Nucleic Acids Research

Survey and Summary

Get checked abstract Eugene V. Koonin and Yuri I. Wolf

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2008 36: 6688-6719; doi:10.1093/nar/gkn668 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chemistry and Synthetic Biology

Get checked abstract Georges Lahoud, Khalil Arar, Ya-Ming Hou, and Howard Gamper

RecA-mediated strand invasion of DNA by oligonucleotides substituted with 2-aminoadenine and 2-thiothymine
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2008 36: 6806-6815; doi:10.1093/nar/gkn755 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Computational Biology

Get checked abstract Umadevi Paila, Rohini Kondam, and Akash Ranjan

Genome bias influences amino acid choices: analysis of amino acid substitution and re-compilation of substitution matrices exclusive to an AT-biased genome
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2008 36: 6664-6675; doi:10.1093/nar/gkn635 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Antonio Starcevic, Jurica Zucko, Jurica Simunkovic, Paul F. Long, John Cullum, and Daslav Hranueli

ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures
Nucleic Acids Research Advance Access published on October 31, 2008
Nucl. Acids Res. 2008 36: 6882-6892; doi:10.1093/nar/gkn685 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gene regulation, Chromatin and Epigenetics

Get checked abstract Renata Z. Jurkowska, Nils Anspach, Claus Urbanke, Da Jia, Richard Reinhardt, Wolfgang Nellen, Xiaodong Cheng, and Albert Jeltsch

Formation of nucleoprotein filaments by mammalian DNA methyltransferase Dnmt3a in complex with regulator Dnmt3L
Nucleic Acids Research Advance Access published on October 22, 2008
Nucl. Acids Res. 2008 36: 6656-6663; doi:10.1093/nar/gkn747 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Maude Guillier and Susan Gottesman

The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2008 36: 6781-6794; doi:10.1093/nar/gkn742 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Mark Koudritsky and Eytan Domany

Positional distribution of human transcription factor binding sites
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2008 36: 6795-6805; doi:10.1093/nar/gkn752 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Sílvia Pérez-Lluch, Sergi Cuartero, Fernando Azorín, and M. Lluïsa Espinàs

Characterization of new regulatory elements within the Drosophila bithorax complex
Nucleic Acids Research Advance Access published on October 31, 2008
Nucl. Acids Res. 2008 36: 6926-6933; doi:10.1093/nar/gkn818 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genome integrity, repair and replication

Get checked abstract Dávid Szüts, Adam P. Marcus, Masayuki Himoto, Shigenori Iwai, and Julian E. Sale

REV1 restrains DNA polymerase to ensure frame fidelity during translesion synthesis of UV photoproducts in vivo
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2008 36: 6767-6780; doi:10.1093/nar/gkn651 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Michael Kappeler, Elisabeth Kranz, Katrina Woolcock, Oleg Georgiev, and Walter Schaffner

Drosophila bloom helicase maintains genome integrity by inhibiting recombination between divergent DNA sequences
Nucleic Acids Research Advance Access published on October 31, 2008
Nucl. Acids Res. 2008 36: 6907-6917; doi:10.1093/nar/gkn793 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics

Get checked abstract Kayole Kazadi, Corinne Loeuillet, Samuel Deutsch, Angela Ciuffi, Miguel Muñoz, Jacques S. Beckmann, Darius Moradpour, Stylianos E. Antonarakis, and Amalio Telenti

Genomic determinants of the efficiency of internal ribosomal entry sites of viral and cellular origin
Nucleic Acids Research Advance Access published on October 31, 2008
Nucl. Acids Res. 2008 36: 6918-6925; doi:10.1093/nar/gkn812 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract Kevin P. Callahan and J. Scott Butler

Evidence for core exosome independent function of the nuclear exoribonuclease Rrp6p
Nucleic Acids Research Advance Access published on October 21, 2008
Nucl. Acids Res. 2008 36: 6645-6655; doi:10.1093/nar/gkn743 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Go Hirokawa, Nobuhiro Iwakura, Akira Kaji, and Hideko Kaji

