| | Survey and Summary Practical lessons from protein structure prediction Krzysztof Ginalski, Nick V. Grishin, Adam Godzik, and Leszek Rychlewski PMCID: PMC1074308 Articles Conservation versus parallel gains in intron evolution Alexander V. Sverdlov, Igor B. Rogozin, Vladimir N. Babenko, and Eugene V. Koonin PMCID: PMC1069513 Solution structure of a modified 2′,5′-linked RNA hairpin involved in an equilibrium with duplex Miha Plevnik, Zofia Gdaniec, and Janez Plavec PMCID: PMC1069515 On the DNA cleavage mechanism of Type I restriction enzymes Eva Jindrova, Stefanie Schmid-Nuoffer, Fabienne Hamburger, Pavel Janscak, and Thomas A. Bickle PMCID: PMC1069518 Post-synthetic and site-specific modification of endocyclic nitrogen atoms of purines in DNA and its potential for biological and structural studies Raman Narukulla, David E. G. Shuker, and Yao-Zhong Xu PMCID: PMC1069512 Influence of the π–π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases Pierre Mignon, Stefan Loverix, Jan Steyaert, and Paul Geerlings PMCID: PMC1069514 Polyamines preferentially interact with bent adenine tracts in double-stranded DNA Søren Lindemose, Peter E. Nielsen, and Niels Erik Møllegaard PMCID: PMC1069516 The archaeal eIF2 homologue: functional properties of an ancient translation initiation factor Nadia Pedullà, Rocco Palermo, David Hasenöhrl, Udo Bläsi, Piero Cammarano, and Paola Londei PMCID: PMC1069517 Dynamic relocalization of hOGG1 during the cell cycle is disrupted in cells harbouring the hOGG1-Cys326 polymorphic variant Luisa Luna, Veslemøy Rolseth, Gunn A. Hildrestrand, Marit Otterlei, Françoise Dantzer, Magnar Bjørås, and Erling Seeberg PMCID: PMC1072800 Torsional restraint: a new twist on frameshifting pseudoknots Ewan P. Plant and Jonathan D. Dinman PMCID: PMC1072802 A computational study of off-target effects of RNA interference Shibin Qiu, Coen M. Adema, and Terran Lane PMCID: PMC1072799 Srs2 and RecQ homologs cooperate in mei-3-mediated homologous recombination repair of Neurospora crassa Keiichiro Suzuki, Akihiro Kato, Yoshiyuki Sakuraba, and Hirokazu Inoue PMCID: PMC1072801 The liver-enriched transcription factor CREB-H is a growth suppressor protein underexpressed in hepatocellular carcinoma King-Tung Chin, Hai-Jun Zhou, Chun-Ming Wong, Joyce Man-Fong Lee, Ching-Ping Chan, Bo-Qin Qiang, Jian-Gang Yuan, Irene Oi-lin Ng, and Dong-Yan Jin PMCID: PMC1072803 Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI Zhe Yang, John R. Horton, Robert Maunus, Geoffrey G. Wilson, Richard J. Roberts, and Xiaodong Cheng PMCID: PMC1074309 tRNA-linked molecular beacons for imaging mRNAs in the cytoplasm of living cells Musa M. Mhlanga, Diana Y. Vargas, Cindy W. Fung, Fred Russell Kramer, and Sanjay Tyagi PMCID: PMC1074395 Mutational comparison of the single-domained APOBEC3C and double-domained APOBEC3F/G anti-retroviral cytidine deaminases provides insight into their DNA target site specificities Marc-André Langlois, Rupert C. L. Beale, Silvestro G. Conticello, and Michael S. Neuberger PMCID: PMC1074398 Regulation of Id2 expression by CCAAT/enhancer binding protein β Kazuhiro Karaya, Seiichi Mori, Hisashi Kimoto, Yoko Shima, Yoshihito Tsuji, Hisanori Kurooka, Shizuo Akira, and Yoshifumi Yokota PMCID: PMC1074397 Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes Robert Castelo, Alexandre Reymond, Carine Wyss, Francisco Câmara, Genís Parra, Stylianos E. Antonarakis, Roderic Guigó, and Eduardo Eyras PMCID: PMC1074396 Tandem oligonucleotide synthesis using linker phosphoramidites Richard T. Pon and Shuyuan Yu PMCID: PMC1074720 Experimental RNomics in Aquifex aeolicus: identification of small non-coding RNAs and the putative 6S RNA homolog Dagmar K. Willkomm, Jens Minnerup, Alexander Hüttenhofer, and Roland K. Hartmann PMCID: PMC1074721 Site-specific incorporation of N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-AAF) into oligonucleotides using modified ‘ultra-mild’ DNA synthesis Ludovic C. J. Gillet, Jawad Alzeer, and Orlando D. Schärer PMCID: PMC1074722 Pre-organized structure of viral DNA at the binding-processing site of HIV-1 integrase Jean-Guillaume Renisio, Sylvain Cosquer, Ilham Cherrak, Saïd El Antri, Olivier Mauffret, and Serge Fermandjian PMCID: PMC1074723 Cyclic changes in the affinity of protein–DNA interactions drive the progression and regulate the outcome of the Tn10 transposition reaction Danxu Liu, Paul Crellin, and Ronald Chalmers PMCID: PMC1074725 Functional roles of 3′-terminal structures