Nucleic Acids Research

Articles:

Ines Krüger, Kai Rothkamm, and Markus Löbrich

Enhanced fidelity for rejoining radiation-induced DNA double-strand breaks in the G₂ phase of Chinese hamster ovary cells
Nucl. Acids Res. 2004 32: 2677-2684; doi:10.1093/nar/gkh586 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Xia Li, Shaoqi Rao, Yadong Wang, and Binsheng Gong

Gene mining: a novel and powerful ensemble decision approach to hunting for disease genes using microarray expression profiling
Nucl. Acids Res. 2004 32: 2685-2694; doi:10.1093/nar/gkh563 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Andrew M. Siwkowski, Leila Malik, Christine C. Esau, Martin A. Maier, Edward V. Wancewicz, Klaus Albertshofer, Brett P. Monia, C. Frank Bennett, and Anne B. Eldrup

Identification and functional validation of PNAs that inhibit murine CD40 expression by redirection of splicing
Nucl. Acids Res. 2004 32: 2695-2706; doi:10.1093/nar/gkh584 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dagmar Klostermeier, Pamela Sears, Chi-Huey Wong, David P. Millar, and James R. Williamson

A three-fluorophore FRET assay for high-throughput screening of small-molecule inhibitors of ribosome assembly
Nucl. Acids Res. 2004 32: 2707-2715; doi:10.1093/nar/gkh588 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Theresa M. Geiman, Umesh T. Sankpal, Andrea K. Robertson, Yue Chen, Manjari Mazumdar, Jason T. Heale, John A. Schmiesing, Wankee Kim, Kyoko Yokomori, Yingming Zhao, and Keith D. Robertson

Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery
Nucl. Acids Res. 2004 32: 2716-2729; doi:10.1093/nar/gkh589 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Maria Manunta, Peng Hong Tan, Pervinder Sagoo, Kirk Kashefi, and Andrew J. T. George

Gene delivery by dendrimers operates via a cholesterol dependent pathway
Nucl. Acids Res. 2004 32: 2730-2739; doi:10.1093/nar/gkh595 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Taku Tanaka, Yasuhiro Tomaru, Yuki Nomura, Hisashi Miura, Masanori Suzuki, and Yoshihide Hayashizaki

Comprehensive search for HNF-1ß-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi
Nucl. Acids Res. 2004 32: 2740-2750; doi:10.1093/nar/gkh597 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Julie Charollais, Marc Dreyfus, and Isabelle Iost

CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit
Nucl. Acids Res. 2004 32: 2751-2759; doi:10.1093/nar/gkh603 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Seisuke Kimura, Yasue Tahira, Toyotaka Ishibashi, Yoko Mori, Toshio Mori, Junji Hashimoto, and Kengo Sakaguchi

DNA repair in higher plants; photoreactivation is the major DNA repair pathway in non-proliferating cells while excision repair (nucleotide excision repair and base excision repair) is active in proliferating cells
Nucl. Acids Res. 2004 32: 2760-2767; doi:10.1093/nar/gkh591 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mickaël Blaise, Hubert Dominique Becker, Gérard Keith, Christian Cambillau, Jacques Lapointe, Richard Giegé, and Daniel Kern

A minimalist glutamyl-tRNA synthetase dedicated to aminoacylation of the tRNA^Asp QUC anticodon
Nucl. Acids Res. 2004 32: 2768-2775; doi:10.1093/nar/gkh608 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jennifer Byrum, Stephen Jordan, Stephen T. Safrany, and William Rodgers

Visualization of inositol phosphate-dependent mobility of Ku: depletion of the DNA–PK cofactor InsP₆ inhibits Ku mobility
Nucl. Acids Res. 2004 32: 2776-2784; doi:10.1093/nar/gkh592 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

N. B. Fredrik Edfeldt, Eric A. Harwood, Snorri Th. Sigurdsson, Paul B. Hopkins, and Brian R. Reid

Solution structure of a nitrous acid induced DNA interstrand cross-link
Nucl. Acids Res. 2004 32: 2785-2794; doi:10.1093/nar/gkh606 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

