| | Articles Comparative genomics and evolution of proteins involved in RNA metabolism Vivek Anantharaman, Eugene V. Koonin, and L. Aravind PMCID: PMC101826 Transcriptional silencing in Saccharomyces cerevisiae and Schizosaccharomyces pombe Ying Huang PMCID: PMC101825 A positively charged residue of ![[var phi]](corehtml/pmc/pmcents/x03C6.gif) 29 DNA polymerase, highly conserved in DNA polymerases from families A and B, is involved in binding the incoming nucleotide Verónica Truniger, José M. Lázaro, Francisco J. Esteban, Luis Blanco, and Margarita Salas PMCID: PMC101840 Physical and functional interactions of the tumor suppressor protein p53 and DNA polymerase α-primase Christian Melle and Heinz-Peter Nasheuer PMCID: PMC101832 NMR structure of a parallel-stranded DNA duplex at atomic resolution V. Rani Parvathy, Sukesh R. Bhaumik, Kandala V. R. Chary, Girjesh Govil, Keliang Liu, Frank B. Howard, and H. Todd Miles PMCID: PMC101824 Receptor-mediated endocytosis of phosphodiester oligonucleotides in the HepG2 cell line: evidence for non-conventional intracellular trafficking Philippe de Diesbach, Francisca N’Kuli, Catherine Berens, Etienne Sonveaux, Michel Monsigny, Annie-Claude Roche, and Pierre J. Courtoy PMCID: PMC101842 Requirements for utilization of CREB binding protein by hypersensitive site two of the β-globin locus control region Kirby D. Johnson, Jason E. Norton, and Emery H. Bresnick PMCID: PMC101831 Correlated alternative side chain conformations in the RNA-recognition motif of heterogeneous nuclear ribonucleoprotein A1 Jacqueline Vitali, Jianzhong Ding, Jianzhong Jiang, Ying Zhang, Adrian R. Krainer, and Rui-Ming Xu PMCID: PMC101846 Rhodobacter sphaeroides LexA has dual activity: optimising and repressing recA gene transcription Angels Tapias, Silvia Fernández, Juan C. Alonso, and Jordi Barbé PMCID: PMC101838 Circular permutation of DNA cytosine-N4 methyltransferases: in vivo coexistence in the BcnI system and in vitro probing by hybrid formation Giedrius Vilkaitis, Arvydas Lubys, EglÇ MerkienÇ, Albertas Timinskas, Arvydas Janulaitis, and Saulius Klimaauskas PMCID: PMC101829 Multiple thiol-anchor capped DNA–gold nanoparticle conjugates Zhi Li, Rongchao Jin, Chad A. Mirkin, and Robert L. Letsinger PMCID: PMC101851 Factors governing loss and rescue of DNA binding upon single and double mutations in the p53 core domain Jon D. Wright, Sergey Yu Noskov, and Carmay Lim PMCID: PMC101848 An efficient algorithm for large-scale detection of protein families A. J. Enright, S. Van Dongen, and C. A. Ouzounis PMCID: PMC101833 A novel DNA polymerase homologous to Escherichia coli DNA polymerase I from a higher plant, rice (Oryza sativa L.) Seisuke Kimura, Yukinobu Uchiyama, Nobuyuki Kasai, Satoshi Namekawa, Ai Saotome, Tadamasa Ueda, Tsuyu Ando, Toyotaka Ishibashi, Masahiko Oshige, Tomoyuki Furukawa, Taichi Yamamoto, Junji Hashimoto, and Kengo Sakaguchi PMCID: PMC101828 Restart of DNA replication in Gram-positive bacteria: functional characterisation of the Bacillus subtilis PriA initiator Patrice Polard, Stéphanie Marsin, Stephen McGovern, Marion Velten, Dale B. Wigley, S. Dusko Ehrlich, and Claude Bruand PMCID: PMC101839 Efficient trans-cleavage by the Schistosoma mansoni SMα1 hammerhead ribozyme in the extreme thermophile Thermus thermophilus Alejandro Vazquez-Tello, Pablo Castán, Renata Moreno, James M. Smith, José Berenguer, and Robert Cedergren PMCID: PMC101841 Immunostimulatory properties of phosphorothioate CpG DNA containing both 3′–5′- and 2′–5′-internucleotide linkages Dong Yu, Ekambar R. Kandimalla, Qiuyan Zhao, Yanping Cong, and Sudhir Agrawal PMCID: PMC101845 SmpB functions in various steps of