/gkl871 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Naoko Shiomi, Masahiko Mori, Hideo Tsuji, Takashi Imai, Hirokazu Inoue, Satoshi Tateishi, Masaru Yamaizumi, and Tadahiro Shiomi

Human RAD18 is involved in S phase-specific single-strand break repair without PCNA monoubiquitination
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: e9; doi:10.1093/nar/gkl979 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract M. S. Brenz Verca, Peter Weber, Christine Mayer, Cornelia Graf, Damián Refojo, Ralf Kühn, Ingrid Grummt, and Beat Lutz

Development of a species-specific RNA polymerase I-based shRNA expression vector
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: e10; doi:10.1093/nar/gkl1045 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yohann Duverger, Jérôme Belougne, Sarah Scaglione, Dominique Brandli, Christophe Beclin, and Jonathan J. Ewbank

A semi-automated high-throughput approach to the generation of transposon insertion mutants in the nematode Caenorhabditis elegans
Nucleic Acids Research Advance Access published on December 12, 2006
Nucl. Acids Res. 2007 35: e11; doi:10.1093/nar/gkl1046 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Scott Mann, Jinyan Li, and Yi-Ping Phoebe Chen

A pHMM-ANN based discriminative approach to promoter identification in prokaryote genomic contexts
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: e12; doi:10.1093/nar/gkl1024 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Chandran R. Sabanayagam and Joseph R. Lakowicz

Increasing the sensitivity of DNA microarrays by metal-enhanced fluorescence using surface-bound silver nanoparticles
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: e13; doi:10.1093/nar/gkl1054 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Erratum

Erratum
Nucl. Acids Res. 2007 35: 704; doi:10.1093/nar/gkm048 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Corrigendum

Thomas Bentin, Georg I. Hansen, and Peter E. Nielsen

Structural diversity of target-specific homopyrimidine peptide nucleic acid–dsDNA complexes
Nucl. Acids Res. 2007 35: 702; doi:10.1093/nar/gkl1167 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Corrigendum
Nucleic Acids Research Advance Access published on January 18, 2007
Nucl. Acids Res. 2007 35: 703; doi:10.1093/nar/gkl1132 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Corrigendum
Nucl. Acids Res. 2007 35: 703; doi:10.1093/nar/gkl760 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

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