| | Molecular Biology Correlation between binding rate constants and individual information of E. coli Fis binding sites Ryan K. Shultzaberger, Lindsey R. Roberts, Ilya G. Lyakhov, Igor A. Sidorov, Andrew G. Stephen, Robert J. Fisher, and Thomas D. Schneider PMCID: PMC2018646 Phospho-epitope binding by the BRCT domains of hPTIP controls multiple aspects of the cellular response to DNA damage Ivan M. Munoz, Paul A. Jowsey, Rachel Toth, and John Rouse PMCID: PMC2018624 Cdc18/CDC6 activates the Rad3-dependent checkpoint in the fission yeast Naomi Fersht, Damien Hermand, Jacqueline Hayles, and Paul Nurse PMCID: PMC2018612 Ubiquitylation-independent degradation of Xeroderma pigmentosum group C protein is required for efficient nucleotide excision repair Qi-En Wang, Mette Prætorius-Ibba, Qianzheng Zhu, Mohamed A. El-Mahdy, Gulzar Wani, Qun Zhao, Song Qin, Srinivas Patnaik, and Altaf A. Wani PMCID: PMC2018625 A persistent RNA·DNA hybrid formed by transcription of the Friedreich ataxia triplet repeat in live bacteria, and by T7 RNAP in vitro Ed Grabczyk, Miriam Mancuso, and Mimi C. Sammarco PMCID: PMC2018641 Protein p56 from the Bacillus subtilis phage ϕ29 inhibits DNA-binding ability of uracil-DNA glycosylase Gemma Serrano-Heras, José A. Ruiz-Masó, Gloria del Solar, Manuel Espinosa, Alicia Bravo, and Margarita Salas PMCID: PMC2018632 MeCP2 interacts with HP1 and modulates its heterochromatin association during myogenic differentiation Noopur Agarwal, Tanja Hardt, Alessandro Brero, Danny Nowak, Ulrich Rothbauer, Annette Becker, Heinrich Leonhardt, and M. Cristina Cardoso PMCID: PMC2018631 Biochemical reconstitution of abasic DNA lesion replication in Xenopus extracts Shuren Liao, Yoshihiro Matsumoto, and Hong Yan PMCID: PMC2018634 Repeat-associated siRNAs cause chromatin silencing of retrotransposons in the Drosophila melanogaster germline Mikhail S. Klenov, Sergey A. Lavrov, Anastasia D. Stolyarenko, Sergey S. Ryazansky, Alexei A. Aravin, Thomas Tuschl, and Vladimir A. Gvozdev PMCID: PMC2018648 Protein/DNA arrays identify nitric oxide-regulated cis-element and trans-factor activities some of which govern neuroblastoma cell viability Saravanakumar Dhakshinamoorthy, Shiva Ranjani Sridharan, Lei Li, Poh Yong Ng, Linda M. Boxer, and Alan G. Porter PMCID: PMC2018649 Hairpin structure within the 3′UTR of DNA polymerase β mRNA acts as a post-transcriptional regulatory element and interacts with Hax-1 Elżbieta Sarnowska, Ewa A. Grzybowska, Krzysztof Sobczak, Ryszard Konopiński, Anna Wilczyńska, Maria Szwarc, Tomasz J. Sarnowski, Włodzimierz J. Krzyżosiak, and Janusz A. Siedlecki PMCID: PMC2018635 β-Catenin binds to the downstream region and regulates the expression C-reactive protein gene Yong Seok Choi, Jung Hur, and Sunjoo Jeong PMCID: PMC2018623 Tup1-Ssn6 and Swi-Snf remodelling activities influence long-range chromatin organization upstream of the yeast SUC2 gene Alastair B. Fleming and Sari Pennings PMCID: PMC2018639 A facilitated tracking and transcription mechanism of long-range enhancer function Xingguo Zhu, Jianhua Ling, Ling Zhang, Wenhu Pi, Min Wu, and Dorothy Tuan PMCID: PMC2018613 Defective DNA base excision repair in brain from individuals with Alzheimer's disease and amnestic mild cognitive impairment Lior Weissman, Dong-Gyu Jo, Martin M. Sørensen, Nadja C. de Souza-Pinto, William R. Markesbery, Mark P. Mattson, and Vilhelm A. Bohr PMCID: PMC2018628 The PMC2NT domain of the catalytic exosome subunit Rrp6p provides the interface for binding with its cofactor Rrp47p, a nucleic acid-binding protein Jonathan A. Stead, Joe L. Costello, Michaela J. Livingstone, and Phil Mitchell PMCID: PMC2018643 RNA Tissue-specific splicing regulator Fox-1 induces exon skipping by interfering E complex formation on the downstream intron of human F1γ gene Kazuhiro Fukumura, Ayako Kato, Yui Jin, Takashi Ideue, Tetsuro Hirose, Naoyuki Kataoka, Toshinobu Fujiwara, Hiroshi Sakamoto, and Kunio Inoue PMCID: PMC2018636 Fluorescent probing for RNA molecules by an unnatural base-pair