| | Molecular Biology PDZ domain-mediated dimerization and homeodomain-directed specificity are required for high-affinity DNA binding by SATB1 Prabhat Kumar Purbey, Sunita Singh, P. Pavan Kumar, Sameet Mehta, K. N. Ganesh, Debashis Mitra, and Sanjeev Galande PMCID: PMC2367706 Lsr2 of Mycobacterium tuberculosis is a DNA-bridging protein Jeffrey M. Chen, Huiping Ren, James E. Shaw, Yu Jing Wang, Ming Li, Andrea S. Leung, Vanessa Tran, Nicolas M. Berbenetz, Dana Kocíncová, Christopher M. Yip, Jean-Marc Reyrat, and Jun Liu PMCID: PMC2367712 Eukaryotic Y-family polymerases bypass a 3-methyl-2′-deoxyadenosine analog in vitro and methyl methanesulfonate-induced DNA damage in vivo Brian S. Plosky, Ekaterina G. Frank, David A. Berry, Graham P. Vennall, John P. McDonald, and Roger Woodgate PMCID: PMC2367705 Trace amounts of 8-oxo-dGTP in mitochondrial dNTP pools reduce DNA polymerase γ replication fidelity Zachary F. Pursell, J. Tyson McDonald, Christopher K. Mathews, and Thomas A. Kunkel PMCID: PMC2367704 Epigenetics of a tandem DNA repeat: chromatin DNaseI sensitivity and opposite methylation changes in cancers Koji Tsumagari, Lixin Qi, Kesmic Jackson, Chunbo Shao, Michelle Lacey, Janet Sowden, Rabi Tawil, Vettaikorumakankav Vedanarayanan, and Melanie Ehrlich PMCID: PMC2367708 Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro Hiroaki Tachiwana, Akihisa Osakabe, Hiroshi Kimura, and Hitoshi Kurumizaka PMCID: PMC2367731 LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated Brian J. Krueger, Célia Jeronimo, Bibhuti Bhusan Roy, Annie Bouchard, Charlotte Barrandon, Sarah A. Byers, Courtney E. Searcey, Jeffrey J. Cooper, Olivier Bensaude, Éric A. Cohen, Benoit Coulombe, and David H. Price PMCID: PMC2367717 Binding of sulphonated indigo derivatives to RepA-WH1 inhibits DNA-induced protein amyloidogenesis Fátima Gasset-Rosa, María Jesús Maté, Cristina Dávila-Fajardo, Jerónimo Bravo, and Rafael Giraldo PMCID: PMC2367726 Nucleocapsid mutations turn HIV-1 into a DNA-containing virus Laurent Houzet, Zakia Morichaud, Ludovic Didierlaurent, Delphine Muriaux, Jean-Luc Darlix, and Marylène Mougel PMCID: PMC2367716 Position effect variegation and imprinting of transgenes in lymphocytes Adam Williams, Nicola Harker, Eleni Ktistaki, Henrique Veiga-Fernandes, Kathleen Roderick, Mauro Tolaini, Trisha Norton, Keith Williams, and Dimitris Kioussis PMCID: PMC2367730 Molecular dissection of mRNA poly(A) tail length control in yeast Nicolas Viphakone, Florence Voisinet-Hakil, and Lionel Minvielle-Sebastia PMCID: PMC2367721 An upstream open reading frame within an IRES controls expression of a specific VEGF-A isoform Amandine Bastide, Zeineb Karaa, Stéphanie Bornes, Corinne Hieblot, Eric Lacazette, Hervé Prats, and Christian Touriol PMCID: PMC2367723 RNA Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect Kumiko Ui-Tei, Yuki Naito, Shuhei Zenno, Kenji Nishi, Kenji Yamato, Fumitaka Takahashi, Aya Juni, and Kaoru Saigo PMCID: PMC2367719 Human branch point consensus sequence is yUnAy Kaiping Gao, Akio Masuda, Tohru Matsuura, and Kinji Ohno PMCID: PMC2367711 Solution structure of a let-7 miRNA:lin-41 mRNA complex from C. elegans Mirko Cevec, Christophe Thibaudeau, and Janez Plavec PMCID: PMC2367737 Requirements for gene silencing mediated by U1 snRNA binding to a target sequence Xabi Abad, Maria Vera, Stephen P. Jung, Evelyn Oswald, Inés Romero, Vaibhav Amin, Puri Fortes, and Samuel I. Gunderson PMCID: PMC2367729 Identification of functional microRNAs released through asymmetrical processing of HIV-1 TAR element Dominique L. Ouellet, Isabelle Plante, Patricia Landry, Corinne Barat, Marie-Ève Janelle, Louis Flamand, Michel J. Tremblay, and Patrick Provost PMCID: PMC2367715 Structural Biology Towards a molecular dynamics consensus view of B-DNA flexibility Alberto Pérez, Filip Lankas, F. Javier Luque, and Modesto Orozco PMCID: PMC2367714 Survey and Summary Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction