| | 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 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 |