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Previous Next 		Contents: Volume 37, Number 6, April 2009   [Index by Author] 

Down Survey and Summary
Down Chemistry and Synthetic Biology
Down Gene Regulation, Chromatin and Epigenetics
Down Genome Integrity, Repair and Replication
Down Genomics
Down Molecular Biology
Down Nucleic Acid Enzymes
Down RNA
Down Structural Biology
Down Methods Online
Down Front-Matter/Back-Matter


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To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.

Survey and Summary Back

Jaroslav Kypr, Iva Kejnovská, Daniel Renciuk, and Michaela Vorlícková
Circular dichroism and conformational polymorphism of DNA
Nucleic Acids Research Advance Access published on February 3, 2009
Nucl. Acids Res. 2009 37: 1713-1725; doi:10.1093/nar/gkp026 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sophie Lemoine, Florence Combes, and Stéphane Le Crom
An evaluation of custom microarray applications: the oligonucleotide design challenge
Nucleic Acids Research Advance Access published on February 10, 2009
Nucl. Acids Res. 2009 37: 1726-1739; doi:10.1093/nar/gkp053 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Chemistry and Synthetic Biology Back

Pedro M. D. Moreno, Malgorzata Wenska, Karin E. Lundin, Örjan Wrange, Roger Strömberg, and C. I. Edvard Smith
A synthetic snRNA m3G-CAP enhances nuclear delivery of exogenous proteins and nucleic acids
Nucleic Acids Research Advance Access published on February 10, 2009
Nucl. Acids Res. 2009 37: 1925-1935; doi:10.1093/nar/gkp048 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gene Regulation, Chromatin and Epigenetics Back

Song Qin, Qien Wang, Alo Ray, Gulzar Wani, Qun Zhao, Sukesh R. Bhaumik, and Altaf A. Wani
Sem1p and Ubp6p orchestrate telomeric silencing by modulating histone H2B ubiquitination and H3 acetylation
Nucleic Acids Research Advance Access published on February 2, 2009
Nucl. Acids Res. 2009 37: 1843-1853; doi:10.1093/nar/gkn1049 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Shouyu Wang, Zhenghua Gong, Rui Chen, Yunru Liu, Aiping Li, Gang Li, and Jianwei Zhou
JWA regulates XRCC1 and functions as a novel base excision repair protein in oxidative-stress-induced DNA single-strand breaks
Nucleic Acids Research Advance Access published on February 10, 2009
Nucl. Acids Res. 2009 37: 1936-1950; doi:10.1093/nar/gkp054 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genome Integrity, Repair and Replication Back

Qiang Fan, Fan Zhang, Briana Barrett, Keqin Ren, and Paul R. Andreassen
A role for monoubiquitinated FANCD2 at telomeres in ALT cells
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1740-1754; doi:10.1093/nar/gkn995 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Stanislav G. Kozmin, Yuliya Sedletska, Anne Reynaud-Angelin, Didier Gasparutto, and Evelyne Sage
The formation of double-strand breaks at multiply damaged sites is driven by the kinetics of excision/incision at base damage in eukaryotic cells
Nucleic Acids Research Advance Access published on January 27, 2009
Nucl. Acids Res. 2009 37: 1767-1777; doi:10.1093/nar/gkp010 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Reto Brem, Feng Li, and Peter Karran
Reactive oxygen species generated by thiopurine/UVA cause irreparable transcription-blocking DNA lesions
Nucleic Acids Research Advance Access published on February 10, 2009
Nucl. Acids Res. 2009 37: 1951-1961; doi:10.1093/nar/gkp070 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Koen Wagner, Geri Moolenaar, John van Noort, and Nora Goosen
Single-molecule analysis reveals two separate DNA-binding domains in the Escherichia coli UvrA dimer
Nucleic Acids Research Advance Access published on February 10, 2009
Nucl. Acids Res. 2009 37: 1962-1972; doi:10.1093/nar/gkp071 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics Back

Gernot Glöckner and Andrew J. Heidel
Centromere sequence and dynamics in Dictyostelium discoideum
Nucleic Acids Research Advance Access published on January 29, 2009
Nucl. Acids Res. 2009 37: 1809-1816; doi:10.1093/nar/gkp017 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology Back