N. B. Fredrik Edfeldt, Eric A. Harwood, Snorri Th. Sigurdsson, Paul B. Hopkins, and Brian R. Reid

Sequence context effect on the structure of nitrous acid induced DNA interstrand cross-links
Nucl. Acids Res. 2004 32: 2795-2801; doi:10.1093/nar/gkh607 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Benjamin S. Edelson, Timothy P. Best, Bogdan Olenyuk, Nicholas G. Nickols, Raymond M. Doss, Shane Foister, Alexander Heckel, and Peter B. Dervan

Influence of structural variation on nuclear localization of DNA-binding polyamide-fluorophore conjugates
Nucl. Acids Res. 2004 32: 2802-2818; doi:10.1093/nar/gkh609 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Richard H. Guenther, Tim L. Sit, Hanna S. Gracz, Michael A. Dolan, Hannah L. Townsend, Guihua Liu, Winnell H. Newman, Paul F. Agris, and Steven A. Lommel

Structural characterization of an intermolecular RNA–RNA interaction involved in the transcription regulation element of a bipartite plant virus
Nucl. Acids Res. 2004 32: 2819-2828; doi:10.1093/nar/gkh585 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jill A. Livengood and Jennifer K. Nyborg

The high-affinity Sp1 binding site in the HTLV-1 promoter contributes to Tax-independent basal expression
Nucl. Acids Res. 2004 32: 2829-2837; doi:10.1093/nar/gkh590 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nalin C. W. Goonesekere and Byungkook Lee

Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function
Nucl. Acids Res. 2004 32: 2838-2843; doi:10.1093/nar/gkh610 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Anton B. Guliaev, Bo Hang, and B. Singer

Structural insights by molecular dynamics simulations into specificity of the major human AP endonuclease toward the benzene-derived DNA adduct, pBQ-C
Nucl. Acids Res. 2004 32: 2844-2852; doi:10.1093/nar/gkh594 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Oliver Schilling, Ines Langbein, Michael Müller, Matthias H. Schmalisch, and Jörg Stülke

A protein-dependent riboswitch controlling ptsGHI operon expression in Bacillus subtilis: RNA structure rather than sequence provides interaction specificity
Nucl. Acids Res. 2004 32: 2853-2864; doi:10.1093/nar/gkh611 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mário Gomes-Pereira and Darren G. Monckton

Chemically induced increases and decreases in the rate of expansion of a CAG·CTG triplet repeat
Nucl. Acids Res. 2004 32: 2865-2872; doi:10.1093/nar/gkh612 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Emil P. Kartalov and Stephen R. Quake

Microfluidic device reads up to four consecutive base pairs in DNA sequencing-by-synthesis
Nucl. Acids Res. 2004 32: 2873-2879; doi:10.1093/nar/gkh613 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Francisco Martínez-Abarca, Antonio Barrientos-Durán, Manuel Fernández-López, and Nicolás Toro

The RmInt1 group II intron has two different retrohoming pathways for mobility using predominantly the nascent lagging strand at DNA replication forks for priming
Nucl. Acids Res. 2004 32: 2880-2888; doi:10.1093/nar/gkh616 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Gabriel Kreiman

Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes
Nucl. Acids Res. 2004 32: 2889-2900; doi:10.1093/nar/gkh614 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sukunath Narayanan, Julia Gall, and Clemens Richert

Clamping down on weak terminal base pairs: oligonucleotides with molecular caps as fidelity-enhancing elements at the 5'- and 3'-terminal residues
Nucl. Acids Res. 2004 32: 2901-2911; doi:10.1093/nar/gkh600 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Anna B. Osipovich, Erica K. White-Grindley, Geoffrey G. Hicks, Michael J. Roshon, Christian Shaffer, Jason H. Moore, and H. Earl Ruley

Activation of cryptic 3' splice sites within introns of cellular genes following gene entrapment
Nucl. Acids Res. 2004 32: 2912-2924; doi:10.1093/nar/gkh604 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nathalie Boucher, François McNicoll, Maxime Laverdière, Annie Rochette, Marie-Noëlle Chou, and Barbara Papadopoulou

The ribosomal RNA gene promoter and adjacent cis-acting DNA sequences govern plasmid DNA partitioning and stable inheritance in the parasitic protozoan Leishmania
Nucl. Acids Res. 2004 32: 2925-2936; doi:10.1093/nar/gkh617 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Virginie Faure, Jean-François Constant, Pascal Dumy, and Murat Saparbaev

