Nucleic Acids Research

Articles:

Thomas Dowler, Denis Bergeron, Anna-Lisa Tedeschi, Luc Paquet, Nicolay Ferrari, and Masad J. Damha

Improvements in siRNA properties mediated by 2'-deoxy-2'-fluoro-ß-D-arabinonucleic acid (FANA)
Nucl. Acids Res. 2006 34: 1669-1675; doi:10.1093/nar/gkl033 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Bernd Schimanski, Jens Brandenburg, Tu Ngoc Nguyen, Melissa Jo Caimano, and Arthur Günzl

A TFIIB-like protein is indispensable for spliced leader RNA gene transcription in Trypanosoma brucei
Nucl. Acids Res. 2006 34: 1676-1684; doi:10.1093/nar/gkl090 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Helen E. Bryant and Thomas Helleday

Inhibition of poly (ADP-ribose) polymerase activates ATM which is required for subsequent homologous recombination repair
Nucl. Acids Res. 2006 34: 1685-1691; doi:10.1093/nar/gkl108 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Iain M. Wallace, Orla O'Sullivan, Desmond G. Higgins, and Cedric Notredame

M-Coffee: combining multiple sequence alignment methods with T-Coffee
Nucl. Acids Res. 2006 34: 1692-1699; doi:10.1093/nar/gkl091 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Peter Schattner and Mark Diekhans

Regions of extreme synonymous codon selection in mammalian genes
Nucl. Acids Res. 2006 34: 1700-1710; doi:10.1093/nar/gkl095 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Lucy E. Catto, Sumita Ganguly, Susan E. Milsom, Abigail J. Welsh, and Stephen E. Halford

Protein assembly and DNA looping by the FokI restriction endonuclease
Nucl. Acids Res. 2006 34: 1711-1720; doi:10.1093/nar/gkl076 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Veronica Albertini, Aklank Jain, Sara Vignati, Sara Napoli, Andrea Rinaldi, Ivo Kwee, Mohammad Nur-e-Alam, Julia Bergant, Francesco Bertoni, Giuseppina M. Carbone, Jürgen Rohr, and Carlo V. Catapano

Novel GC-rich DNA-binding compound produced by a genetically engineered mutant of the mithramycin producer Streptomyces argillaceus exhibits improved transcriptional repressor activity: implications for cancer therapy
Nucl. Acids Res. 2006 34: 1721-1734; doi:10.1093/nar/gkl063 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Sandra Wißmüller, Thomas Kosian, Michael Wolf, Markus Finzsch, and Michael Wegner

The high-mobility-group domain of Sox proteins interacts with DNA-binding domains of many transcription factors
Nucl. Acids Res. 2006 34: 1735-1744; doi:10.1093/nar/gkl105 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Katrin Nowak, Kornelius Kerl, Daniel Fehr, Christoph Kramps, Christine Gessner, Katrin Killmer, Birgit Samans, Bernd Berwanger, Holger Christiansen, and Werner Lutz

BMI1 is a target gene of E2F-1 and is strongly expressed in primary neuroblastomas
Nucl. Acids Res. 2006 34: 1745-1754; doi:10.1093/nar/gkl119 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Qingqing Liu, Victoria Derbyshire, Marlene Belfort, and David R. Edgell

Distance determination by GIY-YIG intron endonucleases: discrimination between repression and cleavage functions
Nucl. Acids Res. 2006 34: 1755-1764; doi:10.1093/nar/gkl079 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Junichi Mineno, Sachiko Okamoto, Tatsuya Ando, Masahiro Sato, Hideto Chono, Hiroyuki Izu, Masanori Takayama, Kiyozo Asada, Oleg Mirochnitchenko, Masayori Inouye, and Ikunoshin Kato

The expression profile of microRNAs in mouse embryos
Nucl. Acids Res. 2006 34: 1765-1771; doi:10.1093/nar/gkl096 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Ren Liu, Junzhuan Qiu, L. David Finger, Li Zheng, and Binghui Shen