system Michiko Kimoto, Tsuneo Mitsui, Yoko Harada, Akira Sato, Shigeyuki Yokoyama, and Ichiro Hirao PMCID: PMC2018647 Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach Kathrin Lang, Renate Rieder, and Ronald Micura PMCID: PMC2018614 Interactions of the G quartet forming semaphorin 3F RNA with the RGG box domain of the fragile X protein family Lakshmi Menon and Mihaela-Rita Mihailescu PMCID: PMC2018618 Translational control of the interferon regulatory factor 2 mRNA by IRES element Debojyoti Dhar, Swagata Roy, and Saumitra Das PMCID: PMC2018642 Muscleblind-like 1 interacts with RNA hairpins in splicing target and pathogenic RNAs Yuan Yuan, Sarah A. Compton, Krzysztof Sobczak, Myrna G. Stenberg, Charles A. Thornton, Jack D. Griffith, and Maurice S. Swanson PMCID: PMC2018611 Ligand recognition determinants of guanine riboswitches Jérôme Mulhbacher and Daniel A. Lafontaine PMCID: PMC2018637 The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift Mélissa Léger, Dominic Dulude, Sergey V. Steinberg, and Léa Brakier-Gingras PMCID: PMC2018615 In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership Éena Jakó, Péter Ittzés, Áron Szenes, Ádám Kun, Eörs Szathmáry, and Gábor Pál PMCID: PMC2018626 Identification of determinants in the protein partners aCBF5 and aNOP10 necessary for the tRNA:Ψ55-synthase and RNA-guided RNA:Ψ-synthase activities Sébastien Muller, Jean-Baptiste Fourmann, Christine Loegler, Bruno Charpentier, and Christiane Branlant PMCID: PMC2018633 Genomics Does distance matter? Variations in alternative 3′ splicing regulation Martin Akerman and Yael Mandel-Gutfreund PMCID: PMC2018619 Methods Online Thermodynamically modulated partially double-stranded linear DNA probe design for homogeneous real-time PCR Shihai Huang, John Salituro, Ning Tang, Ka-Cheung Luk, John Hackett, Jr, Priscilla Swanson, Gavin Cloherty, Wai-Bing Mak, John Robinson, and Klara Abravaya PMCID: PMC2018630 Filtering genes to improve sensitivity in oligonucleotide microarray data analysis Stefano Calza, Wolfgang Raffelsberger, Alexander Ploner, Jose Sahel, Thierry Leveillard, and Yudi Pawitan PMCID: PMC2018638 High-precision mapping of protein–protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform Maria Pajunen, Hilkka Turakainen, Eini Poussu, Johan Peränen, Mauno Vihinen, and Harri Savilahti PMCID: PMC2018616 One step construction of PCR mutagenized libraries for genetic analysis by recombination cloning Al-Muataz Khalil, Jeffrey A. Julius, and Jeff Bachant PMCID: PMC2018627 Avoiding false-positive signals with nuclease-vulnerable molecular beacons in single living cells Antony K. Chen, Mark A. Behlke, and Andrew Tsourkas PMCID: PMC2018645 Choreography for nucleosomes: the conformational freedom of the nucleosomal filament and its limitations Mogens Engelhardt PMCID: PMC2018644 Live cell imaging of repetitive DNA sequences via GFP-tagged polydactyl zinc finger proteins Beatrice I. Lindhout, Paul Fransz, Federico Tessadori, Tobias Meckel, Paul J.J. Hooykaas, and Bert J. van der Zaal PMCID: PMC2018617 Computational Biology A survey of bacterial insertion sequences using IScan Andreas Wagner, Christopher Lewis, and Manuel Bichsel PMCID: PMC2018620 A systematic strategy for large-scale analysis of genotype–phenotype correlations: identification of candidate genes involved in African trypanosomiasis Paul Fisher, Cornelia Hedeler, Katherine Wolstencroft, Helen Hulme, Harry Noyes, Stephen Kemp, Robert Stevens, and Andrew Brass PMCID: PMC2018629 Nucleic Acid Enzymes T4 DNA ligase is more than an effective trap of cyclized dsDNA Chongli Yuan, Xiong Wen Lou, Elizabeth Rhoades, Huimin Chen, and Lynden A. Archer PMCID: PMC2018621 DNA polymerase proofreading: active site switching catalyzed by the bacteriophage T4 DNA polymerase Elizabeth Fidalgo da Silva and Linda J. Reha-Krantz PMCID: PMC2018640 A randomized library approach to identifying functional lox site domains for the Cre recombinase Jamie Sheren, Stephen J. Langer, and Leslie A. Leinwand PMCID: PMC2018622 |