Klara Post, Besik Kankia, Swathi Gopalakrishnan, Victoria Yang, Elizabeth Cramer, Pilar Saladores, Robert J. Gorelick, Jianhui Guo, Karin Musier-Forsyth, and Judith G. Levin
Fidelity of plus-strand priming requires the nucleic acid chaperone activity of HIV-1 nucleocapsid protein
Nucleic Acids Research Advance Access published on January 21, 2009
Nucl. Acids Res. 2009 37: 1755-1766; doi:10.1093/nar/gkn1045 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Marcus Klotzsche, Sabine Ehrt, and Dirk Schnappinger
Improved tetracycline repressors for gene silencing in mycobacteria
Nucleic Acids Research Advance Access published on January 27, 2009
Nucl. Acids Res. 2009 37: 1778-1788; doi:10.1093/nar/gkp015 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Ivana Bratic, Jürgen Hench, Johan Henriksson, Adam Antebi, Thomas R Bürglin, and Aleksandra Trifunovic
Mitochondrial DNA level, but not active replicase, is essential for Caenorhabditis elegans development
Nucleic Acids Research Advance Access published on January 30, 2009
Nucl. Acids Res. 2009 37: 1817-1828; doi:10.1093/nar/gkp018 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Donna A. MacDuff, Zachary L. Demorest, and Reuben S. Harris
AID can restrict L1 retrotransposition suggesting a dual role in innate and adaptive immunity
Nucleic Acids Research Advance Access published on February 2, 2009
Nucl. Acids Res. 2009 37: 1854-1867; doi:10.1093/nar/gkp030 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Sean P. Riley, Tomasz Bykowski, Anne E. Cooley, Logan H. Burns, Kelly Babb, Catherine A. Brissette, Amy Bowman, Matthew Rotondi, M. Clarke Miller, Edward DeMoll, Kap Lim, Michael G. Fried, and Brian Stevenson
Borrelia burgdorferi EbfC defines a newly-identified, widespread family of bacterial DNA-binding proteins
Nucleic Acids Research Advance Access published on February 10, 2009
Nucl. Acids Res. 2009 37: 1973-1983; doi:10.1093/nar/gkp027 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Bi-He Cai, Jang-Yi Chen, Mei-Hua Lu, Li-Tze Chang, Hwang-Chi Lin, Yu-Ming Chang, and Chung-Faye Chao
Functional four-base A/T gap core sequence CATTAG of P53 response elements specifically bound tetrameric P53 differently than two-base A/T gap core sequence CATG bound both dimeric and tetrameric P53
Nucleic Acids Research Advance Access published on February 10, 2009
Nucl. Acids Res. 2009 37: 1984-1990; doi:10.1093/nar/gkp033 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Siu Kai Leung and Joseph T. Y. Wong
The replication of plastid minicircles involves rolling circle intermediates
Nucleic Acids Research Advance Access published on February 10, 2009
Nucl. Acids Res. 2009 37: 1991-2002; doi:10.1093/nar/gkp063 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Keunsoo Kang, Jae Hoon Chung, and Joomyeong Kim
Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites
Nucleic Acids Research Advance Access published on February 10, 2009
Nucl. Acids Res. 2009 37: 2003-2013; doi:10.1093/nar/gkp077 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes Back

Víctor M. Castillo-Acosta, Luis M. Ruiz-Pérez, Wei Yang, Dolores González-Pacanowska, and Antonio E. Vidal
Identification of a residue critical for the excision of 3'-blocking ends in apurinic/apyrimidinic endonucleases of the Xth family
Nucleic Acids Research Advance Access published on January 30, 2009
Nucl. Acids Res. 2009 37: 1829-1842; doi:10.1093/nar/gkp021 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Rajendra Prasad, Matthew J. Longley, Farida S. Sharief, Esther W. Hou, William C. Copeland, and Samuel H. Wilson
Human DNA polymerase {theta} possesses 5'-dRP lyase activity and functions in single-nucleotide base excision repair in vitro
Nucleic Acids Research Advance Access published on February 2, 2009
Nucl. Acids Res. 2009 37: 1868-1877; doi:10.1093/nar/gkp035 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kirk Tevebaugh Ehmsen and Wolf-Dietrich Heyer
A junction branch point adjacent to a DNA backbone nick directs substrate cleavage by Saccharomyces cerevisiae Mus81-Mms4
Nucleic Acids Research Advance Access published on February 11, 2009
Nucl. Acids Res. 2009 37: 2026-2036; doi:10.1093/nar/gkp038 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Shuhei Nakane, Noriko Nakagawa, Seiki Kuramitsu, and Ryoji Masui
Characterization of DNA polymerase X from Thermus thermophilus HB8 reveals the POLXc and PHP domains are both required for 3'–5' exonuclease activity
Nucleic Acids Research Advance Access published on February 11, 2009
Nucl. Acids Res. 2009 37: 2037-2052; doi:10.1093/nar/gkp064 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Kelly J. Neaves, Laurie P. Cooper, John H. White, Stewart M. Carnally, David T. F. Dryden, J. Michael Edwardson, and Robert M. Henderson
Atomic force microscopy of the EcoKI Type I DNA restriction enzyme bound to DNA shows enzyme dimerization and DNA looping
Nucleic Acids Research Advance Access published on February 17, 2009
Nucl. Acids Res. 2009 37: 2053-2063; doi:10.1093/nar/gkp042 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA Back

