| | Molecular Biology Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli Beata Kosmider and Robert D. Wells PMCID: PMC1636463 Systematic characterization of 2′-deoxynucleoside- 5′-triphosphate analogs as substrates for DNA polymerases by polymerase chain reaction and kinetic studies on enzymatic production of modified DNA Masayasu Kuwahara, Jun-ichi Nagashima, Masatoshi Hasegawa, Takehiro Tamura, Rina Kitagata, Kazuo Hanawa, Shin-ichi Hososhima, Toshiyuki Kasamatsu, Hiroaki Ozaki, and Hiroaki Sawai PMCID: PMC1636466 In vivo DNase I sensitivity of the Streptomyces coelicolor chromosome correlates with gene expression: implications for bacterial chromosome structure Michael McArthur and Mervyn Bibb PMCID: PMC1636467 SIR2 modifies histone H4-K16 acetylation and affects superhelicity in the ARS region of plasmid chromatin in Saccharomyces cerevisiae Francesco Chiani, Francesca Di Felice, and Giorgio Camilloni PMCID: PMC1636471 Non-random, individual-specific methylation profiles are present at the sixth CTCF binding site in the human H19/IGF2 imprinting control region Jörg Tost, Hélène Jammes, Jean-Michel Dupont, Christophe Buffat, Brigitte Robert, Thérèse-Marie Mignot, Françoise Mondon, Bruno Carbonne, Umberto Siméoni, Gilles Grangé, Antoine Kerjean, Françoise Ferré, Ivo Glynne Gut, and Daniel Vaiman PMCID: PMC1636469 The Arabidopsis SUVR4 protein is a nucleolar histone methyltransferase with preference for monomethylated H3K9 Tage Thorstensen, Andreas Fischer, Silje V. Sandvik, Sylvia S. Johnsen, Paul E. Grini, Gunter Reuter, and Reidunn B. Aalen PMCID: PMC1636477 Identification of multiple transcription initiation, polyadenylation, and splice sites in the Drosophila melanogaster TART family of telomeric retrotransposons Patrick H. Maxwell, John M. Belote, and Robert W. Levis PMCID: PMC1636488 Multiple signaling pathways regulate the transcriptional activity of the orphan nuclear receptor NURR1 Paola Sacchetti, Rodolphe Carpentier, Pascaline Ségard, Cécile Olivé-Cren, and Philippe Lefebvre PMCID: PMC1636490 Different modes and potencies of translational repression by sequence-specific RNA–protein interaction at the 5′-UTR Minghua Nie and Han Htun PMCID: PMC1635260 PIAS3 induction of PRB sumoylation represses PRB transactivation by destabilizing its retention in the nucleus Jiang-Hong Man, Hui-Yan Li, Pei-Jing Zhang, Tao Zhou, Kun He, Xin Pan, Bing Liang, Ai-Ling Li, Jie Zhao, Wei-Li Gong, Bao-Feng Jin, Qing Xia, Ming Yu, Bei-Fen Shen, and Xue-Min Zhang PMCID: PMC1635300 The Saccharomyces cerevisiae RNA polymerase III recruitment factor subunits Brf1 and Bdp1 impose a strict sequence preference for the downstream half of the TATA box Nick D. Tsihlis and Anne Grove PMCID: PMC1636458 Expression of C-terminal deleted p53 isoforms in neuroblastoma David Goldschneider, Emilie Horvilleur, Louis-François Plassa, Marine Guillaud-Bataille, Karine Million, Evelyne Wittmer-Dupret, Gisèle Danglot, Hughes de Thé, Jean Bénard, Evelyne May, and Sétha Douc-Rasy PMCID: PMC1636465 Specific binding of a hexanucleotide to HIV-1 reverse transcriptase: a novel class of bioactive molecules Alessandra Mescalchin, Winfried Wünsche, Sandra D. Laufer, Dina Grohmann, Tobias