| | Articles Identification of a novel gene encoding a flavin-dependent tRNA:m5U methyltransferase in bacteria—evolutionary implications Jaunius Urbonavičius, Stéphane Skouloubris, Hannu Myllykallio, and Henri Grosjean PMCID: PMC1178002 Syntheses of 4′-thioribonucleosides and thermodynamic stability and crystal structure of RNA oligomers with incorporated 4′-thiocytosine Peter Haeberli, Imre Berger, Pradeep S. Pallan, and Martin Egli PMCID: PMC1178003 Maternal disruption of Ube3a leads to increased expression of Ube3a-ATS in trans Miguel Landers, Margaret A. Calciano, Dan Colosi, Heather Glatt-Deeley, Joseph Wagstaff, and Marc Lalande PMCID: PMC1178004 Interplay between positive and negative activities that influence the role of Bicoid in transcription Dechen Fu and Jun Ma PMCID: PMC1178001 Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains S. Balaji, M. Madan Babu, Lakshminarayan M. Iyer, and L. Aravind PMCID: PMC1178005 Functional studies on the ATM intronic splicing processing element Marzena A. Lewandowska, Cristiana Stuani, Alireza Parvizpur, Francisco E. Baralle, and Franco Pagani PMCID: PMC1178006 Uracil content of 16S rRNA of thermophilic and psychrophilic prokaryotes correlates inversely with their optimal growth temperatures Amit N. Khachane, Kenneth N. Timmis, and Vítor A. P. Martins dos Santos PMCID: PMC1179731 DNA repair factor XPC is modified by SUMO-1 and ubiquitin following UV irradiation Qi-En Wang, Qianzheng Zhu, Gulzar Wani, Mohamed A. El-Mahdy, Jinyou Li, and Altaf A. Wani PMCID: PMC1178000 Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers M. L. Green and P. D. Karp PMCID: PMC1179732 Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages Kyudong Han, Shurjo K. Sen, Jianxin Wang, Pauline A. Callinan, Jungnam Lee, Richard Cordaux, Ping Liang, and Mark A. Batzer PMCID: PMC1179734 Structural and DNA-binding studies on the bovine antimicrobial peptide, indolicidin: evidence for multiple conformations involved in binding to membranes and DNA Chun-Hua Hsu, Chinpan Chen, Maou-Lin Jou, Alan Yueh-Luen Lee, Yu-Ching Lin, Yi-Ping Yu, Wei-Ting Huang, and Shih-Hsiung Wu PMCID: PMC1179735 Length-dependent energetics of (CTG)n and (CAG)n trinucleotide repeats Samir Amrane, Barbara Saccà, Martin Mills, Madhu Chauhan, Horst H. Klump, and Jean-Louis Mergny PMCID: PMC1179733 Contrasting effects of Elg1–RFC and Ctf18–RFC inactivation in the absence of fully functional RFC in fission yeast Jiyoung Kim, Kathryn Robertson, Katie J. L. Mylonas, Fiona C. Gray, Iryna Charapitsa, and Stuart A. MacNeill PMCID: PMC1179736 Topological constraints in nucleic acid hybridization kinetics Justin S. Bois, Suvir Venkataraman, Harry M. T. Choi, Andrew J. Spakowitz, Zhen-Gang Wang, and Niles A. Pierce PMCID: PMC1180668 sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes Jonathan Livny, Michael A. Fogel, Brigid M. Davis, and Matthew K. Waldor PMCID: PMC1180744 A host–guest approach for determining drug–DNA interactions: an example using netropsin Kristie D. Goodwin, Eric C. Long, and Millie M. Georgiadis PMCID: PMC1181240 Incorporation of non-nucleoside triphosphate analogues opposite to an abasic site by human DNA polymerases β and λ Emmanuele Crespan, Samantha Zanoli, Anastasiya Khandazhinskaya, Igor Shevelev, Maxim Jasko, Ludmila Alexandrova, Marina Kukhanova, Giuseppina Blanca, Giuseppe Villani, Ulrich Hübscher, Silvio Spadari, and Giovanni Maga PMCID: PMC1180669 Cloning and characterization of the Schizosaccharomyces pombe homologs of the human protein Translin and the Translin-associated protein TRAX Orly Laufman, Ron Ben Yosef, Noam Adir, and Haim Manor PMCID: PMC1180670 Functional polarity is introduced by Dicer processing of short substrate RNAs Scott D. Rose, Dong-Ho Kim, Mohammed Amarzguioui, Jeremy D. Heidel, Michael A. Collingwood, Mark E. Davis, John J. Rossi, and Mark A. Behlke PMCID: PMC1180746 Induction of transcription within chromosomal DNA loops flanked by MAR elements causes an association of