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Volume 32(9);  2004
Articles
Enhanced fidelity for rejoining radiation-induced DNA double-strand breaks in the G2 phase of Chinese hamster ovary cells
Ines Krüger, Kai Rothkamm, and Markus Löbrich
Nucleic Acids Res. 2004; 32(9): 2677–2684. Published online 2004 May 17. doi: 10.1093/nar/gkh586.
PMCID: PMC419594
Gene mining: a novel and powerful ensemble decision approach to hunting for disease genes using microarray expression profiling
Xia Li, Shaoqi Rao, Yadong Wang, and Binsheng Gong
Nucleic Acids Res. 2004; 32(9): 2685–2694. Published online 2004 May 17. doi: 10.1093/nar/gkh563.
PMCID: PMC419591
Identification and functional validation of PNAs that inhibit murine CD40 expression by redirection of splicing
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
Nucleic Acids Res. 2004; 32(9): 2695–2706. Published online 2004 May 17. doi: 10.1093/nar/gkh584.
PMCID: PMC419592
A three-fluorophore FRET assay for high-throughput screening of small-molecule inhibitors of ribosome assembly
Dagmar Klostermeier, Pamela Sears, Chi-Huey Wong, David P. Millar, and James R. Williamson
Nucleic Acids Res. 2004; 32(9): 2707–2715. Published online 2004 May 17. doi: 10.1093/nar/gkh588.
PMCID: PMC419595
Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery
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
Nucleic Acids Res. 2004; 32(9): 2716–2729. Published online 2004 May 17. doi: 10.1093/nar/gkh589.
PMCID: PMC419596
Gene delivery by dendrimers operates via a cholesterol dependent pathway
Maria Manunta, Peng Hong Tan, Pervinder Sagoo, Kirk Kashefi, and Andrew J. T. George
Nucleic Acids Res. 2004; 32(9): 2730–2739. Published online 2004 May 17. doi: 10.1093/nar/gkh595.
PMCID: PMC419601
Comprehensive search for HNF-1β-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi
Taku Tanaka, Yasuhiro Tomaru, Yuki Nomura, Hisashi Miura, Masanori Suzuki, and Yoshihide Hayashizaki
Nucleic Acids Res. 2004; 32(9): 2740–2750. Published online 2004 May 17. doi: 10.1093/nar/gkh597.
PMCID: PMC419602
CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit
Julie Charollais, Marc Dreyfus, and Isabelle Iost
Nucleic Acids Res. 2004; 32(9): 2751–2759. Published online 2004 May 17. doi: 10.1093/nar/gkh603.
PMCID: PMC419605
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
Seisuke Kimura, Yasue Tahira, Toyotaka Ishibashi, Yoko Mori, Toshio Mori, Junji Hashimoto, and Kengo Sakaguchi
Nucleic Acids Res. 2004; 32(9): 2760–2767. Published online 2004 May 18. doi: 10.1093/nar/gkh591.
PMCID: PMC419598
A minimalist glutamyl-tRNA synthetase dedicated to aminoacylation of the tRNAAsp QUC anticodon
Mickaël Blaise, Hubert Dominique Becker, Gérard Keith, Christian Cambillau, Jacques Lapointe, Richard Giegé, and Daniel Kern
Nucleic Acids Res. 2004; 32(9): 2768–2775. Published online 2004 May 18. doi: 10.1093/nar/gkh608.
PMCID: PMC419609
Visualization of inositol phosphate-dependent mobility of Ku: depletion of the DNA–PK cofactor InsP6 inhibits Ku mobility
Jennifer Byrum, Stephen Jordan, Stephen T. Safrany, and William Rodgers
Nucleic Acids Res. 2004; 32(9): 2776–2784. Published online 2004 May 18. doi: 10.1093/nar/gkh592.
PMCID: PMC419599
Solution structure of a nitrous acid induced DNA interstrand cross-link
N. B. Fredrik Edfeldt, Eric A. Harwood, Snorri Th. Sigurdsson, Paul B. Hopkins, and Brian R. Reid
Nucleic Acids Res. 2004; 32(9): 2785–2794. Published online 2004 May 20. doi: 10.1093/nar/gkh606.
PMCID: PMC419607
Sequence context effect on the structure of nitrous acid induced DNA interstrand cross-links
N. B. Fredrik Edfeldt, Eric A. Harwood, Snorri Th. Sigurdsson, Paul B. Hopkins, and Brian R. Reid
Nucleic Acids Res. 2004; 32(9): 2795–2801. Published online 2004 May 20. doi: 10.1093/nar/gkh607.
