| | Survey and Summary BRCA1: cell cycle checkpoint, genetic instability, DNA damage response and cancer evolution Chu-Xia Deng PMCID: PMC1390683 Articles Inhibitory effects of archetypical nucleic acid ligands on the interactions of HIV-1 nucleocapsid protein with elements of Ψ-RNA Kevin B. Turner, Nathan A. Hagan, and Daniele Fabris PMCID: PMC1390681 Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods Ewy Mathe, Magali Olivier, Shunsuke Kato, Chikashi Ishioka, Pierre Hainaut, and Sean V. Tavtigian PMCID: PMC1390679 Structural and evolutionary classification of G/U wobble basepairs in the ribosome Ali Mokdad, Maryna V. Krasovska, Jiri Sponer, and Neocles B. Leontis PMCID: PMC1390688 An isoform of ZBP-89 predisposes the colon to colitis David J. Law, Edwin M. Labut, Rachael D. Adams, and Juanita L. Merchant PMCID: PMC1390687 The proteasomal ATPase complex is required for stress-induced transcription in yeast Rita Sulahian, Stephen Albert Johnston, and Thomas Kodadek PMCID: PMC1390684 Repression of mutagenesis by Rad51D-mediated homologous recombination John M. Hinz, Robert S. Tebbs, Paul F. Wilson, Peter B. Nham, Edmund P. Salazar, Hatsumi Nagasawa, Salustra S. Urbin, Joel S. Bedford, and Larry H. Thompson PMCID: PMC1390685 In situ fluorescence analysis demonstrates active siRNA exclusion from the nucleus by Exportin 5 Thomas Ohrt, Dennis Merkle, Karin Birkenfeld, Christophe J. Echeverri, and Petra Schwille PMCID: PMC1390680 Controlling RNA self-assembly to form filaments Lorena Nasalean, Stéphanie Baudrey, Neocles B. Leontis, and Luc Jaeger PMCID: PMC1390682 The human Pif1 helicase, a potential Escherichia coli RecD homologue, inhibits telomerase activity Deng-Hong Zhang, Bo Zhou, Yu Huang, Lu-Xia Xu, and Jin-Qiu Zhou PMCID: PMC1390689 Human replication protein A can suppress the intrinsic in vitro mutator phenotype of human DNA polymerase λ Giovanni Maga, Igor Shevelev, Giuseppe Villani, Silvio Spadari, and Ulrich Hübscher PMCID: PMC1390690 Tpk3 and Snf1 protein kinases regulate Rgt1 association with Saccharomyces cerevisiae HXK2 promoter A. Palomino, P. Herrero, and F. Moreno PMCID: PMC1401511 Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family Paul Thaw, Svetlana E. Sedelnikova, Tatyana Muranova, Sebastian Wiese, Sylvia Ayora, Juan C. Alonso, Arie B. Brinkman, Jasper Akerboom, John van der Oost, and John B. Rafferty PMCID: PMC1401507 Structures of ω repressors bound to direct and inverted DNA repeats explain modulation of transcription Wilhelm Andreas Weihofen, Aslan Cicek, Florencia Pratto, Juan Carlos Alonso, and Wolfram Saenger PMCID: PMC1401508 Histone deacetylase 3 binds to and regulates the GCMa transcription factor Hsiao-Ching Chuang, Ching-Wen Chang, Geen-Dong Chang, Tso-Pang Yao, and Hungwen Chen PMCID: PMC1401512 The Rhizobium etli σ70 (SigA) factor recognizes a lax consensus promoter Miguel A. Ramírez-Romero, Irina Masulis, Miguel A. Cevallos, Víctor González, and Guillermo Dávila PMCID: PMC1401509 Single nucleotide RNA choreography Chiaolong Hsiao, Srividya Mohan, Eli Hershkovitz, Allen Tannenbaum, and Loren Dean Williams PMCID: PMC1401506 En masse nascent transcription analysis to elucidate regulatory transcription factors Jinshui Fan, Ming Zhan, Jikui Shen, Jennifer L. Martindale, Xiaoling Yang, Tomoko