Nucleic Acids Research

Editorial

Editorial
Nucleic Acids Research Advance Access published on November 14, 2007
Nucl. Acids Res. 2007 35: 7043; doi:10.1093/nar/gkm1015 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Chemistry

Get checked abstract Daniel J. Fish, M. Todd Horne, Greg P. Brewood, Jim P. Goodarzi, Saba Alemayehu, Ashwini Bhandiwad, Robert P. Searles, and Albert S. Benight

DNA multiplex hybridization on microarrays and thermodynamic stability in solution: a direct comparison
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2007 35: 7197-7208; doi:10.1093/nar/gkm865 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Youngmi Kim, Chaoyong James Yang, and Weihong Tan

Superior structure stability and selectivity of hairpin nucleic acid probes with an L-DNA stem
Nucleic Acids Research Advance Access published on October 24, 2007
Nucl. Acids Res. 2007 35: 7279-7287; doi:10.1093/nar/gkm771 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Computational Biology

Get checked abstract Elmar Pruesse, Christian Quast, Katrin Knittel, Bernhard M. Fuchs, Wolfgang Ludwig, Jörg Peplies, and Frank Oliver Glöckner

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2007 35: 7188-7196; doi:10.1093/nar/gkm864 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Larry N. Singh, Li-San Wang, and Sridhar Hannenhalli

TREMOR—a tool for retrieving transcriptional modules by incorporating motif covariance
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2007 35: 7360-7371; doi:10.1093/nar/gkm885 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics

Get checked abstract Haizheng Hong, Huachuan Cao, and Yinsheng Wang

Formation and genotoxicity of a guanine–cytosine intrastrand cross-link lesion in vivo
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: 7118-7127; doi:10.1093/nar/gkm851 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Salim Charaniya, Sarika Mehra, Wei Lian, Karthik P. Jayapal, George Karypis, and Wei-Shou Hu

Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor
Nucleic Acids Research Advance Access published on October 24, 2007
Nucl. Acids Res. 2007 35: 7222-7236; doi:10.1093/nar/gkm501 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract John F. Reichard, Gregory T. Motz, and Alvaro Puga

Heme oxygenase-1 induction by NRF2 requires inactivation of the transcriptional repressor BACH1
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: 7074-7086; doi:10.1093/nar/gkm638 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jeny Shklover, Shulamit Etzioni, Pnina Weisman-Shomer, Anat Yafe, Eyal Bengal, and Michael Fry

MyoD uses overlapping but distinct elements to bind E-box and tetraplex structures of regulatory sequences of muscle-specific genes
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: 7087-7095; doi:10.1093/nar/gkm746 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yasumasa Iwatani, Denise S.B. Chan, F. Wang, Kristen Stewart Maynard, Wataru Sugiura, Angela M. Gronenborn, Ioulia Rouzina, Mark C. Williams, Karin Musier-Forsyth, and Judith G. Levin

Deaminase-independent inhibition of HIV-1 reverse transcription by APOBEC3G
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: 7096-7108; doi:10.1093/nar/gkm750 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Alberto García-Marcos, Antonio Morreale, Esther Guarinos, Elisa Briones, Miguel Remacha, Angel R. Ortiz, and Juan P. G. Ballesta

In vivo assembling of bacterial ribosomal protein L11 into yeast ribosomes makes the particles sensitive to the prokaryotic specific antibiotic thiostrepton
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: 7109-7117; doi:10.1093/nar/gkm773 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Xiaohong Liu, Hazuki Takahashi, Yoko Harada, Tsukasa Ogawara, Yuta Ogimura, Yoshiyuku Mizushina, Mineo Saneyoshi, and Toyofumi Yamaguchi

3'-Azido-2',3'-dideoxynucleoside 5'-triphosphates inhibit telomerase activity in vitro, and the corresponding nucleosides cause telomere shortening in human HL60 cells
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: 7140-7149; doi:10.1093/nar/gkm859 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jordi Bernués, David Piñeyro, and Ana Kosoy

General, negative feedback mechanism for regulation of Trithorax-like gene expression in vivo: new roles for GAGA factor in flies
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2007 35: 7150-7159; doi:10.1093/nar/gkm590 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Huimei Lu, Jingyin Yue, Xiangbing Meng, Jac A. Nickoloff, and Zhiyuan Shen

BCCIP regulates homologous recombination by distinct domains and suppresses spontaneous DNA damage
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2007 35: 7160-7170; doi:10.1093/nar/gkm732 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Olga Ivanova, Daniel Braas, and Karl-Heinz Klempnauer

Oncogenic point mutations in the Myb DNA-binding domain alter the DNA-binding properties of Myb at a physiological target gene
Nucleic Acids Research Advance Access published on October 24, 2007
Nucl. Acids Res. 2007 35: 7237-7247; doi:10.1093/nar/gkm675 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Alexandra-Viola Bohne, Stephanie Ruf, Thomas Börner, and Ralph Bock

