| | Other Issues: previous | next | latest | archiveChemistry and Synthetic Biology A synthetic snRNA m3G-CAP enhances nuclear delivery of exogenous proteins and nucleic acids Pedro M. D. Moreno, Malgorzata Wenska, Karin E. Lundin, Örjan Wrange, Roger Strömberg, and C. I. Edvard Smith PMCID: PMC2665231 Front-Matter/Back-Matter Nucleic Acids Research: VOLUME 37 ISSUE 6 2009 PMCID: PMC2665247 Nucleic Acids Res. 2009 April; 37(6): ii. Published online 2009 April. doi: 10.1093/nar/gkp245.PMCID: PMC2665246 Nucleic Acids Res. 2009 April; 37(6): iii. Published online 2009 April. doi: 10.1093/nar/gkp247.PMCID: PMC2665248 Gene Regulation, Chromatin and Epigenetics Sem1p and Ubp6p orchestrate telomeric silencing by modulating histone H2B ubiquitination and H3 acetylation Song Qin, Qien Wang, Alo Ray, Gulzar Wani, Qun Zhao, Sukesh R. Bhaumik, and Altaf A. Wani PMCID: PMC2665209 JWA regulates XRCC1 and functions as a novel base excision repair protein in oxidative-stress-induced DNA single-strand breaks Shouyu Wang, Zhenghua Gong, Rui Chen, Yunru Liu, Aiping Li, Gang Li, and Jianwei Zhou PMCID: PMC2665235 Genome Integrity, Repair and Replication A role for monoubiquitinated FANCD2 at telomeres in ALT cells Qiang Fan, Fan Zhang, Briana Barrett, Keqin Ren, and Paul R. Andreassen PMCID: PMC2665210 The formation of double-strand breaks at multiply damaged sites is driven by the kinetics of excision/incision at base damage in eukaryotic cells Stanislav G. Kozmin, Yuliya Sedletska, Anne Reynaud-Angelin, Didier Gasparutto, and Evelyne Sage PMCID: PMC2665211 Reactive oxygen species generated by thiopurine/UVA cause irreparable transcription-blocking DNA lesions Reto Brem, Feng Li, and Peter Karran PMCID: PMC2665240 Single-molecule analysis reveals two separate DNA-binding domains in the Escherichia coli UvrA dimer Koen Wagner, Geri Moolenaar, John van Noort, and Nora Goosen PMCID: PMC2665241 Molecular Biology Fidelity of plus-strand priming requires the nucleic acid chaperone activity of HIV-1 nucleocapsid protein Klara Post, Besik Kankia, Swathi Gopalakrishnan, Victoria Yang, Elizabeth Cramer, Pilar Saladores, Robert J. Gorelick, Jianhui Guo, Karin Musier-Forsyth, and Judith G. Levin PMCID: PMC2665208 Improved tetracycline repressors for gene silencing in mycobacteria Marcus Klotzsche, Sabine Ehrt, and Dirk Schnappinger PMCID: PMC2665214 Mitochondrial DNA level, but not active replicase, is essential for Caenorhabditis elegans development Ivana Bratic, Jürgen Hench, Johan Henriksson, Adam Antebi, Thomas R Bürglin, and Aleksandra Trifunovic PMCID: PMC2665216 AID can restrict L1 retrotransposition suggesting a dual role in innate and adaptive immunity Donna A. MacDuff, Zachary L. Demorest, and Reuben S. Harris PMCID: PMC2665220 Borrelia burgdorferi EbfC defines a newly-identified, widespread family of bacterial DNA-binding proteins 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 PMCID: PMC2665219 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 Bi-He Cai, Jang-Yi Chen, Mei-Hua Lu, Li-Tze Chang, Hwang-Chi Lin, Yu-Ming Chang, and Chung-Faye Chao PMCID: PMC2665222 The replication of plastid minicircles involves rolling circle intermediates Siu Kai Leung and Joseph T. Y. Wong PMCID: PMC2665238 Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites Keunsoo Kang, Jae Hoon Chung, and Joomyeong Kim PMCID: PMC2665242 RNA Molecular dissection of translation termination mechanism identifies two new critical regions in eRF1 Isabelle Hatin, Celine Fabret, Jean-Pierre Rousset, and Olivier Namy PMCID: PMC2665212 Adenylation of plant miRNAs Shanfa Lu, Ying-Hsuan Sun, and Vincent L. Chiang PMCID: PMC2665221 A minimized rRNA-binding site for ribosomal protein S4 and its implications for 30S assembly Deepti L. Bellur and Sarah A. Woodson PMCID: PMC2665224 Kinetoplastid RNA editing involves a 3′ nucleotidyl phosphatase activity Moritz Niemann, Heike Kaibel, Elke