Nucleic Acids Research

Survey and Summary:

Sundar Durai, Mala Mani, Karthikeyan Kandavelou, Joy Wu, Matthew H. Porteus, and Srinivasan Chandrasegaran

Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells
Nucl. Acids Res. 2005 33: 5978-5990; doi:10.1093/nar/gki912 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Articles:

Ursula Wimmer, Ying Wang, Oleg Georgiev, and Walter Schaffner

Two major branches of anti-cadmium defense in the mouse: MTF-1/metallothioneins and glutathione
Nucl. Acids Res. 2005 33: 5715-5727; doi:10.1093/nar/gki881 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jesús de la Cruz, Eloisa Sanz-Martínez, and Miguel Remacha

The essential WD-repeat protein Rsa4p is required for rRNA processing and intra-nuclear transport of 60S ribosomal subunits
Nucl. Acids Res. 2005 33: 5728-5739; doi:10.1093/nar/gki887 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Pedro A. Ortiz and Terri Goss Kinzy

Dominant-negative mutant phenotypes and the regulation of translation elongation factor 2 levels in yeast
Nucl. Acids Res. 2005 33: 5740-5748; doi:10.1093/nar/gki882 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Karim M. Elsawy, Michael K. Hodgson, and Leo S. D. Caves

The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA
Nucl. Acids Res. 2005 33: 5749-5762; doi:10.1093/nar/gki888 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Julia F. Hopkins and Sarah A. Woodson

Molecular beacons as probes of RNA unfolding under native conditions
Nucl. Acids Res. 2005 33: 5763-5770; doi:10.1093/nar/gki877 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Seung Pil Pack, Mitsuru Nonogawa, Tsutomu Kodaki, and Keisuke Makino

Chemical synthesis and thermodynamic characterization of oxanine-containing oligodeoxynucleotides
Nucl. Acids Res. 2005 33: 5771-5780; doi:10.1093/nar/gki865 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Alexandre V. Morozov, James J. Havranek, David Baker, and Eric D. Siggia

Protein–DNA binding specificity predictions with structural models
Nucl. Acids Res. 2005 33: 5781-5798; doi:10.1093/nar/gki875 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Christian Rausch, Tilmann Weber, Oliver Kohlbacher, Wolfgang Wohlleben, and Daniel H. Huson

Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs)
Nucl. Acids Res. 2005 33: 5799-5808; doi:10.1093/nar/gki885 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Kazuki Iwabata, Akiyo Koshiyama, Taiki Yamaguchi, Hiroko Sugawara, Fumika N. Hamada, Satoshi H. Namekawa, Satomi Ishii, Takashi Ishizaki, Hiroyuki Chiku, Takayuki Nara, and Kengo Sakaguchi

DNA topoisomerase II interacts with Lim15/Dmc1 in meiosis
Nucl. Acids Res. 2005 33: 5809-5818; doi:10.1093/nar/gki883 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Victoria Marini, Petros Christofis, Olga Novakova, Jana Kasparkova, Nicholas Farrell, and Viktor Brabec

Conformation, protein recognition and repair of DNA interstrand and intrastrand cross-links of Antitumor trans-[PtCl₂(NH₃)(thiazole)]
Nucl. Acids Res. 2005 33: 5819-5828; doi:10.1093/nar/gki884 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Kevin M. Phillips, Jonathan W. Larson, Gregory R. Yantz, Christina M. D'Antoni, Michael V. Gallo, Kimberly A. Gillis, Nuno M. Goncalves, Lori A. Neely, Steven R. Gullans, and Rudolf Gilmanshin

Application of single molecule technology to rapidly map long DNA and study the conformation of stretched DNA
Nucl. Acids Res. 2005 33: 5829-5837; doi:10.1093/nar/gki895 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Shea N. Gardner, Marisa W. Lam, Jason R. Smith, Clinton L. Torres, and Tom R. Slezak

Draft versus finished sequence data for DNA and protein diagnostic signature development
Nucl. Acids Res. 2005 33: 5838-5850; doi:10.1093/nar/gki896 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Michaela Vorlícková, Jana Chládková, Iva Kejnovská, Markéta Fialová, and Jaroslav Kypr

Guanine tetraplex topology of human telomere DNA is governed by the number of (TTAGGG) repeats
Nucl. Acids Res. 2005 33: 5851-5860; doi:10.1093/nar/gki898 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gong Cheng, Bin Qian, Ram Samudrala, and David Baker

Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design
Nucl. Acids Res. 2005 33: 5861-5867; doi:10.1093/nar/gki894 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Alexander Meissner, Andreas Gnirke, George W. Bell, Bernard Ramsahoye, Eric S. Lander, and Rudolf Jaenisch

Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis
Nucl. Acids Res. 2005 33: 5868-5877; doi:10.1093/nar/gki901 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shuhua Chen, Adelina A. Davies, Daniel Sagan, and Helle D. Ulrich

The RING finger ATPase Rad5p of Saccharomyces cerevisiae contributes to DNA double-strand break repair in a ubiquitin-independent manner
Nucl. Acids Res. 2005 33: 5878-5886; doi:10.1093/nar/gki902 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Mitsunobu Nakamura, Yudai Fukunaga, Kazuhiro Sasa, Yukinori Ohtoshi, Kenji Kanaori, Haruhisa Hayashi, Hidehiko Nakano, and Kazushige Yamana

Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference
Nucl. Acids Res. 2005 33: 5887-5895; doi:10.1093/nar/gki889 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Atanu Maiti and Siddhartha Roy

Switching DNA-binding specificity by unnatural amino acid substitution
Nucl. Acids Res. 2005 33: 5896-5903; doi:10.1093/nar/gki899 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Richard J. Dixon, Ian C. Eperon, Laurence Hall, and Nilesh J. Samani

A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species
Nucl. Acids Res. 2005 33: 5904-5913; doi:10.1093/nar/gki893 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Michael Barnes, Johannes Freudenberg, Susan Thompson, Bruce Aronow, and Paul Pavlidis

Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms
Nucl. Acids Res. 2005 33: 5914-5923; doi:10.1093/nar/gki890 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Rob Knight, Hans De Sterck, Rob Markel, Sandra Smit, Alexander Oshmyansky, and Michael Yarus

Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids
Nucl. Acids Res. 2005 33: 5924-5935; doi:10.1093/nar/gki886 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Karine Pereira de Jésus, Laurence Serre, Charles Zelwer, and Bertrand Castaing

Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA
Nucl. Acids Res. 2005 33: 5936-5944; doi:10.1093/nar/gki879 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fernando Moreno-Herrero, Laurent Holtzer, Daniel A. Koster, Stewart Shuman, Cees Dekker, and Nynke H. Dekker

Atomic force microscopy shows that vaccinia topoisomerase IB generates filaments on DNA in a cooperative fashion
Nucl. Acids Res. 2005 33: 5945-5953; doi:10.1093/nar/gki906 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

A. D. J. Scadden and M. A. O'Connell

Cleavage of dsRNAs hyper-edited by ADARs occurs at preferred editing sites
Nucl. Acids Res. 2005 33: 5954-5964; doi:10.1093/nar/gki909 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Monica Cuccurese, Giulia Russo, Annapina Russo, and Concetta Pietropaolo

Alternative splicing and nonsense-mediated mRNA decay regulate mammalian ribosomal gene expression
Nucl. Acids Res. 2005 33: 5965-5977; doi:10.1093/nar/gki905 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jean-Jacques Favory, Masanori Kobayshi, Kan Tanaka, Gilles Peltier, Martin Kreis, Jean-Gabriel Valay, and Silva Lerbs-Mache

Specific function of a plastid sigma factor for ndhF gene transcription
Nucl. Acids Res. 2005 33: 5991-5999; doi:10.1093/nar/gki908 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Pablo Arrisi Mercado, Youhna M. Ayala, Maurizio Romano, Emanuele Buratti, and Francisco E. Baralle

Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene
Nucl. Acids Res. 2005 33: 6000-6010; doi:10.1093/nar/gki897 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alexander E. F. Smith and Kevin G. Ford

Use of altered-specificity binding Oct-4 suggests an absence of pluripotent cell-specific cofactor usage
Nucl. Acids Res. 2005 33: 6011-6023; doi:10.1093/nar/gki907 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yuexing Zhang, Damilola Akinmade, and Anne W. Hamburger

The ErbB3 binding protein Ebp1 interacts with Sin3A to repress E2F1 and AR-mediated transcription
Nucl. Acids Res. 2005 33: 6024-6033; doi:10.1093/nar/gki903 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Krzysztof Lemke, Marcin Wojciechowski, William Laine, Christian Bailly, Pierre Colson, Maciej Baginski, Annette K. Larsen, and Andrzej Skladanowski

Induction of unique structural changes in guanine-rich DNA regions by the triazoloacridone C-1305, a topoisomerase II inhibitor with antitumor activities
Nucl. Acids Res. 2005 33: 6034-6047; doi:10.1093/nar/gki904 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Petr V. Sergiev, Dmitry V. Lesnyak, Sergey V. Kiparisov, Dmitry E. Burakovsky, Andrei A. Leonov, Alexey A. Bogdanov, Richard Brimacombe, and Olga A. Dontsova

Function of the ribosomal E-site: a mutagenesis study
Nucl. Acids Res. 2005 33: 6048-6056; doi:10.1093/nar/gki910 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Uri Laserson, Hin Hark Gan, and Tamar Schlick

Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs
Nucl. Acids Res. 2005 33: 6057-6069; doi:10.1093/nar/gki911 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Daekyu Sun, Kexiao Guo, Jadrian J. Rusche, and Laurence H. Hurley

Facilitation of a structural transition in the polypurine/polypyrimidine tract within the proximal promoter region of the human VEGF gene by the presence of potassium and G-quadruplex-interactive agents
Nucl. Acids Res. 2005 33: 6070-6080; doi:10.1093/nar/gki917 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Corrigendum:

Peter Macpherson, Flavia Barone, Giovanni Maga, Filomena Mazzei, Peter Karran, and Margherita Bignami

8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutS
Nucl. Acids Res. 2005 33: 6081; doi:10.1093/nar/gki891 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Ming Jiang, Andrey A. Arzumanov, Michael J. Gait, and Jo Milner

A bi-functional siRNA construct induces RNA interference and also primes PCR amplification for its own quantification
Nucl. Acids Res. 2005 33: e151; doi:10.1093/nar/gni144 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sarah J. Lindsay, James K. Bonfield, and Matthew E. Hurles

Shotgun haplotyping: a novel method for surveying allelic sequence variation
Nucl. Acids Res. 2005 33: e152; doi:10.1093/nar/gni152 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ralph Bertram, Martin Köstner, Judith Müller, José Vazquez Ramos, and Wolfgang Hillen

Integrative elements for Bacillus subtilis yielding tetracycline-dependent growth phenotypes
Nucl. Acids Res. 2005 33: e153; doi:10.1093/nar/gni154 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Zhilei Chen and Huimin Zhao

A highly sensitive selection method for directed evolution of homing endonucleases
Nucl. Acids Res. 2005 33: e154; doi:10.1093/nar/gni148 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Junhao Mao, Jeffery Barrow, Jill McMahon, Joe Vaughan, and Andrew P. McMahon

An ES cell system for rapid, spatial and temporal analysis of gene function in vitro and in vivo
Nucl. Acids Res. 2005 33: e155; doi:10.1093/nar/gni146 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chia-Sheng Liao, Gwo-Bin Lee, Hsiao-Sheng Liu, Tsung-Min Hsieh, and Ching-Hsing Luo

Miniature RT–PCR system for diagnosis of RNA-based viruses
Nucl. Acids Res. 2005 33: e156; doi:10.1093/nar/gni157 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Soumyaroop Bhattacharya and Thomas J. Mariani

Transformation of expression intensities across generations of Affymetrix microarrays using sequence matching and regression modeling
Nucl. Acids Res. 2005 33: e157; doi:10.1093/nar/gni159 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ozlem Topaloglu, Paula J. Hurley, Ozlem Yildirim, Curt I. Civin, and Fred Bunz

Improved methods for the generation of human gene knockout and knockin cell lines
Nucl. Acids Res. 2005 33: e158; doi:10.1093/nar/gni160 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jeroen Knijnenburg, Marja van der Burg, Philomeen Nilsson, Hans Kristian Ploos van Amstel, Hans Tanke, and Károly Szuhai

Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms
Nucl. Acids Res. 2005 33: e159; doi:10.1093/nar/gni161 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Christine N. Zanghi, Heather A. Lankes, Birgit Bradel-Tretheway, Jessica Wegman, and Stephen Dewhurst

A simple method for displaying recalcitrant proteins on the surface of bacteriophage lambda
Nucl. Acids Res. 2005 33: e160; doi:10.1093/nar/gni158 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

PokMan Chan, Tony Yuen, Frederique Ruf, Javier Gonzalez-Maeso, and Stuart C. Sealfon

Method for multiplex cellular detection of mRNAs using quantum dot fluorescent in situ hybridization
Nucl. Acids Res. 2005 33: e161; doi:10.1093/nar/gni162 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Supriya Pai, Andrew D. Ellington, and Matthew Levy

Proximity ligation assays with peptide conjugate ‘burrs’ for the sensitive detection of spores
Nucl. Acids Res. 2005 33: e162; doi:10.1093/nar/gni150 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Holly E. Sassi, Stephanie Renihan, Andrew M. Spence, and Ramona L. Cooperstock

Gene CATCHR—Gene Cloning And Tagging for Caenorhabditis elegans using yeast Homologous Recombination: a novel approach for the analysis of gene expression
Nucl. Acids Res. 2005 33: e163; doi:10.1093/nar/gni164 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Anita I. Kishore, Michael R. Mayer, and James H. Prestegard

Partial ¹³C isotopic enrichment of nucleoside monophosphates: useful reporters for NMR structural studies
Nucl. Acids Res. 2005 33: e164; doi:10.1093/nar/gni165 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.