The role of GTP in transient splitting of 70S ribosomes by RRF (ribosome recycling factor) and EF-G (elongation factor G)
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2008 36: 6676-6687; doi:10.1093/nar/gkn647 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Monique E. Beaudoin, Vincent-Joseph Poirel, and Leslie A. Krushel

Regulating amyloid precursor protein synthesis through an internal ribosomal entry site
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2008 36: 6835-6847; doi:10.1093/nar/gkn792 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Terumasa Ikeda, Takeo Ohsugi, Tetsuya Kimura, Shuzo Matsushita, Yosuke Maeda, Shinji Harada, and Atsushi Koito

The antiretroviral potency of APOBEC1 deaminase from small animal species
Nucleic Acids Research Advance Access published on October 29, 2008
Nucl. Acids Res. 2008 36: 6859-6871; doi:10.1093/nar/gkn802 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes

Get checked abstract Richard D. Hutton, Jennifer A. Roberts, J. Carlos Penedo, and Malcolm F. White

PCNA stimulates catalysis by structure-specific nucleases using two distinct mechanisms: substrate targeting and catalytic step
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2008 36: 6720-6727; doi:10.1093/nar/gkn745 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Augusto Simoes-Barbosa, Camila Louly, Octávio L. Franco, Mary A. Rubio, Juan D. Alfonzo, and Patricia J. Johnson

The divergent eukaryote Trichomonas vaginalis has an m⁷G cap methyltransferase capable of a single N2 methylation
Nucleic Acids Research Advance Access published on October 28, 2008
Nucl. Acids Res. 2008 36: 6848-6858; doi:10.1093/nar/gkn706 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Olivier Humbert and Nina R. Salama

The Helicobacter pylori HpyAXII restriction–modification system limits exogenous DNA uptake by targeting GTAC sites but shows asymmetric conservation of the DNA methyltransferase and restriction endonuclease components
Nucleic Acids Research Advance Access published on October 31, 2008
Nucl. Acids Res. 2008 36: 6893-6906; doi:10.1093/nar/gkn718 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA

Get checked abstract Naama Eldad, Yahav Yosefzon, and Yoav Arava

Identification and characterization of extensive intra-molecular associations between 3'-UTRs and their ORFs
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2008 36: 6728-6738; doi:10.1093/nar/gkn754 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Na Li, Yuxuan Wang, Arti Pothukuchy, Angel Syrett, Naeem Husain, Siddharth Gopalakrisha, Pradeepa Kosaraju, and Andrew D. Ellington

Aptamers that recognize drug-resistant HIV-1 reverse transcriptase
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2008 36: 6739-6751; doi:10.1093/nar/gkn775 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Anne Dallas, Svetlana V. Balatskaya, Tai-Chih Kuo, Heini Ilves, Alexander V. Vlassov, Roger L. Kaspar, Kevin O. Kisich, Sergei A. Kazakov, and Brian H. Johnston

Hairpin ribozyme-antisense RNA constructs can act as molecular lassos
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2008 36: 6752-6766; doi:10.1093/nar/gkn637 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Joshua C. Canzoneri and Adegboyega K. Oyelere

Interaction of anthracyclines with iron responsive element mRNAs
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2008 36: 6825-6834; doi:10.1093/nar/gkn774 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Penghui Bao, Qi-Jia Wu, Ping Yin, Yanfei Jiang, Xu Wang, Mao-Hua Xie, Tao Sun, Lin Huang, Ding-Ding Mo, and Yi Zhang

Coordination of two sequential ester-transfer reactions: exogenous guanosine binding promotes the subsequent G binding to a group I intron
Nucleic Acids Research Advance Access published on October 31, 2008
Nucl. Acids Res. 2008 36: 6934-6943; doi:10.1093/nar/gkn824 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Takashi Nagata, Yusuke Takada, Asami Ono, Kayoko Nagata, Yuki Konishi, Takeshi Nukina, Manami Ono, Akimasa Matsugami, Ayako Furukawa, Natsuki Fujimoto, Hirokazu Fukuda, Hitoshi Nakagama, and Masato Katahira

