| | Molecular Biology Impaired function of the phage-type RNA polymerase RpoTp in transcription of chloroplast genes is compensated by a second phage-type RNA polymerase Monika Swiatecka-Hagenbruch, Carola Emanuel, Boris Hedtke, Karsten Liere, and Thomas Börner PMCID: PMC2241911 Dlx2 homeobox gene transcriptional regulation of Trkb neurotrophin receptor expression during mouse retinal development Jimmy de Melo, Qing-Ping Zhou, Qi Zhang, Shunzhen Zhang, Mario Fonseca, Jeffrey T. Wigle, and David D. Eisenstat PMCID: PMC2241891 Probing dynamics of HIV-1 nucleocapsid protein/target hexanucleotide complexes by 2-aminopurine S. V. Avilov, E. Piemont, V. Shvadchak, H. de Rocquigny, and Y. Mély PMCID: PMC2241888 What drives the binding of minor groove-directed ligands to DNA hairpins? Jurij Lah, Igor Drobnak, Marko Dolinar, and Gorazd Vesnaver PMCID: PMC2241884 Human Pcf11 enhances degradation of RNA polymerase II-associated nascent RNA and transcriptional termination Steven West and Nicholas J. Proudfoot PMCID: PMC2241900 Differentiation-dependent lysine 4 acetylation enhances MEF2C binding to DNA in skeletal muscle cells Cecilia Angelelli, Alessandro Magli, Daniela Ferrari, Massimo Ganassi, Vittoria Matafora, Flavia Parise, Giorgia Razzini, Angela Bachi, Stefano Ferrari, and Susanna Molinari PMCID: PMC2241889 Red flag on the white reporter: a versatile insulator abuts the white gene in Drosophila and is omnipresent in mini-white constructs Darya Chetverina, Ekaterina Savitskaya, Oksana Maksimenko, Larisa Melnikova, Olga Zaytseva, Alexander Parshikov, Alexander V. Galkin, and Pavel Georgiev PMCID: PMC2241909 Targeted induction of meiotic double-strand breaks reveals chromosomal domain-dependent regulation of Spo11 and interactions among potential sites of meiotic recombination Tomoyuki Fukuda, Kazuto Kugou, Hiroyuki Sasanuma, Takehiko Shibata, and Kunihiro Ohta PMCID: PMC2241902 Interaction of human tRNA-dihydrouridine synthase-2 with interferon-induced protein kinase PKR Megan Mittelstadt, Andrea Frump, TuAnh Khuu, Vennece Fowlkes, Indhira Handy, Chandrashekhar V. Patel, and Rekha C. Patel PMCID: PMC2241914 ATR protects the genome against CGG·CCG-repeat expansion in Fragile X premutation mice Ali Entezam and Karen Usdin PMCID: PMC2241920 RNA RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae Roland Ivanyi-Nagy, Jean-Pierre Lavergne, Caroline Gabus, Damien Ficheux, and Jean-Luc Darlix PMCID: PMC2241907 Developmentally regulated cleavage of tRNAs in the bacterium Streptomyces coelicolor Henry J. Haiser, Fedor V. Karginov, Gregory J. Hannon, and Marie A. Elliot PMCID: PMC2241913 ERK is a novel regulatory kinase for poly(A) polymerase Seol-Hoon Lee, Hyun-Sook Choi, Hana Kim, and Younghoon Lee PMCID: PMC2241896 The U1, U2 and U5 snRNAs crosslink to the 5′ exon during yeast pre-mRNA splicing Joanne C. McGrail and Raymond T. O’Keefe PMCID: PMC2241886 Modulation of utrophin A mRNA stability in fast versus slow muscles via an AU-rich element and calcineurin signaling Joe V. Chakkalakal, Pedro Miura, Guy Bélanger, Robin N. Michel, and Bernard J. Jasmin PMCID: PMC2241908 Analysis of intermolecular base pair formation of prohead RNA of the phage ø29 DNA packaging motor using NMR spectroscopy Aya Kitamura, Paul J. Jardine, Dwight L. Anderson, Shelley Grimes, and Hiroshi Matsuo PMCID: PMC2241910 Creating a ribonuclease T-tat that preferentially recognizes and hydrolyzes HIV-1 TAR RNA in vitro and in vivo Chen Dow-Tien, Tsai Yuan-Jhih, and Lin Alan PMCID: PMC2241915 Role of poly (A) tail as an identity element for mRNA nuclear export Hiroyuki Fuke and Mutsuhito Ohno PMCID: PMC2241894 Structural Biology Solution structures of 2 : 1 and 1 : 1 DNA polymerase–DNA complexes probed by ultracentrifugation and small-angle X-ray scattering Kuo-Hsiang Tang, Marc Niebuhr, Ann Aulabaugh, and Ming-Daw Tsai PMCID: PMC2241917 Genomics Comprehensive comparison of the interaction