Nucleic Acids Research

Survey and Summary

Get checked abstract Clyde A. Hutchison, III

DNA sequencing: bench to bedside and beyond
Nucleic Acids Research Advance Access published on September 12, 2007
Nucl. Acids Res. 2007 35: 6227-6237; doi:10.1093/nar/gkm688 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genomics

Get checked abstract Yoshiharu Y. Yamamoto, Hiroyuki Ichida, Tomoko Abe, Yutaka Suzuki, Sumio Sugano, and Junichi Obokata

Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis
Nucleic Acids Research Advance Access published on September 12, 2007
Nucl. Acids Res. 2007 35: 6219-6226; doi:10.1093/nar/gkm685 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Benjamin Lang, Nicolas Blot, Emeline Bouffartigues, Malcolm Buckle, Marcel Geertz, Claudio O. Gualerzi, Ramesh Mavathur, Georgi Muskhelishvili, Cynthia L. Pon, Sylvie Rimsky, Stefano Stella, M. Madan Babu, and Andrew Travers

High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2007 35: 6330-6337; doi:10.1093/nar/gkm712 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract Toshiki Murata, Naoki Kadotani, Miki Yamaguchi, Yukio Tosa, Shigeyuki Mayama, and Hitoshi Nakayashiki

siRNA-dependent and -independent post-transcriptional cosuppression of the LTR-retrotransposon MAGGY in the phytopathogenic fungus Magnaporthe oryzae
Nucleic Acids Research Advance Access published on August 28, 2007
Nucl. Acids Res. 2007 35: 5987-5994; doi:10.1093/nar/gkm646 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Walden Ai, Hai Zheng, Xiangdong Yang, Ying Liu, and Timothy C. Wang

Tip60 functions as a potential corepressor of KLF4 in regulation of HDC promoter activity
Nucleic Acids Research Advance Access published on September 7, 2007
Nucl. Acids Res. 2007 35: 6137-6149; doi:10.1093/nar/gkm656 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Wei Chen and Robert G. Roeder

The Mediator subunit MED1/TRAP220 is required for optimal glucocorticoid receptor-mediated transcription activation
Nucleic Acids Research Advance Access published on September 7, 2007
Nucl. Acids Res. 2007 35: 6161-6169; doi:10.1093/nar/gkm661 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Rikke From Frøhlich, Christopher Veigaard, Félicie Faucon Andersen, A. Kathleen McClendon, Amanda C. Gentry, Anni Hangaard Andersen, Neil Osheroff, Tinna Stevnsner, and Birgitta Ruth Knudsen

Tryptophane-205 of human topoisomerase I is essential for camptothecin inhibition of negative but not positive supercoil removal
Nucleic Acids Research Advance Access published on September 7, 2007
Nucl. Acids Res. 2007 35: 6170-6180; doi:10.1093/nar/gkm669 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Osama A. Youssef, Rebecca M. Terns, and Michael P. Terns

Dynamic interactions within sub-complexes of the H/ACA pseudouridylation guide RNP
Nucleic Acids Research Advance Access published on September 12, 2007
Nucl. Acids Res. 2007 35: 6196-6206; doi:10.1093/nar/gkm673 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Abdelaty Saleh, Ayed Al-Abdallat, Ivan Ndamukong, Raul Alvarez-Venegas, and Zoya Avramova

The Arabidopsis homologs of trithorax (ATX1) and enhancer of zeste (CLF) establish ‘bivalent chromatin marks’ at the silent AGAMOUS locus
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2007 35: 6290-6296; doi:10.1093/nar/gkm464 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Karl P. Nightingale, Matthias Baumann, Anton Eberharter, Adamantios Mamais, Peter B. Becker, and Joan Boyes

Acetylation increases access of remodelling complexes to their nucleosome targets to enhance initiation of V(D)J recombination
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2007 35: 6311-6321; doi:10.1093/nar/gkm650 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Nucleic Acid Enzymes

