Nucleic Acids Research

Survey and Summary:

Elizabeth C. Chao and Steven M. Lipkin

Molecular models for the tissue specificity of DNA mismatch repair-deficient carcinogenesis
Nucl. Acids Res. 2006 34: 840-852; doi:10.1093/nar/gkj489 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Vigdis Nygaard and Eivind Hovig

Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling
Nucl. Acids Res. 2006 34: 996-1014; doi:10.1093/nar/gkj499 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Articles:

Manolis Gialitakis, Androniki Kretsovali, Charalampos Spilianakis, Lara Kravariti, Jörg Mages, Reinhard Hoffmann, Antonis K. Hatzopoulos, and Joseph Papamatheakis

Coordinated changes of histone modifications and HDAC mobilization regulate the induction of MHC class II genes by Trichostatin A
Nucl. Acids Res. 2006 34: 765-772; doi:10.1093/nar/gkj462 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Blagovesta Popova, Markus Kuhlmann, Andrea Hinas, Fredrik Söderbom, and Wolfgang Nellen

HelF, a putative RNA helicase acts as a nuclear suppressor of RNAi but not antisense mediated gene silencing
Nucl. Acids Res. 2006 34: 773-784; doi:10.1093/nar/gkj465 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Lihua Wang and Suse Broyde

A new anti conformation for N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) allows Watson–Crick pairing in the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4)
Nucl. Acids Res. 2006 34: 785-795; doi:10.1093/nar/gkj479 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

James C. Samuelson, Richard D. Morgan, Jack S. Benner, Toby E. Claus, Stephanie L. Packard, and Shuang-yong Xu

Engineering a rare-cutting restriction enzyme: genetic screening and selection of NotI variants
Nucl. Acids Res. 2006 34: 796-805; doi:10.1093/nar/gkj483 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chad B. Thomas and Richard I. Gumport

Dimerization of the bacterial RsrI N6-adenine DNA methyltransferase
Nucl. Acids Res. 2006 34: 806-815; doi:10.1093/nar/gkj486 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Rebecca J. Richards, Carla A. Theimer, L. David Finger, and Juli Feigon

Structure of the Tetrahymena thermophila telomerase RNA helix II template boundary element
Nucl. Acids Res. 2006 34: 816-825; doi:10.1093/nar/gkj481 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Xavier Manival, Christophe Charron, Jean-Baptiste Fourmann, François Godard, Bruno Charpentier, and Christiane Branlant

Crystal structure determination and site-directed mutagenesis of the Pyrococcus abyssi aCBF5–aNOP10 complex reveal crucial roles of the C-terminal domains of both proteins in H/ACA sRNP activity
Nucl. Acids Res. 2006 34: 826-839; doi:10.1093/nar/gkj482 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Patrick Wai-Lun Li, Jinfang Li, Stephanie L. Timmerman, Les A. Krushel, and Sandra L. Martin

The dicistronic RNA from the mouse LINE-1 retrotransposon contains an internal ribosome entry site upstream of each ORF: implications for retrotransposition
Nucl. Acids Res. 2006 34: 853-864; doi:10.1093/nar/gkj490 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Romina Oliva, Luigi Cavallo, and Anna Tramontano

Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions
Nucl. Acids Res. 2006 34: 865-879; doi:10.1093/nar/gkj491 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Takashi Hiyama, Mari Katsura, Takashi Yoshihara, Mari Ishida, Aiko Kinomura, Tetsuji Tonda, Toshimasa Asahara, and Kiyoshi Miyagawa

Haploinsufficiency of the Mus81–Eme1 endonuclease activates the intra-S-phase and G₂/M checkpoints and promotes rereplication in human cells
Nucl. Acids Res. 2006 34: 880-892; doi:10.1093/nar/gkj495 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

David H. Ardell and Siv G. E. Andersson

TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase
Nucl. Acids Res. 2006 34: 893-904; doi:10.1093/nar/gkj449 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Eva Freyhult, Vincent Moulton, and David H. Ardell

Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos
Nucl. Acids Res. 2006 34: 905-916; doi:10.1093/nar/gkj478 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Xueping Yu, Jimmy Lin, Tomohiro Masuda, Noriko Esumi, Donald J. Zack, and Jiang Qian

Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae
Nucl. Acids Res. 2006 34: 917-927; doi:10.1093/nar/gkj487 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Barbara Testoni and Roberto Mantovani

Mechanisms of transcriptional repression of cell-cycle G₂/M promoters by p63
Nucl. Acids Res. 2006 34: 928-938; doi:10.1093/nar/gkj477 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

John R. Horton, Xing Zhang, Robert Maunus, Zhe Yang, Geoffrey G. Wilson, Richard J. Roberts, and Xiaodong Cheng

DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion
Nucl. Acids Res. 2006 34: 939-948; doi:10.1093/nar/gkj484 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Yan Xu and Hiroshi Sugiyama

Formation of the G-quadruplex and i-motif structures in retinoblastoma susceptibility genes (Rb)
Nucl. Acids Res. 2006 34: 949-954; doi:10.1093/nar/gkj485 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Björn Titz, Sindhu Thomas, Seesandra V. Rajagopala, Tomoko Chiba, Takashi Ito, and Peter Uetz

Transcriptional activators in yeast
Nucl. Acids Res. 2006 34: 955-967; doi:10.1093/nar/gkj493 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Garrett A. Soukup

Core requirements for glmS ribozyme self-cleavage reveal a putative pseudoknot structure
Nucl. Acids Res. 2006 34: 968-975; doi:10.1093/nar/gkj497 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

J. A. Ferreiro, N. G. Powell, N. Karabetsou, J. Mellor, and R. Waters

Roles for Gcn5p and Ada2p in transcription and nucleotide excision repair at the Saccharomyces cerevisiae MET16 gene
Nucl. Acids Res. 2006 34: 976-985; doi:10.1093/nar/gkj501 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Antoine Graindorge, Raphaël Thuret, Nicolas Pollet, H. Beverley Osborne, and Yann Audic

Identification of post-transcriptionally regulated Xenopus tropicalis maternal mRNAs by microarray
Nucl. Acids Res. 2006 34: 986-995; doi:10.1093/nar/gkj492 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

J. Ross Buchan, Lorna S. Aucott, and Ian Stansfield

tRNA properties help shape codon pair preferences in open reading frames
Nucl. Acids Res. 2006 34: 1015-1027; doi:10.1093/nar/gkj488 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Sarah L. Williams, Laura K. Parkhurst, and Lawrence J. Parkhurst

Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer
Nucl. Acids Res. 2006 34: 1028-1035; doi:10.1093/nar/gkj498 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Cindy Baumann, Gisa S. Boehden, Alexander Bürkle, and Lisa Wiesmüller

Poly(ADP-RIBOSE) polymerase-1 (Parp-1) antagonizes topoisomerase I-dependent recombination stimulation by P53
Nucl. Acids Res. 2006 34: 1036-1049; doi:10.1093/nar/gkj509 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zhengchang Su, Fenglou Mao, Phuongan Dam, Hongwei Wu, Victor Olman, Ian T. Paulsen, Brian Palenik, and Ying Xu

Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102
Nucl. Acids Res. 2006 34: 1050-1065; doi:10.1093/nar/gkj496 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Russell L. Marsden, David Lee, Michael Maibaum, Corin Yeats, and Christine A. Orengo

Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space
Nucl. Acids Res. 2006 34: 1066-1080; doi:10.1093/nar/gkj494 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Corrigendum:

Teca Calcagno Galvão and Jean O. Thomas

Structure-specific binding of MeCP2 to four-way junction DNA through its methyl CpG-binding domain
Nucl. Acids Res. 2006 34: 1081; doi:10.1093/nar/gkj513 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Erratum:

