| | Molecular Biology The role of peptide motifs in the evolution of a protein network Hirohide Saito, Shunnichi Kashida, Tan Inoue, and Kiyotaka Shiba PMCID: PMC2095796 Telomeric co-localization of the modified base J and contingency genes in the protozoan parasite Trypanosoma cruzi Dilrukshi K. Ekanayake, Michael J. Cipriano, and Robert Sabatini PMCID: PMC2095807 In vitro selection and characterization of cellulose-binding DNA aptamers Benjamin J. Boese and Ronald R. Breaker PMCID: PMC2095800 The mitochondrial transcription termination factor mTERF modulates replication pausing in human mitochondrial DNA Anne K. Hyvärinen, Jaakko L. O. Pohjoismäki, Aurelio Reyes, Sjoerd Wanrooij, Takehiro Yasukawa, Pekka J. Karhunen, Johannes N. Spelbrink, Ian J. Holt, and Howard T. Jacobs PMCID: PMC2095818 Telomere dynamics and fusion of critically shortened telomeres in plants lacking DNA ligase IV Michelle L. Heacock, Rachel A. Idol, Joanna D. Friesner, Anne B. Britt, and Dorothy E. Shippen PMCID: PMC2095805 Generation of a transgenic zebrafish model of Tauopathy using a novel promoter element derived from the zebrafish eno2 gene Qing Bai, Jessica A. Garver, Neil A. Hukriede, and Edward A. Burton PMCID: PMC2095798 Different genetic requirements for repair of replication-born double-strand breaks by sister-chromatid recombination and break-induced replication Felipe Cortés-Ledesma, Cristina Tous, and Andrés Aguilera PMCID: PMC2095809 Subcellular distribution of human RDM1 protein isoforms and their nucleolar accumulation in response to heat shock and proteotoxic stress Lydia Messaoudi, Yun-Gui Yang, Aiko Kinomura, Diana A. Stavreva, Gonghong Yan, Marie-Line Bortolin-Cavaillé, Hiroshi Arakawa, Jean-Marie Buerstedde, Pierre Hainaut, Jérome Cavaillé, Minoru Takata, and Eric Van Dyck PMCID: PMC2095821 The ePHD protein SPBP interacts with TopBP1 and together they co-operate to stimulate Ets1-mediated transcription Eva Sjøttem, Cecilie Rekdal, Gunbjørg Svineng, Sylvia Sagen Johnsen, Helle Klenow, Rebecca Dale Uglehus, and Terje Johansen PMCID: PMC2095823 LATERAL ORGAN BOUNDARIES defines a new family of DNA-binding transcription factors and can interact with specific bHLH proteins Aman Husbands, Elizabeth M. Bell, Bin Shuai, Harley M.S. Smith, and Patricia S. Springer PMCID: PMC2095788 RNA Global control of aberrant splice-site activation by auxiliary splicing sequences: evidence for a gradient in exon and intron definition Jana Královičová and Igor Vořechovský PMCID: PMC2095810 Human ribosomal protein S13 regulates expression of its own gene at the splicing step by a feedback mechanism Alexey A. Malygin, Natalia M. Parakhnevitch, Anton V. Ivanov, Ian C. Eperon, and Galina G. Karpova PMCID: PMC2095825 Interactions between subunits of Saccharomyces cerevisiae RNase MRP support a conserved eukaryotic RNase P/MRP architecture Tanya V. Aspinall, James M.B. Gordon, Hayley J. Bennett, Panagiotis Karahalios, John-Paul Bukowski, Scott C. Walker, David R. Engelke, and Johanna M. Avis PMCID: PMC2095792 Translation of non-capped mRNAs in a eukaryotic cell-free system: acceleration of initiation rate in the course of polysome formation Olga M. Alekhina, Konstantin S. Vassilenko, and Alexander S. Spirin PMCID: PMC2095793 Reduced levels of Ago2 expression result in increased siRNA competition in mammalian cells Timothy A. Vickers, Walt F. Lima, Josh G. Nichols, and Stanley T. Crooke PMCID: PMC2095815 Structural Biology Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme Feng Li, Pradeep S. Pallan, Martin A. Maier, Kallanthottathil G. Rajeev, Steven L. Mathieu, Christoph Kreutz, Yupeng Fan, Jayodita Sanghvi, Ronald Micura, Eriks Rozners, Muthiah Manoharan, and Martin Egli PMCID: PMC2095806 Papillomavirus E1 helicase assembly maintains an asymmetric state in the absence of DNA and nucleotide cofactors Cyril M. Sanders, Oleg V. Kovalevskiy, Dmytro Sizov, Andrey A. Lebedev, Michail N. Isupov, and Alfred A. Antson PMCID: PMC2095799 Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution Anh Tuân Phan, Vitaly Kuryavyi, Kim Ngoc Luu, and Dinshaw J. Patel PMCID: PMC2095816 Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing Pradeep S. Pallan, Paolo Lubini, Martin Bolli, and Martin