2'-Deoxyribonolactone lesion produces GA transitions in Escherichia coli
Nucl. Acids Res. 2004 32: 2937-2946; doi:10.1093/nar/gkh622 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ian M. Fingerman, Kristina Sutphen, Sherwin P. Montano, Millie M. Georgiadis, and Andrew K. Vershon

Characterization of critical interactions between Ndt80 and MSE DNA defining a novel family of Ig-fold transcription factors
Nucl. Acids Res. 2004 32: 2947-2956; doi:10.1093/nar/gkh625 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nicole Montreau, Sabine Vaur, Francois Dautry, and Yannick Andéol

Coupled amplification and degradation of exogenous RNA injected in amphibian oocytes
Nucl. Acids Res. 2004 32: 2957-2965; doi:10.1093/nar/gkh620 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Alexander V. Vlassov, Brian H. Johnston, Laura F. Landweber, and Sergei A. Kazakov

Ligation activity of fragmented ribozymes in frozen solution: implications for the RNA world
Nucl. Acids Res. 2004 32: 2966-2974; doi:10.1093/nar/gkh601 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

NAR Methods Online:

Kwong-Kwok Wong, Yvonne T. M. Tsang, Jianhe Shen, Rita S. Cheng, Yi-Mieng Chang, Tsz-Kwong Man, and Ching C. Lau

Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA
Nucl. Acids Res. 2004 32: e69; doi:10.1093/nar/gnh072 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

F. Fixe, V. Chu, D. M. F. Prazeres, and J. P. Conde

An on-chip thin film photodetector for the quantification of DNA probes and targets in microarrays
Nucl. Acids Res. 2004 32: e70; doi:10.1093/nar/gnh066 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

J. Guillermo Paez, Ming Lin, Rameen Beroukhim, Jeffrey C. Lee, Xiaojun Zhao, Daniel J. Richter, Stacey Gabriel, Paula Herman, Hidefumi Sasaki, David Altshuler, Cheng Li, Matthew Meyerson, and William R. Sellers

Genome coverage and sequence fidelity of 29 polymerase-based multiple strand displacement whole genome amplification
Nucl. Acids Res. 2004 32: e71; doi:10.1093/nar/gnh069 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Salvatore A. E. Marras, Benjamin Gold, Fred Russell Kramer, Issar Smith, and Sanjay Tyagi

Real-time measurement of in vitro transcription
Nucl. Acids Res. 2004 32: e72; doi:10.1093/nar/gnh068 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Noëlle Pouget, Cynthia Dennis, Catherine Turlan, Mikhail Grigoriev, Michaël Chandler, and Laurence Salomé

Single-particle tracking for DNA tether length monitoring
Nucl. Acids Res. 2004 32: e73; doi:10.1093/nar/gnh073 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Brigham H. Mecham, Gregory T. Klus, Jeffrey Strovel, Meena Augustus, David Byrne, Peter Bozso, Daniel Z. Wetmore, Thomas J. Mariani, Isaac S. Kohane, and Zoltan Szallasi

Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements
Nucl. Acids Res. 2004 32: e74; doi:10.1093/nar/gnh071 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Fang Yu, Danfeng Yao, and Wolfgang Knoll

Oligonucleotide hybridization studied by a surface plasmon diffraction sensor (SPDS)
Nucl. Acids Res. 2004 32: e75; doi:10.1093/nar/gnh067 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Gang Wang, Cameron Brennan, Martha Rook, Jia Liu Wolfe, Christopher Leo, Lynda Chin, Hongjie Pan, Wei-Hua Liu, Brendan Price, and G. Mike Makrigiorgos

Balanced-PCR amplification allows unbiased identification of genomic copy changes in minute cell and tissue samples
Nucl. Acids Res. 2004 32: e76; doi:10.1093/nar/gnh070 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sandrine Baghdoyan, Yoann Roupioz, Amandine Pitaval, David Castel, Elena Khomyakova, Alexandre Papine, Françoise Soussaline, and Xavier Gidrol

Quantitative analysis of highly parallel transfection in cell microarrays
Nucl. Acids Res. 2004 32: e77; doi:10.1093/nar/gnh074 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Michael Paulus, Martin Haslbeck, and Manfred Watzele

RNA stem–loop enhanced expression of previously non-expressible genes
Nucl. Acids Res. 2004 32: e78; doi:10.1093/nar/gnh076 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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