Restle, and Georg Sczakiel PMCID: PMC1635251 RNA Molecular dynamics simulations of human  : the role of modified bases in mRNA recognition Nina E. McCrate, Mychel E. Varner, Kenneth I. Kim, and Maria C. Nagan PMCID: PMC1636460 Controlling bacteriophage phi29 DNA-packaging motor by addition or discharge of a peptide at N-terminus of connector protein that interacts with pRNA Jianhe Sun, Ying Cai, Wulf-Dieter Moll, and Peixuan Guo PMCID: PMC1636484 Effects of the trinucleotide preceding the self-cleavage site on eggplant latent viroid hammerheads: differences in co- and post-transcriptional self-cleavage may explain the lack of trinucleotide AUC in most natural hammerheads Alberto Carbonell, Marcos De la Peña, Ricardo Flores, and Selma Gago PMCID: PMC1636495 Codeine-binding RNA aptamers and rapid determination of their binding constants using a direct coupling surface plasmon resonance assay Maung Nyan Win, Joshua S. Klein, and Christina D. Smolke PMCID: PMC1636496 The majority of Escherichia coli mRNAs undergo post-transcriptional modification in exponentially growing cells Bijoy K. Mohanty and Sidney R. Kushner PMCID: PMC1636475 β-Catenin stabilizes Cyclooxygenase-2 mRNA by interacting with AU-rich elements of 3′-UTR Hee Kyu Lee and Sunjoo Jeong PMCID: PMC1636482 Structural Biology Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus Sherwin P. Montaño, Marie L. Coté, Monica J. Roth, and Millie M. Georgiadis PMCID: PMC1636480 Collision events between RNA polymerases in convergent transcription studied by atomic force microscopy Neal Crampton, William A. Bonass, Jennifer Kirkham, Claudio Rivetti, and Neil H. Thomson PMCID: PMC1636470 Structural analysis of aligned RNAs Björn Voß PMCID: PMC1636479 RusA Holliday junction resolvase: DNA complex structure—insights into selectivity and specificity Rachel Macmaster, Svetlana Sedelnikova, Patrick J. Baker, Edward L. Bolt, Robert G. Lloyd, and John B. Rafferty PMCID: PMC1636454 Different loop arrangements of intramolecular human telomeric (3+1) G-quadruplexes in K+ solution Anh Tuân Phan, Kim Ngoc Luu, and Dinshaw J. Patel PMCID: PMC1635308 Survey and Summary Quadruplex DNA: sequence, topology and structure Sarah Burge, Gary N. Parkinson, Pascale Hazel, Alan K. Todd, and Stephen Neidle PMCID: PMC1636468 Alu elements as regulators of gene expression Julien Häsler and Katharina Strub PMCID: PMC1636486 Human sat III and Drosophila hsrω transcripts: a common paradigm for regulation of nuclear RNA processing in stressed cells Caroline Jolly and Subhash C. Lakhotia PMCID: PMC1636489 Chemistry Quantitative analysis of the oxidative DNA lesion, 2,2-diamino-4-(2-deoxy-β-d-erythro-pentofuranosyl)amino]-5(2H)-oxazolone (oxazolone), in vitro and in vivo by isotope dilution-capillary HPLC-ESI-MS/MS Brock Matter, Danuta Malejka-Giganti, A. Saari Csallany, and Natalia Tretyakova PMCID: PMC1636462 Methods Online Robust analysis of 5′-transcript ends (5′-RATE): a novel technique for transcriptome analysis and genome annotation Malali Gowda, Haumeng Li, Joe Alessi, Feng Chen, Richard Pratt, and Guo-Liang Wang PMCID: PMC1636456 In vitro evolution of single-chain antibodies using mRNA display Isao Fukuda, Kanehisa Kojoh, Noriko