| | Articles Catalytic mechanism of Escherichia coli ribonuclease III: kinetic and inhibitor evidence for the involvement of two magnesium ions in RNA phosphodiester hydrolysis Weimei Sun, Alexandre Pertzev, and Allen W. Nicholson PMCID: PMC549391 Homology-extended sequence alignment V. A. Simossis, J. Kleinjung, and J. Heringa PMCID: PMC549400 Splicing of human immunodeficiency virus RNA is position-dependent suggesting sequential removal of introns from the 5′ end Jens Bohne, Harald Wodrich, and Hans-Georg Kräusslich PMCID: PMC549389 Distinct transcriptional responses of RNA polymerases I, II and III to aptamers that bind TBP Xiaochun Fan, Hua Shi, and John T. Lis PMCID: PMC549393 A potential role for RNA interference in controlling the activity of the human LINE-1 retrotransposon Harris S. Soifer, Adriana Zaragoza, Maany Peyvan, Mark A. Behlke, and John J. Rossi PMCID: PMC549394 Site-specific Tn7 transposition into the human genome Prasad N. Kuduvalli, Rupak Mitra, and Nancy L. Craig PMCID: PMC549396 Linking disease-associated genes to regulatory networks via promoter organization S. Döhr, A. Klingenhoff, H. Maier, M. Hrabé de Angelis, T. Werner, and R. Schneider PMCID: PMC549397 Sam68 is absolutely required for Rev function and HIV-1 production Suhasini Modem, Kameswara R. Badri, Thomas C. Holland, and Thipparthi R. Reddy PMCID: PMC549398 A novel method for accurate operon predictions in all sequenced prokaryotes Morgan N. Price, Katherine H. Huang, Eric J. Alm, and Adam P. Arkin PMCID: PMC549399 The p80 homology region of TEP1 is sufficient for its association with the telomerase and vault RNAs, and the vault particle Michael J. Poderycki, Leonard H. Rome, Lea Harrington, and Valerie A. Kickhoefer PMCID: PMC549401 Design of nucleic acid sequences for DNA computing based on a thermodynamic approach Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, and Azuma Ohuchi PMCID: PMC549402 Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides Karen L. Buchmueller, Andrew M. Staples, Peter B. Uthe, Cameron M. Howard, Kimberly A. O. Pacheco, Kari K. Cox, James A. Henry, Suzanna L. Bailey, Sarah M. Horick, Binh Nguyen, W. David Wilson, and Moses Lee PMCID: PMC549405 A new computational method for the detection of horizontal gene transfer events Aristotelis Tsirigos and Isidore Rigoutsos PMCID: PMC549390 Long-range oscillation in a periodic DNA sequence motif may influence nucleosome array formation Yamini Dalal, Tomara J. Fleury, Alfred Cioffi, and Arnold Stein PMCID: PMC549395 Protein coding potential of retroviruses and other transposable elements in vertebrate genomes Evgeny M. Zdobnov, Mónica Campillos, Eoghan D. Harrington, David Torrents, and Peer Bork PMCID: PMC549403 mRNA sequence features that contribute to translational regulation in Arabidopsis Riki Kawaguchi and Julia Bailey-Serres PMCID: PMC549406 Toxin–antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes Deo Prakash Pandey and Kenn Gerdes PMCID: PMC549392 HIV-1 integrase crosslinked oligomers are active in vitro Aurélie Faure, Christina Calmels, Cécile Desjobert, Michel Castroviejo, Anne Caumont-Sarcos, Laura Tarrago-Litvak, Simon Litvak, and Vincent Parissi PMCID: PMC549407 Direct transcriptional repression of the genes encoding the zinc-finger proteins Gfi1b and Gfi1 by Gfi1b Lothar Vassen, Katharina Fiolka, Stefan Mahlmann, and Tarik Möröy PMCID: PMC549408 Characterization of the ATPase and unwinding activities of the yeast DEAD-box protein Has1p and the analysis of the roles of the conserved motifs Sanda Rocak, Bertrand Emery, N. Kyle Tanner, and Patrick Linder PMCID: PMC549409 The relationship between the prothrombin upstream sequence element and the G20210A polymorphism: the influence of a competitive environment for mRNA 3′-end formation Mythily Sachchithananthan, Stan J. Stasinopoulos, Jeffrey Wilusz, and Robert L. Medcalf PMCID: PMC549410 Mms22p protects Saccharomyces cerevisiae from DNA damage induced by topoisomerase II E. L. Baldwin, A. C. Berger, A. H. Corbett, and N. Osheroff PMCID: PMC549411 8-vinyl-deoxyadenosine, an alternative fluorescent nucleoside analog to 2′-deoxyribosyl-2-aminopurine with improved properties Nouha Ben Gaied, Nicole Glasser, Nick Ramalanjaona, Hervé Beltz, Philippe Wolff, Roland Marquet, Alain