Nucleic Acids Research

Survey and Summary:

Susan M. Bailey and John P. Murnane

Telomeres, chromosome instability and cancer
Nucl. Acids Res. 2006 34: 2408-2417; doi:10.1093/nar/gkl303 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Articles:

Tomoko Hiroki, Young-Han Song, Stephen A. Liebhaber, and Nancy E. Cooke

The human vitamin D-binding protein gene contains locus control determinants sufficient for autonomous activation in hepatic chromatin
Nucl. Acids Res. 2006 34: 2154-2165; doi:10.1093/nar/gkl174 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jeffrey J. Tabor, Matthew Levy, and Andrew D. Ellington

Deoxyribozymes that recode sequence information
Nucl. Acids Res. 2006 34: 2166-2172; doi:10.1093/nar/gkl176 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Freddie R. Salsbury, Jr, Jill E. Clodfelter, Michael B. Gentry, Thomas Hollis, and Karin Drotschmann Scarpinato

The molecular mechanism of DNA damage recognition by MutS homologs and its consequences for cell death response
Nucl. Acids Res. 2006 34: 2173-2185; doi:10.1093/nar/gkl238 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

R. Krishna, G. P. Manjunath, P. Kumar, A. Surolia, Nagasuma R. Chandra, K. Muniyappa, and M. Vijayan

Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery
Nucl. Acids Res. 2006 34: 2186-2195; doi:10.1093/nar/gkl107 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Baskaran Anand, Sunil Kumar Verma, and Balaji Prakash

Structural stabilization of GTP-binding domains in circularly permuted GTPases: Implications for RNA binding
Nucl. Acids Res. 2006 34: 2196-2205; doi:10.1093/nar/gkl178 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Pavlina Konstantinova, Peter de Haan, Atze T. Das, and Ben Berkhout

Hairpin-induced tRNA-mediated (HITME) recombination in HIV-1
Nucl. Acids Res. 2006 34: 2206-2218; doi:10.1093/nar/gkl226 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yan Ling, Abigail J. Smith, and Garry T. Morgan

A sequence motif conserved in diverse nuclear proteins identifies a protein interaction domain utilised for nuclear targeting by human TFIIS
Nucl. Acids Res. 2006 34: 2219-2229; doi:10.1093/nar/gkl239 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Caroline J. Dobson and Sarah L. Allinson

The phosphatase activity of mammalian polynucleotide kinase takes precedence over its kinase activity in repair of single strand breaks
Nucl. Acids Res. 2006 34: 2230-2237; doi:10.1093/nar/gkl275 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chaolin Zhang, Zhenyu Xuan, Stefanie Otto, John R. Hover, Sean R. McCorkle, Gail Mandel, and Michael Q. Zhang

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome
Nucl. Acids Res. 2006 34: 2238-2246; doi:10.1093/nar/gkl248 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Vladimir A. Efimov, Klara R. Birikh, Dmitri B. Staroverov, Sergei A. Lukyanov, Maria B. Tereshina, Andrey G. Zaraisky, and Oksana G. Chakhmakhcheva

Hydroxyproline-based DNA mimics provide an efficient gene silencing in vitro and in vivo
Nucl. Acids Res. 2006 34: 2247-2257; doi:10.1093/nar/gkl249 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Anetta Nowosielska, Stephen A. Smith, Bevin P. Engelward, and M. G. Marinus

Homologous recombination prevents methylation-induced toxicity in Escherichia coli
Nucl. Acids Res. 2006 34: 2258-2268; doi:10.1093/nar/gkl222 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Csanád Z. Bachrati, Rhona H. Borts, and Ian D. Hickson

Mobile D-loops are a preferred substrate for the Bloom's syndrome helicase
Nucl. Acids Res. 2006 34: 2269-2279; doi:10.1093/nar/gkl258 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Miloslava Fojtová, Annick Bleys, Jana Bedrichová, Helena Van Houdt, Katerina Krízová, Anna Depicker, and Ales Kovarík

The trans-silencing capacity of invertedly repeated transgenes depends on their epigenetic state in tobacco
Nucl. Acids Res. 2006 34: 2280-2293; doi:10.1093/nar/gkl180 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Scott Davis, Bridget Lollo, Susan Freier, and Christine Esau

