| | Articles Mechanisms of P/CAF auto-acetylation Helena Santos-Rosa, Ester Valls, Tony Kouzarides, and Marian Martínez-Balbás PMCID: PMC169960 Functional characterization of cis- and trans-regulatory elements involved in expression of phospholipid hydroperoxide glutathione peroxidase Christoph Ufer, Astrid Borchert, and Hartmut Kuhn PMCID: PMC169948 Functional conservation between members of an ancient duplicated transcription factor family, LSF/Grainyhead Kavitha Venkatesan, Heather R. McManus, Craig C. Mello, Temple F. Smith, and Ulla Hansen PMCID: PMC169928 Divalent metal-dependent catalysis and cleavage specificity of CSP41, a chloroplast endoribonuclease belonging to the short chain dehydrogenase/reductase superfamily Thomas J. Bollenbach and David B. Stern PMCID: PMC169913 Solution structure of the HIV-1 frameshift inducing stem–loop RNA David W. Staple and Samuel E. Butcher PMCID: PMC169958 Fep1 represses expression of the fission yeast Schizosaccharomyces pombe siderophore-iron transport system Benoit Pelletier, Jude Beaudoin, Caroline C. Philpott, and Simon Labbé PMCID: PMC169938 Transposases are responsible for the target specificity of IS1397 and ISKpn1 for two different types of palindromic units (PUs) Caroline Wilde, Frédéric Escartin, Susumu Kokeguchi, Patricia Latour-Lambert, Aude Lectard, and Jean-Marie Clément PMCID: PMC169884 Intracellular mRNA cleavage by 3′ tRNase under the direction of 2′-O-methyl RNA heptamers Masato Tamura, Chikako Nashimoto, Noriko Miyake, Yasushi Daikuhara, Kozo Ochi, and Masayuki Nashimoto PMCID: PMC169917 Mutagenesis of a light-regulated psbA intron reveals the importance of efficient splicing for photosynthetic growth Jaesung Lee and David L. Herrin PMCID: PMC169925 Yeast recombination pathways triggered by topoisomerase II-mediated DNA breaks Michelle Sabourin, John L. Nitiss, Karin C. Nitiss, Kazuo Tatebayashi, Hideo Ikeda, and Neil Osheroff PMCID: PMC169887 The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination Anton Buzdin, Elena Gogvadze, Elena Kovalskaya, Pavel Volchkov, Svetlana Ustyugova, Anna Illarionova, Alexey Fushan, Tatiana Vinogradova, and Eugene Sverdlov PMCID: PMC169886 Structural and functional homology between the RNAPI subunits A14/A43 and the archaeal RNAP subunits E/F Hedije Meka, Gregoire Daoust, Kristine Bourke Arnvig, Finn Werner, Peter Brick, and Silvia Onesti PMCID: PMC169954 Structural diversification and neo-functionalization during floral MADS-box gene evolution by C-terminal frameshift mutations Michiel Vandenbussche, Günter Theissen, Yves Van de Peer, and Tom Gerats PMCID: PMC169922 Hydropathic analysis of the free energy differences in anthracycline antibiotic binding to DNA Derek J. Cashman, J. Neel Scarsdale, and Glen E. Kellogg PMCID: PMC169931 The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides Rosel Kretschmer-Kazemi Far and Georg Sczakiel PMCID: PMC169945 Spurious spatial periodicity of co-expression in microarray data due to printing design Gábor Balázsi, Krin A. Kay, Albert-László Barabási, and Zoltán N. Oltvai PMCID: PMC169875 DNA polymerase III χ subunit ties single-stranded DNA binding protein to the bacterial replication machinery Gregor Witte, Claus Urbanke, and Ute Curth PMCID: PMC169888 Lack of sugar discrimination by human Pol µ requires a single glycine residue José F. Ruiz, Raquel Juárez, Miguel García-Díaz, Gloria Terrados, Angel J. Picher, Sergio González-Barrera, Antonio R. Fernández de Henestrosa, and Luis Blanco PMCID: PMC169901 Microenvironment analysis and identification of magnesium binding sites in RNA D. Rey Banatao, Russ B. Altman, and Teri E. Klein PMCID: PMC169872 The synthesis of oligoribonucleotides containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines via post-synthetic modification of precursor oligomers Elzbieta Kierzek and Ryszard Kierzek PMCID: PMC169891 The thermodynamic stability of RNA duplexes and hairpins containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines Elzbieta Kierzek and Ryszard Kierzek PMCID: PMC169893 Double-stranded RNA-mediated gene silencing in fission yeast Mitch Raponi and Greg M. Arndt PMCID: PMC169874 Global methylation screening in the Arabidopsis thaliana and Mus musculus genome: applications of virtual image restriction landmark genomic scanning (Vi-RLGS) Tomoki Matsuyama, Makoto T. Kimura, Kuniaki Koike, Tomoko Abe, Takeshi Nakano, Tadao Asami, Toshikazu Ebisuzaki, William A. Held, Shigeo Yoshida, and Hiroki Nagase PMCID: PMC169878 Oligoamine–acridine conjugates for promotion of gap-selective DNA hydrolysis by Ce(IV)/EDTA complex Yoji Yamamoto, Wataru Tsuboi, and Makoto Komiyama PMCID: PMC169895 Evolutionary clues to DNA polymerase III β clamp structural mechanisms Andrew F. Neuwald PMCID: PMC169876 Transcription increases multiple spontaneous point mutations in Salmonella enterica Richard Ellis Hudson, Ulfar Bergthorsson, and Howard