| | Articles DNA binding by yeast Mlh1 and Pms1: implications for DNA mismatch repair Mark C. Hall, Polina V. Shcherbakova, John M. Fortune, Christoph H. Borchers, J. Michael Dial, Kenneth B. Tomer, and Thomas A. Kunkel PMCID: PMC153752 Differential use of multiple replication origins in the ribosomal DNA episome of the protozoan parasite Entamoeba histolytica Soma Ghosh, S. Satish, Sonika Tyagi, Alok Bhattacharya, and Sudha Bhattacharya PMCID: PMC153748 A novel uracil-DNA glycosylase family related to the helix–hairpin–helix DNA glycosylase superfamily Ji Hyung Chung, Eun Kyoung Im, Hyun-Young Park, Jun Hye Kwon, Seahyoung Lee, Jaewon Oh, Ki-Chul Hwang, Jong Ho Lee, and Yangsoo Jang PMCID: PMC153747 Subunit interactions in the assembly of Saccharomyces cerevisiae DNA polymerase α Subhasis B. Biswas, Sujata M. Khopde, Fan xiu Zhu, and Esther E. Biswas PMCID: PMC153739 Tuning of conformational preorganization in model 2′,5′- and 3′,5′-linked oligonucleotides by 3′- and 2′-O-methoxyethyl modification Matjaž Polak, Muthiah Manoharan, Gopal B. Inamati, and Janez Plavec PMCID: PMC153733 Structural basis of replication origin recognition by the DnaA protein Norie Fujikawa, Hitoshi Kurumizaka, Osamu Nureki, Takaho Terada, Mikako Shirouzu, Tsutomu Katayama, and Shigeyuki Yokoyama PMCID: PMC153737 Formation of the P1.1 pseudoknot is critical for both the cleavage activity and substrate specificity of an antigenomic trans-acting hepatitis delta ribozyme Patrick Deschênes, Jonathan Ouellet, Jonathan Perreault, and Jean-Pierre Perreault PMCID: PMC153735 Biophysical and biological properties of quadruplex oligodeoxyribonucleotides Virna Đapić, Vedra Abdomerović, Rachel Marrington, Jemma Peberdy, Alison Rodger, John O. Trent, and Paula J. Bates PMCID: PMC153744 The fission yeast TFIIB-related factor limits RNA polymerase III to a TATA-dependent pathway of TBP recruitment Ying Huang, Edward McGillicuddy, Michael Weindel, Steven Dong, and Richard J. Maraia PMCID: PMC153730 Independent combinatorial effect of antisense oligonucleotides and RNAi-mediated specific inhibition of the recombinant Rat P2X3 receptor Maja Hemmings-Mieszczak, Gabriele Dorn, François J. Natt, Jonathan Hall, and William L. Wishart PMCID: PMC153750 Vertebrate TBP-like protein (TLP/TRF2/TLF) stimulates TATA-less terminal deoxynucleotidyl transferase promoters in a transient reporter assay, and TFIIA-binding capacity of TLP is required for this function T. Ohbayashi, M. Shimada, T. Nakadai, T. Wada, H. Handa, and T. Tamura PMCID: PMC153743 Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae T. D. Read, G. S. A. Myers, R. C. Brunham, W. C. Nelson, I. T. Paulsen, J. Heidelberg, E. Holtzapple, H. Khouri, N. B. Federova, H. A. Carty, L. A. Umayam, D. H. Haft, J. Peterson, M. J. Beanan, O. White, S. L. Salzberg, R. -c. Hsia, G. McClarty, R. G. Rank, P. M. Bavoil, and C. M. Fraser PMCID: PMC153749 Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures Louis Droogmans, Martine Roovers, Janusz M. Bujnicki, Catherine Tricot, Thomas Hartsch, Victor Stalon, and Henri Grosjean PMCID: PMC153742 Impact of DNA ligase IV on the fidelity of end joining in human cells Julianne Smith, Enriqueta Riballo, Boris Kysela, Celine Baldeyron, Kostas