Nucleic Acids Research

Survey and Summary:

George W. Owttrim

RNA helicases and abiotic stress
Nucl. Acids Res. 2006 34: 3220-3230; doi:10.1093/nar/gkl408 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Articles:

Dayal Saran, Daniel M. Held, and Donald H. Burke

Multiple-turnover thio-ATP hydrolase and phospho-enzyme intermediate formation activities catalyzed by an RNA enzyme
Nucl. Acids Res. 2006 34: 3201-3208; doi:10.1093/nar/gkl413 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shani Blanga-Kanfi, Michal Amitsur, Abdussalam Azem, and Gabriel Kaufmann

PrrC-anticodon nuclease: functional organization of a prototypical bacterial restriction RNase
Nucl. Acids Res. 2006 34: 3209-3219; doi:10.1093/nar/gkl415 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mallikarjuna Reddy Putta, FuGang Zhu, Yukui Li, Lakshmi Bhagat, YanPing Cong, Ekambar R. Kandimalla, and Sudhir Agrawal

Novel oligodeoxynucleotide agonists of TLR9 containing N³-Me-dC or N¹-Me-dG modifications
Nucl. Acids Res. 2006 34: 3231-3238; doi:10.1093/nar/gkl430 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Anna K. Shchyolkina, Dmitry N. Kaluzhny, Donna J. Arndt-Jovin, Thomas M. Jovin, and Victor B. Zhurkin

Recombination R-triplex: H-bonds contribution to stability as revealed with minor base substitutions for adenine
Nucl. Acids Res. 2006 34: 3239-3245; doi:10.1093/nar/gkl431 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ning Shen, Litao Guo, Bei Yang, Youxin Jin, and Jianping Ding

Structure of human tryptophanyl-tRNA synthetase in complex with tRNA^Trp reveals the molecular basis of tRNA recognition and specificity
Nucl. Acids Res. 2006 34: 3246-3258; doi:10.1093/nar/gkl441 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Angel J. Picher, Miguel García-Díaz, Katarzyna Bebenek, Lars C. Pedersen, Thomas A. Kunkel, and Luis Blanco

Promiscuous mismatch extension by human DNA polymerase lambda
Nucl. Acids Res. 2006 34: 3259-3266; doi:10.1093/nar/gkl377 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sergio de la Fuente van Bentem, Dorothea Anrather, Elisabeth Roitinger, Armin Djamei, Thomas Hufnagl, Andrea Barta, Edina Csaszar, Ilse Dohnal, David Lecourieux, and Heribert Hirt

Phosphoproteomics reveals extensive in vivo phosphorylation of Arabidopsis proteins involved in RNA metabolism
Nucl. Acids Res. 2006 34: 3267-3278; doi:10.1093/nar/gkl429 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Alison Zimon, Anna Erat, Tiffany Von Wald, Brad Bissell, Anna Koulova, Chu H. Choi, Dimcho Bachvarov, Richard H. Reindollar, and Anny Usheva

Genes invoked in the ovarian transition to menopause
Nucl. Acids Res. 2006 34: 3279-3287; doi:10.1093/nar/gkl387 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

K. M. Viiri, H. Korkeamäki, M. K. Kukkonen, L. K. Nieminen, K. Lindfors, P. Peterson, M. Mäki, H. Kainulainen, and O. Lohi

SAP30L interacts with members of the Sin3A corepressor complex and targets Sin3A to the nucleolus
Nucl. Acids Res. 2006 34: 3288-3298; doi:10.1093/nar/gkl401 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

David M. Lehmann, Chad A. Galloway, Mark P. Sowden, and Harold C. Smith

Metabolic regulation of ApoB mRNA editing is associated with phosphorylation of APOBEC-1 complementation factor
Nucl. Acids Res. 2006 34: 3299-3308; doi:10.1093/nar/gkl417 [Abstract] [Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Christophe Dessimoz, Brigitte Boeckmann, Alexander C. J. Roth, and Gaston H. Gonnet

Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Nucl. Acids Res. 2006 34: 3309-3316; doi:10.1093/nar/gkl433 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Marc van Dijk, Aalt D. J. van Dijk, Victor Hsu, Rolf Boelens, and Alexandre M. J. J. Bonvin

Information-driven protein–DNA docking using HADDOCK: it is a matter of flexibility
Nucl. Acids Res. 2006 34: 3317-3325; doi:10.1093/nar/gkl412 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ling Zhang, Olga Rechkoblit, Lihua Wang, Dinshaw J. Patel, Robert Shapiro, and Suse Broyde

