Nucleic Acids Research

Survey and Summary:

Krzysztof Ginalski, Nick V. Grishin, Adam Godzik, and Leszek Rychlewski

Practical lessons from protein structure prediction
Nucl. Acids Res. 2005 33: 1874-1891; doi:10.1093/nar/gki327 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Articles:

Alexander V. Sverdlov, Igor B. Rogozin, Vladimir N. Babenko, and Eugene V. Koonin

Conservation versus parallel gains in intron evolution
Nucl. Acids Res. 2005 33: 1741-1748; doi:10.1093/nar/gki316 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Miha Plevnik, Zofia Gdaniec, and Janez Plavec

Solution structure of a modified 2',5'-linked RNA hairpin involved in an equilibrium with duplex
Nucl. Acids Res. 2005 33: 1749-1759; doi:10.1093/nar/gki318 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Eva Jindrova, Stefanie Schmid-Nuoffer, Fabienne Hamburger, Pavel Janscak, and Thomas A. Bickle

On the DNA cleavage mechanism of Type I restriction enzymes
Nucl. Acids Res. 2005 33: 1760-1766; doi:10.1093/nar/gki322 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Raman Narukulla, David E. G. Shuker, and Yao-Zhong Xu

Post-synthetic and site-specific modification of endocyclic nitrogen atoms of purines in DNA and its potential for biological and structural studies
Nucl. Acids Res. 2005 33: 1767-1778; doi:10.1093/nar/gki315 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Pierre Mignon, Stefan Loverix, Jan Steyaert, and Paul Geerlings

Influence of the – interaction on the hydrogen bonding capacity of stacked DNA/RNA bases
Nucl. Acids Res. 2005 33: 1779-1789; doi:10.1093/nar/gki317 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Søren Lindemose, Peter E. Nielsen, and Niels Erik Møllegaard

Polyamines preferentially interact with bent adenine tracts in double-stranded DNA
Nucl. Acids Res. 2005 33: 1790-1803; doi:10.1093/nar/gki319 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Nadia Pedullà, Rocco Palermo, David Hasenöhrl, Udo Bläsi, Piero Cammarano, and Paola Londei

The archaeal eIF2 homologue: functional properties of an ancient translation initiation factor
Nucl. Acids Res. 2005 33: 1804-1812; doi:10.1093/nar/gki321 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Luisa Luna, Veslemøy Rolseth, Gunn A. Hildrestrand, Marit Otterlei, Françoise Dantzer, Magnar Bjørås, and Erling Seeberg

Dynamic relocalization of hOGG1 during the cell cycle is disrupted in cells harbouring the hOGG1-Cys³²⁶ polymorphic variant
Nucl. Acids Res. 2005 33: 1813-1824; doi:10.1093/nar/gki325 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ewan P. Plant and Jonathan D. Dinman

Torsional restraint: a new twist on frameshifting pseudoknots
Nucl. Acids Res. 2005 33: 1825-1833; doi:10.1093/nar/gki329 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shibin Qiu, Coen M. Adema, and Terran Lane

A computational study of off-target effects of RNA interference
Nucl. Acids Res. 2005 33: 1834-1847; doi:10.1093/nar/gki324 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Keiichiro Suzuki, Akihiro Kato, Yoshiyuki Sakuraba, and Hirokazu Inoue

Srs2 and RecQ homologs cooperate in mei-3-mediated homologous recombination repair of Neurospora crassa
Nucl. Acids Res. 2005 33: 1848-1858; doi:10.1093/nar/gki326 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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

The liver-enriched transcription factor CREB-H is a growth suppressor protein underexpressed in hepatocellular carcinoma
Nucl. Acids Res. 2005 33: 1859-1873; doi:10.1093/nar/gki332 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zhe Yang, John R. Horton, Robert Maunus, Geoffrey G. Wilson, Richard J. Roberts, and Xiaodong Cheng

Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI
Nucl. Acids Res. 2005 33: 1892-1901; doi:10.1093/nar/gki337 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Musa M. Mhlanga, Diana Y. Vargas, Cindy W. Fung, Fred Russell Kramer, and Sanjay Tyagi

tRNA-linked molecular beacons for imaging mRNAs in the cytoplasm of living cells
Nucl. Acids Res. 2005 33: 1902-1912; doi:10.1093/nar/gki302 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Marc-André Langlois, Rupert C. L. Beale, Silvestro G. Conticello, and Michael S. Neuberger

