| | Articles SURVEY AND SUMMARY: Mutagenic potentials of damaged nucleic acids produced by reactive oxygen/nitrogen species: approaches using synthetic oligonucleotides and nucleotides Hiroyuki Kamiya PMCID: PMC140503 SURVEY AND SUMMARY: Structural classification of zinc fingers S. Sri Krishna, Indraneel Majumdar, and Nick V. Grishin PMCID: PMC140525 Mutational analysis of the Chlamydia trachomatis dnaK promoter defines the optimal –35 promoter element Chris S. Schaumburg and Ming Tan PMCID: PMC140514 Cellular uptake of Antennapedia Penetratin peptides is a two-step process in which phase transfer precedes a tryptophan-dependent translocation Geneviève Dom, Chloë Shaw-Jackson, Christelle Matis, Olivier Bouffioux, Jacques J. Picard, Alain Prochiantz, Marie-Paule Mingeot-Leclercq, Robert Brasseur, and René Rezsohazy PMCID: PMC140524 Basal transcriptional regulation of human damage-specific DNA-binding protein genes DDB1 and DDB2 by Sp1, E2F, N-myc and NF1 elements Anne F. Nichols, Toshiki Itoh, Francesca Zolezzi, Stephanie Hutsell, and Stuart Linn PMCID: PMC140516 Identification and functional characterization of a new member of the human Mcm protein family: hMcm8 Devrim Gozuacik, Mounia Chami, David Lagorce, Jamila Faivre, Yoshiki Murakami, Olivier Poch, Esther Biermann, Rolf Knippers, Christian Bréchot, and Patrizia Paterlini-Bréchot PMCID: PMC140502 Site-directed mutagenesis analysis of the structural interaction of the single-strand-break repair protein, X-ray cross-complementing group 1, with DNA polymerase β Assen Marintchev, Michael R. Gryk, and Gregory P. Mullen PMCID: PMC140523 Tolerance for mutations and chemical modifications in a siRNA Mohammed Amarzguioui, Torgeir Holen, Eshrat Babaie, and Hans Prydz PMCID: PMC140512 The pathogenic U3271C human mitochondrial tRNALeu(UUR) mutation disrupts a fragile anticodon stem Lisa M. Wittenhagen, Marc D. Roy, and Shana O. Kelley PMCID: PMC140497 Human RNase 7: a new cationic ribonuclease of the RNase A superfamily Jianzhi Zhang, Kimberly D. Dyer, and Helene F. Rosenberg PMCID: PMC140521 Identification of a cis-acting element required for shunt-mediated translational initiation of the Sendai virus Y proteins Sylvain de Breyne, Viviane Simonet, Thierry Pelet, and Joseph Curran PMCID: PMC140508 Putative subunits of the maize origin of replication recognition complex ZmORC1–ZmORC5 Xiaohong Witmer, Raul Alvarez-Venegas, Phillip San-Miguel, Olga Danilevskaya, and Zoya Avramova PMCID: PMC140504 Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations Wen Li, Buyong Ma, and Bruce A. Shapiro PMCID: PMC140513 Polypyrimidine tract binding protein and poly r(C) binding protein 1 interact with the BAG-1 IRES and stimulate its activity in vitro and in vivo Becky M. Pickering, Sally A. Mitchell, Joanne R. Evans, and Anne E. Willis PMCID: PMC140511 Putative proteins related to group II intron reverse transcriptase/maturases are encoded by nuclear genes in higher plants Georg Mohr and Alan M. Lambowitz PMCID: PMC140517 The phylogenetic diversity of eukaryotic transcription Richard M. R. Coulson and Christos A. Ouzounis PMCID: PMC140520 Selections for constituting new RNA–protein interactions in catalytic RNP Shota Atsumi, Yoshiya Ikawa, Hideaki Shiraishi, and Tan Inoue PMCID: PMC140506 Functional studies of the PI(3)-kinase signalling pathway employing synthetic and expressed siRNA Frank Czauderna, Melanie Fechtner, Hüseyin Aygün, Wolfgang Arnold, Anke Klippel, Klaus Giese, and Jörg Kaufmann PMCID: PMC140507 Finding weak similarities between proteins by sequence profile comparison Anna R. Panchenko PMCID: PMC140518 Enp1, a yeast protein associated with U3 and U14 snoRNAs, is required for pre-rRNA processing and 40S subunit synthesis Weidong Chen, Jean Bucaria, David A. Band, Ann Sutton, and