| | Molecular Biology A comparison of the DNA binding and bending capacities and the oligomeric states of the immunity repressors of heteroimmune coliphages P2 and WΦ Alexandra Ahlgren-Berg, Petri Henriksson-Peltola, Wilhelmina Sehlén, and Elisabeth Haggård-Ljungquist PMCID: PMC1904263 Determination of the DNA-binding kinetics of three related but heteroimmune bacteriophage repressors using EMSA and SPR analysis Petri Henriksson-Peltola, Wilhelmina Sehlén, and Elisabeth Haggård-Ljungquist PMCID: PMC1904268 Genomewide and biochemical analyses of DNA-binding activity of Cdc6/Orc1 and Mcm proteins in Pyrococcus sp. Fujihiko Matsunaga, Annie Glatigny, Marie-Hélène Mucchielli-Giorgi, Nicolas Agier, Hervé Delacroix, Laetitia Marisa, Patrice Durosay, Yoshizumi Ishino, Lawrence Aggerbeck, and Patrick Forterre PMCID: PMC1904270 Differential regulation of repeated histone genes during the fission yeast cell cycle Yuko Takayama and Kohta Takahashi PMCID: PMC1904272 Expression of catalytic mutants of the mtDNA helicase Twinkle and polymerase POLG causes distinct replication stalling phenotypes Sjoerd Wanrooij, Steffi Goffart, Jaakko L.O. Pohjoismäki, Takehiro Yasukawa, and Johannes N. Spelbrink PMCID: PMC1904276 Interplay between DNA N-glycosylases/AP lyases at multiply damaged sites and biological consequences Grégory Éot-Houllier, Marta Gonera, Didier Gasparutto, Céline Giustranti, and Evelyne Sage PMCID: PMC1904269 Complexities associated with expression of Epstein–Barr virus (EBV) lytic origins of DNA replication Shao-An Xue and Beverly E. Griffin PMCID: PMC1904260 Sequences in attB that affect the ability of ϕC31 integrase to synapse and to activate DNA cleavage Milind Gupta, Rob Till, and Margaret C. M. Smith PMCID: PMC1904298 Structural elements defining elongation factor Tu mediated suppression of codon ambiguity Hervé Roy, Hubert Dominique Becker, Marie-Hélène Mazauric, and Daniel Kern PMCID: PMC1904265 Transcription-coupled deposition of histone modifications during MHC class II gene activation Natalia Rybtsova, Elisa Leimgruber, Queralt Seguin-Estévez, Isabelle Dunand-Sauthier, Michal Krawczyk, and Walter Reith PMCID: PMC1904273 Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1 Jeong Do Kim, Christopher Faulk, and Joomyeong Kim PMCID: PMC1904287 Transcription of the human cell cycle regulated BUB1B gene requires hStaf/ZNF143 Evelyne Myslinski, Marie-Aline Gérard, Alain Krol, and Philippe Carbon PMCID: PMC1904299 Rational design of an estrogen receptor mutant with altered DNA-binding specificity Denis Nguyen, Martine Bail, Genevieve Pesant, Virginie N. Dupont, Étienne Rouault, Julie Deschênes, Walter Rocha, Geneviève Melançon, Sergey V. Steinberg, and Sylvie Mader PMCID: PMC1904296 Trypanosoma brucei homologous recombination is dependent on substrate length and homology, though displays a differential dependence on mismatch repair as substrate length decreases Rebecca L. Barnes and Richard McCulloch PMCID: PMC1904282 RNA A bona fide La protein is required for embryogenesis in Arabidopsis thaliana Sophie Fleurdépine, Jean-Marc Deragon, Martine Devic, Jocelyne Guilleminot, and Cécile Bousquet-Antonelli PMCID: PMC1904278 Pan-eukaryote ITS2 homologies revealed by RNA secondary structure Annette W. Coleman PMCID: PMC1904279 Post-transcriptional modification mapping in the Clostridium acetobutylicum 16S rRNA by mass spectrometry and reverse transcriptase assays Gert Emmerechts, Sofie Barbé, Piet Herdewijn, Jozef Anné, and Jef Rozenski PMCID: PMC1904277 Structural Biology DNA sequence-specific recognition by a transcriptional regulator requires indirect readout of A-tracts Jesús Mendieta, Laura Pérez-Lago, Margarita Salas, and Ana Camacho PMCID: PMC1904284 The C-terminal loop of the homing endonuclease I-CreI is essential for site recognition, DNA binding and cleavage Jesús Prieto, Pilar Redondo, Daniel Padró, Sylvain Arnould, Jean-Charles Epinat, Frédéric Pâques, Francisco J. Blanco, and Guillermo Montoya PMCID: PMC1904291 Defining the mode, energetics and specificity with which a macrocyclic hexaoxazole binds to human telomeric G-quadruplex DNA Christopher M. Barbieri, Annankoil R. Srinivasan, Suzanne G. Rzuczek, Joseph E. Rice, Edmond J. LaVoie, and Daniel S. Pilch PMCID: PMC1904271 Theoretical study of large conformational transitions in DNA: the B↔A conformational change in water and ethanol/water Agnes Noy, Alberto Pérez, Charles A. Laughton, and Modesto Orozco PMCID: PMC1904281 Transcription activator structure reveals redox control of a replication initiation