The DNA–protein interaction modes of FEN-1 with gap substrates and their implication in preventing duplication mutations
Nucl. Acids Res. 2006 34: 1772-1784; doi:10.1093/nar/gkl106 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Daniel Strahs, Chang-Xi Zhu, Bokun Cheng, Jason Chen, and Yuk-Ching Tse-Dinh

Experimental and computational investigations of Ser10 and Lys13 in the binding and cleavage of DNA substrates by Escherichia coli DNA topoisomerase I
Nucl. Acids Res. 2006 34: 1785-1797; doi:10.1093/nar/gkl109 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Joachim Meraner, Markus Lechner, Adele Loidl, Maria Goralik-Schramel, Renate Voit, Ingrid Grummt, and Peter Loidl

Acetylation of UBF changes during the cell cycle and regulates the interaction of UBF with RNA polymerase I
Nucl. Acids Res. 2006 34: 1798-1806; doi:10.1093/nar/gkl101 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Cornelia Brunner and Thomas Wirth

Btk expression is controlled by Oct and BOB.1/OBF.1
Nucl. Acids Res. 2006 34: 1807-1815; doi:10.1093/nar/gkl131 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Christian Marck, Rym Kachouri-Lafond, Ingrid Lafontaine, Eric Westhof, Bernard Dujon, and Henri Grosjean

The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications
Nucl. Acids Res. 2006 34: 1816-1835; doi:10.1093/nar/gkl085 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Chad C. Bjorklund and William B. Davis

Attenuation of DNA charge transport by compaction into a nucleosome core particle
Nucl. Acids Res. 2006 34: 1836-1846; doi:10.1093/nar/gkl030 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Sylvie Nonin-Lecomte, Brice Felden, and Frédéric Dardel

NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation
Nucl. Acids Res. 2006 34: 1847-1853; doi:10.1093/nar/gkl111 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Jeong-Hoon Kim, Hee-Dai Kim, Gi-Hyuck Ryu, Do-Hyung Kim, Jerard Hurwitz, and Yeon-Soo Seo

Isolation of human Dna2 endonuclease and characterization of its enzymatic properties
Nucl. Acids Res. 2006 34: 1854-1864; doi:10.1093/nar/gkl102 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Taro Masuda-Sasa, Osamu Imamura, and Judith L. Campbell

Biochemical analysis of human Dna2
Nucl. Acids Res. 2006 34: 1865-1875; doi:10.1093/nar/gkl070 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yu Fu and Wei Xiao

Identification and characterization of CRT10 as a novel regulator of Saccharomyces cerevisiae ribonucleotide reductase genes
Nucl. Acids Res. 2006 34: 1876-1883; doi:10.1093/nar/gkl100 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Takayuki Shibata, Nicola Glynn, T. Brian H. McMurry, R. Stanley McElhinney, Geoffrey P. Margison, and David M. Williams

Novel synthesis of O⁶-alkylguanine containing oligodeoxyribonucleotides as substrates for the human DNA repair protein, O⁶-methylguanine DNA methyltransferase (MGMT)
Nucl. Acids Res. 2006 34: 1884-1891; doi:10.1093/nar/gkl117 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Ji Hyun Yang, So Jeong Han, Eun Kyung Yoon, and Woo Sung Lee

‘Evidence of an auxin signal pathway, microRNA167-ARF8-GH3, and its response to exogenous auxin in cultured rice cells’
Nucl. Acids Res. 2006 34: 1892-1899; doi:10.1093/nar/gkl118 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Maria Duca, Dominique Guianvarc'h, Kahina Oussedik, Ludovic Halby, Anna Garbesi, Daniel Dauzonne, Claude Monneret, Neil Osheroff, Carine Giovannangeli, and Paola B. Arimondo