Mutational comparison of the single-domained APOBEC3C and double-domained APOBEC3F/G anti-retroviral cytidine deaminases provides insight into their DNA target site specificities
Nucl. Acids Res. 2005 33: 1913-1923; doi:10.1093/nar/gki343 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Kazuhiro Karaya, Seiichi Mori, Hisashi Kimoto, Yoko Shima, Yoshihito Tsuji, Hisanori Kurooka, Shizuo Akira, and Yoshifumi Yokota

Regulation of Id2 expression by CCAAT/enhancer binding protein ß
Nucl. Acids Res. 2005 33: 1924-1934; doi:10.1093/nar/gki339 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Robert Castelo, Alexandre Reymond, Carine Wyss, Francisco Câmara, Genís Parra, Stylianos E. Antonarakis, Roderic Guigó, and Eduardo Eyras

Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes
Nucl. Acids Res. 2005 33: 1935-1939; doi:10.1093/nar/gki328 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Richard T. Pon and Shuyuan Yu

Tandem oligonucleotide synthesis using linker phosphoramidites
Nucl. Acids Res. 2005 33: 1940-1948; doi:10.1093/nar/gki333 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Dagmar K. Willkomm, Jens Minnerup, Alexander Hüttenhofer, and Roland K. Hartmann

Experimental RNomics in Aquifex aeolicus: identification of small non-coding RNAs and the putative 6S RNA homolog
Nucl. Acids Res. 2005 33: 1949-1960; doi:10.1093/nar/gki334 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ludovic C. J. Gillet, Jawad Alzeer, and Orlando D. Schärer

Site-specific incorporation of N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-AAF) into oligonucleotides using modified ‘ultra-mild’ DNA synthesis
Nucl. Acids Res. 2005 33: 1961-1969; doi:10.1093/nar/gki335 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jean-Guillaume Renisio, Sylvain Cosquer, Ilham Cherrak, Saïd El Antri, Olivier Mauffret, and Serge Fermandjian

Pre-organized structure of viral DNA at the binding-processing site of HIV-1 integrase
Nucl. Acids Res. 2005 33: 1970-1981; doi:10.1093/nar/gki346 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Danxu Liu, Paul Crellin, and Ronald Chalmers

Cyclic changes in the affinity of protein–DNA interactions drive the progression and regulate the outcome of the Tn10 transposition reaction
Nucl. Acids Res. 2005 33: 1982-1992; doi:10.1093/nar/gki348 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tomohiro Anzai, Mizuko Osanai, Mitsuhiro Hamada, and Haruhiko Fujiwara

Functional roles of 3'-terminal structures of template RNA during in vivo retrotransposition of non-LTR retrotransposon, R1Bm
Nucl. Acids Res. 2005 33: 1993-2002; doi:10.1093/nar/gki347 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yvonne Ihle, Oliver Ohlenschläger, Sabine Häfner, Elke Duchardt, Martin Zacharias, Simone Seitz, Roland Zell, Ramadurai Ramachandran, and Matthias Görlach

A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA
Nucl. Acids Res. 2005 33: 2003-2011; doi:10.1093/nar/gki501 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ema Kikovska, Mathias Brännvall, Joanna Kufel, and Leif A. Kirsebom

Substrate discrimination in RNase P RNA-mediated cleavage: importance of the structural environment of the RNase P cleavage site
Nucl. Acids Res. 2005 33: 2012-2021; doi:10.1093/nar/gki344 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Iulian N. Rujan, J. Carlin Meleney, and Philip H. Bolton

Vertebrate telomere repeat DNAs favor external loop propeller quadruplex structures in the presence of high concentrations of potassium
Nucl. Acids Res. 2005 33: 2022-2031; doi:10.1093/nar/gki345 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jonathan Perreault, Jean-François Noël, Francis Brière, Benoit Cousineau, Jean-François Lucier, Jean-Pierre Perreault, and Gilles Boire

Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs
Nucl. Acids Res. 2005 33: 2032-2041; doi:10.1093/nar/gki504 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Åsa B. Birgisdottir and Steinar Johansen

Site-specific reverse splicing of a HEG-containing group I intron in ribosomal RNA
Nucl. Acids Res. 2005 33: 2042-2051; doi:10.1093/nar/gki341 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alla I. Kalmykova, Mikhail S. Klenov, and Vladimir A. Gvozdev