Schlüter, Kerstin Weitzel, Michael Brecht, and H. Ulrich Göringer PMCID: PMC2665232 U1-independent pre-mRNA splicing contributes to the regulation of alternative splicing Kazuhiro Fukumura, Ichiro Taniguchi, Hiroshi Sakamoto, Mutsuhito Ohno, and Kunio Inoue PMCID: PMC2665233 Structural Biology Structural insights into TDP-43 in nucleic-acid binding and domain interactions Pan-Hsien Kuo, Lyudmila G. Doudeva, Yi-Ting Wang, Che-Kun James Shen, and Hanna S. Yuan PMCID: PMC2665213 Crystal structure of KorA bound to operator DNA: insight into repressor cooperation in RP4 gene regulation Bettina König, Jürgen J. Müller, Erich Lanka, and Udo Heinemann PMCID: PMC2665229 The regulatory domain of the RIG-I family ATPase LGP2 senses double-stranded RNA Diana A. Pippig, Johannes C. Hellmuth, Sheng Cui, Axel Kirchhofer, Katja Lammens, Alfred Lammens, Andreas Schmidt, Simon Rothenfusser, and Karl-Peter Hopfner PMCID: PMC2665237 Survey and Summary Circular dichroism and conformational polymorphism of DNA Jaroslav Kypr, Iva Kejnovská, Daniel Renčiuk, and Michaela Vorlíčková PMCID: PMC2665218 An evaluation of custom microarray applications: the oligonucleotide design challenge Sophie Lemoine, Florence Combes, and Stéphane Le Crom PMCID: PMC2665234 Genomics Centromere sequence and dynamics in Dictyostelium discoideum Gernot Glöckner and Andrew J. Heidel PMCID: PMC2665215 Methods Online A library-based method to rapidly analyse chromatin accessibility at multiple genomic regions Asjad Basheer, Harald Berger, Yazmid Reyes-Dominguez, Markus Gorfer, and Joseph Strauss PMCID: PMC2665225 Vectors expressing efficient RNA decoys achieve the long-term suppression of specific microRNA activity in mammalian cells Takeshi Haraguchi, Yuka Ozaki, and Hideo Iba PMCID: PMC2665227 Manipulating transgenes using a chromosome vector Masashi Ikeno, Nobutaka Suzuki, Yoshinori Hasegawa, and Tsuneko Okazaki PMCID: PMC2665236 Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data J. M. Ruijter, C. Ramakers, W. M. H. Hoogaars, Y. Karlen, O. Bakker, M. J. B. van den Hoff, and A. F. M. Moorman PMCID: PMC2665230 Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing Jane M. Liu, Jonathan Livny, Michael S. Lawrence, Marc D. Kimball, Matthew K. Waldor, and Andrew Camilli PMCID: PMC2665243 Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data Hiroshi Nakayama, Misaki Akiyama, Masato Taoka, Yoshio Yamauchi, Yuko Nobe, Hideaki Ishikawa, Nobuhiro Takahashi, and Toshiaki Isobe PMCID: PMC2665244 Identification of RNA molecules by specific enzyme digestion and mass spectrometry: software for and implementation of RNA mass mapping Rune Matthiesen and Finn Kirpekar PMCID: PMC2665245 Nucleic Acid Enzymes Identification of a residue critical for the excision of 3′-blocking ends in apurinic/apyrimidinic endonucleases of the Xth family Víctor M. Castillo-Acosta, Luis M. Ruiz-Pérez, Wei Yang, Dolores González-Pacanowska, and Antonio E. Vidal PMCID: PMC2665217 Human DNA polymerase θ possesses 5′-dRP lyase activity and functions in single-nucleotide base excision repair in vitro Rajendra Prasad, Matthew J. Longley, Farida S. Sharief, Esther W. Hou, William C. Copeland, and Samuel H. Wilson PMCID: PMC2665223 A junction branch point adjacent to a DNA backbone nick directs substrate cleavage by Saccharomyces cerevisiae Mus81-Mms4 Kirk Tevebaugh Ehmsen and Wolf-Dietrich Heyer PMCID: PMC2665226 Characterization of DNA polymerase X from Thermus thermophilus HB8 reveals the POLXc and PHP domains are both required for 3′–5′ exonuclease activity Shuhei Nakane, Noriko Nakagawa, Seiki Kuramitsu, and Ryoji Masui PMCID: PMC2665239 Atomic force microscopy of the EcoKI Type I DNA restriction enzyme bound to DNA shows enzyme dimerization and DNA looping Kelly J. Neaves, Laurie P. Cooper, John H. White, Stewart M. Carnally, David T. F. Dryden, J. Michael Edwardson, and Robert M. Henderson PMCID: PMC2665228 |