Isabelle Hatin, Celine Fabret, Jean-Pierre Rousset, and Olivier Namy
Molecular dissection of translation termination mechanism identifies two new critical regions in eRF1
Nucleic Acids Research Advance Access published on January 27, 2009
Nucl. Acids Res. 2009 37: 1789-1798; doi:10.1093/nar/gkp012 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Shanfa Lu, Ying-Hsuan Sun, and Vincent L. Chiang
Adenylation of plant miRNAs
Nucleic Acids Research Advance Access published on February 2, 2009
Nucl. Acids Res. 2009 37: 1878-1885; doi:10.1093/nar/gkp031 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Deepti L. Bellur and Sarah A. Woodson
A minimized rRNA-binding site for ribosomal protein S4 and its implications for 30S assembly
Nucleic Acids Research Advance Access published on February 3, 2009
Nucl. Acids Res. 2009 37: 1886-1896; doi:10.1093/nar/gkp036 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Moritz Niemann, Heike Kaibel, Elke Schlüter, Kerstin Weitzel, Michael Brecht, and H. Ulrich Göringer
Kinetoplastid RNA editing involves a 3' nucleotidyl phosphatase activity
Nucleic Acids Research Advance Access published on February 3, 2009
Nucl. Acids Res. 2009 37: 1897-1906; doi:10.1093/nar/gkp049 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Kazuhiro Fukumura, Ichiro Taniguchi, Hiroshi Sakamoto, Mutsuhito Ohno, and Kunio Inoue
U1-independent pre-mRNA splicing contributes to the regulation of alternative splicing
Nucleic Acids Research Advance Access published on February 3, 2009
Nucl. Acids Res. 2009 37: 1907-1914; doi:10.1093/nar/gkp050 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology Back

Pan-Hsien Kuo, Lyudmila G. Doudeva, Yi-Ting Wang, Che-Kun James Shen, and Hanna S. Yuan
Structural insights into TDP-43 in nucleic-acid binding and domain interactions
Nucleic Acids Research Advance Access published on January 27, 2009
Nucl. Acids Res. 2009 37: 1799-1808; doi:10.1093/nar/gkp013 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Bettina König, Jürgen J. Müller, Erich Lanka, and Udo Heinemann
Crystal structure of KorA bound to operator DNA: insight into repressor cooperation in RP4 gene regulation
Nucleic Acids Research Advance Access published on February 3, 2009
Nucl. Acids Res. 2009 37: 1915-1924; doi:10.1093/nar/gkp044 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Diana A. Pippig, Johannes C. Hellmuth, Sheng Cui, Axel Kirchhofer, Katja Lammens, Alfred Lammens, Andreas Schmidt, Simon Rothenfusser, and Karl-Peter Hopfner
The regulatory domain of the RIG-I family ATPase LGP2 senses double-stranded RNA
Nucleic Acids Research Advance Access published on February 10, 2009
Nucl. Acids Res. 2009 37: 2014-2025; doi:10.1093/nar/gkp059 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online Back

Asjad Basheer, Harald Berger, Yazmid Reyes-Dominguez, Markus Gorfer, and Joseph Strauss
A library-based method to rapidly analyse chromatin accessibility at multiple genomic regions
Nucleic Acids Research Advance Access published on February 27, 2009
Nucl. Acids Res. 2009 37: e42; doi:10.1093/nar/gkp037 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Takeshi Haraguchi, Yuka Ozaki, and Hideo Iba
Vectors expressing efficient RNA decoys achieve the long-term suppression of specific microRNA activity in mammalian cells
Nucleic Acids Research Advance Access published on February 17, 2009
Nucl. Acids Res. 2009 37: e43; doi:10.1093/nar/gkp040 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Masashi Ikeno, Nobutaka Suzuki, Yoshinori Hasegawa, and Tsuneko Okazaki
Manipulating transgenes using a chromosome vector
Nucleic Acids Research Advance Access published on February 17, 2009
Nucl. Acids Res. 2009 37: e44; doi:10.1093/nar/gkp058 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

J. M. Ruijter, C. Ramakers, W. M. H. Hoogaars, Y. Karlen, O. Bakker, M. J. B. van den Hoff, and A. F. M. Moorman
Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data
Nucleic Acids Research Advance Access published on February 22, 2009
Nucl. Acids Res. 2009 37: e45; doi:10.1093/nar/gkp045 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jane M. Liu, Jonathan Livny, Michael S. Lawrence, Marc D. Kimball, Matthew K. Waldor, and Andrew Camilli
Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing
Nucleic Acids Research Advance Access published on February 17, 2009
Nucl. Acids Res. 2009 37: e46; doi:10.1093/nar/gkp080 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Hiroshi Nakayama, Misaki Akiyama, Masato Taoka, Yoshio Yamauchi, Yuko Nobe, Hideaki Ishikawa, Nobuhiro Takahashi, and Toshiaki Isobe
Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data
Nucleic Acids Research Advance Access published on March 6, 2009
Nucl. Acids Res. 2009 37: e47; doi:10.1093/nar/gkp099 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Rune Matthiesen and Finn Kirpekar
Identification of RNA molecules by specific enzyme digestion and mass spectrometry: software for and implementation of RNA mass mapping
Nucleic Acids Research Advance Access published on March 5, 2009
Nucl. Acids Res. 2009 37: e48; doi:10.1093/nar/gkp139 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Front-Matter/Back-Matter Back

Nucleic Acids Research: VOLUME 37 ISSUE 6 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkp246 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkp245 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkp247 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.