Nucleic Acids Research

Survey and Summary:

A. Lescoute and E. Westhof

The interaction networks of structured RNAs
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2006 34: 6587-6604; doi:10.1093/nar/gkl963 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Chemistry:

Yuan Li, Hye Jin Lee, and Robert M. Corn

Fabrication and characterization of RNA aptamer microarrays for the study of protein–aptamer interactions with SPR imaging
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: 6416-6424; doi:10.1093/nar/gkl738 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Montserrat Puig, Andrzej Grajkowski, Malgorzata Boczkowska, Cristina Ausín, Serge L. Beaucage, and Daniela Verthelyi

Use of thermolytic protective groups to prevent G-tetrad formation in CpG ODN type D: structural studies and immunomodulatory activity in primates
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: 6488-6495; doi:10.1093/nar/gkl867 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Computational Biology:

Chien-Hua Peng, Jeh-Ting Hsu, Yun-Sheng Chung, Yen-Jen Lin, Wei-Yuan Chow, D. Frank Hsu, and Chuan Yi Tang

Identification of degenerate motifs using position restricted selection and hybrid ranking combination
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: 6379-6391; doi:10.1093/nar/gkl658 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Oanh T. P. Kim, Kei Yura, and Nobuhiro Go

Amino acid residue doublet propensity in the protein–RNA interface and its application to RNA interface prediction
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: 6450-6460; doi:10.1093/nar/gkl819 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Walter Pirovano, K. Anton Feenstra, and Jaap Heringa

Sequence comparison by sequence harmony identifies subtype-specific functional sites
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: 6540-6548; doi:10.1093/nar/gkl901 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Omar J. Jabado, Gustavo Palacios, Vishal Kapoor, Jeffrey Hui, Neil Renwick, Junhui Zhai, Thomas Briese, and W. Ian Lipkin

Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2006 34: 6605-6611; doi:10.1093/nar/gkl966 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Genomics:

M. Madan Babu, Lakshminarayan M. Iyer, S. Balaji, and L. Aravind

The natural history of the WRKY–GCM1 zinc fingers and the relationship between transcription factors and transposons
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: 6505-6520; doi:10.1093/nar/gkl888 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Molecular Biology:

Chun Sung Kim, Hack Sun Choi, Cheol Kyu Hwang, Kyu Young Song, Byung-Kwon Lee, Ping-Yee Law, Li-Na Wei, and Horace H. Loh

Evidence of the neuron-restrictive silencer factor (NRSF) interaction with Sp3 and its synergic repression to the mu opioid receptor (MOR) gene
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: 6392-6403; doi:10.1093/nar/gkl724 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Katharina Maniura-Weber, Mark Helm, Katrin Engemann, Sabrina Eckertz, Myriam Möllers, Matthias Schauen, Armine Hayrapetyan, Jürgen-Christoph von Kleist-Retzow, Robert N. Lightowlers, Laurence A. Bindoff, and Rudolf J. Wiesner

Molecular dysfunction associated with the human mitochondrial 3302A>G mutation in the MTTL1 (mt-tRNA^Leu(UUR)) gene
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: 6404-6415; doi:10.1093/nar/gkl727 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Tetsuya Suzuki, Kei Moriyama, Chie Otsuka, David Loakes, and Kazuo Negishi

Template properties of mutagenic cytosine analogues in reverse transcription
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: 6438-6449; doi:10.1093/nar/gkl761 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Stéphane Ouellet, François Vigneault, Maryse Lessard, Steeve Leclerc, Régen Drouin, and Sylvain L. Guérin

Transcriptional regulation of the cyclin-dependent kinase inhibitor 1A (p21) gene by NFI in proliferating human cells
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: 6472-6487; doi:10.1093/nar/gkl861 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fernando M. García-Rodríguez, Barbara Schrammeijer, and Paul J. J. Hooykaas

The Agrobacterium VirE3 effector protein: a potential plant transcriptional activator
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: 6496-6504; doi:10.1093/nar/gkl877 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Markus Christmann, Maja T. Tomicic, Judith Origer, Dorthe Aasland, and Bernd Kaina

c-Fos is required for excision repair of UV-light induced DNA lesions by triggering the re-synthesis of XPF
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: 6530-6539; doi:10.1093/nar/gkl895 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Guido Plotz, Christoph Welsch, Luis Giron-Monzon, Peter Friedhoff, Mario Albrecht, Albrecht Piiper, Ricardo M. Biondi, Thomas Lengauer, Stefan Zeuzem, and Jochen Raedle

Mutations in the MutS interaction interface of MLH1 can abolish DNA mismatch repair
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2006 34: 6574-6586; doi:10.1093/nar/gkl944 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Vishwanie S. Budhram-Mahadeo, Samantha Bowen, Sonia Lee, Christina Perez-Sanchez, Elizabeth Ensor, Peter J. Morris, and David S. Latchman

Brn-3b enhances the pro-apoptotic effects of p53 but not its induction of cell cycle arrest by cooperating in trans-activation of bax expression
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2006 34: 6640-6652; doi:10.1093/nar/gkl878 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Catherine Lavazec, Sohini Sanyal, and Thomas J. Templeton

Hypervariability within the Rifin, Stevor and Pfmc-2TM superfamilies in Plasmodium falciparum
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2006 34: 6696-6707; doi:10.1093/nar/gkl942 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Nucleic Acid Enzymes:

Sylvain Durand, Graziella Richard, Marco Bisaglia, Soumaya Laalami, François Bontems, and Marc Uzan

