| | Articles A critical role for the Sp1-binding sites in the transforming growth factor-β-mediated inhibition of lipoprotein lipase gene expression in macrophages Scott A. Irvine, Pelagia Foka, Sarah A. Rogers, James R. Mead, and Dipak P. Ramji PMCID: PMC1062872 Regulated chromatin domain comprising cluster of co-expressed genes in Drosophila melanogaster Alla I. Kalmykova, Dmitry I. Nurminsky, Dmirty V. Ryzhov, and Yuri Y. Shevelyov PMCID: PMC1062873 NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence Thomas A. Down and Tim J. P. Hubbard PMCID: PMC1064142 Expression of complementary RNA from chloroplast transgenes affects editing efficiency of transgene and endogenous chloroplast transcripts Carla E. Hegeman, Christine P. Halter, Thomas G. Owens, and Maureen R. Hanson PMCID: PMC1062874 Conformational flexibility revealed by the crystal structure of a crenarchaeal RadA Antonio Ariza, Derek J. Richard, Malcolm F. White, and Charles S. Bond PMCID: PMC1062875 Translation of the F protein of hepatitis C virus is initiated at a non-AUG codon in a +1 reading frame relative to the polyprotein Martin Baril and Léa Brakier-Gingras PMCID: PMC1062877 Characterizing the function and structural organization of the 5′ tRNA-like motif within the hepatitis C virus quasispecies Maria Piron, Nerea Beguiristain, Anna Nadal, Encarnación Martínez-Salas, and Jordi Gómez PMCID: PMC1062876 Developmentally regulated instability of the GPI-PLC mRNA is dependent on a short-lived protein factor Helena Webb, Roisin Burns, Louise Ellis, Nicola Kimblin, and Mark Carrington PMCID: PMC1062878 Identification of the ‘NORE’ (N-Oct-3 responsive element), a novel structural motif and composite element Robert Alazard, Magali Blaud, Shmouel Elbaz, Christine Vossen, Guillaume Icre, Gérard Joseph, Laurence Nieto, and Monique Erard PMCID: PMC1065252 Dimeric configuration of SeqA protein bound to a pair of hemi-methylated GATC sequences Sukhyun Kang, Joo Seok Han, Keun Pill Kim, Hye Yoon Yang, Kyung Yong Lee, Choo Bong Hong, and Deog Su Hwang PMCID: PMC1065253 Hybridization properties and enzymatic replication of oligonucleotides containing the photocleavable 7-nitroindole base analog Caroline Crey-Desbiolles, Nathalie Berthet, Mitsuharu Kotera, and Pascal Dumy PMCID: PMC1065254 Integration of text- and data-mining using ontologies successfully selects disease gene candidates Nicki Tiffin, Janet F. Kelso, Alan R. Powell, Hong Pan, Vladimir B. Bajic, and Winston A. Hide PMCID: PMC1065256 Characterization of the frameshift signal of Edr, a mammalian example of programmed −1 ribosomal frameshifting Emily Manktelow, Kazuhiro Shigemoto, and Ian Brierley PMCID: PMC1065257 The post-transcriptional gene silencing machinery functions independently of DNA methylation to repress a LINE1-like retrotransposon in Neurospora crassa Tony Nolan, Laura Braccini, Gianluca Azzalin, Arianna De Toni, Giuseppe Macino, and Carlo Cogoni PMCID: PMC1065258 Gene conversion and deletion frequencies during double-strand break repair in human cells are controlled by the distance between direct repeats Ezra Schildkraut, Cheryl A. Miller, and Jac A. Nickoloff PMCID: PMC1065255 Differential role of RB in response to UV and IR damage Emily E. Bosco and Erik S. Knudsen PMCID: PMC1065251 Generation of 5-(2′-deoxycytidyl)methyl radical and the formation of intrastrand cross-link lesions in oligodeoxyribonucleotides Qibin Zhang and Yinsheng Wang PMCID: PMC1065259 Structural roles of CTG repeats in slippage expansion during DNA replication Lai Man Chi and Sik Lok Lam PMCID: PMC1065260 Chemical engineering of the peptidyl transferase center reveals an important role of the 2′-hydroxyl group of A2451 Matthias D. Erlacher, Kathrin Lang, Nisha Shankaran, Brigitte Wotzel, Alexander Hüttenhofer, Ronald Micura, Alexander S. Mankin, and Norbert Polacek PMCID: PMC1065261 Two modes of microsatellite instability in human cancer: differential connection of defective DNA mismatch repair to dinucleotide repeat instability Shinya Oda, Yoshihiko Maehara, Yoichi Ikeda, Eiji Oki, Akinori Egashira, Yoshikazu Okamura, Ikuo Takahashi, Yoshihiro Kakeji, Yasushi Sumiyoshi, Kaname Miyashita, Yu Yamada, Yan Zhao, Hiroyoshi Hattori, Ken-ichi Taguchi, Tatsuro Ikeuchi, Teruhisa Tsuzuki, Mutsuo Sekiguchi, Peter Karran, and Mitsuaki A. Yoshida PMCID: PMC1067522 The effect of the 2-amino group of 