of the E2 master regulator with its cognate target DNA sites in 73 human papillomavirus types by sequence statistics Ignacio E. Sánchez, Mariano Dellarole, Kevin Gaston, and Gonzalo de Prat Gay PMCID: PMC2241901 Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells Jairo Rodriguez, Laura Vives, Mireia Jordà, Cristina Morales, Mar Muñoz, Elisenda Vendrell, and Miguel A. Peinado PMCID: PMC2241897 Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes So Nakagawa, Yoshihito Niimura, Takashi Gojobori, Hiroshi Tanaka, and Kin-ichiro Miura PMCID: PMC2241899 Chemistry Oxidation of single-stranded oligonucleotides by carbonate radical anions: generating intrastrand cross-links between guanine and thymine bases separated by cytosines Conor Crean, Yuriy Uvaydov, Nicholas E. Geacintov, and Vladimir Shafirovich PMCID: PMC2241916 2′-Methylseleno-modified oligoribonucleotides for X-ray crystallography synthesized by the ACE RNA solid-phase approach Barbara Puffer, Holger Moroder, Michaela Aigner, and Ronald Micura PMCID: PMC2241898 Methods Online Quantitative telomeric overhang determination using a double-strand specific nuclease Yong Zhao, Hirotoshi Hoshiyama, Jerry W. Shay, and Woodring E. Wright PMCID: PMC2241892 μChIP—a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies John Arne Dahl and Philippe Collas PMCID: PMC2241883 Codon choice in genes depends on flanking sequence information—implications for theoretical reverse translation Karthikeyan Sivaraman, AswinSaiNarain Seshasayee, Patrick M. Tarwater, and Alexander M. Cole PMCID: PMC2241905 Microplate-based chromatin immunoprecipitation method, Matrix ChIP: a platform to study signaling of complex genomic events Steve Flanagin, Joel D. Nelson, David G. Castner, Oleg Denisenko, and Karol Bomsztyk PMCID: PMC2241906 Short-hairpin RNAs synthesized by T7 phage polymerase do not induce interferon Takuma Gondai, Kazuya Yamaguchi, Naoko Miyano-Kurosaki, Yuichirou Habu, and Hiroshi Takaku PMCID: PMC2241887 PAP-LMPCR for improved, allele-specific footprinting and automated chromatin fine structure analysis R. Ingram, C. Gao, J. LeBon, Q. Liu, R. J. Mayoral, S. S. Sommer, M. Hoogenkamp, A. D. Riggs, and C. Bonifer PMCID: PMC2241904 Computational Biology Ab initio thermodynamic modeling of distal multisite transcription regulation Leonor Saiz and Jose M. G. Vilar PMCID: PMC2241893 Nucleic Acid Enzymes Uracil recognition by replicative DNA polymerases is limited to the archaea, not occurring with bacteria and eukarya Josephine Wardle, Peter M. J. Burgers, Isaac K. O. Cann, Kate Darley, Pauline Heslop, Erik Johansson, Li-Jung Lin, Peter McGlynn, Jonathan Sanvoisin, Carrie M. Stith, and Bernard A. Connolly PMCID: PMC2241895 Site specific phosphorylation of yeast RNA polymerase I Jochen Gerber, Alarich Reiter, Robert Steinbauer, Steffen Jakob, Claus-Dieter Kuhn, Patrick Cramer, Joachim Griesenbeck, Philipp Milkereit, and Herbert Tschochner PMCID: PMC2241885 Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family Giedrius Gasiunas, Giedrius Sasnauskas, Gintautas Tamulaitis, Claus Urbanke, Dalia Razaniene, and Virginijus Siksnys PMCID: PMC2241918 Structure-function analysis of the RNA helicase maleless Annalisa Izzo, Catherine Regnard, Violette Morales, Elisabeth Kremmer, and Peter B. Becker PMCID: PMC2241912 AZT resistance of simian foamy virus reverse transcriptase is based on the excision of AZTMP in the presence of ATP Maximilian J. Hartl, Benedikt Kretzschmar, Anne Frohn, Ali Nowrouzi, Axel Rethwilm, and Birgitta M. Wöhrl PMCID: PMC2241919 Mutation adjacent to the active site tyrosine can enhance DNA cleavage and cell killing by the TOPRIM Gly to Ser mutant of bacterial topoisomerase I Bokun Cheng, Elena P. Sorokin, and Yuk-Ching Tse-Dinh PMCID: PMC2241903 HU binds and folds single-stranded DNA Dmitri Kamashev, Anna Balandina, Alexey K. Mazur, Paola B. Arimondo, and Josette Rouviere-Yaniv PMCID: PMC2241890 |