Tabata, Nobuhide Doi, Hideaki Takashima, Etsuko Miyamoto-Sato, and Hiroshi Yanagawa PMCID: PMC1636464 A novel endonuclease IV post-PCR genotyping system Igor V. Kutyavin, Dave Milesi, Yevgeniy Belousov, Mikhail Podyminogin, Alexei Vorobiev, Vladimir Gorn, Eugeny A. Lukhtanov, Nicolaas M. J. Vermeulen, and Walt Mahoney PMCID: PMC1636472 Using DNA pools for genotyping trios Kenneth B. Beckman, Kenneth J. Abel, Andreas Braun, and Eran Halperin PMCID: PMC1636483 Analysis of protein sequence and interaction data for candidate disease gene prediction Richard A. George, Jason Y. Liu, Lina L. Feng, Robert J. Bryson-Richardson, Diane Fatkin, and Merridee A. Wouters PMCID: PMC1636487 Assessing incomplete deprotection of microarray oligonucleotides in situ Holly K. Dressman, Lise Barley-Maloney, Laura-Leigh Rowlette, Paul F. Agris, and Mariano A. Garcia-Blanco PMCID: PMC1636491 Antibody binding loop insertions as diversity elements Csaba Kiss, Hugh Fisher, Emanuele Pesavento, Minghua Dai, Rosa Valero, Milan Ovecka, Rhiannon Nolan, M. Lisa Phipps, Nileena Velappan, Leslie Chasteen, Jennifer S. Martinez, Geoffrey S. Waldo, Peter Pavlik, and Andrew R.M. Bradbury PMCID: PMC1635297 DeepSAGE—digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples Kåre L. Nielsen, Annabeth Laursen Høgh, and Jeppe Emmersen PMCID: PMC1636492 A high throughput method for genome-wide analysis of retroviral integration Julie Mantovani, Nathalie Holic, Kelly Martinez, Olivier Danos, and Javier Perea PMCID: PMC1636494 Troubleshooting coupled in vitro transcription–translation system derived from Escherichia coli cells: synthesis of high-yield fully active proteins Madina B. Iskakova, Witold Szaflarski, Marc Dreyfus, Jaanus Remme, and Knud H. Nierhaus PMCID: PMC1636455 Computational Biology MetaGene: prokaryotic gene finding from environmental genome shotgun sequences Hideki Noguchi, Jungho Park, and Toshihisa Takagi PMCID: PMC1636498 Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials Nils B. Becker, Lars Wolff, and Ralf Everaers PMCID: PMC1636474 Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation Yu Shao, Yan Wu, Chi Yu Chan, Kathleen McDonough, and Ye Ding PMCID: PMC1636493 Nucleic Acid Enzymes Purification of the yeast Slx5–Slx8 protein complex and characterization of its DNA-binding activity Litao Yang, Janet R. Mullen, and Steven J. Brill PMCID: PMC1635298 Glutamate racemase from Mycobacterium tuberculosis inhibits DNA gyrase by affecting its DNA-binding Sugopa Sengupta, Meera Shah, and Valakunja Nagaraja PMCID: PMC1635304 Functional characterization of a 48 kDa Trypanosoma brucei cap 2 RNA methyltransferase Megan P. Hall and C. Kiong Ho PMCID: PMC1636459 The key DNA-binding residues in the C-terminal domain of Mycobacterium tuberculosis DNA gyrase A subunit (GyrA) You-Yi Huang, Jiao-Yu Deng, Jing Gu, Zhi-Ping Zhang, Anthony Maxwell, Li-Jun Bi, Yuan-Yuan Chen, Ya-Feng Zhou, Zi-Niu Yu, and Xian-En Zhang PMCID: PMC1636481 Evolutionarily conserved and non-conserved retrovirus restriction activities of artiodactyl APOBEC3F proteins Stefán R. Jónsson, Guylaine Haché, Mark D. Stenglein, Scott C. Fahrenkrug, Valgerdur Andrésdóttir, and Reuben S. Harris PMCID: PMC1636497 |