PMCID: PMC419608
Influence of structural variation on nuclear localization of DNA-binding polyamide-fluorophore conjugates
Benjamin S. Edelson, Timothy P. Best, Bogdan Olenyuk, Nicholas G. Nickols, Raymond M. Doss, Shane Foister, Alexander Heckel, and Peter B. Dervan
Nucleic Acids Res. 2004; 32(9): 2802–2818. Published online 2004 May 20. doi: 10.1093/nar/gkh609.
PMCID: PMC419610
Structural characterization of an intermolecular RNA–RNA interaction involved in the transcription regulation element of a bipartite plant virus
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
Nucleic Acids Res. 2004; 32(9): 2819–2828. Published online 2004 May 20. doi: 10.1093/nar/gkh585.
PMCID: PMC419593
The high-affinity Sp1 binding site in the HTLV-1 promoter contributes to Tax-independent basal expression
Jill A. Livengood and Jennifer K. Nyborg
Nucleic Acids Res. 2004; 32(9): 2829–2837. Published online 2004 May 20. doi: 10.1093/nar/gkh590.
PMCID: PMC419597
Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function
Nalin C. W. Goonesekere and Byungkook Lee
Nucleic Acids Res. 2004; 32(9): 2838–2843. Published online 2004 May 20. doi: 10.1093/nar/gkh610.
PMCID: PMC419611
Structural insights by molecular dynamics simulations into specificity of the major human AP endonuclease toward the benzene-derived DNA adduct, pBQ-C
Anton B. Guliaev, Bo Hang, and B. Singer
Nucleic Acids Res. 2004; 32(9): 2844–2852. Published online 2004 May 20. doi: 10.1093/nar/gkh594.
PMCID: PMC419600
A protein-dependent riboswitch controlling ptsGHI operon expression in Bacillus subtilis: RNA structure rather than sequence provides interaction specificity
Oliver Schilling, Ines Langbein, Michael Müller, Matthias H. Schmalisch, and Jörg Stülke
Nucleic Acids Res. 2004; 32(9): 2853–2864. Published online 2004 May 20. doi: 10.1093/nar/gkh611.
PMCID: PMC419612
Chemically induced increases and decreases in the rate of expansion of a CAG·CTG triplet repeat
Mário Gomes-Pereira and Darren G. Monckton
Nucleic Acids Res. 2004; 32(9): 2865–2872. Published online 2004 May 20. doi: 10.1093/nar/gkh612.
PMCID: PMC419613
Microfluidic device reads up to four consecutive base pairs in DNA sequencing-by-synthesis
Emil P. Kartalov and Stephen R. Quake
Nucleic Acids Res. 2004; 32(9): 2873–2879. Published online 2004 May 20. doi: 10.1093/nar/gkh613.
PMCID: PMC419614
The RmInt1 group II intron has two different retrohoming pathways for mobility using predominantly the nascent lagging strand at DNA replication forks for priming
Francisco Martínez-Abarca, Antonio Barrientos-Durán, Manuel Fernández-López, and Nicolás Toro
Nucleic Acids Res. 2004; 32(9): 2880–2888. Published online 2004 May 20. doi: 10.1093/nar/gkh616.
PMCID: PMC419616
Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes
Gabriel Kreiman
Nucleic Acids Res. 2004; 32(9): 2889–2900. Published online 2004 May 20. doi: 10.1093/nar/gkh614.
PMCID: PMC419615
Clamping down on weak terminal base pairs: oligonucleotides with molecular caps as fidelity-enhancing elements at the 5′- and 3′-terminal residues
Sukunath Narayanan, Julia Gall, and Clemens Richert
Nucleic Acids Res. 2004; 32(9): 2901–2911. Published online 2004 May 20. doi: 10.1093/nar/gkh600.
PMCID: PMC419603
Activation of cryptic 3′ splice sites within introns of cellular genes following gene entrapment
Anna B. Osipovich, Erica K. White-Grindley, Geoffrey G. Hicks, Michael J. Roshon, Christian Shaffer, Jason H. Moore, and H. Earl Ruley
Nucleic Acids Res. 2004; 32(9): 2912–2924. Published online 2004 May 20. doi: 10.1093/nar/gkh604.
PMCID: PMC419606
The ribosomal RNA gene promoter and adjacent cis-acting DNA sequences govern plasmid DNA partitioning and stable inheritance in the parasitic protozoan Leishmania
Nathalie Boucher, François McNicoll, Maxime Laverdière, Annie Rochette, Marie-Noëlle Chou, and Barbara Papadopoulou
Nucleic Acids Res. 2004; 32(9): 2925–2936. Published online 2004 May 25. doi: 10.1093/nar/gkh617.