Hinanit Koltai and Carmiya Weingarten-Baror PMCID: PMC2367720 Genomics The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera, subsection Oenothera: I. Sequence evaluation and plastome evolution Stephan Greiner, Xi Wang, Uwe Rauwolf, Martina V. Silber, Klaus Mayer, Jörg Meurer, Georg Haberer, and Reinhold G. Herrmann PMCID: PMC2367718 Methods Online Elevated α-synuclein mRNA levels in individual UV-laser-microdissected dopaminergic substantia nigra neurons in idiopathic Parkinson's disease Jan Gründemann, Falk Schlaudraff, Olga Haeckel, and Birgit Liss PMCID: PMC2367701 High-resolution array comparative genomic hybridization of single micrometastatic tumor cells Christine Fuhrmann, Oleg Schmidt-Kittler, Nikolas H. Stoecklein, Karina Petat-Dutter, Christian Vay, Kerstin Bockler, Richard Reinhardt, Thomas Ragg, and Christoph A. Klein PMCID: PMC2367728 Labeling of unique sequences in double-stranded DNA at sites of vicinal nicks generated by nicking endonucleases Heiko Kuhn and Maxim D. Frank-Kamenetskii PMCID: PMC2373456 wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data Patrick Cahan, Laura E. Godfrey, Peggy S. Eis, Todd A. Richmond, Rebecca R. Selzer, Michael Brent, Howard L. McLeod, Timothy J. Ley, and Timothy A. Graubert PMCID: PMC2367727 Sensitive Melting Analysis after Real Time- Methylation Specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection Lasse S. Kristensen, Thomas Mikeska, Michael Krypuy, and Alexander Dobrovic PMCID: PMC2367707 Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions Katleen De Preter, Roland Barriot, Frank Speleman, Jo Vandesompele, and Yves Moreau PMCID: PMC2367735 Generation of ρ0 cells utilizing a mitochondrially targeted restriction endonuclease and comparative analyses Alexandra Kukat, Christian Kukat, Jan Brocher, Ingo Schäfer, Georg Krohne, Ian A. Trounce, Gaetano Villani, and Peter Seibel PMCID: PMC2367725 Computational Biology Phylogenetic classification of short environmental DNA fragments Lutz Krause, Naryttza N. Diaz, Alexander Goesmann, Scott Kelley, Tim W. Nattkemper, Forest Rohwer, Robert A. Edwards, and Jens Stoye PMCID: PMC2367736 Accurate statistical model of comparison between multiple sequence alignments Ruslan I. Sadreyev and Nick V. Grishin PMCID: PMC2367703 Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites Jeremy Curuksu, Krystyna Zakrzewska, and Martin Zacharias PMCID: PMC2367702 Empirical comparison of ab initio repeat finding programs Surya Saha, Susan Bridges, Zenaida V. Magbanua, and Daniel G. Peterson PMCID: PMC2367713 PROMALS3D: a tool for multiple protein sequence and structure alignments Jimin Pei, Bong-Hyun Kim, and Nick V. Grishin PMCID: PMC2367709 PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction Arif Ozgun Harmanci, Gaurav Sharma, and David H. Mathews PMCID: PMC2367733 SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines Francesca Demichelis, Heidi Greulich, Jill A. Macoska, Rameen Beroukhim, William R. Sellers, Levi Garraway, and Mark A. Rubin PMCID: PMC2367734 Nucleic Acid Enzymes Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences Emmanuel Fajardo-Sanchez, François Stricher, Frédéric Pâques, Mark Isalan, and Luis Serrano PMCID: PMC2367722 Saccharomyces cerevisiae Mus81-Mms4 is a catalytic, DNA structure-selective endonuclease Kirk Tevebaugh Ehmsen and Wolf-Dietrich Heyer PMCID: PMC2367710 Single-molecule observations of topotecan-mediated TopIB activity at a unique DNA sequence Daniel A. Koster, Fabian Czerwinski, Ludovic Halby, Aurélien Crut, Pierre Vekhoff, Komaraiah Palle, Paola B. Arimondo, and Nynke H. Dekker PMCID: PMC2367732 Corrigendum The Molecule Pages Database Brian Saunders, Stephen Lyon, Matthew Day, Brenda Riley, Emily Chenette, and Shankar Subramaniam PMCID: PMC2367724 Corrects: Brian Saunders, et al. The Molecule Pages database. Nucleic Acids Res. 2008 January; 36(Database issue): D700–D706. |