Manolis, Christel Masson, Michael R. Lieber, Dora Papadopoulo, and Penny Jeggo PMCID: PMC153745 Repression of E2F1-mediated transcription by the ErbB3 binding protein Ebp1 involves histone deacetylases Yuexing Zhang, Nicholas Woodford, Xianmin Xia, and Anne W. Hamburger PMCID: PMC153746 Ensemble and single-molecule fluorescence spectroscopic study of the binding modes of the bis-benzimidazole derivative Hoechst 33258 with DNA Amitava Adhikary, Volker Buschmann, Christian Müller, and Markus Sauer PMCID: PMC153736 GenDB—an open source genome annotation system for prokaryote genomes Folker Meyer, Alexander Goesmann, Alice C. McHardy, Daniela Bartels, Thomas Bekel, Jörn Clausen, Jörn Kalinowski, Burkhard Linke, Oliver Rupp, Robert Giegerich, and Alfred Pühler PMCID: PMC153740 Phosphorylation of Kruppel-like factor 5 (KLF5/IKLF) at the CBP interaction region enhances its transactivation function Zhiping Zhang and Christina T. Teng PMCID: PMC153738 Transcriptional stimulation by the DNA binding protein Hap46/BAG-1M involves hsp70/hsc70 molecular chaperones Yilmaz Niyaz, Irina Frenz, Gabriele Petersen, and Ulrich Gehring PMCID: PMC153731 Transcript identification by analysis of short sequence tags—influence of tag length, restriction site and transcript database Per Unneberg, Anders Wennborg, and Magnus Larsson PMCID: PMC153741 Mechanistic aspects of CoII(HAPP)(TFA)2 in DNA bulge-specific recognition Chien-Chung Cheng, Wei-Chun Huang-Fu, Kuo-Chan Hung, Po-Jui Chen, Wen Jwu Wang, and Yu-Ju Chen PMCID: PMC153751 Revised Escherichia coli selenocysteine insertion requirements determined by in vivo screening of combinatorial libraries of SECIS variants Karen E. Sandman, Daniel F. Tardiff, Lori A. Neely, and Christopher J. Noren PMCID: PMC153732 Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models Ronald Jansen, Harmen J. Bussemaker, and Mark Gerstein PMCID: PMC153734 NAR Methods Online On-line integration of PCR and cycle sequencing in capillaries: from human genomic DNA directly to called bases Masahiko Hashimoto, Yan He, and Edward S. Yeung PMCID: PMC153753 A functional analysis of disease-associated mutations in the androgen receptor gene Sean D. Mooney, Teri E. Klein, Russ B. Altman, Mark A. Trifiro, and Bruce Gottlieb PMCID: PMC153754 Multiplexed SNP genotyping using the Qbead™ system: a quantum dot-encoded microsphere-based assay Hongxia Xu, Michael Y. Sha, Edith Y. Wong, Janet Uphoff, Yanzhang Xu, Joseph A. Treadway, Anh Truong, Eamonn O’Brien, Steven Asquith, Michael Stubbins, Nigel K. Spurr, Eric H. Lai, and Walt Mahoney PMCID: PMC153755 Tagging muscle cell lineages in development and tail regeneration using Cre recombinase in transgenic Xenopus Gerhart U. Ryffel, Dagmar Werdien, Gülüzar Turan, Andrea Gerhards, Stefan Gooßes, and Sabine Senkel PMCID: PMC153756 A new minor groove binding asymmetric cyanine reporter dye for real-time PCR Martin Bengtsson, H. Jonas Karlsson, Gunnar Westman, and Mikael Kubista PMCID: PMC153757 The hepatitis C virus internal ribosome entry site facilitates efficient protein synthesis in blood vessel endothelium during tumour angiogenesis Grace T. Y. Chung, Yoshihiro Yamada, Richard Pannell, Alan Forster, and Terence H. Rabbitts PMCID: PMC153758 |