Egli PMCID: PMC2095819 Survey and Summary An RNA toolbox for single-molecule force spectroscopy studies Igor D. Vilfan, Wiecher Kamping, Michiel van den Hout, Andrea Candelli, Susanne Hage, and Nynke H. Dekker PMCID: PMC2095808 Genomics Multiple conserved regulatory elements with overlapping functions determine Sox10 expression in mouse embryogenesis Torsten Werner, Alexander Hammer, Mandy Wahlbuhl, Michael R. Bösl, and Michael Wegner PMCID: PMC2095789 Phosphorylated serine 28 of histone H3 is associated with destabilized nucleosomes in transcribed chromatin Jian-Min Sun, Hou Yu Chen, Paula S. Espino, and James R. Davie PMCID: PMC2095820 Chemistry Termination of DNA synthesis by N6-alkylated, not 3′-O-alkylated, photocleavable 2′-deoxyadenosine triphosphates Weidong Wu, Brian P. Stupi, Vladislav A. Litosh, Dena Mansouri, Demetra Farley, Sidney Morris, Sherry Metzker, and Michael L. Metzker PMCID: PMC2095803 Methods Online Direct observation of the reversible unwinding of a single DNA molecule caused by the intercalation of ethidium bromide Masahito Hayashi and Yoshie Harada PMCID: PMC2095801 Cre reconstitution allows for DNA recombination selectively in dual-marker-expressing cells in transgenic mice Yanwen Xu, Gang Xu, Bindong Liu, and Guoqiang Gu PMCID: PMC2095822 Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature Haukur Gudnason, Martin Dufva, D.D. Bang, and Anders Wolff PMCID: PMC2095797 Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D Fabiana Perocchi, Zhenyu Xu, Sandra Clauder-Münster, and Lars M. Steinmetz PMCID: PMC2095812 Ultrasound-mediated DNA transfer for bacteria Yizhi Song, Thomas Hahn, Ian P. Thompson, Timothy J. Mason, Gail M. Preston, Guanghe Li, Larysa Paniwnyk, and Wei E. Huang PMCID: PMC2095817 A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing Poornima Parameswaran, Roxana Jalili, Li Tao, Shadi Shokralla, Baback Gharizadeh, Mostafa Ronaghi, and Andrew Z. Fire PMCID: PMC2095802 FLAG assay as a novel method for real-time signal generation during PCR: application to detection and genotyping of KRAS codon 12 mutations Giulia Amicarelli, Erlet Shehi, G. Mike Makrigiorgos, and Daniel Adlerstein PMCID: PMC2095824 A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells Hedda A. Meijer, Martin Bushell, Kirsti Hill, Timothy W. Gant, Anne E. Willis, Peter Jones, and Cornelia H. de Moor PMCID: PMC2095794 In vivo construction of recombinant molecules within the Caenorhabditis elegans germ line using short regions of terminal homology Benedict J. Kemp, Julia Hatzold, Laura A. Sternick, Joshua Cornman-Homonoff, Jessica M. Whitaker, Pamela J. Tieu, and Eric J. Lambie PMCID: PMC2095804 Computational Biology Organismal complexity, cell differentiation and gene expression: human over mouse Alexander E. Vinogradov and Olga V. Anatskaya PMCID: PMC2095826 Nucleic Acid Enzymes Molecular cloning and characterization of the human RNase κ, an ortholog of Cc RNase Marie-angela I. Economopoulou, Emmanouel G. Fragoulis, and Diamantis C. Sideris PMCID: PMC2095791 Identification of key structural determinants of the IntI1 integron integrase that influence attC × attI1 recombination efficiency Gaëlle Demarre, Clara Frumerie, Deshmukh N. Gopaul, and Didier Mazel PMCID: PMC2095811 The restriction endonuclease R.NmeDI from Neisseria meningitidis that recognizes a palindromic sequence and cuts the DNA on both sides of the recognition sequence Agnieszka Kwiatek and Andrzej Piekarowicz PMCID: PMC2095814 The eukaryotic leading and lagging strand DNA polymerases are loaded onto primer-ends via separate mechanisms but have comparable processivity in the presence of PCNA Olga Chilkova, Peter Stenlund, Isabelle Isoz, Carrie M. Stith, Pawel Grabowski, Else-Britt Lundström, Peter M. Burgers, and Erik Johansson PMCID: PMC2095795 Escherichia coli HU protein has a role in the repair of abasic sites in DNA Yoke W. Kow, Barry Imhoff, Bernard Weiss, David C. I. Hung, Antreas A. Hindoyan, Randall M. Story, and Steven D. Goodman PMCID: PMC2095813 A hexanucleotide sequence (dC1–dC6 tract) restricts the dC-specific cleavage of single-stranded DNA by endonuclease IV of bacteriophage T4 Hiroyuki Ohshima, Nobutaka Hirano, and Hideo Takahashi PMCID: PMC2095790 |
