| | Survey and Summary Advances in mechanisms of genetic instability related to hereditary neurological diseases Robert D. Wells, Ruhee Dere, Micheal L. Hebert, Marek Napierala, and Leslie S. Son PMCID: PMC1174910 Articles A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes Aristotelis Tsirigos and Isidore Rigoutsos PMCID: PMC1174904 Characterization of a novel transcriptionally active domain in the transforming growth factor β-regulated Smad3 protein Vassiliki Prokova, Sofia Mavridou, Paraskevi Papakosta, and Dimitris Kardassis PMCID: PMC1169234 Localization of mitochondrial DNA base excision repair to an inner membrane-associated particulate fraction J. A. Stuart, S. Mayard, K. Hashiguchi, N. C. Souza-Pinto, and V. A. Bohr PMCID: PMC1174906 Stable transmission of targeted gene modification using single-stranded oligonucleotides with flanking LNAs Charlotte Andrieu-Soler, Mariana Casas, Anne-Marie Faussat, Christelle Gandolphe, Marc Doat, Denis Tempé, Carine Giovannangeli, Francine Behar-Cohen, and Jean-Paul Concordet PMCID: PMC1174897 DNA looping induced by a transcriptional enhancer in vivo Michael Petrascheck, Dominik Escher, Tokameh Mahmoudi, C. Peter Verrijzer, Walter Schaffner, and Alcide Barberis PMCID: PMC1174898 Heterologous gene expression using self-assembled supra-molecules with high affinity for HSP70 chaperone Ji-Young Ahn, Hyung Choi, Yang-Hoon Kim, Kyung-Yeon Han, Jin-Seung Park, Sung-Sik Han, and Jeewon Lee PMCID: PMC1174908 Regulation of expression by promoters versus internal ribosome entry site in the 5′-untranslated sequence of the human cyclin-dependent kinase inhibitor p27kip1 Zhaoqian Liu, Zizheng Dong, Baoguang Han, Youyun Yang, Yang Liu, and Jian-Ting Zhang PMCID: PMC1174905 A sequence sub-sampling algorithm increases the power to detect distant homologues Catrióna R. Johnston and Denis C. Shields PMCID: PMC1174907 Mammalian enzymes for preventing transcriptional errors caused by oxidative damage Toru Ishibashi, Hiroshi Hayakawa, Riyoko Ito, Masayuki Miyazawa, Yuriko Yamagata, and Mutsuo Sekiguchi PMCID: PMC1174896 Methyl methanesulfonate (MMS) produces heat-labile DNA damage but no detectable in vivo DNA double-strand breaks Cecilia Lundin, Matthew North, Klaus Erixon, Kevin Walters, Dag Jenssen, Alastair S. H. Goldman, and Thomas Helleday PMCID: PMC1174933 Contrahelicase activity of the mitochondrial transcription termination factor mtDBP Paola Loguercio Polosa, Stefania Deceglie, Marina Roberti, Maria Nicola Gadaleta, and Palmiro Cantatore PMCID: PMC1174909 A highly distinctive mechanical property found in the majority of human promoters and its transcriptional relevance Yoshiro Fukue, Noriyuki Sumida, Jun-ichi Tanase, and Takashi Ohyama PMCID: PMC1175459 Investigation of the DNA-dependent cyclohexenyl nucleic acid polymerization and the cyclohexenyl nucleic acid-dependent DNA polymerization Veerle Kempeneers, Marleen Renders, Matheus Froeyen, and Piet Herdewijn PMCID: PMC1175020 Inhibition of O6-methylguanine-DNA methyltransferase by an alkyltransferase-like protein from Escherichia coli Steven J. Pearson, Jennifer Ferguson, Mauro Santibanez-Koref, and Geoffrey P. Margison PMCID: PMC1175458 NFAT5 binds to the TNF promoter distinctly from NFATp, c, 3 and 4, and activates TNF transcription during hypertonic stress alone Jonathan H. Esensten, Alla V. Tsytsykova, Cristina Lopez-Rodriguez, Filipa A. Ligeiro, Anjana Rao, and Anne E. Goldfeld PMCID: PMC1175021 Identification and