| | Molecular Biology Recovery of bisulfite-converted genomic sequences in the methylation-sensitive QPCR Kristofer Munson, Jarrod Clark, Katarzyna Lamparska-Kupsik, and Steven S. Smith PMCID: PMC1888819 Recruitment of DNA repair synthesis machinery to sites of DNA damage/repair in living human cells Kazunari Hashiguchi, Yoshihiro Matsumoto, and Akira Yasui PMCID: PMC1888830 DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites Jingdan Liang, Zhijun Wang, Xinyi He, Jialiang Li, Xiufen Zhou, and Zixin Deng PMCID: PMC1888814 All APOBEC3 family proteins differentially inhibit LINE-1 retrotransposition Masanobu Kinomoto, Takayuki Kanno, Mari Shimura, Yukihito Ishizaka, Asato Kojima, Takeshi Kurata, Tetsutaro Sata, and Kenzo Tokunaga PMCID: PMC1888823 Complex translational regulation of BACE1 involves upstream AUGs and stimulatory elements within the 5′ untranslated region Marija Mihailovich, Rolf Thermann, Fabio Grohovaz, Matthias W. Hentze, and Daniele Zacchetti PMCID: PMC1888809 RNA polymerase III transcription is repressed in response to the tumour suppressor ARF Jennifer P. Morton, Theodoros Kantidakis, and Robert J. White PMCID: PMC1888803 Mechanism for the TtDnaA–Tt-oriC cooperative interaction at high temperature and duplex opening at an unusual AT-rich region in Thermoanaerobacter tengcongensis Huadong Pei, Jingfang Liu, Jie Li, Aobo Guo, Jian Zhou, and Hua Xiang PMCID: PMC1888806 Actin-related protein Arp4 functions in kinetochore assembly Hideaki Ogiwara, Ayako Ui, Satoshi Kawashima, Kazuto Kugou, Fumitoshi Onoda, Hitoshi Iwahashi, Masahiko Harata, Kunihiro Ohta, Takemi Enomoto, and Masayuki Seki PMCID: PMC1888834 RNA Use of a novel Förster resonance energy transfer method to identify locations of site-bound metal ions in the U2–U6 snRNA complex Faqing Yuan, Laura Griffin, LauraJane Phelps, Volker Buschmann, Kenneth Weston, and Nancy L. Greenbaum PMCID: PMC1888832 Specificity, duplex degradation and subcellular localization of antagomirs Jan Krützfeldt, Satoru Kuwajima, Ravi Braich, Kallanthottathil G. Rajeev, John Pena, Thomas Tuschl, Muthiah Manoharan, and Markus Stoffel PMCID: PMC1888827 Thermodynamics and kinetics for base-pair opening in the P1 duplex of the Tetrahymena group I ribozyme Joon-Hwa Lee and Arthur Pardi PMCID: PMC1891724 CAF1 plays an important role in mRNA deadenylation separate from its contact to CCR4 Takbum Ohn, Yueh-Chin Chiang, Darren J. Lee, Gang Yao, Chongxu Zhang, and Clyde L. Denis PMCID: PMC1888822 Escherichia coli ribosomal protein L20 binds as a single monomer to its own mRNA bearing two potential binding sites F. Allemand, J. Haentjens, C. Chiaruttini, C. Royer, and M. Springer PMCID: PMC1888825 Base-specific spin-labeling of RNA for structure determination Nelly Piton, Yuguang Mu, Gerhard Stock, Thomas F. Prisner, Olav Schiemann, and Joachim W. Engels PMCID: PMC1891445 Identification of conserved secondary structures and expansion segments in enod40 RNAs reveals new enod40 homologues in plants Alexander P. Gultyaev and Andreas Roussis PMCID: PMC1888808 Structural Biology Solution structure of Domains IVa and V of the τ subunit of Escherichia coli DNA polymerase III and interaction with the α subunit Xun-Cheng Su, Slobodan Jergic, Max A. Keniry, Nicholas E. Dixon, and Gottfried Otting PMCID: PMC1888800 Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization Chunlai Chen, Wenjuan Wang, Zhang Wang, Fang Wei, and Xin Sheng Zhao PMCID: PMC1888818 Solution structure and dynamics of DNA duplexes containing the universal base analogues 5-nitroindole and 5-nitroindole 3-carboxamide José Gallego and David Loakes PMCID: PMC1888824 The open state of human topoisomerase I as probed by molecular dynamics simulation Giovanni Chillemi, Alessandro Bruselles, Paola Fiorani, Susana Bueno, and Alessandro Desideri PMCID: PMC1888835 Guanines are a quartet's best friend: impact of base substitutions on the kinetics and stability of tetramolecular quadruplexes Julien Gros, Frédéric Rosu, Samir Amrane, Anne De Cian, Valérie Gabelica, Laurent Lacroix, and Jean-Louis Mergny PMCID: PMC1888817 The 1.4-Å crystal structure of the S. pombe Pop2p deadenylase subunit unveils the configuration of an active enzyme Anette Thyssen Jonstrup, Kasper R. Andersen, Lan B. Van, and Ditlev E. Brodersen PMCID: PMC1888821 Genomics