| | Chemistry and Synthetic Biology Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2′,4′-bridged nucleosides Masayasu Kuwahara, Satoshi Obika, Jun-ichi Nagashima, Yuki Ohta, Yoshiyuki Suto, Hiroaki Ozaki, Hiroaki Sawai, and Takeshi Imanishi PMCID: PMC2490744 Editorial Nucleic Acids Res. 2008 August; 36(13): 4221. Published online 2008 August. doi: 10.1093/nar/gkn478.PMCID: PMC2490764 Gene Regulation, Chromatin and Epigenetics Physical and functional characterization of the genetic locus of IBtk, an inhibitor of Bruton's tyrosine kinase: evidence for three protein isoforms of IBtk Carmen Spatuzza, Marco Schiavone, Emanuela Di Salle, Elzbieta Janda, Marco Sardiello, Giuseppe Fiume, Olga Fierro, Marco Simonetta, Notis Argiriou, Raffaella Faraonio, Rosanna Capparelli, Ileana Quinto, and Giuseppe Scala PMCID: PMC2490745 TAp73β and DNp73β activate the expression of the pro-survival caspase-2S Wen Hong Toh, Emmanuelle Logette, Laurent Corcos, and Kanaga Sabapathy PMCID: PMC2490756 Requirement of histone deacetylase1 (HDAC1) in signal transducer and activator of transcription 3 (STAT3) nucleocytoplasmic distribution Sutapa Ray, Chang Lee, Tieying Hou, Istvan Boldogh, and Allan R. Brasier PMCID: PMC2490754 Molecular Biology p73α isoforms drive opposite transcriptional and post-transcriptional regulation of MYCN expression in neuroblastoma cells Emilie Horvilleur, Matthieu Bauer, David Goldschneider, Xénia Mergui, Alix de La Motte, Jean Bénard, Sétha Douc-Rasy, and David Cappellen PMCID: PMC2490757 Minigene-like inhibition of protein synthesis mediated by hungry codons near the start codon Eva Jacinto-Loeza, Serafín Vivanco-Domínguez, Gabriel Guarneros, and Javier Hernández-Sánchez PMCID: PMC2490762 Filament formation and robust strand exchange activities of the rice DMC1A and DMC1B proteins Isao Sakane, Chiaki Kamataki, Yoshimasa Takizawa, Marina Nakashima, Seiichi Toki, Hiroaki Ichikawa, Shukuko Ikawa, Takehiko Shibata, and Hitoshi Kurumizaka PMCID: PMC2490746 The Zur of Xanthomonas campestris functions as a repressor and an activator of putative zinc homeostasis genes via recognizing two distinct sequences within its target promoters Dong-Liang Huang, Dong-Jie Tang, Qing Liao, Heng-Cong Li, Qi Chen, Yong-Qiang He, Jia-Xun Feng, Bo-Le Jiang, Guang-Tao Lu, Baoshan Chen, and Ji-Liang Tang PMCID: PMC2490734 YacG from Escherichia coli is a specific endogenous inhibitor of DNA gyrase Sugopa Sengupta and Valakunja Nagaraja PMCID: PMC2490753 The Ty1 integrase protein can exploit the classical nuclear protein import machinery for entry into the nucleus Laura M. McLane, Kanika F. Pulliam, Scott E. Devine, and Anita H. Corbett PMCID: PMC2490736 A new APE1/Ref-1-dependent pathway leading to reduction of NF-κB and AP-1, and activation of their DNA-binding activity Kozue Ando, Satoshi Hirao, Yasuaki Kabe, Yuji Ogura, Iwao Sato, Yuki Yamaguchi, Tadashi Wada, and Hiroshi Handa PMCID: PMC2490748 Nuclear epidermal growth factor receptor (EGFR) interacts with signal transducer and activator of transcription 5 (STAT5) in activating Aurora-A gene expression Liang-Yi Hung, Joseph T. Tseng, Yi-Chao Lee, Weiya Xia, Ying-Nai Wang, Min-Li Wu, Yu-Hsuan Chuang, Chein-Hsien Lai, and Wen-Chang Chang PMCID: PMC2490761 Subnanomolar antisense activity of phosphonate-peptide nucleic acid (PNA) conjugates delivered by cationic lipids to HeLa cells Takehiko Shiraishi, Ramin Hamzavi, and Peter E. Nielsen PMCID: PMC2490735 The structure of the 5′-end of the protein-tyrosine phosphatase PTPRJ mRNA reveals a novel mechanism for translation attenuation Luchezar Karagyozov, Rinesh Godfrey, Sylvia-Annette Böhmer, Astrid Petermann, Sebastian Hölters, Arne Östman, and Frank-D. Böhmer PMCID: PMC2490741 PARP inhibition versus PARP-1 silencing: different outcomes in terms of single-strand break repair and radiation susceptibility