| | Survey and Summary A second look at cellular mRNA sequences said to function as internal ribosome entry sites Marilyn Kozak PMCID: PMC1298923 Articles Role of the Bombyx mori R2 element N-terminal domain in the target-primed reverse transcription (TPRT) reaction Shawn M. Christensen, Arkadiusz Bibillo, and Thomas H. Eickbush PMCID: PMC1283540 Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination Takao Kasuga, Jeffrey P. Townsend, Chaoguang Tian, Luz B. Gilbert, Gertrud Mannhaupt, John W. Taylor, and N. Louise Glass PMCID: PMC1283539 Kernel-based machine learning protocol for predicting DNA-binding proteins Nitin Bhardwaj, Robert E. Langlois, Guijun Zhao, and Hui Lu PMCID: PMC1283538 Gene identification in novel eukaryotic genomes by self-training algorithm Alexandre Lomsadze, Vardges Ter-Hovhannisyan, Yury O. Chernoff, and Mark Borodovsky PMCID: PMC1298918 The K-loop, a general feature of the Pyrococcus C/D guide RNAs, is an RNA structural motif related to the K-turn Sophie Nolivos, Agamemnon J. Carpousis, and Béatrice Clouet-d'Orval PMCID: PMC1289080 Synthesis of novel poly(dG)–poly(dG)–poly(dC) triplex structure by Klenow exo− fragment of DNA polymerase I Alexander Kotlyar, Natalia Borovok, Tatiana Molotsky, Dmitry Klinov, Benjamin Dwir, and Eli Kapon PMCID: PMC1292991 The excess of 5′ introns in eukaryotic genomes Kui Lin and Da-Yong Zhang PMCID: PMC1292992 Activation of Sp1-mediated transcription by Rta of Epstein–Barr virus via an interaction with MCAF1 Li-Kwan Chang, Jian-Ying Chung, Yi-Ren Hong, Takaya Ichimura, Mitsuyoshi Nakao, and Shih-Tung Liu PMCID: PMC1298921 StpA protein from Escherichia coli condenses supercoiled DNA in preference to linear DNA and protects it from digestion by DNase I and EcoKI S. A. Keatch, P. G. Leonard, J. E. Ladbury, and D. T. F. Dryden PMCID: PMC1289078 Chimeric peptide nucleic acid compounds modulate splicing of the bcl-x gene in vitro and in vivo Jeremy E. Wilusz, Sean C. Devanney, and Massimo Caputi PMCID: PMC1289079 Human Bex2 interacts with LMO2 and regulates the transcriptional activity of a novel DNA-binding complex Chunyu Han, Hao Liu, Jin Liu, Kang Yin, Yi Xie, Xiao Shen, Yong Wang, Jiangang Yuan, Boqing Qiang, Yong-Jian Liu, and Xiaozhong Peng PMCID: PMC1298925 SIP1/ZEB2 induces EMT by repressing genes of different epithelial cell–cell junctions Cindy Vandewalle, Joke Comijn, Bram De Craene, Petra Vermassen, Erik Bruyneel, Henriette Andersen, Eugene Tulchinsky, Frans Van Roy, and Geert Berx PMCID: PMC1298926 The PSEA promoter element of the Drosophila U1 snRNA gene is sufficient to bring DmSNAPc into contact with 20 base pairs of downstream DNA Hsien-Tsung Lai, Hsiang Chen, Cheng Li, Kathleen J. McNamara-Schroeder, and William E. Stumph PMCID: PMC1292993 A thermodynamic model of transcriptome formation Tomokazu Konishi PMCID: PMC1298927 Structure-specific binding of MeCP2 to four-way junction DNA through its methyl CpG-binding domain Teca Calcagno Galvão and Jean O. Thomas PMCID: PMC1298929 Minimal pre-mRNA substrates with natural and converted sites for full-round U insertion and U deletion RNA editing in trypanosomes Catherine Cifuentes-Rojas, Kari Halbig, Anastasia Sacharidou, Monica De Nova-Ocampo, and Jorge Cruz-Reyes PMCID: PMC1298919 Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation Levent Sari and Ioan Andricioaei PMCID: PMC1298917 A haploid-specific transcriptional response to irradiation in Saccharomyces cerevisiae G. Mercier, N. Berthault, N. Touleimat, F. Képès, G. Fourel, E. Gilson, and M. Dutreix PMCID: PMC1298924 AP endonuclease deficiency results in extreme sensitivity to thymidine deprivation Ken Dornfeld and Monika Johnson PMCID: PMC1298931 A retrocopy of a gene can functionally displace the source gene in evolution Aleksey N. Krasnov, Maria M. Kurshakova, Vasily E. Ramensky, Pavel V. Mardanov, Elena N. Nabirochkina, and Sofia G. Georgieva PMCID: PMC1298928 DNA end-directed and processive nuclease activities of the archaeal XPF enzyme Jennifer A. Roberts and Malcolm F. White PMCID: PMC1298930 Methods Online Towards systematic identification of Plasmodium essential genes by transposon shuttle mutagenesis Hiroshi Sakamoto, Sabine Thiberge, Susan Akerman, Chris J. Janse, Teresa Gil Carvalho, and Robert Ménard PMCID: PMC1283541 Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data Manhong Dai, Pinglang Wang, Andrew D. Boyd, Georgi Kostov, Brian Athey, Edward G. Jones, William E. Bunney, Richard M. Myers, Terry P. Speed, Huda Akil, Stanley J. Watson, and Fan Meng PMCID: PMC1283542 Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level Mehrnaz Fatemi, Martha M. Pao, Shinwu Jeong, Einav Nili Gal-Yam, Gerda Egger, Daniel J. Weisenberger, and Peter A. Jones PMCID: PMC1292996 Bis-aptazyme sensors for hepatitis C virus replicase and helicase without blank signal Suhyung Cho, Ji-Eun Kim, Bo-Rahm Lee, June-Hyung Kim, and Byung-Gee Kim PMCID: PMC1292994 In vivo selection of engineered homing endonucleases using double-strand break induced homologous recombination Patrick Chames, Jean-Charles Epinat, Sophie Guillier, Amélie Patin, Emmanuel Lacroix, and Frédéric Pâques PMCID: PMC1289081 Real-time quantification of microRNAs by stem–loop RT–PCR Caifu Chen, Dana A. Ridzon, Adam J. Broomer, Zhaohui Zhou, Danny H. Lee, Julie T. Nguyen, Maura Barbisin, Nan Lan Xu, Vikram R. Mahuvakar, Mark R. Andersen, Kai Qin Lao, Kenneth J. Livak, and Karl J. Guegler PMCID: PMC1292995 Multiplexed tandem PCR: gene profiling from small amounts of RNA using SYBR Green detection Keith K. Stanley and Elektra Szewczuk PMCID: PMC1298933 PCR inhibition by reverse transcriptase leads to an overestimation of amplification efficiency Oleg Suslov and Dennis A. Steindler PMCID: PMC1298932 Erratum Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids PMCID: PMC1298920 Corrects: Rob Knight, et al. Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids. Nucleic Acids Res. 2005; 33(18): 5924–5935. |