Molecular basis of the targeting of topoisomerase II-mediated DNA cleavage by VP16 derivatives conjugated to triplex-forming oligonucleotides
Nucl. Acids Res. 2006 34: 1900-1911; doi:10.1093/nar/gkl126 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Gérard Roizès

Human centromeric alphoid domains are periodically homogenized so that they vary substantially between homologues. Mechanism and implications for centromere functioning
Nucl. Acids Res. 2006 34: 1912-1924; doi:10.1093/nar/gkl137 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ingrid Zegers, Daniel Gigot, Françoise van Vliet, Catherine Tricot, Stéphane Aymerich, Janusz M. Bujnicki, Jan Kosinski, and Louis Droogmans

Crystal structure of Bacillus subtilis TrmB, the tRNA (m⁷G46) methyltransferase
Nucl. Acids Res. 2006 34: 1925-1934; doi:10.1093/nar/gkl116 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Marc Hallier, Jessie Desreac, and Brice Felden

Small protein B interacts with the large and the small subunits of a stalled ribosome during trans-translation
Nucl. Acids Res. 2006 34: 1935-1943; doi:10.1093/nar/gkl097 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Corrigendum:

Paul Thaw, Svetlana E. Sedelnikova, Tatyana Muranova, Sebastian Wiese, Sylvia Ayora, Juan C. Alonso, Arie B. Brinkman, Jasper Akerboom, John van der Oost, and John B. Rafferty

Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family
Nucl. Acids Res. 2006 34: 1944; doi:10.1093/nar/gkl152 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Srinivasa Rao Meneni, Rhijuta D'Mello, Gregory Norigian, Gregory Baker, Lan Gao, M. Paul Chiarelli, and Bongsup P. Cho

Sequence effects of aminofluorene-modified DNA duplexes: thermodynamic and circular dichroism properties
Nucl. Acids Res. 2006 34: 1945; doi:10.1093/nar/gkl153 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Tania Tabone, Georgina Sallmann, Elizabeth Webb, and Richard G. H. Cotton

Detection of 100% of mutations in 124 individuals using a standard UV/Vis microplate reader: a novel concept for mutation scanning
Nucl. Acids Res. 2006 34: e45; doi:10.1093/nar/gkl077 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jean-Philippe Pichon, Bertrand Bonnaud, Philippe Cleuziat, and François Mallet

Multiplex degenerate PCR coupled with an oligo sorbent array for human endogenous retrovirus expression profiling
Nucl. Acids Res. 2006 34: e46; doi:10.1093/nar/gkl086 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Bernd Liedert, Dick Pluim, Jan Schellens, and Jürgen Thomale

Adduct-specific monoclonal antibodies for the measurement of cisplatin-induced DNA lesions in individual cell nuclei
Nucl. Acids Res. 2006 34: e47; doi:10.1093/nar/gkl051 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Inna Shcherbakova, Somdeb Mitra, Robert H. Beer, and Michael Brenowitz

Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins
Nucl. Acids Res. 2006 34: e48; doi:10.1093/nar/gkl055 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Erik Pettersson, Mats Lindskog, Joakim Lundeberg, and Afshin Ahmadian

Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA
Nucl. Acids Res. 2006 34: e49; doi:10.1093/nar/gkl103 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Angel A. Martí, Steffen Jockusch, Zengmin Li, Jingyue Ju, and Nicholas J. Turro

Molecular beacons with intrinsically fluorescent nucleotides
Nucl. Acids Res. 2006 34: e50; doi:10.1093/nar/gkl134 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sewon Ki, Fuminori Sugihara, Koji Kasahara, Hidehito Tochio, Azusa Okada-Marubayashi, Setsuko Tomita, Masahito Morita, Mitsunori Ikeguchi, Masahiro Shirakawa, and Tetsuro Kokubo

A novel magnetic resonance-based method to measure gene expression in living cells
Nucl. Acids Res. 2006 34: e51; doi:10.1093/nar/gkl135 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

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