| | Articles Improvements in siRNA properties mediated by 2′-deoxy-2′-fluoro-β-d-arabinonucleic acid (FANA) Thomas Dowler, Denis Bergeron, Anna-Lisa Tedeschi, Luc Paquet, Nicolay Ferrari, and Masad J. Damha PMCID: PMC1409815 A TFIIB-like protein is indispensable for spliced leader RNA gene transcription in Trypanosoma brucei Bernd Schimanski, Jens Brandenburg, Tu Ngoc Nguyen, Melissa Jo Caimano, and Arthur Günzl PMCID: PMC1409817 Inhibition of poly (ADP-ribose) polymerase activates ATM which is required for subsequent homologous recombination repair Helen E. Bryant and Thomas Helleday PMCID: PMC1410911 M-Coffee: combining multiple sequence alignment methods with T-Coffee Iain M. Wallace, Orla O'Sullivan, Desmond G. Higgins, and Cedric Notredame PMCID: PMC1410914 Regions of extreme synonymous codon selection in mammalian genes Peter Schattner and Mark Diekhans PMCID: PMC1410912 Protein assembly and DNA looping by the FokI restriction endonuclease Lucy E. Catto, Sumita Ganguly, Susan E. Milsom, Abigail J. Welsh, and Stephen E. Halford PMCID: PMC1410913 Novel GC-rich DNA-binding compound produced by a genetically engineered mutant of the mithramycin producer Streptomyces argillaceus exhibits improved transcriptional repressor activity: implications for cancer therapy Veronica Albertini, Aklank Jain, Sara Vignati, Sara Napoli, Andrea Rinaldi, Ivo Kwee, Mohammad Nur-e-Alam, Julia Bergant, Francesco Bertoni, Giuseppina M. Carbone, Jürgen Rohr, and Carlo V. Catapano PMCID: PMC1420802 The high-mobility-group domain of Sox proteins interacts with DNA-binding domains of many transcription factors Sandra Wißmüller, Thomas Kosian, Michael Wolf, Markus Finzsch, and Michael Wegner PMCID: PMC1421504 BMI1 is a target gene of E2F-1 and is strongly expressed in primary neuroblastomas Katrin Nowak, Kornelius Kerl, Daniel Fehr, Christoph Kramps, Christine Gessner, Katrin Killmer, Birgit Samans, Bernd Berwanger, Holger Christiansen, and Werner Lutz PMCID: PMC1421501 Distance determination by GIY-YIG intron endonucleases: discrimination between repression and cleavage functions Qingqing Liu, Victoria Derbyshire, Marlene Belfort, and David R. Edgell PMCID: PMC1421500 The expression profile of microRNAs in mouse embryos Junichi Mineno, Sachiko Okamoto, Tatsuya Ando, Masahiro Sato, Hideto Chono, Hiroyuki Izu, Masanori Takayama, Kiyozo Asada, Oleg Mirochnitchenko, Masayori Inouye, and Ikunoshin Kato PMCID: PMC1421506 The DNA–protein interaction modes of FEN-1 with gap substrates and their implication in preventing duplication mutations Ren Liu, Junzhuan Qiu, L. David Finger, Li Zheng, and Binghui Shen PMCID: PMC1421507 Experimental and computational investigations of Ser10 and Lys13 in the binding and cleavage of DNA substrates by Escherichia coli DNA topoisomerase I Daniel Strahs, Chang-Xi Zhu, Bokun Cheng, Jason Chen, and Yuk-Ching Tse-Dinh PMCID: PMC1421505 Acetylation of UBF changes during the cell cycle and regulates the interaction of UBF with RNA polymerase I Joachim Meraner, Markus Lechner, Adele Loidl, Maria Goralik-Schramel, Renate Voit, Ingrid Grummt, and Peter Loidl PMCID: PMC1421502 Btk expression is controlled by Oct and BOB.1/OBF.1 Cornelia Brunner and Thomas Wirth PMCID: PMC1421503 The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications Christian Marck, Rym Kachouri-Lafond, Ingrid Lafontaine, Eric Westhof, Bernard Dujon, and Henri Grosjean PMCID: PMC1447645 Attenuation of DNA charge transport by compaction into a nucleosome core particle Chad C. Bjorklund and William B. Davis PMCID: PMC1428796 NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation Sylvie Nonin-Lecomte, Brice Felden, and Frédéric Dardel PMCID: PMC1428798 Isolation of human Dna2 endonuclease and characterization of its enzymatic properties Jeong-Hoon Kim, Hee-Dai Kim, Gi-Hyuck Ryu, Do-Hyung Kim, Jerard Hurwitz, and Yeon-Soo Seo PMCID: PMC1428795 