of template RNA during in vivo retrotransposition of non-LTR retrotransposon, R1Bm Tomohiro Anzai, Mizuko Osanai, Mitsuhiro Hamada, and Haruhiko Fujiwara PMCID: PMC1074724 A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA Yvonne Ihle, Oliver Ohlenschläger, Sabine Häfner, Elke Duchardt, Martin Zacharias, Simone Seitz, Roland Zell, Ramadurai Ramachandran, and Matthias Görlach PMCID: PMC1074726 Substrate discrimination in RNase P RNA-mediated cleavage: importance of the structural environment of the RNase P cleavage site Ema Kikovska, Mathias Brännvall, Joanna Kufel, and Leif A. Kirsebom PMCID: PMC1074746 Vertebrate telomere repeat DNAs favor external loop propeller quadruplex structures in the presence of high concentrations of potassium Iulian N. Rujan, J. Carlin Meleney, and Philip H. Bolton PMCID: PMC1074753 Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs Jonathan Perreault, Jean-François Noël, Francis Brière, Benoit Cousineau, Jean-François Lucier, Jean-Pierre Perreault, and Gilles Boire PMCID: PMC1074747 Site-specific reverse splicing of a HEG-containing group I intron in ribosomal RNA Åsa B. Birgisdottir and Steinar Johansen PMCID: PMC1074745 Argonaute protein PIWI controls mobilization of retrotransposons in the Drosophila male germline Alla I. Kalmykova, Mikhail S. Klenov, and Vladimir A. Gvozdev PMCID: PMC1074743 Methods Online Analysis of host response to bacterial infection using error model based gene expression microarray experiments Dov J. Stekel, Donatella Sarti, Victor Trevino, Lihong Zhang, Mike Salmon, Chris D. Buckley, Mark Stevens, Mark J. Pallen, Charles Penn, and Francesco Falciani PMCID: PMC1072804 A GFP-based reporter system to monitor nonsense-mediated mRNA decay Alexandra Paillusson, Nadine Hirschi, Claudio Vallan, Claus M. Azzalin, and Oliver Mühlemann PMCID: PMC1072805 Correcting errors in synthetic DNA through consensus shuffling Brock F. Binkowski, Kathryn E. Richmond, James Kaysen, Michael R. Sussman, and Peter J. Belshaw PMCID: PMC1072806 Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces Sandrine Imbeaud, Esther Graudens, Virginie Boulanger, Xavier Barlet, Patrick Zaborski, Eric Eveno, Odilo Mueller, Andreas Schroeder, and Charles Auffray PMCID: PMC1072807 L1 retrotransposon-mediated stable gene silencing Nuo Yang, Lin Zhang, and Haig H. Kazazian, Jr PMCID: PMC1072808 Removal of mismatched bases from synthetic genes by enzymatic mismatch cleavage Markus Fuhrmann, Wolfgang Oertel, Peter Berthold, and Peter Hegemann PMCID: PMC1072809 Efficient and seamless DNA recombineering using a thymidylate synthase A selection system in Escherichia coli Queenie N. Y. Wong, Vivian C. W. Ng, Marie C. M. Lin, Hsiang-fu Kung, Danny Chan, and Jian-Dong Huang PMCID: PMC1072810 An ultrasensitive site-specific DNA recombination assay based on dual-color fluorescence cross-correlation spectroscopy Michael Jahnz and Petra Schwille PMCID: PMC1074182 Determination of tumor necrosis factor receptor-associated factor trimerization in living cells by CFP→YFP→mRFP FRET detected by flow cytometry Liusheng He, Xiaoli Wu, James Simone, Derek Hewgill, and Peter E. Lipsky PMCID: PMC1074310 An RNA polymerase II construct synthesizes short-hairpin RNA with a quantitative indicator and mediates highly efficient RNAi Hongxia Zhou, Xu Gang Xia, and Zuoshang Xu PMCID: PMC1074311 Comparison of single regulated lentiviral vectors with rtTA expression driven by an autoregulatory loop or a constitutive promoter David Markusic, Ronald Oude-Elferink, Atze T. Das, Ben Berkhout, and Jurgen Seppen PMCID: PMC1074399 Proximity extension of circular DNA aptamers with real-time protein detection Daniel A. Di Giusto, Wjatschesslaw A. Wlassoff, J. Justin Gooding, Barbara A. Messerle, and Garry C. King PMCID: PMC1074748 Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription Daiji Endoh, Tetsuya Mizutani, Rikio Kirisawa, Yoshiyuki Maki, Hidetoshi Saito, Yasuhiro Kon, Shigeru Morikawa, and Masanobu Hayashi PMCID: PMC1074749 Corrigendum Efficient isolation of targeted Caenorhabditis elegans deletion strains using highly thermostable restriction endonucleases and PCR Aguan Wei, Alex Yuan, Gloria Fawcett, Alice Butler, Theodore Davis, Shuang-yong Xu, and Lawrence Salkoff PMCID: PMC1074744 Corrects: Aguan Wei, et al. Efficient isolation of targeted Caenorhabditis elegans deletion strains using highly thermostable restriction endonucleases and PCR. Nucleic Acids Res. 2002 October 15; 30(20): e110. |