Camille Godon, Fabrice P. Cordelières, Denis Biard, Nicole Giocanti, Frédérique Mégnin-Chanet, Janet Hall, and Vincent Favaudon PMCID: PMC2490739 RNA Dispatched Homolog 2 is targeted by miR-214 through a combination of three weak microRNA recognition sites Nan Li, Alex S. Flynt, H. Rosemary Kim, Lilianna Solnica-Krezel, and James G. Patton PMCID: PMC2490740 Destabilization of the TAR hairpin affects the structure and function of the HIV-1 leader RNA Martine M. Vrolijk, Marcel Ooms, Alex Harwig, Atze T. Das, and Ben Berkhout PMCID: PMC2490758 Mrd1p binds to pre-rRNA early during transcription independent of U3 snoRNA and is required for compaction of the pre-rRNA into small subunit processomes Åsa Segerstolpe, Pär Lundkvist, Yvonne N. Osheim, Ann L. Beyer, and Lars Wieslander PMCID: PMC2490760 p100 increases AT1R expression through interaction with AT1R 3′-UTR Kirsi Paukku, Nisse Kalkkinen, Olli Silvennoinen, Kimmo K. Kontula, and Jukka Y. A. Lehtonen PMCID: PMC2490763 Structural Biology A protein functional leap: how a single mutation reverses the function of the transcription regulator TetR Marcus Resch, Harald Striegl, Eva Maria Henssler, Madhumati Sevvana, Claudia Egerer-Sieber, Emile Schiltz, Wolfgang Hillen, and Yves A. Muller PMCID: PMC2490752 Effect of loop length variation on quadruplex-Watson Crick duplex competition Niti Kumar, Bankanidhi Sahoo, K. A. S. Varun, Sudipta Maiti, and Souvik Maiti PMCID: PMC2490738 Survey and Summary See me, feel me: methods to concurrently visualize and manipulate single DNA molecules and associated proteins Joost van Mameren, Erwin J. G. Peterman, and Gijs J. L. Wuite PMCID: PMC2490750 Genomics Effect of polymorphisms within probe–target sequences on olignonucleotide microarray experiments David Benovoy, Tony Kwan, and Jacek Majewski PMCID: PMC2490733 Methods Online Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx) Amy J. Baldwin, Kathy Busse, Alan M. Simm, and D. Dafydd Jones PMCID: PMC2490759 Linking the functions of unrelated proteins using a novel directed evolution domain insertion method Wayne R. Edwards, Kathy Busse, Rudolf K. Allemann, and D. Dafydd Jones PMCID: PMC2490766 Primase-based whole genome amplification Ying Li, Hyun-Jin Kim, Chunyang Zheng, Wing Huen A. Chow, Jeonghwa Lim, Brendan Keenan, Xiaojing Pan, Bertrand Lemieux, and Huimin Kong PMCID: PMC2490742 Impact of whole genome amplification on analysis of copy number variants T. J. Pugh, A. D. Delaney, N. Farnoud, S. Flibotte, M. Griffith, H. I. Li, H. Qian, P. Farinha, R. D. Gascoyne, and M. A. Marra PMCID: PMC2490749 Quick identification of Type I restriction enzyme isoschizomers using newly developed pTypeI and reference plasmids Junichi Ryu and Edward Rowsell PMCID: PMC2490747 Long-range, high-throughput haplotype determination via haplotype-fusion PCR and ligation haplotyping Daniel J. Turner, Chris Tyler-Smith, and Matthew E. Hurles PMCID: PMC2490767 Conditional gene vectors regulated in cis Dagmar Pich, Sibille Humme, Mark-Peter Spindler, Aloys Schepers, and Wolfgang Hammerschmidt PMCID: PMC2490737 Computational Biology Global investigation of protein–protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences S. Pitre, C. North, M. Alamgir, M. Jessulat, A. Chan, X. Luo, J. R. Green, M. Dumontier, F. Dehne, and A. Golshani PMCID: PMC2490765 MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs Jianfei Hu, Haiyan Hu, and Xiaoman Li PMCID: PMC2490743 Nucleic Acid Enzymes Mechanism and substrate specificity of telomeric protein POT1 stimulation of the Werner syndrome helicase Gregory Sowd, Ming Lei, and Patricia L. Opresko PMCID: PMC2490755 TbMP42 is a structure-sensitive ribonuclease that likely follows a metal ion catalysis mechanism Moritz Niemann, Michael Brecht, Elke Schlüter, Kerstin Weitzel, Martin Zacharias, and H. Ulrich Göringer PMCID: PMC2490751 |