Get checked abstract Arnaud Hecker, Nicolas Leulliot, Danièle Gadelle, Marc Graille, Anthony Justome, Pierre Dorlet, Céline Brochier, Sophie Quevillon-Cheruel, Eric Le Cam, Herman van Tilbeurgh, and Patrick Forterre

An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro
Nucleic Acids Research Advance Access published on August 30, 2007
Nucl. Acids Res. 2007 35: 6042-6051; doi:10.1093/nar/gkm554 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract H. Zhang, W. Cao, E. Zakharova, W. Konigsberg, and E. M. De La Cruz

Fluorescence of 2-aminopurine reveals rapid conformational changes in the RB69 DNA polymerase-primer/template complexes upon binding and incorporation of matched deoxynucleoside triphosphates
Nucleic Acids Research Advance Access published on August 30, 2007
Nucl. Acids Res. 2007 35: 6052-6062; doi:10.1093/nar/gkm587 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Sara N. Richter, Giulia Giaretta, Valentina Comuzzi, Elisabetta Leo, Lesley A. Mitchenall, L. Mark Fisher, Anthony Maxwell, and Manlio Palumbo

Hot-spot consensus of fluoroquinolone-mediated DNA cleavage by Gram-negative and Gram-positive type II DNA topoisomerases
Nucleic Acids Research Advance Access published on August 30, 2007
Nucl. Acids Res. 2007 35: 6075-6085; doi:10.1093/nar/gkm653 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Corinne D. Hausmann, Mette Prætorius-Ibba, and Michael Ibba

An aminoacyl-tRNA synthetase:elongation factor complex for substrate channeling in archaeal translation
Nucleic Acids Research Advance Access published on September 1, 2007
Nucl. Acids Res. 2007 35: 6094-6102; doi:10.1093/nar/gkm534 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract James Hejna, Sahaayaruban Philip, Jesse Ott, Craig Faulkner, and Robb Moses

The hSNM1 protein is a DNA 5'-exonuclease
Nucleic Acids Research Advance Access published on September 5, 2007
Nucl. Acids Res. 2007 35: 6115-6123; doi:10.1093/nar/gkm530 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Michael Stahl, Marco Retzlaff, Michael Nassal, and Jürgen Beck

Chaperone activation of the hepadnaviral reverse transcriptase for template RNA binding is established by the Hsp70 and stimulated by the Hsp90 system
Nucleic Acids Research Advance Access published on September 5, 2007
Nucl. Acids Res. 2007 35: 6124-6136; doi:10.1093/nar/gkm628 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Xin Guan, Amrita Madabushi, Dau-Yin Chang, Megan E. Fitzgerald, Gouli Shi, Alexander C. Drohat, and A-Lien Lu

The human checkpoint sensor Rad9–Rad1–Hus1 interacts with and stimulates DNA repair enzyme TDG glycosylase
Nucleic Acids Research Advance Access published on September 12, 2007
Nucl. Acids Res. 2007 35: 6207-6218; doi:10.1093/nar/gkm678 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Siu-hong Chan, Yongming Bao, Ewa Ciszak, Sophie Laget, and Shuang-yong Xu

Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities
Nucleic Acids Research Advance Access published on September 13, 2007
Nucl. Acids Res. 2007 35: 6238-6248; doi:10.1093/nar/gkm665 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Amanda Nga-Sze Mak, Yuen-Ting Wong, Young-Jun An, Sun-Shin Cha, Kong-Hung Sze, Shannon Wing-Ngor Au, Kam-Bo Wong, and Pang-Chui Shaw

Structure-function study of maize ribosome-inactivating protein: implications for the internal inactivation region and the sole glutamate in the active site
Nucleic Acids Research Advance Access published on September 13, 2007
Nucl. Acids Res. 2007 35: 6259-6267; doi:10.1093/nar/gkm687 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Rong-Bing Guo, Pascal Rigolet, Hua Ren, Bo Zhang, Xing-Dong Zhang, Shuo-Xing Dou, Peng-Ye Wang, Mounira Amor-Gueret, and Xu Guang Xi