trans-translation Kyoko Hanawa-Suetsugu, Mitsuru Takagi, Hachiro Inokuchi, Hyouta Himeno, and Akira Muto PMCID: PMC101834 Response of human REV1 to different DNA damage: preferential dCMP insertion opposite the lesion Yanbin Zhang, Xiaohua Wu, Olga Rechkoblit, Nicholas E. Geacintov, John-Stephen Taylor, and Zhigang Wang PMCID: PMC101843 Preparation of partially 2H/13C-labelled RNA for NMR studies. Stereo-specific deuteration of the H5′′ in nucleotides Jenny Cromsigt, Jürgen Schleucher, Tomas Gustafsson, Jan Kihlberg, and Sybren Wijmenga PMCID: PMC101849 Sequence requirements for terminators and antiterminators in the T box transcription antitermination system: disparity between conservation and functional requirements Frank J. Grundy, Tessa R. Moir, Margaret T. Haldeman, and Tina M. Henkin PMCID: PMC101844 A dual reporter screening system identifies the amino acid at position 82 in Flp site-specific recombinase as a determinant for target specificity Yuri Voziyanov, A. Francis Stewart, and Makkuni Jayaram PMCID: PMC101850 Post-transcriptional suppression of gene expression in Xenopus embryos by small interfering RNA Yuan Zhou, Yick-Pang Ching, Kin Hang Kok, Hsiang-fu Kung, and Dong-Yan Jin PMCID: PMC101847 The zinc ion in the HNH motif of the endonuclease domain of colicin E7 is not required for DNA binding but is essential for DNA hydrolysis Wen-Yen Ku, Yu-Wen Liu, Ya-Chein Hsu, Chen-Chung Liao, Po-Huang Liang, Hanna S. Yuan, and Kin-Fu Chak PMCID: PMC101835 dNTP versus NTP discrimination by phenylalanine 451 in duck hepatitis B virus P protein indicates a common structure of the dNTP-binding pocket with other reverse transcriptases Jürgen Beck, Maren Vogel, and Michael Nassal PMCID: PMC101827 Induction of RNA interference in Caenorhabditis elegans by RNAs derived from plants exhibiting post-transcriptional gene silencing Alexandra Boutla, Kriton Kalantidis, Nektarios Tavernarakis, Mina Tsagris, and Martin Tabler PMCID: PMC101830 The terminase subunits pUL56 and pUL89 of human cytomegalovirus are DNA-metabolizing proteins with toroidal structure Hanno Scheffczik, Christos G. W. Savva, Andreas Holzenburg, Larissa Kolesnikova, and Elke Bogner PMCID: PMC101837 Structural analysis of conserved base pairs in protein–DNA complexes Leonid A. Mirny and Mikhail S. Gelfand PMCID: PMC101836 NAR Methods Online Methylome profiling of cancer cells by amplification of inter-methylated sites (AIMS) Jordi Frigola, Maria Ribas, Rosa-Ana Risques, and Miguel A. Peinado PMCID: PMC101852 An in vivo selection system for homing endonuclease activity Mathias Gruen, Kathy Chang, Irina Serbanescu, and David R. Liu PMCID: PMC101853 An assessment of Motorola CodeLink™ microarray performance for gene expression profiling applications Ramesh Ramakrishnan, David Dorris, Anna Lublinsky, Allen Nguyen, Marc Domanus, Anna Prokhorova, Linn Gieser, Edward Touma, Randall Lockner, Murthy Tata, Xiaomei Zhu, Marcus Patterson, Richard Shippy, Timothy J. Sendera, and Abhijit Mazumder PMCID: PMC101854 Multiplex Pyrosequencing Nader Pourmand, Elahe Elahi, Ronald W. Davis, and Mostafa Ronaghi PMCID: PMC101855 Glass bead purification of plasmid template DNA for high throughput sequencing of mammalian genomes Debra A. Dederich, Geoffrey Okwuonu, Toni Garner, Amanda Denn, Angelica Sutton, Michael Escotto, Ashley Martindale, Oliver Delgado, Donna M. Muzny, Richard A. Gibbs, and Michael L. Metzker PMCID: PMC101856 TspGWI, a thermophilic class-IIS restriction endonuclease from Thermus sp., recognizes novel asymmetric sequence 5′-ACGGA(N11/9)-3′ Agnieszka üylicz-Stachula, Renata I. Harasimowicz-Sßowiáska, Ireneusz Sobolewski, and Piotr M. Skowron PMCID: PMC101857 |