Mutagenic nucleotide incorporation and hindered translocation by a food carcinogen C8-dG adduct in Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): modeling and dynamics studies
Nucl. Acids Res. 2006 34: 3326-3337; doi:10.1093/nar/gkl425 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Amanda S. O'Toole, Stacy Miller, Nathan Haines, M. Coleen Zink, and Martin J. Serra

Comprehensive thermodynamic analysis of 3' double-nucleotide overhangs neighboring Watson–Crick terminal base pairs
Nucl. Acids Res. 2006 34: 3338-3344; doi:10.1093/nar/gkl428 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ana Vasileva, R. Michael Linden, and Rolf Jessberger

Homologous recombination is required for AAV-mediated gene targeting
Nucl. Acids Res. 2006 34: 3345-3360; doi:10.1093/nar/gkl455 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Prajna R. Kulkarni, Xiaohui Cui, Joshua W. Williams, Ann M. Stevens, and Rahul V. Kulkarni

Prediction of CsrA-regulating small RNAs in bacteria and their experimental verification in Vibrio fischeri
Nucl. Acids Res. 2006 34: 3361-3369; doi:10.1093/nar/gkl439 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Yang Gao, Lauren K. Wolf, and Rosina M. Georgiadis

Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison
Nucl. Acids Res. 2006 34: 3370-3377; doi:10.1093/nar/gkl422 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Yutaka Satou, Makoto Hamaguchi, Keisuke Takeuchi, Kenneth E. M. Hastings, and Nori Satoh

Genomic overview of mRNA 5'-leader trans-splicing in the ascidian Ciona intestinalis
Nucl. Acids Res. 2006 34: 3378-3388; doi:10.1093/nar/gkl418 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Hideaki Ogiwara, Ayako Ui, Fumitoshi Onoda, Shusuke Tada, Takemi Enomoto, and Masayuki Seki

Dpb11, the budding yeast homolog of TopBP1, functions with the checkpoint clamp in recombination repair
Nucl. Acids Res. 2006 34: 3389-3398; doi:10.1093/nar/gkl411 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fiona Innes, Ben Ramsbottom, and Robert J. White

A test of the model that RNA polymerase III transcription is regulated by selective induction of the 110 kDa subunit of TFIIIC
Nucl. Acids Res. 2006 34: 3399-3407; doi:10.1093/nar/gkl432 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Lilia Ganova-Raeva, Xinjian Zhang, Fengli Cao, Howard Fields, and Yury Khudyakov

Primer Extension Enrichment Reaction (PEER): a new subtraction method for identification of genetic differences between biological specimens
Nucl. Acids Res. 2006 34: e76; doi:10.1093/nar/gkl391 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Pavel Neuzil, Chunyan Zhang, Juergen Pipper, Sharon Oh, and Lang Zhuo

Ultra fast miniaturized real-time PCR: 40 cycles in less than six minutes
Nucl. Acids Res. 2006 34: e77; doi:10.1093/nar/gkl416 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Richard J. Shaw, Emily K. Akufo-Tetteh, Janet M. Risk, John K. Field, and Triantafillos Liloglou

Methylation enrichment pyrosequencing: combining the specificity of MSP with validation by pyrosequencing
Nucl. Acids Res. 2006 34: e78; doi:10.1093/nar/gkl424 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Philipp Wenter, Luc Reymond, Sigrid D. Auweter, Frédéric H.-T. Allain, and Stefan Pitsch

Short, synthetic and selectively ¹³C-labeled RNA sequences for the NMR structure determination of protein–RNA complexes
Nucl. Acids Res. 2006 34: e79; doi:10.1093/nar/gkl427 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Paul J. Farrow, Lee B. Barrett, Mark Stevenson, Kerry D. Fisher, Jonathan Finn, Rachel Spice, Michael A. Allan, Martin Berry, Ann Logan, Leonard W. Seymour, and Martin L. Read

Cytoplasmic expression systems triggered by mRNA yield increased gene expression in post-mitotic neurons
Nucl. Acids Res. 2006 34: e80; doi:10.1093/nar/gkl442 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jizu Yi, Wandi Zhang, and David Y. Zhang

Molecular Zipper: a fluorescent probe for real-time isothermal DNA amplification
Nucl. Acids Res. 2006 34: e81; doi:10.1093/nar/gkl261 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Claudia Gebhard, Lucia Schwarzfischer, Thu Hang Pham, Reinhard Andreesen, Andreas Mackensen, and Michael Rehli

Rapid and sensitive detection of CpG-methylation using methyl-binding (MB)-PCR
Nucl. Acids Res. 2006 34: e82; doi:10.1093/nar/gkl437 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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