Elucidation of the mode of interaction in the UP1–telomerase RNA–telomeric DNA ternary complex which serves to recruit telomerase to telomeric DNA and to enhance the telomerase activity
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2008 36: 6816-6824; doi:10.1093/nar/gkn767 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Xiuna Yang, Masahiro Morita, Hui Wang, Toru Suzuki, Wen Yang, Yunhai Luo, Cong Zhao, Yue Yu, Mark Bartlam, Tadashi Yamamoto, and Zihe Rao

Crystal structures of human BTG2 and mouse TIS21 involved in suppression of CAF1 deadenylase activity
Nucleic Acids Research Advance Access published on October 30, 2008
Nucl. Acids Res. 2008 36: 6872-6881; doi:10.1093/nar/gkn825 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Corrigendum

Henri de Martimprey, Jean-Remi Bertrand, Alfredo Fusco, Massimo Santoro, Patrick Couvreur, Christine Vauthier, and Claude Malvy

siRNA nanoformulation against the Ret/PTC1 junction oncogene is efficient in an in vivo model of papillary thyroid carcinoma
Nucl. Acids Res. 2008 36: 6944; doi:10.1093/nar/gkn882 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online

Get checked abstract Kai Wang, Zhen Chen, Mahlet G. Tadesse, Joseph Glessner, Struan F. A. Grant, Hakon Hakonarson, Maja Bucan, and Mingyao Li

Modeling genetic inheritance of copy number variations
Nucleic Acids Research Advance Access published on October 2, 2008
Nucl. Acids Res. 2008 36: e138; doi:10.1093/nar/gkn641 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jürgen Stech, Olga Stech, Astrid Herwig, Hermann Altmeppen, Jana Hundt, Sandra Gohrbandt, Anne Kreibich, Siegfried Weber, Hans-Dieter Klenk, and Thomas C. Mettenleiter

Rapid and reliable universal cloning of influenza A virus genes by target-primed plasmid amplification
Nucleic Acids Research Advance Access published on October 2, 2008
Nucl. Acids Res. 2008 36: e139; doi:10.1093/nar/gkn646 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Peter Wettstein, Michael Strausbauch, Terry Therneau, and Nancy Borson

The application of real-time PCR to the analysis of T cell repertoires
Nucleic Acids Research Advance Access published on October 3, 2008
Nucl. Acids Res. 2008 36: e140; doi:10.1093/nar/gkn634 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Peter A. C. 't Hoen, Yavuz Ariyurek, Helene H. Thygesen, Erno Vreugdenhil, Rolf H. A. M. Vossen, Renée X. de Menezes, Judith M. Boer, Gert-Jan B. van Ommen, and Johan T. den Dunnen

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
Nucleic Acids Research Advance Access published on October 15, 2008
Nucl. Acids Res. 2008 36: e141; doi:10.1093/nar/gkn705 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Gary B. Fogel, V. William Porto, Gabor Varga, Ernst R. Dow, Andrew M. Craven, David M. Powers, Harry B. Harlow, Eric W. Su, Jude E. Onyia, and Chen Su

Evolutionary computation for discovery of composite transcription factor binding sites
Nucleic Acids Research Advance Access published on October 15, 2008
Nucl. Acids Res. 2008 36: e142; doi:10.1093/nar/gkn738 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Pieter Mestdagh, Tom Feys, Nathalie Bernard, Simone Guenther, Caifu Chen, Frank Speleman, and Jo Vandesompele

High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA
Nucleic Acids Research Advance Access published on October 21, 2008
Nucl. Acids Res. 2008 36: e143; doi:10.1093/nar/gkn725 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Romina Ponzielli, Paul C. Boutros, Sigal Katz, Angelina Stojanova, Adam P. Hanley, Fereshteh Khosravi, Christina Bros, Igor Jurisica, and Linda Z. Penn

Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies
Nucleic Acids Research Advance Access published on October 21, 2008
Nucl. Acids Res. 2008 36: e144; doi:10.1093/nar/gkn735 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 36 ISSUE 21 2008
Nucl. Acids Res. 2008 36: i; doi:10.1093/nar/gkn984 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2008 36: ii; doi:10.1093/nar/gkn983 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2008 36: iii; doi:10.1093/nar/gkn989 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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