Ochman PMCID: PMC169952 Low pH enhances Sp1 DNA binding activity and interaction with TBP Takayuki Torigoe, Hiroto Izumi, Yoichiro Yoshida, Hiroshi Ishiguchi, Takashi Okamoto, Hideaki Itoh, and Kimitoshi Kohno PMCID: PMC169877 Patterns of sequence conservation at termini of long terminal repeat (LTR) retrotransposons and DNA transposons in the human genome: lessons from phage Mu Insuk Lee and Rasika M. Harshey PMCID: PMC169890 Roles of Saccharomyces cerevisiae DNA polymerases Polη and Polζ in response to irradiation by simulated sunlight Stanislav G. Kozmin, Youri I. Pavlov, Thomas A. Kunkel, and Evelyne Sage PMCID: PMC169879 The computational analysis of scientific literature to define and recognize gene expression clusters Soumya Raychaudhuri, Jeffrey T. Chang, Farhad Imam, and Russ B. Altman PMCID: PMC169898 Identification, characterization and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome Wei Zhu and Volker Brendel PMCID: PMC169882 Repair of clustered uracil DNA damages in Escherichia coli Dwain I. D’souza and Lynn Harrison PMCID: PMC169883 The ERV-9 LTR enhancer is not blocked by the HS5 insulator and synthesizes through the HS5 site non-coding, long RNAs that regulate LTR enhancer function Jianhua Ling, Wenhu Pi, Xiuping Yu, Chikh Bengra, Qiaoming Long, Huaqian Jin, Andreas Seyfang, and Dorothy Tuan PMCID: PMC169934 The essential transcription factor Reb1p interacts with the CLB2 UAS outside of the G2/M control region Ceri Van Slyke and Elizabeth J. Grayhack PMCID: PMC169905 Controlling nucleic acid secondary structure by intercalation: effects of DNA strand length on coralyne-driven duplex disproportionation Swapan S. Jain, Matjaž Polak, and Nicholas V. Hud PMCID: PMC169941 The quakingviable mutation affects qkI mRNA expression specifically in myelin-producing cells of the nervous system Zifan Lu, Youyi Zhang, Li Ku, Houping Wang, Amir Ahmadian, and Yue Feng PMCID: PMC169897 Structural details (kinks and non-α conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors Isidore Rigoutsos, Peter Riek, Robert M. Graham, and Jiri Novotny PMCID: PMC169910 Protein families and Tribes in genome sequence space Anton J. Enright, Victor Kunin, and Christos A. Ouzounis PMCID: PMC169885 Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis Flavio Mignone, Giorgio Grillo, Sabino Liuni, and Graziano Pesole PMCID: PMC169873 Retrotransposon-mediated restoration of Chlorella telomeres: accumulation of Zepp retrotransposons at termini of newly formed minichromosomes Yoshitaka Yamamoto, Yuhki Fujimoto, Ryota Arai, Makoto Fujie, Shoji Usami, and Takashi Yamada PMCID: PMC169880 Functional similarity of Knirps CtBP-dependent and CtBP-independent transcriptional repressor activities Jae-Ryeon Ryu and David N. Arnosti PMCID: PMC169881 Correcting errors in shotgun sequences Martti T. Tammi, Erik Arner, Ellen Kindlund, and Björn Andersson PMCID: PMC169956 NAR Methods Online Establishment of conditional vectors for hairpin siRNA knockdowns Shiro Matsukura, Peter A. Jones, and Daiya Takai PMCID: PMC169962 Highly stable and efficient mRNA templates for mRNA–protein fusions and C-terminally labeled proteins Etsuko Miyamoto-Sato, Hideaki Takashima, Shinichiro Fuse, Kaori Sue, Masamichi Ishizaka, Seiji Tateyama, Kenichi Horisawa, Tatsuya Sawasaki, Yaeta Endo, and Hiroshi Yanagawa PMCID: PMC169963 Fast and accurate determination of sites along the FUT2 in vitro transcript that are accessible to antisense oligonucleotides by application of secondary structure predictions and RNase H in combination with MALDI-TOF mass spectrometry Angelika Gabler, Stefan Krebs, Doris Seichter, and Martin Förster PMCID: PMC169965 A simple two-step, ‘hit and fix’ method to generate subtle mutations in BACs using short denatured PCR fragments Yongping Yang and Shyam K. Sharan PMCID: PMC169966 Combination of overlapping bacterial artificial chromosomes by a two-step recombinogenic engineering method Xin-Mei Zhang and Jian-Dong Huang PMCID: PMC169968 General plasmids for producing RNA in vitro transcripts with homogeneous ends Scott C. Walker, Johanna M. Avis, and Graeme L. Conn PMCID: PMC169970 Development of a rapid, small-scale DNA repair assay for use on clinical samples Christine P. Diggle, Johanne Bentley, and Anne E. Kiltie PMCID: PMC169971 Parallel competition analysis of Saccharomyces cerevisiae strains differing by a single base using polymerase colonies Joshua Merritt, Jason R. DiTonno, Robi D. Mitra, George M. Church, and Jeremy S. Edwards PMCID: PMC169973 Stable and heritable gene silencing in the malaria vector Anopheles stephensi Anthony E. Brown, Laurence Bugeon, Andrea Crisanti, and Flaminia Catteruccia PMCID: PMC169974 Induction of cre recombinase activity using modified androgen receptor ligand binding domains: a sensitive assay for ligand-receptor interactions Stanislaw J. Kaczmarczyk and Jeffrey E. Green PMCID: PMC169976 |