Faithful transcription initiation from a mitochondrial promoter in transgenic plastids
Nucleic Acids Research Advance Access published on October 24, 2007
Nucl. Acids Res. 2007 35: 7256-7266; doi:10.1093/nar/gkm679 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Amra Grudic, Åsne Jul-Larsen, Stuart J. Haring, Marc S. Wold, Per Eystein Lønning, Rolf Bjerkvig, and Stig Ove Bøe

Replication protein A prevents accumulation of single-stranded telomeric DNA in cells that use alternative lengthening of telomeres
Nucleic Acids Research Advance Access published on October 24, 2007
Nucl. Acids Res. 2007 35: 7267-7278; doi:10.1093/nar/gkm738 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Gui-deng Li, Jin-xu Fang, Hang-zi Chen, Jie Luo, Zhong-hui Zheng, Yue-mao Shen, and Qiao Wu

Negative regulation of transcription coactivator p300 by orphan receptor TR3
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2007 35: 7348-7359; doi:10.1093/nar/gkm870 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Stéphanie Renaud, Elena M. Pugacheva, M. Dolores Delgado, Richard Braunschweig, Ziedulla Abdullaev, Dmitri Loukinov, Jean Benhattar, and Victor Lobanenkov

Expression of the CTCF-paralogous cancer-testis gene, brother of the regulator of imprinted sites (BORIS), is regulated by three alternative promoters modulated by CpG methylation and by CTCF and p53 transcription factors
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2007 35: 7372-7388; doi:10.1093/nar/gkm896 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Svetlana Tishchenko, Ekaterina Nikonova, Vladislav Kljashtorny, Olga Kostareva, Natalia Nevskaya, Wolfgang Piendl, Natalia Davydova, Victor Streltsov, Maria Garber, and Stanislav Nikonov

Domain I of ribosomal protein L1 is sufficient for specific RNA binding
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2007 35: 7389-7395; doi:10.1093/nar/gkm898 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nucleic Acid Enzymes

Get checked abstract Brian A. McKinley and Maxim V. Sukhodolets

Escherichia coli RNA polymerase-associated SWI/SNF protein RapA: evidence for RNA-directed binding and remodeling activity
Nucleic Acids Research Advance Access published on October 2, 2007
Nucl. Acids Res. 2007 35: 7044-7060; doi:10.1093/nar/gkm747 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Patricia Pérez-Arnaiz, Elisa Longás, Laurentino Villar, José M. Lázaro, Margarita Salas, and Miguel de Vega

Involvement of phage 29 DNA polymerase and terminal protein subdomains in conferring specificity during initiation of protein-primed DNA replication
Nucleic Acids Research Advance Access published on October 2, 2007
Nucl. Acids Res. 2007 35: 7061-7073; doi:10.1093/nar/gkm749 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Judith Miné, Ludovic Disseau, Masayuki Takahashi, Giovanni Cappello, Marie Dutreix, and Jean-Louis Viovy

Real-time measurements of the nucleation, growth and dissociation of single Rad51–DNA nucleoprotein filaments
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2007 35: 7171-7187; doi:10.1093/nar/gkm752 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jennifer H. Eastberg, Audrey McConnell Smith, Lei Zhao, Justin Ashworth, Betty W. Shen, and Barry L. Stoddard

Thermodynamics of DNA target site recognition by homing endonucleases
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2007 35: 7209-7221; doi:10.1093/nar/gkm867 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Hang Gyeong Chin, Pierre-Olivier Estève, Mihika Pradhan, Jack Benner, Debasis Patnaik, Michael F. Carey, and Sriharsa Pradhan

Automethylation of G9a and its implication in wider substrate specificity and HP1 binding
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2007 35: 7313-7323; doi:10.1093/nar/gkm726 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA

Get checked abstract Serena Bernacchi, Séverine Freisz, Clarisse Maechling, Bernard Spiess, Roland Marquet, Philippe Dumas, and Eric Ennifar

Aminoglycoside binding to the HIV-1 RNA dimerization initiation site: thermodynamics and effect on the kissing-loop to duplex conversion
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: 7128-7139; doi:10.1093/nar/gkm856 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Daisuke Kurita, Rumi Sasaki, Akira Muto, and Hyouta Himeno

Interaction of SmpB with ribosome from directed hydroxyl radical probing
Nucleic Acids Research Advance Access published on October 24, 2007
Nucl. Acids Res. 2007 35: 7248-7255; doi:10.1093/nar/gkm677 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Chunjuan Tian, Tao Wang, Wenyan Zhang, and Xiao-Fang Yu