PMCID: PMC419617
2′-Deoxyribonolactone lesion produces G→A transitions in Escherichia coli
Virginie Faure, Jean-François Constant, Pascal Dumy, and Murat Saparbaev
Nucleic Acids Res. 2004; 32(9): 2937–2946. Published online 2004 May 24. doi: 10.1093/nar/gkh622.
PMCID: PMC419619
Characterization of critical interactions between Ndt80 and MSE DNA defining a novel family of Ig-fold transcription factors
Ian M. Fingerman, Kristina Sutphen, Sherwin P. Montano, Millie M. Georgiadis, and Andrew K. Vershon
Nucleic Acids Res. 2004; 32(9): 2947–2956. Published online 2004 May 25. doi: 10.1093/nar/gkh625.
PMCID: PMC419620
Coupled amplification and degradation of exogenous RNA injected in amphibian oocytes
Nicole Montreau, Sabine Vaur, Francois Dautry, and Yannick Andéol
Nucleic Acids Res. 2004; 32(9): 2957–2965. Published online 2004 May 25. doi: 10.1093/nar/gkh620.
PMCID: PMC419618
Ligation activity of fragmented ribozymes in frozen solution: implications for the RNA world
Alexander V. Vlassov, Brian H. Johnston, Laura F. Landweber, and Sergei A. Kazakov
Nucleic Acids Res. 2004; 32(9): 2966–2974. Published online 2004 May 25. doi: 10.1093/nar/gkh601.
PMCID: PMC419604
NAR Methods Online
Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA
Kwong-Kwok Wong, Yvonne T. M. Tsang, Jianhe Shen, Rita S. Cheng, Yi-Mieng Chang, Tsz-Kwong Man, and Ching C. Lau
Nucleic Acids Res. 2004; 32(9): e69. Published online 2004 May 17. doi: 10.1093/nar/gnh072.
PMCID: PMC419627
An on-chip thin film photodetector for the quantification of DNA probes and targets in microarrays
F. Fixe, V. Chu, D. M. F. Prazeres, and J. P. Conde
Nucleic Acids Res. 2004; 32(9): e70. Published online 2004 May 17. doi: 10.1093/nar/gnh066.
PMCID: PMC419621
Genome coverage and sequence fidelity of [var phi]29 polymerase-based multiple strand displacement whole genome amplification
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
Nucleic Acids Res. 2004; 32(9): e71. Published online 2004 May 18. doi: 10.1093/nar/gnh069.
PMCID: PMC419624
Real-time measurement of in vitro transcription
Salvatore A. E. Marras, Benjamin Gold, Fred Russell Kramer, Issar Smith, and Sanjay Tyagi
Nucleic Acids Res. 2004; 32(9): e72. Published online 2004 May 20. doi: 10.1093/nar/gnh068.
PMCID: PMC419623
Single-particle tracking for DNA tether length monitoring
Noëlle Pouget, Cynthia Dennis, Catherine Turlan, Mikhail Grigoriev, Michaël Chandler, and Laurence Salomé
Nucleic Acids Res. 2004; 32(9): e73. Published online 2004 May 20. doi: 10.1093/nar/gnh073.
PMCID: PMC419628
Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements
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
Nucleic Acids Res. 2004; 32(9): e74. Published online 2004 May 25. doi: 10.1093/nar/gnh071.
PMCID: PMC419626
Oligonucleotide hybridization studied by a surface plasmon diffraction sensor (SPDS)
Fang Yu, Danfeng Yao, and Wolfgang Knoll
Nucleic Acids Res. 2004; 32(9): e75. Published online 2004 May 20. doi: 10.1093/nar/gnh067.
PMCID: PMC419622
Balanced-PCR amplification allows unbiased identification of genomic copy changes in minute cell and tissue samples
Gang Wang, Cameron Brennan, Martha Rook, Jia Liu Wolfe, Christopher Leo, Lynda Chin, Hongjie Pan, Wei-Hua Liu, Brendan Price, and G. Mike Makrigiorgos
Nucleic Acids Res. 2004; 32(9): e76. Published online 2004 May 21. doi: 10.1093/nar/gnh070.
PMCID: PMC419625
Quantitative analysis of highly parallel transfection in cell microarrays
Sandrine Baghdoyan, Yoann Roupioz, Amandine Pitaval, David Castel, Elena Khomyakova, Alexandre Papine, Françoise Soussaline, and Xavier Gidrol
Nucleic Acids Res. 2004; 32(9): e77. Published online 2004 May 21. doi: 10.1093/nar/gnh074.
PMCID: PMC419629
RNA stem–loop enhanced expression of previously non-expressible genes
Michael Paulus, Martin Haslbeck, and Manfred Watzele
Nucleic Acids Res. 2004; 32(9): e78. Published online 2004 May 26. doi: 10.1093/nar/gnh076.
PMCID: PMC419630
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