Burger, and Yves Mély PMCID: PMC549415 Detection of 5′- and 3′-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli Mitsuoki Kawano, April A. Reynolds, Juan Miranda-Rios, and Gisela Storz PMCID: PMC549416 Relative predicted protein levels of functionally associated proteins are conserved across organisms Gila Lithwick and Hanah Margalit PMCID: PMC549420 Investigation of Mg2+- and temperature-dependent folding of the hairpin ribozyme by photo-crosslinking: effects of photo-crosslinker tether length and chemistry Emily J. Borda and Snorri Th. Sigurdsson PMCID: PMC549404 Plant promoter prediction with confidence estimation I. A. Shahmuradov, V. V. Solovyev, and A. J. Gammerman PMCID: PMC549412 The mouse RNase 4 and RNase 5/ang 1 locus utilizes dual promoters for tissue-specific expression Kimberly D. Dyer and Helene F. Rosenberg PMCID: PMC549413 Mutant p53 proteins bind DNA in a DNA structure-selective mode Thomas Göhler, Stefan Jäger, Gabriele Warnecke, Hideyo Yasuda, Ella Kim, and Wolfgang Deppert PMCID: PMC549414 The SAF-box domain of chromatin protein DEK Friederike Böhm, Ferdinand Kappes, Ingo Scholten, Nicole Richter, Hiroshi Matsuo, Rolf Knippers, and Tanja Waldmann PMCID: PMC549417 The unusually large Plasmodium telomerase reverse-transcriptase localizes in a discrete compartment associated with the nucleolus Luisa M. Figueiredo, Eduardo P. C. Rocha, Liliana Mancio-Silva, Christine Prevost, Danièle Hernandez-Verdun, and Artur Scherf PMCID: PMC549419 Biochemical characterization and DNA repair pathway interactions of Mag1-mediated base excision repair in Schizosaccharomyces pombe
Ingrun Alseth, Fikret Osman, Hanne Korvald, Irina Tsaneva, Matthew C. Whitby, Erling Seeberg, and Magnar Bjørås PMCID: PMC549418 Functional characterization of the mitochondrial 12S rRNA C1494T mutation associated with aminoglycoside-induced and non-syndromic hearing loss Hui Zhao, Wie-Yen Young, Qingfeng Yan, Ronghua Li, Juyang Cao, Qiuju Wang, Xiaoming Li, Jennifer L. Peters, Dongyi Han, and Min-Xin Guan PMCID: PMC549421 Methods Online Transposon-mediated generation of targeting vectors for the production of gene knockouts Chunfang Zhang, Danny Kitsberg, Hun Chy, Qi Zhou, and John R. Morrison PMCID: PMC549422 A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays Claire L. Simpson, Joanne Knight, Lee M. Butcher, Valerie K. Hansen, Emma Meaburn, Leonard C. Schalkwyk, Ian W. Craig, John F. Powell, Pak C. Sham, and Ammar Al-Chalabi PMCID: PMC549427 Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome S. Dinel, C. Bolduc, P. Belleau, A. Boivin, M. Yoshioka, E. Calvo, B. Piedboeuf, E. E. Snyder, F. Labrie, and J. St-Amand PMCID: PMC549424 Use of mRNA- and protein-destabilizing elements to develop a highly responsive reporter system Dominic C. Voon, Lily S. Subrata, Svetlana Baltic, Marco P. Leu, Joanna M. Whiteway, Agnes Wong, Samuel A. Knight, Frank T. Christiansen, and John M. Daly PMCID: PMC549429 Identification of antisense nucleic acid hybridization sites in mRNA molecules with self-quenching fluorescent reporter molecules Lida K. Gifford, Joanna B. Opalinska, David Jordan, Vikram Pattanayak, Paul Greenham, Anna Kalota, Michelle Robbins, Kathy Vernovsky, Lesbeth C. Rodriguez, Bao T. Do, Ponzy Lu, and Alan M. Gewirtz PMCID: PMC549423 Effective transcriptome amplification for expression profiling on sense-oriented oligonucleotide microarrays Joerg Schlingemann, Olaf Thuerigen, Carina Ittrich, Grischa Toedt, Heidi Kramer, Meinhard Hahn, and Peter Lichter PMCID: PMC549428 siRNA target site secondary structure predictions using local stable substructures Bret S. E. Heale, Harris S. Soifer, Chauncey Bowers, and John J. Rossi PMCID: PMC549425 A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array Jeremy Harbig, Robert Sprinkle, and Steven A. Enkemann PMCID: PMC549426 Discovery of active proteins directly from combinatorial randomized protein libraries without display, purification or sequencing: identification of novel zinc finger proteins Marcus D. Hughes, Zhan-Ren Zhang, Andrew J. Sutherland, Albert F. Santos, and Anna V. Hine PMCID: PMC549430 Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays Mazen W. Karaman, Susan Groshen, Chi-Chiang Lee, Brian L. Pike, and Joseph G. Hacia PMCID: PMC549431 |