Kawai, and Myriam Gorospe PMCID: PMC1408309 C5′- and C3′-sugar radicals produced via photo-excitation of one-electron oxidized adenine in 2′-deoxyadenosine and its derivatives Amitava Adhikary, David Becker, Sean Collins, Jessica Koppen, and Michael D. Sevilla PMCID: PMC1401510 LINE-1 RNA splicing and influences on mammalian gene expression Victoria P. Belancio, Dale J. Hedges, and Prescott Deininger PMCID: PMC1415225 Dual inhibitory effects of APOBEC family proteins on retrotransposition of mammalian endogenous retroviruses Cécile Esnault, Jean Millet, Olivier Schwartz, and Thierry Heidmann PMCID: PMC1401513 A new method for gene discovery in large-scale microarray data Kentaro Yano, Kazuhide Imai, Akifumi Shimizu, and Takao Hanashita PMCID: PMC1401514 Synthesis and characterization of oligonucleotides containing 2′-fluorinated thymidine glycol as inhibitors of the endonuclease III reaction Yusuke Doi, Atsushi Katafuchi, Yoshie Fujiwara, Kenichi Hitomi, John A. Tainer, Hiroshi Ide, and Shigenori Iwai PMCID: PMC1409675 Role of the tryptophan residue in the vicinity of the catalytic center of exonuclease III family AP endonucleases: AP site recognition mechanism Kohichi Kaneda, Junichi Sekiguchi, and Toshio Shida PMCID: PMC1408312 Excess of charged tRNALys maintains low levels of peptidyl-tRNA hydrolase in pth(Ts) mutants at a non-permissive temperature Serafin Vivanco-Domínguez, Luis Rogelio Cruz-Vera, and Gabriel Guarneros PMCID: PMC1408313 Spectral clustering of protein sequences Alberto Paccanaro, James A. Casbon, and Mansoor A. S. Saqi PMCID: PMC1409676 A modular DNA signal translator for the controlled release of a protein by an aptamer Stefan Beyer and Friedrich C. Simmel PMCID: PMC1409677 Bacterial single-stranded DNA-binding proteins are phosphorylated on tyrosine Ivan Mijakovic, Dina Petranovic, Boris Macek, Tina Cepo, Matthias Mann, Julian Davies, Peter R. Jensen, and Dusica Vujaklija PMCID: PMC1405823 mAMSA resistant human topoisomerase IIβ mutation G465D has reduced ATP hydrolysis activity Kathryn L. Gilroy, Chrysoula Leontiou, Kay Padget, Jeremy H. Lakey, and Caroline A. Austin PMCID: PMC1405819 Microarray missing data imputation based on a set theoretic framework and biological knowledge Xiangchao Gan, Alan Wee-Chung Liew, and Hong Yan PMCID: PMC1409680 Dimerization and opposite base-dependent catalytic impairment of polymorphic S326C OGG1 glycosylase Jeff W. Hill and Michele K. Evans PMCID: PMC1405821 Genome wide distribution of illegitimate recombination events in Kluyveromyces lactis Andreas Kegel, Paula Martinez, Sidney D. Carter, and Stefan U. Åström PMCID: PMC1405753 Systematic identification of microRNA functions by combining target prediction and expression profiling Xiaowei Wang and Xiaohui Wang PMCID: PMC1405822 A tripartite DNA-binding element, comprised of the nuclear localization signal and two AT-hook motifs, mediates the association of LEDGF/p75 with chromatin in vivo Fanny Turlure, Goedele Maertens, Shaila Rahman, Peter Cherepanov, and Alan Engelman PMCID: PMC1405818 Methods Online Homogeneous point mutation detection by quantum dot-mediated two-color fluorescence coincidence analysis Hsin-Chih Yeh, Yi-Ping Ho, Ie-Ming Shih, and Tza-Huei Wang PMCID: PMC1390686 Co-expression of anti-NFκB RNA aptamers