Improved targeting of miRNA with antisense oligonucleotides
Nucl. Acids Res. 2006 34: 2294-2304; doi:10.1093/nar/gkl183 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

M. Abul Kalam, Kazuhiro Haraguchi, Sushil Chandani, Edward L. Loechler, Maasaki Moriya, Marc M. Greenberg, and Ashis K. Basu

Genetic effects of oxidative DNA damages: comparative mutagenesis of the imidazole ring-opened formamidopyrimidines (Fapy lesions) and 8-oxo-purines in simian kidney cells
Nucl. Acids Res. 2006 34: 2305-2315; doi:10.1093/nar/gkl099 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Limor Kozobay-Avraham, Sergey Hosid, and Alexander Bolshoy

Involvement of DNA curvature in intergenic regions of prokaryotes
Nucl. Acids Res. 2006 34: 2316-2327; doi:10.1093/nar/gkl230 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Eric Ennifar, Jean-Christophe Paillart, Anne Bodlenner, Philippe Walter, Jean-Marc Weibel, Anne-Marie Aubertin, Patrick Pale, Philippe Dumas, and Roland Marquet

Targeting the dimerization initiation site of HIV-1 RNA with aminoglycosides: from crystal to cell
Nucl. Acids Res. 2006 34: 2328-2339; doi:10.1093/nar/gkl317 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Sébastien Lemieux and François Major

Automated extraction and classification of RNA tertiary structure cyclic motifs
Nucl. Acids Res. 2006 34: 2340-2346; doi:10.1093/nar/gkl120 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Steven J. Pearson, Stephen Wharton, Amanda J. Watson, Ghazala Begum, Amna Butt, Nicola Glynn, David M. Williams, Takayuki Shibata, Mauro F. Santibáñez-Koref, and Geoffrey P. Margison

A novel DNA damage recognition protein in Schizosaccharomyces pombe
Nucl. Acids Res. 2006 34: 2347-2354; doi:10.1093/nar/gkl270 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Clemens Stockklausner, Stephen Breit, Gabriele Neu-Yilik, Nicole Echner, Matthias W. Hentze, Andreas E. Kulozik, and Niels H. Gehring

The uORF-containing thrombopoietin mRNA escapes nonsense-mediated decay (NMD)
Nucl. Acids Res. 2006 34: 2355-2363; doi:10.1093/nar/gkl277 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Undine Mechold, Vasily Ogryzko, Saravuth Ngo, and Antoine Danchin

Oligoribonuclease is a common downstream target of lithium-induced pAp accumulation in Escherichia coli and human cells
Nucl. Acids Res. 2006 34: 2364-2373; doi:10.1093/nar/gkl247 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Julien Häsler and Katharina Strub

Alu RNP and Alu RNA regulate translation initiation in vitro
Nucl. Acids Res. 2006 34: 2374-2385; doi:10.1093/nar/gkl246 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Jean-Louis Mergny, Anne De Cian, Samir Amrane, and Mateus Webba da Silva

Kinetics of double-chain reversals bridging contiguous quartets in tetramolecular quadruplexes
Nucl. Acids Res. 2006 34: 2386-2397; doi:10.1093/nar/gkl098 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Jing-Yi Huang, Wei-Hao Chen, Ya-Ling Chang, Hsiao-Ting Wang, Wan-ting Chuang, and Sheng-Chung Lee

Modulation of nucleosome-binding activity of FACT by poly(ADP-ribosyl)ation
Nucl. Acids Res. 2006 34: 2398-2407; doi:10.1093/nar/gkl241 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Dongsheng Che, Guojun Li, Fenglou Mao, Hongwei Wu, and Ying Xu

Detecting uber-operons in prokaryotic genomes
Nucl. Acids Res. 2006 34: 2418-2427; doi:10.1093/nar/gkl294 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Svetlana A. Shabalina, Aleksey Y. Ogurtsov, and Nikolay A. Spiridonov

A periodic pattern of mRNA secondary structure created by the genetic code
Nucl. Acids Res. 2006 34: 2428-2437; doi:10.1093/nar/gkl287 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Jing Shi, Pedro R. Romero, Gary K. Schoolnik, Alfred M. Spormann, and Peter D. Karp