Activation of RegB endoribonuclease by S1 ribosomal protein requires an 11 nt conserved sequence
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: 6549-6560; doi:10.1093/nar/gkl911 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Rigu Gupta, Sudha Sharma, Kevin M. Doherty, Joshua A. Sommers, Sharon B. Cantor, and Robert M. Brosh, Jr

Inhibition of BACH1 (FANCJ) helicase by backbone discontinuity is overcome by increased motor ATPase or length of loading strand
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2006 34: 6673-6683; doi:10.1093/nar/gkl964 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Ross J. Molinaro, Babal Kant Jha, Krishnamurthy Malathi, Sooryanarayana Varambally, Arul M. Chinnaiyan, and Robert H. Silverman

Selection and cloning of poly(rC)-binding protein 2 and Raf kinase inhibitor protein RNA activators of 2',5'-oligoadenylate synthetase from prostate cancer cells
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2006 34: 6684-6695; doi:10.1093/nar/gkl968 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

RNA:

Navtej Toor, Aaron R. Robart, Joshua Christianson, and Steven Zimmerly

Self-splicing of a group IIC intron: 5' exon recognition and alternative 5' splicing events implicate the stem–loop motif of a transcriptional terminator
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: 6461-6471; doi:10.1093/nar/gkl820 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sandra Veldhoen, Sandra D. Laufer, Alexander Trampe, and Tobias Restle

Cellular delivery of small interfering RNA by a non-covalently attached cell-penetrating peptide: quantitative analysis of uptake and biological effect
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2006 34: 6561-6573; doi:10.1093/nar/gkl941 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Kathryn S. Sciabica and Klemens J. Hertel

The splicing regulators Tra and Tra2 are unusually potent activators of pre-mRNA splicing
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2006 34: 6612-6620; doi:10.1093/nar/gkl984 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Structural Biology:

Veronica S. DeGuzman, Clarence C. Lee, David W. Deamer, and Wenonah A. Vercoutere

Sequence-dependent gating of an ion channel by DNA hairpin molecules
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: 6425-6437; doi:10.1093/nar/gkl754 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yu Zeng and Yinsheng Wang

Sequence-dependent formation of intrastrand crosslink products from the UVB irradiation of duplex DNA containing a 5-bromo-2'-deoxyuridine or 5-bromo-2'-deoxycytidine
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: 6521-6529; doi:10.1093/nar/gkl892 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Peng Zhang, Jiamu Du, Bingfa Sun, Xianchi Dong, Guoliang Xu, Jinqiu Zhou, Qingqiu Huang, Qun Liu, Quan Hao, and Jianping Ding

Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2006 34: 6621-6628; doi:10.1093/nar/gkl989 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zhi-Jie Tan and Shi-Jie Chen

Electrostatic free energy landscapes for nucleic acid helix assembly
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2006 34: 6629-6639; doi:10.1093/nar/gkl810 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [supplementary data] [Request Permissions]  

Luigi Martino, Ada Virno, Antonio Randazzo, Antonella Virgilio, Veronica Esposito, Concetta Giancola, Mariarosaria Bucci, Giuseppe Cirino, and Luciano Mayol

A new modified thrombin binding aptamer containing a 5'–5' inversion of polarity site
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2006 34: 6653-6662; doi:10.1093/nar/gkl915 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Nicholas H. Hopcroft, Anna L. Brogden, Mark Searcey, and Christine J. Cardin

X-ray crystallographic study of DNA duplex cross-linking: simultaneous binding to two d(CGTACG)₂ molecules by a bis(9-aminoacridine-4-carboxamide) derivative
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2006 34: 6663-6672; doi:10.1093/nar/gkl930 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary material] [Request Permissions]  

Roman Fedorov, Gregor Witte, Claus Urbanke, Dietmar J. Manstein, and Ute Curth

3D structure of Thermus aquaticus single-stranded DNA–binding protein gives insight into the functioning of SSB proteins
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2006 34: 6708-6717; doi:10.1093/nar/gkl1002 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

James P. Orengo, Donnie Bundman, and Thomas A. Cooper

A bichromatic fluorescent reporter for cell-based screens of alternative splicing
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2006 34: e148; doi:10.1093/nar/gkl967 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Julianne Smith, Sylvestre Grizot, Sylvain Arnould, Aymeric Duclert, Jean-Charles Epinat, Patrick Chames, Jesús Prieto, Pilar Redondo, Francisco J. Blanco, Jerónimo Bravo, Guillermo Montoya, Frédéric Pâques, and Philippe Duchateau

A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: e149; doi:10.1093/nar/gkl720 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Keith I. E. McLuckie, John H. Lamb, Jatinderpal K. Sandhu, Helen L. Pearson, Karen Brown, Peter B. Farmer, and Donald J. L. Jones

Development of a novel site-specific mutagenesis assay using MALDI-ToF MS (SSMA-MS)
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: e150; doi:10.1093/nar/gkl745 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Vishal Saxena, Dennis Orgill, and Isaac Kohane

Absolute enrichment: gene set enrichment analysis for homeostatic systems
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: e151; doi:10.1093/nar/gkl766 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Andreas Martin Lisewski and Olivier Lichtarge

Rapid detection of similarity in protein structure and function through contact metric distances
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2006 34: e152; doi:10.1093/nar/gkl788 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Corrigendum:

Corrigendum
Nucl. Acids Res. 2006 34: 6718; doi:10.1093/nar/gkl1020 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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