Argonaute protein PIWI controls mobilization of retrotransposons in the Drosophila male germline
Nucl. Acids Res. 2005 33: 2052-2059; doi:10.1093/nar/gki323 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Corrigendum:

Aguan Wei, Alex Yuan, Gloria Fawcett, Alice Butler, Theodore Davis, Shuang-yong Xu, and Lawrence Salkoff

Efficient isolation of targeted Caenorhabditis elegans deletion strains using highly thermostable restriction endonucleases and PCR
Nucl. Acids Res. 2005 33: 2060; doi:10.1093/nar/gki340 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Dov J. Stekel, Donatella Sarti, Victor Trevino, Lihong Zhang, Mike Salmon, Chris D. Buckley, Mark Stevens, Mark J. Pallen, Charles Penn, and Francesco Falciani

Analysis of host response to bacterial infection using error model based gene expression microarray experiments
Nucl. Acids Res. 2005 33: e53; doi:10.1093/nar/gni050 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alexandra Paillusson, Nadine Hirschi, Claudio Vallan, Claus M. Azzalin, and Oliver Mühlemann

A GFP-based reporter system to monitor nonsense-mediated mRNA decay
Nucl. Acids Res. 2005 33: e54; doi:10.1093/nar/gni052 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Brock F. Binkowski, Kathryn E. Richmond, James Kaysen, Michael R. Sussman, and Peter J. Belshaw

Correcting errors in synthetic DNA through consensus shuffling
Nucl. Acids Res. 2005 33: e55; doi:10.1093/nar/gni053 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Sandrine Imbeaud, Esther Graudens, Virginie Boulanger, Xavier Barlet, Patrick Zaborski, Eric Eveno, Odilo Mueller, Andreas Schroeder, and Charles Auffray

Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces
Nucl. Acids Res. 2005 33: e56; doi:10.1093/nar/gni054 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Nuo Yang, Lin Zhang, and Haig H. Kazazian, Jr

L1 retrotransposon-mediated stable gene silencing
Nucl. Acids Res. 2005 33: e57; doi:10.1093/nar/gni056 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Markus Fuhrmann, Wolfgang Oertel, Peter Berthold, and Peter Hegemann

Removal of mismatched bases from synthetic genes by enzymatic mismatch cleavage
Nucl. Acids Res. 2005 33: e58; doi:10.1093/nar/gni058 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Queenie N. Y. Wong, Vivian C. W. Ng, Marie C. M. Lin, Hsiang-fu Kung, Danny Chan, and Jian-Dong Huang

Efficient and seamless DNA recombineering using a thymidylate synthase A selection system in Escherichia coli
Nucl. Acids Res. 2005 33: e59; doi:10.1093/nar/gni059 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Michael Jahnz and Petra Schwille

An ultrasensitive site-specific DNA recombination assay based on dual-color fluorescence cross-correlation spectroscopy
Nucl. Acids Res. 2005 33: e60; doi:10.1093/nar/gni060 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Liusheng He, Xiaoli Wu, James Simone, Derek Hewgill, and Peter E. Lipsky

Determination of tumor necrosis factor receptor-associated factor trimerization in living cells by CFPYFPmRFP FRET detected by flow cytometry
Nucl. Acids Res. 2005 33: e61; doi:10.1093/nar/gni057 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hongxia Zhou, Xu Gang Xia, and Zuoshang Xu

An RNA polymerase II construct synthesizes short-hairpin RNA with a quantitative indicator and mediates highly efficient RNAi
Nucl. Acids Res. 2005 33: e62; doi:10.1093/nar/gni061 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

David Markusic, Ronald Oude-Elferink, Atze T. Das, Ben Berkhout, and Jurgen Seppen

Comparison of single regulated lentiviral vectors with rtTA expression driven by an autoregulatory loop or a constitutive promoter
Nucl. Acids Res. 2005 33: e63; doi:10.1093/nar/gni062 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Daniel A. Di Giusto, Wjatschesslaw A. Wlassoff, J. Justin Gooding, Barbara A. Messerle, and Garry C. King

Proximity extension of circular DNA aptamers with real-time protein detection
Nucl. Acids Res. 2005 33: e64; doi:10.1093/nar/gni063 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Daiji Endoh, Tetsuya Mizutani, Rikio Kirisawa, Yoshiyuki Maki, Hidetoshi Saito, Yasuhiro Kon, Shigeru Morikawa, and Masanobu Hayashi

Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription
Nucl. Acids Res. 2005 33: e65; doi:10.1093/nar/gni064 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

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