characterization of the mouse nuclear export factor (Nxf) family members Wei Tan, Andrei S. Zolotukhin, Irina Tretyakova, Jenifer Bear, Susan Lindtner, Sergey V. Smulevitch, and Barbara K. Felber PMCID: PMC1175460 HnRNP H inhibits nuclear export of mRNA containing expanded CUG repeats and a distal branch point sequence Dong-Ho Kim, Marc-Andre Langlois, Kwang-Back Lee, Arthur D. Riggs, Jack Puymirat, and John J. Rossi PMCID: PMC1176012 Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members Lakshminarayan M. Iyer, Eugene V. Koonin, Detlef D. Leipe, and L. Aravind PMCID: PMC1176014 Exonization of AluYa5 in the human ACE gene requires mutations in both 3′ and 5′ splice sites and is facilitated by a conserved splicing enhancer Haixin Lei, Ian N. M. Day, and Igor Vořechovský PMCID: PMC1175817 A-tract clusters may facilitate DNA packaging in bacterial nucleoid Michael Y. Tolstorukov, Konstantin M. Virnik, Sankar Adhya, and Victor B. Zhurkin PMCID: PMC1176013 Kinetics of substrate recognition and cleavage by human 8-oxoguanine-DNA glycosylase Nikita A. Kuznetsov, Vladimir V. Koval, Dmitry O. Zharkov, Georgy A. Nevinsky, Kenneth T. Douglas, and Olga S. Fedorova PMCID: PMC1176011 The Bloom's syndrome helicase promotes the annealing of complementary single-stranded DNA Chit Fang Cheok, Leonard Wu, Patrick L. Garcia, Pavel Janscak, and Ian D. Hickson PMCID: PMC1176015 Bacillus subtilis RecU Holliday-junction resolvase modulates RecA activities Begoña Carrasco, Silvia Ayora, Rudi Lurz, and Juan C. Alonso PMCID: PMC1176016 Methods Online Improved microarray methods for profiling the yeast knockout strain collection Daniel S. Yuan, Xuewen Pan, Siew Loon Ooi, Brian D. Peyser, Forrest A. Spencer, Rafael A. Irizarry, and Jef D. Boeke PMCID: PMC1169235 A gene truncation strategy generating N- and C-terminal deletion variants of proteins for functional studies: mapping of the Sec1p binding domain in yeast Mso1p by a Mu in vitro transposition-based approach Eini Poussu, Jussi Jäntti, and Harri Savilahti PMCID: PMC1174911 A universal BMV-based RNA recombination system—how to search for general rules in RNA recombination Magdalena Alejska, Magdalena Figlerowicz, Nelli Malinowska, Anna Urbanowicz, and Marek Figlerowicz PMCID: PMC1174899 DNA microarrays on nanoscale-controlled surface Bong Jin Hong, Vijaya Sunkara, and Joon Won Park PMCID: PMC1174902 A novel mammalian expression system derived from components coordinating nicotine degradation in arthrobacter nicotinovorans pAO1 Laetitia Malphettes, Cornelia C. Weber, Marie Daoud El-Baba, Ronald G. Schoenmakers, Dominique Aubel, Wilfried Weber, and Martin Fussenegger PMCID: PMC1174900 A novel method of screening thrombin-inhibiting DNA aptamers using an evolution-mimicking algorithm Kazunori Ikebukuro, Yuji Okumura, Koichi Sumikura, and Isao Karube PMCID: PMC1174901 A novel high-throughput (HTP) cloning strategy for site-directed designed chimeragenesis and mutation using the Gateway cloning system Yasuhiro Suzuki, Naoko Kagawa, Toru Fujino, Tsuyoshi Sumiya, Taichi Andoh, Kumiko Ishikawa, Rie Kimura, Kiyokazu Kemmochi, Tsutomu Ohta, and Shigeo Tanaka PMCID: PMC1174934 Corrigendum Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation Jiang Qian, Noriko Esumi, Yangjian Chen, Qingliang Wang, Itay Chowers, and Donald J. Zack PMCID: PMC1176017 Corrects: Jiang Qian, et al. Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation. Nucleic Acids Res. 2005; 33(11): 3479–3491. |