Structural and functional analyses of disease-causing missense mutations in Bloom syndrome protein
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2007 35: 6297-6310; doi:10.1093/nar/gkm536 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA

Get checked abstract Kentaro Sahashi, Akio Masuda, Tohru Matsuura, Jun Shinmi, Zhujun Zhang, Yasuhiro Takeshima, Masafumi Matsuo, Gen Sobue, and Kinji Ohno

In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites
Nucleic Acids Research Advance Access published on August 28, 2007
Nucl. Acids Res. 2007 35: 5995-6003; doi:10.1093/nar/gkm647 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Lakshminarasimhan Pavithra, Shravanti Rampalli, Surajit Sinha, Kadreppa Sreenath, Richard G. Pestell, and Samit Chattopadhyay

Stabilization of SMAR1 mRNA by PGA2 involves a stem–loop structure in the 5' UTR
Nucleic Acids Research Advance Access published on August 28, 2007
Nucl. Acids Res. 2007 35: 6004-6016; doi:10.1093/nar/gkm649 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Ernesto Simón and Bertrand Séraphin

A specific role for the C-terminal region of the Poly(A)-binding protein in mRNA decay
Nucleic Acids Research Advance Access published on August 30, 2007
Nucl. Acids Res. 2007 35: 6017-6028; doi:10.1093/nar/gkm452 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Sven N. Hobbie, Sarath K. Kalapala, Subramanian Akshay, Christian Bruell, Sebastian Schmidt, Sabine Dabow, Andrea Vasella, Peter Sander, and Erik C. Böttger

Engineering the rRNA decoding site of eukaryotic cytosolic ribosomes in bacteria
Nucleic Acids Research Advance Access published on August 30, 2007
Nucl. Acids Res. 2007 35: 6086-6093; doi:10.1093/nar/gkm658 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Nikolai B. Ulyanov, Kinneret Shefer, Thomas L. James, and Yehuda Tzfati

Pseudoknot structures with conserved base triples in telomerase RNAs of ciliates
Nucleic Acids Research Advance Access published on September 7, 2007
Nucl. Acids Res. 2007 35: 6150-6160; doi:10.1093/nar/gkm660 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Andrew M. Parrott and Michael B. Mathews

Novel rapidly evolving hominid RNAs bind nuclear factor 90 and display tissue-restricted distribution
Nucleic Acids Research Advance Access published on September 13, 2007
Nucl. Acids Res. 2007 35: 6249-6258; doi:10.1093/nar/gkm668 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Ruth Canavan and Ursula Bond

Deletion of the nuclear exosome component RRP6 leads to continued accumulation of the histone mRNA HTB1 in S-phase of the cell cycle in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on September 13, 2007
Nucl. Acids Res. 2007 35: 6268-6279; doi:10.1093/nar/gkm691 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yogev Brown, Mira Abraham, Sivan Pearl, Majdi M. Kabaha, Elhanan Elboher, and Yehuda Tzfati

A critical three-way junction is conserved in budding yeast and vertebrate telomerase RNAs
Nucleic Acids Research Advance Access published on September 13, 2007
Nucl. Acids Res. 2007 35: 6280-6289; doi:10.1093/nar/gkm713 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Qing Dai, Robert Fong, Mridusmita Saikia, David Stephenson, Yi-tao Yu, Tao Pan, and Joseph A. Piccirilli

Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N⁶-methyladenosine
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2007 35: 6322-6329; doi:10.1093/nar/gkm657 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Hua Ren, Shuo-Xing Dou, Pascal Rigolet, Ye Yang, Peng-Ye Wang, Mounira Amor-Gueret, and Xu Guang Xi

The arginine finger of the Bloom syndrome protein: its structural organization and its role in energy coupling
Nucleic Acids Research Advance Access published on August 30, 2007
Nucl. Acids Res. 2007 35: 6029-6041; doi:10.1093/nar/gkm544 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Satoshi Fujii, Hidetoshi Kono, Shigeori Takenaka, Nobuhiro Go, and Akinori Sarai

