Nucleic Acids Research

Survey and Summary

Get checked abstract Ivaylo P. Ivanov and John F. Atkins

Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation
Nucleic Acids Research Advance Access published on March 1, 2007
Nucl. Acids Res. 2007 35: 1842-1858; doi:10.1093/nar/gkm035 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Chemistry

Get checked abstract Katerina Chválová, Viktor Brabec, and Jana Kaspárková

Mechanism of the formation of DNA–protein cross-links by antitumor cisplatin
Nucleic Acids Research Advance Access published on February 28, 2007
Nucl. Acids Res. 2007 35: 1812-1821; doi:10.1093/nar/gkm032 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Computational Biology

Get checked abstract Julia R. Gog, Emmanuel Dos Santos Afonso, Rosa M. Dalton, India Leclercq, Laurence Tiley, Debra Elton, Johann C. von Kirchbach, Nadia Naffakh, Nicolas Escriou, and Paul Digard

Codon conservation in the influenza A virus genome defines RNA packaging signals
Nucleic Acids Research Advance Access published on March 1, 2007
Nucl. Acids Res. 2007 35: 1897-1907; doi:10.1093/nar/gkm087 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Stefano Colella, Christopher Yau, Jennifer M. Taylor, Ghazala Mirza, Helen Butler, Penny Clouston, Anne S. Bassett, Anneke Seller, Christopher C. Holmes, and Jiannis Ragoussis

QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data
Nucleic Acids Research Advance Access published on March 6, 2007
Nucl. Acids Res. 2007 35: 2013-2025; doi:10.1093/nar/gkm076 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Genomics

Get checked abstract Mauro A. A. Castro, José C. M. Mombach, Rita M. C. de Almeida, and José C. F. Moreira

Impaired expression of NER gene network in sporadic solid tumors
Nucleic Acids Research Advance Access published on March 1, 2007
Nucl. Acids Res. 2007 35: 1859-1867; doi:10.1093/nar/gkm061 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Virginie Moucadel, Fabrice Lopez, Takeshi Ara, Philippe Benech, and Daniel Gautheret

Beyond the 3' end: experimental validation of extended transcript isoforms
Nucleic Acids Research Advance Access published on March 4, 2007
Nucl. Acids Res. 2007 35: 1947-1957; doi:10.1093/nar/gkm062 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Monica Jain, Jeff Shrager, Elizabeth H. Harris, Renee Halbrook, Arthur R. Grossman, Charles Hauser, and Olivier Vallon

EST assembly supported by a draft genome sequence: an analysis of the Chlamydomonas reinhardtii transcriptome
Nucleic Acids Research Advance Access published on March 13, 2007
Nucl. Acids Res. 2007 35: 2074-2083; doi:10.1093/nar/gkm081 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Molecular Biology

Get checked abstract Giacomo Cattaruzzi, Sandro Altamura, Michela A. Tessari, Alessandra Rustighi, Vincenzo Giancotti, Carlo Pucillo, and Guidalberto Manfioletti

The second AT-hook of the architectural transcription factor HMGA2 is determinant for nuclear localization and function
Nucleic Acids Research Advance Access published on February 25, 2007
Nucl. Acids Res. 2007 35: 1751-1760; doi:10.1093/nar/gkl1106 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Brian Boer, Janel Kopp, Sunil Mallanna, Michelle Desler, Harini Chakravarthy, Phillip J. Wilder, Cory Bernadt, and Angie Rizzino

Elevating the levels of Sox2 in embryonal carcinoma cells and embryonic stem cells inhibits the expression of Sox2:Oct-3/4 target genes
Nucleic Acids Research Advance Access published on February 25, 2007
Nucl. Acids Res. 2007 35: 1773-1786; doi:10.1093/nar/gkm059 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Sangyong Lim, Jiae Yun, Hyunjin Yoon, Chehwee Park, Boowon Kim, Byeonghwa Jeon, Dongho Kim, and Sangryeol Ryu

Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression
Nucleic Acids Research Advance Access published on February 28, 2007
Nucl. Acids Res. 2007 35: 1822-1832; doi:10.1093/nar/gkm060 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Zheqiong Yang, Yang Sui, Shiqin Xiong, Sean S. Liour, Andrew C. Phillips, and Lan Ko