loop DNA with the nuclear matrix Olga V. Iarovaia, Sergey B. Akopov, Lev G. Nikolaev, Eugene D. Sverdlov, and Sergey V. Razin PMCID: PMC1180747 MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences Julie D. Thompson, Stephen R. Holbrook, Kazutaka Katoh, Patrice Koehl, Dino Moras, Eric Westhof, and Olivier Poch PMCID: PMC1180671 Solution structure of the DNA-binding domain of RPA from Saccharomyces cerevisiae and its interaction with single-stranded DNA and SV40 T antigen Chin-Ju Park, Joon-Hwa Lee, and Byong-Seok Choi PMCID: PMC1180672 Preferential binding of a G-quadruplex ligand to human chromosome ends Christine Granotier, Gaëlle Pennarun, Lydia Riou, Françoise Hoffschir, Laurent R. Gauthier, Anne De Cian, Dennis Gomez, Eliane Mandine, Jean-François Riou, Jean-Louis Mergny, Patrick Mailliet, Bernard Dutrillaux, and François D. Boussin PMCID: PMC1181860 GDNF-inducible zinc finger protein 1 is a sequence-specific transcriptional repressor that binds to the HOXA10 gene regulatory region Takatoshi Morinaga, Atsushi Enomoto, Yohei Shimono, Fumiko Hirose, Naoyuki Fukuda, Atsushi Dambara, Mayumi Jijiwa, Kumi Kawai, Katsunori Hashimoto, Masatoshi Ichihara, Naoya Asai, Yoshiki Murakumo, Seiichi Matsuo, and Masahide Takahashi PMCID: PMC1180748 The involvement of the aspartate triad of the active center in all catalytic activities of multisubunit RNA polymerase Vasily Sosunov, Savva Zorov, Ekaterina Sosunova, Anatoly Nikolaev, Irina Zakeyeva, Irina Bass, Alex Goldfarb, Vadim Nikiforov, Konstantin Severinov, and Arkady Mustaev PMCID: PMC1180743 Cooperative binding of DNA and CBFβ to the Runt domain of the CBFα studied via MD simulations Bahru Habtemariam, Victor M. Anisimov, and Alexander D. MacKerell, Jr PMCID: PMC1180745 Intercalator conjugates of pyrimidine locked nucleic acid-modified triplex-forming oligonucleotides: improving DNA binding properties and reaching cellular activities Erika Brunet, Maddalena Corgnali, Loïc Perrouault, Victoria Roig, Ulysse Asseline, Mads D. Sørensen, B. Ravindra Babu, Jesper Wengel, and Carine Giovannangeli PMCID: PMC1181241 Assigning functions to genes: identification of S-phase expressed genes in Leishmania major based on post-transcriptional control elements Aviad Zick, Itay Onn, Rachel Bezalel, Hanah Margalit, and Joseph Shlomai PMCID: PMC1181863 Specific binding of the methyl binding domain protein 2 at the BRCA1-NBR2 locus Emilie Auriol, Lise-Marie Billard, Frédérique Magdinier, and Robert Dante PMCID: PMC1181861 Large-scale structural analysis of the core promoter in mammalian and plant genomes Kobe Florquin, Yvan Saeys, Sven Degroeve, Pierre Rouzé, and Yves Van de Peer PMCID: PMC1181242 An atypical RNA pseudoknot stimulator and an upstream attenuation signal for −1 ribosomal frameshifting of SARS coronavirus Mei-Chi Su, Chung-Te Chang, Chiu-Hui Chu, Ching-Hsiu Tsai, and Kung-Yao Chang PMCID: PMC1182165 FAST DB: a website resource for the study of the expression regulation of human gene products Pierre de la Grange, Martin Dutertre, Natalia Martin, and Didier Auboeuf PMCID: PMC1181862 Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for virus infectivity Véronique Goffin, Dominique Demonté, Caroline Vanhulle, Stéphane de Walque, Yvan de Launoit, Arsène Burny, Yves Collette, and Carine Van Lint PMCID: PMC1182164 The proliferating cell nuclear antigen regulates retinoic acid receptor transcriptional activity through direct protein–protein interaction Perrine J. Martin, Virginie Lardeux, and Philippe Lefebvre PMCID: PMC1182168 Determination of protein–DNA binding constants and specificities from statistical analyses of single molecules: MutS–DNA interactions Yong Yang, Lauryn E. Sass, Chunwei Du, Peggy Hsieh, and Dorothy A. Erie PMCID: PMC1182163 miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST You Jung Kim, Andrew Boyd, Brian D. Athey, and Jignesh M. Patel PMCID: PMC1182166 Anti-HIV-1 activity of anti-TAR polyamide nucleic acid conjugated with various membrane