Robert J. Fisher, Matthew J. Fivash, Andrew G. Stephen, Nathan A. Hagan, Shilpa R. Shenoy, Maxine V. Medaglia, Lindsey R. Smith, Karen M. Worthy, John T. Simpson, Robert Shoemaker, Karen L. McNitt, Donald G. Johnson, Catherine V. Hixson, Robert J. Gorelick, Daniele Fabris, Louis E. Henderson, and Alan Rein

Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides
Nucl. Acids Res. 2006 34: 1082; doi:10.1093/nar/gkj506 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Romulo Martin Brena, Herbert Auer, Karl Kornacker, Björn Hackanson, Aparna Raval, John C. Byrd, and Christoph Plass

Accurate quantification of DNA methylation using combined bisulfite restriction analysis coupled with the Agilent 2100 Bioanalyzer platform
Nucl. Acids Res. 2006 34: e17; doi:10.1093/nar/gnj017 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Florence Mauger, Olivier Jaunay, Valérie Chamblain, Fred Reichert, Keith Bauer, Ivo G. Gut, and David H. Gelfand

SNP genotyping using alkali cleavage of RNA/DNA chimeras and MALDI time-of-flight mass spectrometry
Nucl. Acids Res. 2006 34: e18; doi:10.1093/nar/gnj021 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Srinivasan Yegnasubramanian, Xiaohui Lin, Michael C. Haffner, Angelo M. DeMarzo, and William G. Nelson

Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation
Nucl. Acids Res. 2006 34: e19; doi:10.1093/nar/gnj022 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gholam Khodakaramian, Sarah Lissenden, Bertolt Gust, Laura Moir, Paul A. Hoskisson, Keith F. Chater, and Margaret C. M. Smith

Expression of Cre recombinase during transient phage infection permits efficient marker removal in Streptomyces
Nucl. Acids Res. 2006 34: e20; doi:10.1093/nar/gnj019 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ya-Ming Hou, Zhi Li, and Howard Gamper

Isolation of a site-specifically modified RNA from an unmodified transcript
Nucl. Acids Res. 2006 34: e21; doi:10.1093/nar/gnj018 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Milan Fedurco, Anthony Romieu, Scott Williams, Isabelle Lawrence, and Gerardo Turcatti

BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies
Nucl. Acids Res. 2006 34: e22; doi:10.1093/nar/gnj023 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Volker Wiesenthal, Achim Leutz, and Cornelis F. Calkhoven

A translation control reporter system (TCRS) for the analysis of translationally controlled processes in the vertebrate cell
Nucl. Acids Res. 2006 34: e23; doi:10.1093/nar/gnj029 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Vicente Marchán, Samuel Ortega, Daniel Pulido, Enrique Pedroso, and Anna Grandas

Diels-Alder cycloadditions in water for the straightforward preparation of peptide–oligonucleotide conjugates
Nucl. Acids Res. 2006 34: e24; doi:10.1093/nar/gnj020 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Silke De-Zolt, Frank Schnütgen, Claudia Seisenberger, Jens Hansen, Melanie Hollatz, Thomas Floss, Patricia Ruiz, Wolfgang Wurst, and Harald von Melchner

High-throughput trapping of secretory pathway genes in mouse embryonic stem cells
Nucl. Acids Res. 2006 34: e25; doi:10.1093/nar/gnj026 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Lukas M. Wick, Jean Marie Rouillard, Thomas S. Whittam, Erdogan Gulari, James M. Tiedje, and Syed A. Hashsham

On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes
Nucl. Acids Res. 2006 34: e26; doi:10.1093/nar/gnj024 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Seiji Tateyama, Kenichi Horisawa, Hideaki Takashima, Etsuko Miyamoto-Sato, Nobuhide Doi, and Hiroshi Yanagawa

Affinity selection of DNA-binding protein complexes using mRNA display
Nucl. Acids Res. 2006 34: e27; doi:10.1093/nar/gnj025 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

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