Switched alternative splicing of oncogene CoAA during embryonal carcinoma stem cell differentiation
Nucleic Acids Research Advance Access published on March 1, 2007
Nucl. Acids Res. 2007 35: 1919-1932; doi:10.1093/nar/gkl1092 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Ester Valls, Noemí Blanco-García, Naiara Aquizu, David Piedra, Conchi Estarás, Xavier de la Cruz, and Marian A. Martínez-Balbás

Involvement of chromatin and histone deacetylation in SV40 T antigen transcription regulation
Nucleic Acids Research Advance Access published on March 6, 2007
Nucl. Acids Res. 2007 35: 1958-1968; doi:10.1093/nar/gkl1113 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Matjaz Barboric, Jasper H. N. Yik, Nadine Czudnochowski, Zhiyuan Yang, Ruichuan Chen, Xavier Contreras, Matthias Geyer, B. Matija Peterlin, and Qiang Zhou

Tat competes with HEXIM1 to increase the active pool of P-TEFb for HIV-1 transcription
Nucleic Acids Research Advance Access published on March 6, 2007
Nucl. Acids Res. 2007 35: 2003-2012; doi:10.1093/nar/gkm063 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Yong-Heng Chen, Catherine K. Yang, Meng Xia, Chen-Yin Ou, and Michael R. Stallcup

Role of GAC63 in transcriptional activation mediated by ß-catenin
Nucleic Acids Research Advance Access published on March 7, 2007
Nucl. Acids Res. 2007 35: 2084-2092; doi:10.1093/nar/gkm095 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Faina Vikhanskaya, Ming Kei Lee, Marco Mazzoletti, Massimo Broggini, and Kanaga Sabapathy

Cancer-derived p53 mutants suppress p53-target gene expression—potential mechanism for gain of function of mutant p53
Nucleic Acids Research Advance Access published on March 7, 2007
Nucl. Acids Res. 2007 35: 2093-2104; doi:10.1093/nar/gkm099 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acid Enzymes

Get checked abstract Abigail J. Smith, Mark D. Szczelkun, and Nigel J. Savery

Controlling the motor activity of a transcription-repair coupling factor: autoinhibition and the role of RNA polymerase
Nucleic Acids Research Advance Access published on February 28, 2007
Nucl. Acids Res. 2007 35: 1802-1811; doi:10.1093/nar/gkm019 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Jana Sefcikova, Maryna V. Krasovska, Jirí Sponer, and Nils G. Walter

The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis
Nucleic Acids Research Advance Access published on March 2, 2007
Nucl. Acids Res. 2007 35: 1933-1946; doi:10.1093/nar/gkl1104 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Jurate Bitinaite, Michelle Rubino, Kamini Hingorani Varma, Ira Schildkraut, Romualdas Vaisvila, and Rita Vaiskunaite

USER^TM friendly DNA engineering and cloning method by uracil excision
Nucleic Acids Research Advance Access published on March 6, 2007
Nucl. Acids Res. 2007 35: 1992-2002; doi:10.1093/nar/gkm041 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

RNA

Get checked abstract Wen-Cheng Chang, Yung-Chia Chen, Kuo-Ming Lee, and Woan-Yuh Tarn

Alternative splicing and bioinformatic analysis of human U12-type introns
Nucleic Acids Research Advance Access published on March 1, 2007
Nucl. Acids Res. 2007 35: 1833-1841; doi:10.1093/nar/gkm026 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract A. Cléry, V. Bourguignon-Igel, C. Allmang, A. Krol, and C. Branlant

An improved definition of the RNA-binding specificity of SECIS-binding protein 2, an essential component of the selenocysteine incorporation machinery
Nucleic Acids Research Advance Access published on March 1, 2007
Nucl. Acids Res. 2007 35: 1868-1884; doi:10.1093/nar/gkm066 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Nina Gildehaus, Thomas Neußer, Reinhild Wurm, and Rolf Wagner