Evidence supporting predicted metabolic pathways for Vibrio cholerae: gene expression data and clinical tests
Nucl. Acids Res. 2006 34: 2438-2444; doi:10.1093/nar/gkl310 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Kenny Schlosser, Jeffrey C.F. Lam, and Yingfu Li

Characterization of long RNA-cleaving deoxyribozymes with short catalytic cores: the effect of excess sequence elements on the outcome of in vitro selection
Nucl. Acids Res. 2006 34: 2445-2454; doi:10.1093/nar/gkl276 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sandeep Krishna, Anna M. C. Andersson, Szabolcs Semsey, and Kim Sneppen

Structure and function of negative feedback loops at the interface of genetic and metabolic networks
Nucl. Acids Res. 2006 34: 2455-2462; doi:10.1093/nar/gkl140 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Rakhi Rajan, James W. Wisler, and Charles E. Bell

Probing the DNA sequence specificity of Escherichia coli RECA protein
Nucl. Acids Res. 2006 34: 2463-2471; doi:10.1093/nar/gkl302 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Peter Kosa, Matus Valach, Lubomir Tomaska, Kenneth H. Wolfe, and Jozef Nosek

Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: insight into the evolution of linear DNA genomes from mitochondrial telomere mutants
Nucl. Acids Res. 2006 34: 2472-2481; doi:10.1093/nar/gkl327 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Corrigendum:

Rita Sulahian, Stephen Albert Johnston, and Thomas Kodadek

The proteasomal ATPase complex is required for stress-induced transcription in yeast
Nucl. Acids Res. 2006 34: 2482; doi:10.1093/nar/gkl367 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Retraction:

H. Kawasaki, E. Suyama, M. Iyo, and K. Taira

siRNAs generated by recombinant human Dicer induce specific and significant but target site-independent gene silencing in human cells
Nucl. Acids Res. 2006 34: 2153; doi:10.1093/nar/gkl306 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Michael Seringhaus, Anuj Kumar, John Hartigan, Michael Snyder, and Mark Gerstein

Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae
Nucl. Acids Res. 2006 34: e57; doi:10.1093/nar/gkl184 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

G. Hamilton, N. Brown, V. Oseroff, B. Huey, R. Segraves, D. Sudar, J. Kumler, D. Albertson, and D. Pinkel

A large field CCD system for quantitative imaging of microarrays
Nucl. Acids Res. 2006 34: e58; doi:10.1093/nar/gkl160 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Philipp Schatz, Jürgen Distler, Kurt Berlin, and Matthias Schuster

Novel method for high throughput DNA methylation marker evaluation using PNA-probe library hybridization and MALDI-TOF detection
Nucl. Acids Res. 2006 34: e59; doi:10.1093/nar/gkl218 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yong You, Bernardo G. Moreira, Mark A. Behlke, and Richard Owczarzy

Design of LNA probes that improve mismatch discrimination
Nucl. Acids Res. 2006 34: e60; doi:10.1093/nar/gkl175 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Inchul Yang, In Young Park, Sung-Moon Jang, Lian Hua Shi, Hyung-Keun Ku, and Sang-Ryoul Park

Rapid quantification of DNA methylation through dNMP analysis following bisulfite-PCR
Nucl. Acids Res. 2006 34: e61; doi:10.1093/nar/gkl257 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yong-Chao Guo, Ya-Feng Zhou, Xian-En Zhang, Zhi-Ping Zhang, Yan-Mei Qiao, Li-Jun Bi, Ji-Kai Wen, Mi-Fang Liang, and Ji-Bin Zhang

Phage display mediated immuno-PCR
Nucl. Acids Res. 2006 34: e62; doi:10.1093/nar/gkl260 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Hitoshi Suzuki, Yuhong Zuo, Jinhua Wang, Michael Q. Zhang, Arun Malhotra, and Akila Mayeda

Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing
Nucl. Acids Res. 2006 34: e63; doi:10.1093/nar/gkl151 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tadepalli Adilakshmi, Richard A. Lease, and Sarah A. Woodson

Hydroxyl radical footprinting in vivo: mapping macromolecular structures with synchrotron radiation
Nucl. Acids Res. 2006 34: e64; doi:10.1093/nar/gkl291 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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