Sequence-dependent DNA deformability studied using molecular dynamics simulations
Nucleic Acids Research Advance Access published on August 30, 2007
Nucl. Acids Res. 2007 35: 6063-6074; doi:10.1093/nar/gkm627 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Isabelle Lebars, Tristan Richard, Carmelo Di Primo, and Jean-Jacques Toulmé

NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA-modified aptamer
Nucleic Acids Research Advance Access published on September 3, 2007
Nucl. Acids Res. 2007 35: 6103-6114; doi:10.1093/nar/gkm655 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Manjori Ganguly, Feng Wang, Mahima Kaushik, Michael P. Stone, Luis A. Marky, and Barry Gold

A study of 7-deaza-2'-deoxyguanosine–2'-deoxycytidine base pairing in DNA
Nucleic Acids Research Advance Access published on September 12, 2007
Nucl. Acids Res. 2007 35: 6181-6195; doi:10.1093/nar/gkm670 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Corrigendum

T1DBase: integration and presentation of complex data for type 1 diabetes research
Nucl. Acids Res. 2007 35: 6338; doi:10.1093/nar/gkm715 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online

Get checked abstract Traci Kiesling, Kendra Cox, Eugene A. Davidson, Kenneth Dretchen, Guy Grater, Shannon Hibbard, Roger S. Lasken, Jonathan Leshin, Evan Skowronski, and Mark Danielsen

Sequence specific detection of DNA using nicking endonuclease signal amplification (NESA)
Nucleic Acids Research Advance Access published on September 7, 2007
Nucl. Acids Res. 2007 35: e117; doi:10.1093/nar/gkm654 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Shen Mynn Tan, Siew Tein Wang, Hannes Hentze, and Peter Dröge

A UTF1-based selection system for stable homogeneously pluripotent human embryonic stem cell cultures
Nucleic Acids Research Advance Access published on September 12, 2007
Nucl. Acids Res. 2007 35: e118; doi:10.1093/nar/gkm704 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Marcel W. Coolen, Aaron L. Statham, Margaret Gardiner-Garden, and Susan J. Clark

Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements
Nucleic Acids Research Advance Access published on September 13, 2007
Nucl. Acids Res. 2007 35: e119; doi:10.1093/nar/gkm662 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Zongzhi Liu, Catherine Lozupone, Micah Hamady, Frederic D. Bushman, and Rob Knight

Short pyrosequencing reads suffice for accurate microbial community analysis
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2007 35: e120; doi:10.1093/nar/gkm541 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Ricardo Soto Rifo, Emiliano P. Ricci, Didier Décimo, Olivier Moncorgé, and Théophile Ohlmann

Back to basics: the untreated rabbit reticulocyte lysate as a competitive system to recapitulate cap/poly(A) synergy and the selective advantage of IRES-driven translation
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2007 35: e121; doi:10.1093/nar/gkm682 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Laurent Bianchetti, Yan Wu, Eric Guerin, Frédéric Plewniak, and Olivier Poch

SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages
Nucleic Acids Research Advance Access published on September 20, 2007
Nucl. Acids Res. 2007 35: e122; doi:10.1093/nar/gkm648 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Masatoshi Ichihara, Yoshiki Murakumo, Akio Masuda, Toru Matsuura, Naoya Asai, Mayumi Jijiwa, Maki Ishida, Jun Shinmi, Hiroshi Yatsuya, Shanlou Qiao, Masahide Takahashi, and Kinji Ohno

Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities
Nucleic Acids Research Advance Access published on September 20, 2007
Nucl. Acids Res. 2007 35: e123; doi:10.1093/nar/gkm699 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Supplementary Data]  

Get checked abstract Anne Järve, Julius Müller, Il-Han Kim, Karl Rohr, Caroline MacLean, Gert Fricker, Ulrich Massing, Florian Eberle, Alexander Dalpke, Roger Fischer, Michael F. Trendelenburg, and Mark Helm

Surveillance of siRNA integrity by FRET imaging
Nucleic Acids Research Advance Access published on September 22, 2007
Nucl. Acids Res. 2007 35: e124; doi:10.1093/nar/gkm694 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

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