Studies on the function of the riboregulator 6S RNA from E. coli: RNA polymerase binding, inhibition of in vitro transcription and synthesis of RNA-directed de novo transcripts
Nucleic Acids Research Advance Access published on March 1, 2007
Nucl. Acids Res. 2007 35: 1885-1896; doi:10.1093/nar/gkm085 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Andrei Yu. Kobitski, Alexander Nierth, Mark Helm, Andres Jäschke, and G. Ulrich Nienhaus

Mg²⁺-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis
Nucleic Acids Research Advance Access published on March 7, 2007
Nucl. Acids Res. 2007 35: 2047-2059; doi:10.1093/nar/gkm072 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Barbara Wegscheid and Roland K. Hartmann

In vivo and in vitro investigation of bacterial type B RNase P interaction with tRNA 3'-CCA
Nucleic Acids Research Advance Access published on March 13, 2007
Nucl. Acids Res. 2007 35: 2060-2073; doi:10.1093/nar/gkm005 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Structural Biology

Get checked abstract Donald F. Senear, Vira Tretyachenko-Ladokhina, Michael L. Opel, Kimberly A. Aeling, G. Wesley Hatfield, Laurie M. Franklin, Reuben C. Darlington, and J.B. Alexander Ross

Pressure dissociation of integration host factor–DNA complexes reveals flexibility-dependent structural variation at the protein–DNA interface
Nucleic Acids Research Advance Access published on February 25, 2007
Nucl. Acids Res. 2007 35: 1761-1772; doi:10.1093/nar/gkl1122 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Li-Tzu Chen, Tzu-Ping Ko, Yuan-Chih Chang, Kuei-An Lin, Chia-Seng Chang, Andrew H.-J. Wang, and Ting-Fang Wang

Crystal structure of the left-handed archaeal RadA helical filament: identification of a functional motif for controlling quaternary structures and enzymatic functions of RecA family proteins
Nucleic Acids Research Advance Access published on February 28, 2007
Nucl. Acids Res. 2007 35: 1787-1801; doi:10.1093/nar/gkl1131 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Ken-ichi Miyazono, Miki Watanabe, Jan Kosinski, Ken Ishikawa, Masayuki Kamo, Tatsuya Sawasaki, Koji Nagata, Janusz M. Bujnicki, Yaeta Endo, Masaru Tanokura, and Ichizo Kobayashi

Novel protein fold discovered in the PabI family of restriction enzymes
Nucleic Acids Research Advance Access published on March 1, 2007
Nucl. Acids Res. 2007 35: 1908-1918; doi:10.1093/nar/gkm091 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Ella Czarina Magat Juan, Jiro Kondo, Takeshi Kurihara, Takanori Ito, Yoshihito Ueno, Akira Matsuda, and Akio Takénaka

Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules
Nucleic Acids Research Advance Access published on March 6, 2007
Nucl. Acids Res. 2007 35: 1969-1977; doi:10.1093/nar/gkl821 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Melissa Maderia, Shilpa Shenoy, Que N. Van, Victor E. Marquez, and Joseph J. Barchi, Jr

Biophysical studies of DNA modified with conformationally constrained nucleotides: comparison of 2'-exo (north) and 3'-exo (south) ‘locked’ templates
Nucleic Acids Research Advance Access published on March 6, 2007
Nucl. Acids Res. 2007 35: 1978-1991; doi:10.1093/nar/gkm025 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Anwer Mujeeb, Nikolai B. Ulyanov, Stefanos Georgantis, Ivan Smirnov, Janet Chung, Tristram G. Parslow, and Thomas L. James

Nucleocapsid protein-mediated maturation of dimer initiation complex of full-length SL1 stemloop of HIV-1: sequence effects and mechanism of RNA refolding
Nucleic Acids Research Advance Access published on March 6, 2007
Nucl. Acids Res. 2007 35: 2026-2034; doi:10.1093/nar/gkm097 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Magdalena Kaus-Drobek, Honorata Czapinska, Monika Sokolowska, Gintautas Tamulaitis, Roman H. Szczepanowski, Claus Urbanke, Virginijus Siksnys, and Matthias Bochtler

Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically
Nucleic Acids Research Advance Access published on March 7, 2007
Nucl. Acids Res. 2007 35: 2035-2046; doi:10.1093/nar/gkm064 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Methods Online

Get checked abstract Rory M. Watt, Jing Wang, Meikid Leong, Hsiang-fu Kung, Kathryn S.E. Cheah, Depei Liu, Antoine Danchin, and Jian-Dong Huang

Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes
Nucleic Acids Research Advance Access published on January 31, 2007
Nucl. Acids Res. 2007 35: e37; doi:10.1093/nar/gkl1158 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Hirohide Saito, Tamiko Minamisawa, and Kiyotaka Shiba

Motif programming: a microgene-based method for creating synthetic proteins containing multiple functional motifs
Nucleic Acids Research Advance Access published on February 7, 2007
Nucl. Acids Res. 2007 35: e38; doi:10.1093/nar/gkm017 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Emeline Bouffartigues, Hervé Leh, Marielle Anger-Leroy, Sylvie Rimsky, and Malcolm Buckle

Rapid coupling of Surface Plasmon Resonance (SPR and SPRi) and ProteinChip^TM based mass spectrometry for the identification of proteins in nucleoprotein interactions
Nucleic Acids Research Advance Access published on February 7, 2007
Nucl. Acids Res. 2007 35: e39; doi:10.1093/nar/gkm030 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Jong-Yoon Chun, Kyoung-Joong Kim, In-Taek Hwang, Yun-Jee Kim, Dae-Hoon Lee, In-Kyoung Lee, and Jong-Kee Kim

Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene
Nucleic Acids Research Advance Access published on February 7, 2007
Nucl. Acids Res. 2007 35: e40; doi:10.1093/nar/gkm051 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Tomasz K. Wojdacz and Alexander Dobrovic

Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation
Nucleic Acids Research Advance Access published on February 8, 2007
Nucl. Acids Res. 2007 35: e41; doi:10.1093/nar/gkm013 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract A. Macaskill, A. A. Chernonosov, V. V. Koval, E. A. Lukyanets, O. S. Fedorova, W. E. Smith, K. Faulds, and D. Graham

Quantitative surface-enhanced resonance Raman scattering of phthalocyanine-labelled oligonucleotides
Nucleic Acids Research Advance Access published on February 8, 2007
Nucl. Acids Res. 2007 35: e42; doi:10.1093/nar/gkm042 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Christoph Scheich, Daniel Kümmel, Dimitri Soumailakakis, Udo Heinemann, and Konrad Büssow

Vectors for co-expression of an unrestricted number of proteins
Nucleic Acids Research Advance Access published on February 20, 2007
Nucl. Acids Res. 2007 35: e43; doi:10.1093/nar/gkm067 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Luisa Orsini, Maria Pajunen, Ilkka Hanski, and Harri Savilahti

SNP discovery by mismatch-targeting of Mu transposition
Nucleic Acids Research Advance Access published on February 20, 2007
Nucl. Acids Res. 2007 35: e44; doi:10.1093/nar/gkm070 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Nick S. Berrow, David Alderton, Sarah Sainsbury, Joanne Nettleship, Rene Assenberg, Nahid Rahman, David I. Stuart, and Raymond J. Owens

A versatile ligation-independent cloning method suitable for high-throughput expression screening applications
Nucleic Acids Research Advance Access published on February 22, 2007
Nucl. Acids Res. 2007 35: e45; doi:10.1093/nar/gkm047 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Arryn Craney, Tobias Hohenauer, Ye Xu, Naveen Kumar Navani, Yingfu Li, and Justin Nodwell

A synthetic luxCDABE gene cluster optimized for expression in high-GC bacteria
Nucleic Acids Research Advance Access published on March 1, 2007
Nucl. Acids Res. 2007 35: e46; doi:10.1093/nar/gkm086 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Corrigendum

Julian L. Huppert and Shankar Balasubramanian

G-quadruplexes in promoters throughout the human genome
Nucleic Acids Research Advance Access published on February 28, 2007
Nucl. Acids Res. 2007 35: 2105; doi:10.1093/nar/gkm109 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

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