7,8-dihydro-8-oxo-2′-deoxyguanosine on translesion synthesis and duplex stability Natsuhisa Oka and Marc M. Greenberg PMCID: PMC1067523 Conversion of DNA methyltransferases into azidonucleosidyl transferases via synthetic cofactors Lindsay R. Comstock and Scott R. Rajski PMCID: PMC1067524 Modification at position 9 with 1-methyladenosine is crucial for structure and function of nematode mitochondrial tRNAs lacking the entire T-arm Masayuki Sakurai, Takashi Ohtsuki, and Kimitsuna Watanabe PMCID: PMC1069008 Single-stranded DNA-binding protein of Deinococcus radiodurans: a biophysical characterization Gregor Witte, Claus Urbanke, and Ute Curth PMCID: PMC1069009 A systematic analysis of the silencing effects of an active siRNA at all single-nucleotide mismatched target sites Quan Du, Håkan Thonberg, Jue Wang, Claes Wahlestedt, and Zicai Liang PMCID: PMC1069010 Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB Taras Afonyushkin, Branislav Večerek, Isabella Moll, Udo Bläsi, and Vladimir R. Kaberdin PMCID: PMC1069011 The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen Cheng-Hsun Chiu, Petrus Tang, Chishih Chu, Songnian Hu, Qiyu Bao, Jun Yu, Yun-Ying Chou, Hsin-Shih Wang, and Ying-Shiung Lee PMCID: PMC1069006 Formation of linear inverted repeat amplicons following targeting of an essential gene in Leishmania Paul-André Genest, Bas ter Riet, Carole Dumas, Barbara Papadopoulou, Henri G. A. M. van Luenen, and Piet Borst PMCID: PMC1069007 Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms Suganthi Balasubramanian, Yu Xia, Elizaveta Freinkman, and Mark Gerstein PMCID: PMC1069129 Transcriptional regulation of two stage-specifically expressed genes in the protozoan parasite Toxoplasma gondii Michael K. Kibe, Alexandra Coppin, Najoua Dendouga, Gabrielle Oria, Edwige Meurice, Marlène Mortuaire, Edwige Madec, and Stanislas Tomavo PMCID: PMC1903550 Methods Online Methylation profiles of genes utilizing newly developed CpG island methylation microarray on colorectal cancer patients Naoki Kimura, Takeshi Nagasaka, Jun Murakami, Hiromi Sasamoto, Masahiro Murakami, Noriaki Tanaka, and Nagahide Matsubara PMCID: PMC1064143 A microarray configuration to quantify expression levels and relative abundance of splice variants Pascale Fehlbaum, Caroline Guihal, Laurent Bracco, and Olivier Cochet PMCID: PMC1064144 Competitive enzymatic reaction to control allele-specific extensions Emilie Hultin, Max Käller, Afshin Ahmadian, and Joakim Lundeberg PMCID: PMC1065263 A dual-fluorescence reporter system for high-throughput clone characterization and selection by cell sorting Juno Choe, Haiwei H. Guo, and Ger van den Engh PMCID: PMC1065264 Genome physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis: a robust physical map of Penicillium chrysogenum Zhanyou Xu, Marco A. van den Berg, Chantel Scheuring, Lina Covaleda, Hong Lu, Felipe A. Santos, Taesik Uhm, Mi-Kyung Lee, Chengcang Wu, Steve Liu, and Hong-Bin Zhang PMCID: PMC1065262 Conditional and inducible transgene expression in mice through the combinatorial use of Cre-mediated recombination and tetracycline induction Gusztav Belteki, Jody Haigh, Nikolett Kabacs, Katharina Haigh, Karen Sison, Frank Costantini, Jeff Whitsett, Susan E. Quaggin, and Andras Nagy PMCID: PMC1069131 Simple and straightforward construction of a mouse gene targeting vector using in vitro transposition reactions Minako Aoyama, Kazuko Agari, Ge-Hong Sun-Wada, Masamitsu Futai, and Yoh Wada PMCID: PMC1069132 Corrigenda siRNAdb: a database of siRNA sequences Alistair M. Chalk, Richard E. Warfinge, Patrick Georgii-Hemming, and Erik L. L. Sonnhammer PMCID: PMC1069128 Corrects: Alistair M. Chalk, et al. siRNAdb: a database of siRNA sequences. Nucleic Acids Res. 2005 January 1; 33(Database Issue): D131–D134. Cadmium inhibits mismatch repair by blocking the ATPase activity of the MSH2–MSH6 complex Sreeparna Banerjee and Hernan Flores-Rozas PMCID: PMC1069130 Corrects: Sreeparna Banerjee, et al. Cadmium inhibits mismatch repair by blocking the ATPase activity of the MSH2–MSH6 complex. Nucleic Acids Res. 2005; 33(4): 1410–1419. Erratum Human pol II promoter prediction: time series descriptors and machine learning Rajeev Gangal and Pankaj Sharma PMCID: PMC1069632 Corrects: Rajeev Gangal, et al. Human pol II promoter prediction: time series descriptors and machine learning. Nucleic Acids Res. 2005; 33(4): 1332–1336. |