Rolf Sternglanz PMCID: PMC140510 Short hairpin type of dsRNAs that are controlled by tRNAVal promoter significantly induce RNAi-mediated gene silencing in the cytoplasm of human cells Hiroaki Kawasaki and Kazunari Taira PMCID: PMC140522 Fluoride-cleavable biotinylation phosphoramidite for 5′-end-labeling and affinity purification of synthetic oligonucleotides Shiyue Fang and Donald E. Bergstrom PMCID: PMC140496 The complete nucleotide sequence of the hornwort (Anthoceros formosae) chloroplast genome: insight into the earliest land plants Masanori Kugita, Akira Kaneko, Yuhei Yamamoto, Yuko Takeya, Tohoru Matsumoto, and Koichi Yoshinaga PMCID: PMC140519 Comparison of the capacity of different viral internal ribosome entry segments to direct translation initiation in poly(A)-dependent reticulocyte lysates Sylvie Paulous, Cécile E. Malnou, Yanne M. Michel, Katherine M. Kean, and Andrew M. Borman PMCID: PMC140495 Antisense oligonucleotides targeted to the domain IIId of the hepatitis C virus IRES compete with 40S ribosomal subunit binding and prevent in vitro translation Béatrice Tallet-Lopez, Lydia Aldaz-Carroll, Sandrine Chabas, Eric Dausse, Cathy Staedel, and Jean-Jacques Toulmé PMCID: PMC140505 Esp1396I restriction–modification system: structural organization and mode of regulation Eglė Česnavičienė, Goda Mitkaitė, Kornelijus Stankevičius, Arvydas Janulaitis, and Arvydas Lubys PMCID: PMC140501 Prioritized selection of oligodeoxyribonucleotide probes for efficient hybridization to RNA transcripts Kevin J. Luebke, Robert P. Balog, and Harold R. Garner PMCID: PMC140499 A comparison of three fission yeast mitochondrial genomes C. E. Bullerwell, J. Leigh, L. Forget, and B. F. Lang PMCID: PMC140500 Characterization of fragmented mitochondrial ribosomal RNAs of the colorless green alga Polytomella parva Jinshui Fan, Murray N. Schnare, and Robert W. Lee PMCID: PMC140509 Fingerprinting of prokaryotic 16S rRNA genes using oligodeoxyribonucleotide microarrays and virtual hybridization Miguel Ángel Reyes-López, Alfonso Méndez-Tenorio, Rogelio Maldonado-Rodríguez, Mitchel J. Doktycz, James T. Fleming, and Kenneth L. Beattie PMCID: PMC140498 Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information Christian Blouin, Yan Boucher, and Andrew J. Roger PMCID: PMC140515 NAR Methods Online Specificity assessment from fractionation experiments (SAFE): a novel method to evaluate microarray probe specificity based on hybridisation stringencies Alexei L. Drobyshev, Christine Machka, Marion Horsch, Matthias Seltmann, Volkmar Liebscher, Martin Hrabé de Angelis, and Johannes Beckers PMCID: PMC140526 Capillary electrophoretic analysis of genomic DNA methylation levels Dirk Stach, Oliver J. Schmitz, Stephan Stilgenbauer, Axel Benner, Hartmut Döhner, Manfred Wiessler, and Frank Lyko PMCID: PMC140527 SYBR Green real-time telomeric repeat amplification protocol for the rapid quantification of telomerase activity Henning Wege, Michael S. Chui, Hai T. Le, Julie M. Tran, and Mark A. Zern PMCID: PMC140528 A rapid biosensor chip assay for measuring of telomerase activity using surface plasmon resonance Chihaya Maesawa, Toru Inaba, Hidetoshi Sato, Sin Iijima, Kaoru Ishida, Masanori Terashima, Ryo Sato, Michihiro Suzuki, Akiko Yashima, Satoshi Ogasawara, Hiroki Oikawa, Nobuhiro Sato, Kazuyoshi Saito, and Tomoyuki Masuda PMCID: PMC140529 NotI passporting to identify species composition of complex microbial systems Veronika Zabarovska, Alexey S. Kutsenko, Lev Petrenko, Gelena Kilosanidze, Olle Ljungqvist, Elisabeth Norin, Tore Midtvedt, Gösta Winberg, Roland Möllby, Vladimir I. Kashuba, Ingemar Ernberg, and Eugene R. Zabarovsky PMCID: PMC140530 Improving baculovirus recombination Yuguang Zhao, David A. G. Chapman, and Ian M. Jones PMCID: PMC140531 |
