| | Articles Biochemical characterisation of the clamp/clamp loader proteins from the euryarchaeon Archaeoglobus fulgidus Anja Seybert, David J. Scott, Sarah Scaife, Martin R. Singleton, and Dale B. Wigley PMCID: PMC137147 Comparative genomic analysis of equilibrative nucleoside transporters suggests conserved protein structure despite limited sequence identity Narendra Sankar, Jerry Machado, Parween Abdulla, Arthur J. Hilliker, and Imogen R. Coe PMCID: PMC137128 A new family of highly variable proteins in the Chlamydophila pneumoniae genome Eduardo P. C. Rocha, Olivier Pradillon, Hung Bui, Chalom Sayada, and Erick Denamur PMCID: PMC137135 Mutations in genes of Saccharomyces cerevisiae encoding pre-mRNA splicing factors cause cell cycle arrest through activation of the spindle checkpoint Orna Dahan and Martin Kupiec PMCID: PMC137127 NMR structure of the 3′ stem–loop from human U4 snRNA Luis R. Comolli, Nikolai B. Ulyanov, Ana Maria Soto, Luis A. Marky, Thomas L. James, and William H. Gmeiner PMCID: PMC137124 A PIWI homolog is one of the proteins expressed exclusively during macronuclear development in the ciliate Stylonychia lemnae Christian P. Fetzer, Daniel J. Hogan, and Hans J. Lipps PMCID: PMC137143 Characterization of DNA synthesis catalyzed by bacteriophage T4 replication complexes reconstituted on synthetic circular substrates Farid A. Kadyrov and John W. Drake PMCID: PMC137140 IRES-driven translation is stimulated separately by the FMDV 3′-NCR and poly(A) sequences Sonia López de Quinto, Margarita Sáiz, Diana de la Morena, Francisco Sobrino, and Encarnación Martínez-Salas PMCID: PMC137133 The Drosophila transcription factor tramtrack (TTK) interacts with Trithorax-like (GAGA) and represses GAGA-mediated activation Sara Pagans, Miguel Ortiz-Lombardía, Ma Lluïsa Espinás, Jordi Bernués, and Fernando Azorín PMCID: PMC137134 Expression of the human RNA-binding protein HuR in Trypanosoma brucei increases the abundance of mRNAs containing AU-rich regulatory elements Luis Quijada, Cristina Guerra-Giraldez, Maciej Drozdz, Claudia Hartmann, Henriette Irmer, Claudia Ben-Dov, Marina Cristodero, Martina Ding, and Christine Clayton PMCID: PMC137141 DNA end-binding specificity of human Rad50/Mre11 is influenced by ATP Martijn de Jager, Claire Wyman, Dik C. van Gent, and Roland Kanaar PMCID: PMC137138 Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157 Qi Jin, Zhenghong Yuan, Jianguo Xu, Yu Wang, Yan Shen, Weichuan Lu, Jinhua Wang, Hong Liu, Jian Yang, Fan Yang, Xiaobing Zhang, Jiyu Zhang, Guowei Yang, Hongtao Wu, Di Qu, Jie Dong, Lilian Sun, Ying Xue, Ailan Zhao, Yishan Gao, Junping Zhu, Biao Kan, Keyue Ding, Shuxia Chen, Hongsong Cheng, Zhijian Yao, Bingkun He, Runsheng Chen, Dalong Ma, Boqin Qiang, Yumei Wen, Yunde Hou, and Jun Yu PMCID: PMC137130 Additivity in protein–DNA interactions: how good an approximation is it? Panayiotis V. Benos, Martha L. Bulyk, and Gary D. Stormo PMCID: PMC137142 The role of the phosphorus BI–BII transition in protein–DNA recognition: the NF-κB complex K. Wecker, M. C. Bonnet, E. F. Meurs, and M. Delepierre PMCID: PMC137123 ‘Immunomers’—novel 3′–3′-linked CpG oligodeoxyribonucleotides as potent immunomodulatory agents Dong Yu, Ekambar R. Kandimalla, Lakshmi Bhagat, Jin-Yan Tang, Yanping Cong, Jimmy Tang, and Sudhir Agrawal PMCID: PMC137145 Minimum length requirement of the alignment domain of human telomerase RNA to sustain catalytic activity in vitro Gérald Gavory, Mark Farrow, and Shankar Balasubramanian PMCID: PMC137139 Identification of critical amino acid residues on human dihydrofolate reductase protein that mediate RNA recognition Ningwen Tai, Yuyan Ding, John C. Schmitz, and Edward Chu PMCID: PMC137126 Gene