Virion packaging determinants and reverse transcription of SRP RNA in HIV-1 particles
Nucleic Acids Research Advance Access published on October 24, 2007
Nucl. Acids Res. 2007 35: 7288-7302; doi:10.1093/nar/gkm816 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Marc S. Weinberg, Samantha Barichievy, Lana Schaffer, Jiang Han, and Kevin V. Morris

An RNA targeted to the HIV-1 LTR promoter modulates indiscriminate off-target gene activation
Nucleic Acids Research Advance Access published on October 24, 2007
Nucl. Acids Res. 2007 35: 7303-7312; doi:10.1093/nar/gkm847 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jaime Villegas, Veronica Burzio, Claudio Villota, Eduardo Landerer, Ronny Martinez, Marcela Santander, Rodrigo Martinez, Rodrigo Pinto, María I. Vera, Enrique Boccardo, Luisa L. Villa, and Luis O. Burzio

Expression of a novel non-coding mitochondrial RNA in human proliferating cells
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2007 35: 7336-7347; doi:10.1093/nar/gkm863 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Tripti Shrivastava and Ravishankar Ramachandran

Mechanistic insights from the crystal structures of a feast/famine regulatory protein from Mycobacterium tuberculosis H37Rv
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2007 35: 7324-7335; doi:10.1093/nar/gkm850 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Erratum

Saïd Abes, John J. Turner, Gabriela D. Ivanova, David Owen, Donna Williams, Andrey Arzumanov, Philippe Clair, Michael J. Gait, and Bernard Lebleu

Efficient splicing correction by PNA conjugation to an R6-Penetratin delivery peptide
Nucl. Acids Res. 2007 35: 7396; doi:10.1093/nar/gkm1115 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online

Get checked abstract Khirud Gogoi, Meenakshi V. Mane, Sunita S. Kunte, and Vaijayanti A. Kumar

A versatile method for the preparation of conjugates of peptides with DNA/PNA/analog by employing chemo-selective click reaction in water
Nucleic Acids Research Advance Access published on November 2, 2007
Nucl. Acids Res. 2007 35: e139; doi:10.1093/nar/gkm935 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Miho Tagawa, Koh-ichiroh Shohda, Kenzo Fujimoto, Tadashi Sugawara, and Akira Suyama

Heat-resistant DNA tile arrays constructed by template-directed photoligation through 5-carboxyvinyl-2'-deoxyuridine
Nucleic Acids Research Advance Access published on November 3, 2007
Nucl. Acids Res. 2007 35: e140; doi:10.1093/nar/gkm872 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Alex R. Hastie and Steven C. Pruitt

Yeast two-hybrid interaction partner screening through in vivo Cre-mediated Binary Interaction Tag generation
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2007 35: e141; doi:10.1093/nar/gkm894 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Claudia Bex, Katja Knauth, Silvia Dambacher, and Alexander Buchberger

A yeast two-hybrid system reconstituting substrate recognition of the von Hippel-Lindau tumor suppressor protein
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2007 35: e142; doi:10.1093/nar/gkm932 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jörg Fahrer, Ramon Kranaster, Matthias Altmeyer, Andreas Marx, and Alexander Bürkle

Quantitative analysis of the binding affinity of poly(ADP-ribose) to specific binding proteins as a function of chain length
Nucleic Acids Research Advance Access published on November 8, 2007
Nucl. Acids Res. 2007 35: e143; doi:10.1093/nar/gkm944 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Christina Dahl and Per Guldberg

A ligation assay for multiplex analysis of CpG methylation using bisulfite-treated DNA
Nucleic Acids Research Advance Access published on November 12, 2007
Nucl. Acids Res. 2007 35: e144; doi:10.1093/nar/gkm984 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Liu Yang, Kemin Wang, Weihong Tan, Huimin Li, Xiaohai Yang, Changbei Ma, and Hongxing Tang

Using force spectroscopy analysis to improve the properties of the hairpin probe
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2007 35: e145; doi:10.1093/nar/gkm983 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Germán Gastón Leparc and Robi David Mitra

A sensitive procedure to detect alternatively spliced mRNA in pooled-tissue samples
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2007 35: e146; doi:10.1093/nar/gkm989 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Todd W. Roy and A. S. Bhagwat

Kinetic studies of Escherichia coli AlkB using a new fluorescence-based assay for DNA demethylation
Nucleic Acids Research Advance Access published on November 14, 2007
Nucl. Acids Res. 2007 35: e147; doi:10.1093/nar/gkm1031 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Gagan A. Pandya, Michael H. Holmes, Sirisha Sunkara, Andrew Sparks, Yun Bai, Kathleen Verratti, Kelly Saeed, Pratap Venepally, Behnam Jarrahi, Robert D. Fleischmann, and Scott N. Peterson

A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip® whole-genome resequencing platform
Nucleic Acids Research Advance Access published on November 15, 2007
Nucl. Acids Res. 2007 35: e148; doi:10.1093/nar/gkm918 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

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