Mapping translocation breakpoints using a wheat microarray Prasanna R. Bhat, Adam Lukaszewski, Xinping Cui, Jin Xu, Jan T. Svensson, Steve Wanamaker, J. Giles Waines, and Timothy J. Close PMCID: PMC1888831 Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets Buyong Ma, Yongping Pan, Jie Zheng, Arnold J. Levine, and Ruth Nussinov PMCID: PMC1888811 Mitochondrial diversity within modern human populations Robert W. Carter PMCID: PMC1888801 Chemistry Investigation of spectral conversion of d(TTAGGG)4 and d(TTAGGG)13 upon potassium titration by a G-quadruplex recognizer BMVC molecule Cheng-Chung Chang, Chih-Wei Chien, Yi-Hsueh Lin, Chi-Chih Kang, and Ta-Chau Chang PMCID: PMC1888807 Methods Online A hybrid CMV-H1 construct improves efficiency of PEI-delivered shRNA in the mouse brain Zahra Hassani, Jean-Christophe François, Gladys Alfama, Ghislaine Morvan Dubois, Mathilde Paris, Carine Giovannangeli, and Barbara A. Demeneix PMCID: PMC1888798 An in vitro selection scheme for oligonucleotide probes to discriminate between closely related DNA sequences Ivan Brukner, Razan El-Ramahi, Izabella Gorska-Flipot, Maja Krajinovic, and Damian Labuda PMCID: PMC1888810 Comparison of RNAi efficiency mediated by tetracycline-responsive H1 and U6 promoter variants in mammalian cell lines Jørn R. Henriksen, Cecilie Løkke, Martin Hammerø, Dirk Geerts, Rogier Versteeg, Trond Flægstad, and Christer Einvik PMCID: PMC1888813 An exonuclease I hydrolysis assay for evaluating G-quadruplex stabilization by small molecules Yuan Yao, Quan Wang, Yu-hua Hao, and Zheng Tan PMCID: PMC1888815 Error-pooling-based statistical methods for identifying novel temporal replication profiles of human chromosomes observed by DNA tiling arrays Taesung Park, Youngchul Kim, Stefan Bekiranov, and Jae K. Lee PMCID: PMC1888820 Revision of the nonequilibrium thermal dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarrays Alex E. Pozhitkov, Robert D. Stedtfeld, Syed A. Hashsham, and Peter A. Noble PMCID: PMC1888805 An adaptation of the LMS method to determine expression variations in profiling data Paul Chuchana, Dorian Marchand, Mélanie Nugoli, Carmen Rodriguez, Nicolas Molinari, and Jose A. Garcia-Sanz PMCID: PMC1888829 Computational Biology RNAmmer: consistent and rapid annotation of ribosomal RNA genes Karin Lagesen, Peter Hallin, Einar Andreas Rødland, Hans-Henrik Stærfeldt, Torbjørn Rognes, and David W. Ussery PMCID: PMC1888812 Nucleic Acid Enzymes The unstructured C-terminus of the τ subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the α subunit Slobodan Jergic, Kiyoshi Ozawa, Neal K. Williams, Xun-Cheng Su, Daniel D. Scott, Samir M. Hamdan, Jeffrey A. Crowther, Gottfried Otting, and Nicholas E. Dixon PMCID: PMC1888804 The domain structure of Helicobacter pylori DnaB helicase: the N-terminal domain can be dispensable for helicase activity whereas the extreme C-terminal region is essential for its function Ram Gopal Nitharwal, Subhankar Paul, Ashraf Dar, Nirupam Roy Choudhury, Rajesh K Soni, Dhaneswar Prusty, Sukrat Sinha, Tara Kashav, Gauranga Mukhopadhyay, Tapan Kumar Chaudhuri, Samudrala Gourinath, and Suman Kumar Dhar PMCID: PMC1888833 Loop II of DNA polymerase beta is important for polymerization activity and fidelity George C. Lin, Joachim Jaeger, and Joann B. Sweasy PMCID: PMC1888816 Domain swapping between FEN-1 and XPG defines regions in XPG that mediate nucleotide excision repair activity and substrate specificity Marcel Hohl, Isabelle Dunand-Sauthier, Lidija Staresincic, Pascale Jaquier-Gubler, Fabrizio Thorel, Mauro Modesti, Stuart G. Clarkson, and Orlando D. Schärer PMCID: PMC1888826 Regulation of B family DNA polymerase fidelity by a conserved active site residue: characterization of M644W, M644L and M644F mutants of yeast DNA polymerase ε Zachary F. Pursell, Isabelle Isoz, Else-Britt Lundström, Erik Johansson, and Thomas A. Kunkel PMCID: PMC1888828 Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages Zunyi Yang, A. Michael Sismour, and Steven A. Benner PMCID: PMC1888802 Corrigendum An efficient method for multi-locus molecular haplotyping Bernard A. Konfortov, Alan T. Bankier, and Paul H. Dear PMCID: PMC1888799 Corrects: Bernard A. Konfortov, et al. An efficient method for multi-locus molecular haplotyping. Nucleic Acids Res. 2007 January; 35(1): e6. |