reaction Cyril M. Sanders, Dmytro Sizov, Philippa R. Seavers, Miguel Ortiz-Lombardía, and Alfred A. Antson PMCID: PMC1904295 Genomics Repeat-induced epigenetic changes in intron 1 of the frataxin gene and its consequences in Friedreich ataxia Eriko Greene, Lata Mahishi, Ali Entezam, Daman Kumari, and Karen Usdin PMCID: PMC1904289 Chemistry Chemical synthesis of a very long oligoribonucleotide with 2-cyanoethoxymethyl (CEM) as the 2′-O-protecting group: structural identification and biological activity of a synthetic 110mer precursor-microRNA candidate Yoshinobu Shiba, Hirofumi Masuda, Naoki Watanabe, Takeshi Ego, Kazuchika Takagaki, Kouichi Ishiyama, Tadaaki Ohgi, and Junichi Yano PMCID: PMC1904286 On the stability of peptide nucleic acid duplexes in the presence of organic solvents Anjana Sen and Peter E. Nielsen PMCID: PMC1904262 Methods Online Three methods for optimization of cross-laboratory and cross-platform microarray expression data Phillip Stafford and Marcel Brun PMCID: PMC1904274 Subtractive hybridization identifies novel differentially expressed ncRNA species in EBV-infected human B cells Jan Mrázek, Simone B. Kreutmayer, Friedrich A. Grässer, Norbert Polacek, and Alexander Hüttenhofer PMCID: PMC1904266 Lateral flow microarrays: a novel platform for rapid nucleic acid detection based on miniaturized lateral flow chromatography Darren J. Carter and R. Bruce Cary PMCID: PMC1904290 Sequence specificity of single-stranded DNA-binding proteins: a novel DNA microarray approach Hugh P. Morgan, Peter Estibeiro, Martin A. Wear, Klaas E.A. Max, Udo Heinemann, Liza Cubeddu, Maurice P. Gallagher, Peter J. Sadler, and Malcolm D. Walkinshaw PMCID: PMC1904285 Tentacle probes: eliminating false positives without sacrificing sensitivity Brent C. Satterfield, Jay A.A. West, and Michael R. Caplan PMCID: PMC1904288 A facile method for attaching nitroxide spin labels at the 5′ terminus of nucleic acids Gian Paola G. Grant and Peter Z. Qin PMCID: PMC1904292 Assisted large fragment insertion by Red/ET-recombination (ALFIRE)—an alternative and enhanced method for large fragment recombineering Adolfo Rivero-Müller, Svetlana Lajić, and Ilpo Huhtaniemi PMCID: PMC1904275 Sequence analysis and editing for bisulphite genomic sequencing projects Ian M. Carr, Elizabeth M. A. Valleley, Sarah F. Cordery, Alexander F. Markham, and David T. Bonthron PMCID: PMC1904293 Computational Biology Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human German Gaston Leparc and Robi David Mitra PMCID: PMC1904267 Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation Saran Vardhanabhuti, Junwen Wang, and Sridhar Hannenhalli PMCID: PMC1904283 Evolutionary rates vary among rRNA structural elements S. Smit, J. Widmann, and R. Knight PMCID: PMC1904297 LOMETS: A local meta-threading-server for protein structure prediction Sitao Wu and Yang Zhang PMCID: PMC1904280 Nucleic Acid Enzymes Amino acid residues of the Escherichia coli tRNA(m5U54)methyltransferase (TrmA) critical for stability, covalent binding of tRNA and enzymatic activity Jaunius Urbonavičius, Gunilla Jäger, and Glenn R. Björk PMCID: PMC1904294 Corrigenda Transcriptional regulation of human MAP2 gene in melanoma: role of neuronal bHLH factors and Notch1 signaling Kumar M. R. Bhat, Nityanand Maddodi, Cooduvalli Shashikant, and Vijayasaradhi Setaluri PMCID: PMC1904264 Corrects: Kumar M. R. Bhat, et al. Transcriptional regulation of human MAP2 gene in melanoma: role of neuronal bHLH factors and Notch1 signaling. Nucleic Acids Res. 2006; 34(13): 3819–3832. Primer extension enrichment reaction (PEER): a new subtraction method for identification of genetic differences between biological specimens Lilia Ganova-Raeva, Xinjian Zhang, Fengli Cao, Howard Fields, and Yury Khudyakov PMCID: PMC1904259 Corrects: Lilia Ganova-Raeva, et al. Primer Extension Enrichment Reaction (PEER): a new subtraction method for identification of genetic differences between biological specimens. Nucleic Acids Res. 2006; 34(11): e76. The proteins encoded by the pogo-like Lemi1 element bind the TIRs and subterminal repeated motifs of the Arabidopsis Emigrant MITE. Consequences for the transposition mechanism of MITEs Céline Loot, Néstor Santiago, Alicia Sanz, and Josep M. Casacuberta PMCID: PMC1904261 Corrects: Céline Loot, et al. The proteins encoded by the pogo-like Lemi1 element bind the TIRs and subterminal repeated motifs of the Arabidopsis Emigrant MITE: consequences for the transposition mechanism of MITEs. Nucleic Acids Res. 2006 October; 34(18): 5238–5246. |