Biochemical analysis of human Dna2 Taro Masuda-Sasa, Osamu Imamura, and Judith L. Campbell PMCID: PMC1428797 Identification and characterization of CRT10 as a novel regulator of Saccharomyces cerevisiae ribonucleotide reductase genes Yu Fu and Wei Xiao PMCID: PMC1447646 Novel synthesis of O6-alkylguanine containing oligodeoxyribonucleotides as substrates for the human DNA repair protein, O6-methylguanine DNA methyltransferase (MGMT) Takayuki Shibata, Nicola Glynn, T. Brian H. McMurry, R. Stanley McElhinney, Geoffrey P. Margison, and David M. Williams PMCID: PMC1435717 ‘Evidence of an auxin signal pathway, microRNA167-ARF8-GH3, and its response to exogenous auxin in cultured rice cells’ Ji Hyun Yang, So Jeong Han, Eun Kyung Yoon, and Woo Sung Lee PMCID: PMC1447648 Molecular basis of the targeting of topoisomerase II-mediated DNA cleavage by VP16 derivatives conjugated to triplex-forming oligonucleotides Maria Duca, Dominique Guianvarc'h, Kahina Oussedik, Ludovic Halby, Anna Garbesi, Daniel Dauzonne, Claude Monneret, Neil Osheroff, Carine Giovannangeli, and Paola B. Arimondo PMCID: PMC1447649 Human centromeric alphoid domains are periodically homogenized so that they vary substantially between homologues. Mechanism and implications for centromere functioning Gérard Roizès PMCID: PMC1447651 Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase Ingrid Zegers, Daniel Gigot, Françoise van Vliet, Catherine Tricot, Stéphane Aymerich, Janusz M. Bujnicki, Jan Kosinski, and Louis Droogmans PMCID: PMC1447647 Small protein B interacts with the large and the small subunits of a stalled ribosome during trans-translation Marc Hallier, Jessie Desreac, and Brice Felden PMCID: PMC1435831 Methods Online Detection of 100% of mutations in 124 individuals using a standard UV/Vis microplate reader: a novel concept for mutation scanning Tania Tabone, Georgina Sallmann, Elizabeth Webb, and Richard G. H. Cotton PMCID: PMC1409816 Multiplex degenerate PCR coupled with an oligo sorbent array for human endogenous retrovirus expression profiling Jean-Philippe Pichon, Bertrand Bonnaud, Philippe Cleuziat, and François Mallet PMCID: PMC1409818 Adduct-specific monoclonal antibodies for the measurement of cisplatin-induced DNA lesions in individual cell nuclei Bernd Liedert, Dick Pluim, Jan Schellens, and Jürgen Thomale PMCID: PMC1420801 Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins Inna Shcherbakova, Somdeb Mitra, Robert H. Beer, and Michael Brenowitz PMCID: PMC1421499 Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA Erik Pettersson, Mats Lindskog, Joakim Lundeberg, and Afshin Ahmadian PMCID: PMC1421508 Molecular beacons with intrinsically fluorescent nucleotides Angel A. Martí, Steffen Jockusch, Zengmin Li, Jingyue Ju, and Nicholas J. Turro PMCID: PMC1428799 A novel magnetic resonance-based method to measure gene expression in living cells Sewon Ki, Fuminori Sugihara, Koji Kasahara, Hidehito Tochio, Azusa Okada-Marubayashi, Setsuko Tomita, Masahito Morita, Mitsunori Ikeguchi, Masahiro Shirakawa, and Tetsuro Kokubo PMCID: PMC1447650 Corrigenda Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family Paul Thaw, Svetlana E. Sedelnikova, Tatyana Muranova, Sebastian Wiese, Sylvia Ayora, Juan C. Alonso, Arie B. Brinkman, Jasper Akerboom, John van der Oost, and John B. Rafferty PMCID: PMC1435830 Corrects: Paul Thaw, et al. Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family. Nucleic Acids Res. 2006; 34(5): 1439–1449. Sequence effects of aminofluorene-modified DNA duplexes: thermodynamic and circular dichroism properties Srinivasa Rao Meneni, Rhijuta D'Mello, Gregory Norigian, Gregory Baker, Lan Gao, M. Paul Chiarelli, and Bongsup P. Cho PMCID: PMC1435832 Corrects: Srinivasa Rao Meneni, et al. Sequence effects of aminofluorene-modified DNA duplexes: thermodynamic and circular dichroism properties. Nucleic Acids Res. 2006; 34(2): 755–763. |