transducing peptides Snehlata Tripathi, Binay Chaubey, Sabyasachi Ganguly, Dylan Harris, Ralph A Casale, and Virendra N. Pandey PMCID: PMC1182329 An Oct-1 binding site mediates activation of the gata2 promoter by BMP signaling Tal Oren, Ingrid Torregroza, and Todd Evans PMCID: PMC1182169 The 5S rRNA maturase, ribonuclease M5, is a Toprim domain family member Frédéric Allemand, Nathalie Mathy, Dominique Brechemier-Baey, and Ciarán Condon PMCID: PMC1182330 Methods Online A novel PCR strategy for high-efficiency, automated site-directed mutagenesis Wu Wu, Zongchao Jia, Ping Liu, Zhigang Xie, and Qun Wei PMCID: PMC1178011 Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks Felix Naef and Joerg Huelsken PMCID: PMC1178007 Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5′-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi Ken Ishikawa, Miki Watanabe, Toshihiro Kuroita, Ikuo Uchiyama, Janusz M. Bujnicki, Bunsei Kawakami, Masaru Tanokura, and Ichizo Kobayashi PMCID: PMC1178009 Generation of subspecies level-specific microbial diagnostic microarrays using genes amplified from subtractive suppression hybridization as microarray probes Jin-Woo Bae, Sung-Keun Rhee, Young-Do Nam, and Yong-Ha Park PMCID: PMC1178008 Four new type I restriction enzymes identified in Escherichia coli clinical isolates Julie K. A. Kasarjian, Yoshiaki Kodama, Masatake Iida, Katsura Matsuda, and Junichi Ryu PMCID: PMC1178010 Genome-wide selection of unique and valid oligonucleotides Heikki Hyyrö, Martti Juhola, and Mauno Vihinen PMCID: PMC1180749 I-ApeI: a novel intron-encoded LAGLIDADG homing endonuclease from the archaeon, Aeropyrum pernix K1 Norimichi Nomura, Yayoi Morinaga, Nobuaki Shirai, and Yoshihiko Sako PMCID: PMC1180750 Nucleotide exchange and excision technology (NExT) DNA shuffling: a robust method for DNA fragmentation and directed evolution Kristian M. Müller, Sabine C. Stebel, Susanne Knall, Gregor Zipf, Hubert S. Bernauer, and Katja M. Arndt PMCID: PMC1182171 Minimal cross-recombination between wild-type and loxP511 sites in vivo facilitates truncating both ends of large DNA inserts in pBACe3.6 and related vectors Leighcraft A. Shakes, Douglas M. Garland, Deepak K. Srivastava, Ken R. Harewood, and Pradeep K. Chatterjee PMCID: PMC1182172 Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan Peter A. Dickson, Grant W. Montgomery, Anjali Henders, Megan J. Campbell, Nicholas G. Martin, and Michael R. James PMCID: PMC1182175 Characterization of zebrafish Rad52 and replication protein A for oligonucleotide-mediated mutagenesis Nobuhiro Takahashi and Igor B. Dawid PMCID: PMC1182173 Simultaneous detection of microsatellite repeats and SNPs in the macrophage migration inhibitory factor (MIF) gene by thin-film biosensor chips and application to rural field studies Xiao-bo Zhong, Lin Leng, Anna Beitin, Rui Chen, Courtney McDonald, Betty Hsiao, Robert D. Jenison, Insoo Kang, Sung-Hwan Park, Annette Lee, Peter Gregersen, Philip Thuma, Patricia Bray-Ward, David C. Ward, and Richard Bucala PMCID: PMC1182331 SiteFinding-PCR: a simple and efficient PCR method for chromosome walking Guihong Tan, Yin Gao, Miao Shi, Xinyue Zhang, Shanping He, Zhangliang Chen, and Chengcai An PMCID: PMC1182332 An ultrasensitive photoelectrochemical nucleic acid biosensor Zhiqiang Gao and Natalia C. Tansil PMCID: PMC1182174 Corrigenda CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes Anil G. Jegga, Ashima Gupta, Sivakumar Gowrisankar, Mrunal A. Deshmukh, Steven Connolly, Kevin Finley, and Bruce J. Aronow PMCID: PMC1182167 Corrects: Anil G. Jegga, et al. CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes. Nucleic Acids Res. 2005 July 1; 33(Web Server issue): W408–W411. Human POL II promoter prediction: time series descriptors and machine learning Rajeev Gangal and Pankaj Sharma PMCID: PMC1182170 Corrects: Rajeev Gangal, et al. Human pol II promoter prediction: time series descriptors and machine learning. Nucleic Acids Res. 2005; 33(4): 1332–1336. |