expression of TPA induced differentiation in HL-60 cells by DNA microarray analysis Xi Zheng, Roald Ravatn, Yong Lin, Wei-Chung Shih, Arnold Rabson, Roger Strair, Eliezer Huberman, Allan Conney, and Khew-Voon Chin PMCID: PMC137144 La autoantigen is required for the internal ribosome entry site-mediated translation of Coxsackievirus B3 RNA Partho Sarothi Ray and Saumitra Das PMCID: PMC137146 Induction of sporulation in Saccharomyces cerevisiae leads to the formation of N6-methyladenosine in mRNA: a potential mechanism for the activity of the IME4 gene Mary J. Clancy, Mary Eileen Shambaugh, Candace S. Timpte, and Joseph A. Bokar PMCID: PMC137137 Complex formation of the neuron-specific ELAV-like Hu RNA-binding proteins Katsumi Kasashima, Eiji Sakashita, Kuniaki Saito, and Hiroshi Sakamoto PMCID: PMC137131 Endonucleolytic activation directs dark-induced chloroplast mRNA degradation Sacha Baginsky and Wilhelm Gruissem PMCID: PMC137125 Slipped-strand DNAs formed by long (CAG)·(CTG) repeats: slipped-out repeats and slip-out junctions Christopher E. Pearson, Mandy Tam, Yuh-Hwa Wang, S. Erin Montgomery, Arvin C. Dar, John D. Cleary, and Kerrie Nichol PMCID: PMC137136 Use and misuse of correspondence analysis in codon usage studies Guy Perrière and Jean Thioulouse PMCID: PMC137129 Analyses of single-copy Arabidopsis T-DNA-transformed lines show that the presence of vector backbone sequences, short inverted repeats and DNA methylation is not sufficient or necessary for the induction of transgene silencing Trine J. Meza, Biljana Stangeland, Inderjit S. Mercy, Magne Skårn, Dag A. Nymoen, Anita Berg, Melinka A. Butenko, Anne-Mari Håkelien, Camilla Haslekås, Leonardo A. Meza-Zepeda, and Reidunn B. Aalen PMCID: PMC137132 Thermodynamic characterization of the multivalent binding of chartreusin to DNA Francisca Barceló, Damiana Capó, and José Portugal PMCID: PMC137122 GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing J. Lin, J. Qian, D. Greenbaum, P. Bertone, R. Das, N. Echols, A. Senes, B. Stenger, and M. Gerstein PMCID: PMC137121 NAR Methods Online Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis Adel M. Talaat, Susan T. Howard, Walker Hale IV, Rick Lyons, Harold Garner, and Stephen Albert Johnston PMCID: PMC137148 A one-step method for in vitro production of tRNA transcripts Dragana Korenčić, Dieter Söll, and Alexandre Ambrogelly PMCID: PMC137149 A computational framework for optimal masking in the synthesis of oligonucleotide microarrays Simon Kasif, Zhiping Weng, Adnan Derti, Richard Beigel, and Charles DeLisi PMCID: PMC137150 Optimized in situ construction of oligomers on an array surface Andrew C. Tolonen, Dinu F. Albeanu, Julia F. Corbett, Heather Handley, Charlotte Henson, and Pratap Malik PMCID: PMC137151 Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer J. Colin Cox, Andrew Hayhurst, Jay Hesselberth, Travis S. Bayer, George Georgiou, and Andrew D. Ellington PMCID: PMC137152 A double reporter assay for detecting changes in the ratio of spliced and unspliced mRNA in mammalian cells Md. Talat Nasim, H. M. Chowdhury, and I. C. Eperon PMCID: PMC137153 Efficient isolation of targeted Caenorhabditis elegans deletion strains using highly thermostable restriction endonucleases and PCR Aguan Wei, Alex Yuan, Gloria Fawcett, Alice Butler, Theodore Davis, Shuang-yong Xu, and Lawrence Salkoff PMCID: PMC137154 The effects of sequence length and oligonucleotide mismatches on 5′ exonuclease assay efficiency Steve Smith, Linda Vigilant, and Phillip A. Morin PMCID: PMC137155 A continuous kinetic assay for RNA-cleaving deoxyribozymes, exploiting ethidium bromide as an extrinsic fluorescent probe Davide Ferrari and Alessio Peracchi PMCID: PMC137156 |