and siRNAs leads to maximal suppression of NFκB activity in mammalian cells Robert Chan, Madaline Gilbert, Kristin M. Thompson, H. Nicholas Marsh, David M. Epstein, and P. Shannon Pendergrast PMCID: PMC1390692 Control of small inhibitory RNA levels and RNA interference by doxycycline induced activation of a minimal RNA polymerase III promoter Lahouari Amar, Mathieu Desclaux, Nicole Faucon-Biguet, Jacques Mallet, and Roland Vogel PMCID: PMC1390691 A novel normalization method for effective removal of systematic variation in microarray data Su-Wen Chua, Praveen Vijayakumar, Peter M. Nissom, Chew-Yeam Yam, Victor V.T. Wong, and He Yang PMCID: PMC1415275 Development and application of a positive–negative selectable marker system for use in reverse genetics in Plasmodium Joanna A. M. Braks, Blandine Franke-Fayard, Hans Kroeze, Chris J. Janse, and Andrew P. Waters PMCID: PMC1401515 Enhancement of the efficiency of non-viral gene delivery by application of pulsed magnetic field Sarah W. Kamau, Paul O. Hassa, Benedikt Steitz, Alke Petri-Fink, Heinrich Hofmann, Margarethe Hofmann-Amtenbrink, Brigitte von Rechenberg, and Michael O. Hottiger PMCID: PMC1408310 Fusoselect: cell–cell fusion activity engineered by directed evolution of a retroviral glycoprotein Christoph A. Merten, Jörn Stitz, Gundula Braun, Julia Medvedovska, Klaus Cichutek, and Christian J. Buchholz PMCID: PMC1408311 An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis Kazuki Kurimoto, Yukihiro Yabuta, Yasuhide Ohinata, Yukiko Ono, Kenichiro D. Uno, Rikuhiro G. Yamada, Hiroki R. Ueda, and Mitinori Saitou PMCID: PMC1409679 BENA435, a new cell-permeant photoactivated green fluorescent DNA probe Alexandra Erve, Yasmina Saoudi, Sylvie Thirot, Corinne Guetta-Landras, Jean-Claude Florent, Chi-Hung Nguyen, David S. Grierson, and Andrei V. Popov PMCID: PMC1409678 In vitro selection of tRNAs for efficient four-base decoding to incorporate non-natural amino acids into proteins in an Escherichia coli cell-free translation system Hikaru Taira, Takahiro Hohsaka, and Masahiko Sisido PMCID: PMC1405820 Corrigenda Polη, Polζ and Rev1 together are required for G to T transversion mutations induced by the (+)- and (−)-trans-anti-BPDE-N2-dG DNA adducts in yeast cells Bo Zhao, Jillian Wang, Nicholas E. Geacintov, and Zhigang Wang PMCID: PMC1520514 Corrects: Bo Zhao, et al. Polη, Polζ and Rev1 together are required for G to T transversion mutations induced by the (+)- and (−)-trans-anti-BPDE-N2-dG DNA adducts in yeast cells. Nucleic Acids Res. 2006; 34(2): 417–425. Mer1p is a modular splicing factor whose function depends on the conserved U2 snRNP protein Snu17p Marc Spingola, Javier Armisen, and Manuel Ares, Jr PMCID: PMC1520515 Corrects: Marc Spingola, et al. Mer1p is a modular splicing factor whose function depends on the conserved U2 snRNP protein Snu17p. Nucleic Acids Res. 2004; 32(3): 1242–1250. Diels-Alder cycloadditions in water for the straightforward preparation of peptide–oligonucleotide conjugates Vicente Marcha´n, Samuel Ortega, Daniel Pulido, Enrique Pedroso, and Anna Grandas PMCID: PMC1520516 Corrects: Vicente Marchán, et al. Diels-Alder cycloadditions in water for the straightforward preparation of peptide–oligonucleotide conjugates. Nucleic Acids Res. 2006; 34(3): e24. |
