| | Survey and Summary How do site-specific DNA-binding proteins find their targets? Stephen E. Halford and John F. Marko Nucleic Acids Res. 2004; 32(10): 3040–3052. Published online 2004 June 3. doi: 10.1093/nar/gkh624.PMCID: PMC434431 Articles Nucleic Acids Res. 2004; 32(10): 2975–2976. Published online 2004 June 2. doi: 10.1093/nar/gkh647.PMCID: PMC434451 DnaG interacts with a linker region that joins the N- and C-domains of DnaB and induces the formation of 3-fold symmetric rings Jenny Thirlway, Ian J. Turner, Christopher T. Gibson, Laurence Gardiner, Kevin Brady, Stephanie Allen, Clive J. Roberts, and Panos Soultanas Nucleic Acids Res. 2004; 32(10): 2977–2986. Published online 2004 June 1. doi: 10.1093/nar/gkh628.PMCID: PMC434434 3′-Box-dependent processing of human pre-U1 snRNA requires a combination of RNA and protein co-factors Patricia Uguen and Shona Murphy Nucleic Acids Res. 2004; 32(10): 2987–2994. Published online 2004 June 1. doi: 10.1093/nar/gkh619.PMCID: PMC434428 The highly conserved region of the co-repressor Sin3A functionally interacts with the co-repressor Alien Udo Moehren, Uwe Dressel, Christina A. Reeb, Sami Väisänen, Thomas W. Dunlop, Carsten Carlberg, and Aria Baniahmad Nucleic Acids Res. 2004; 32(10): 2995–3004. Published online 2004 June 1. doi: 10.1093/nar/gkh621.PMCID: PMC434429 The C-terminal zinc finger of the catalytic subunit of DNA polymerase δ is responsible for direct interaction with the B-subunit Javier Sanchez Garcia, Leonora F. Ciufo, Xiaowen Yang, Stephen E. Kearsey, and Stuart A. MacNeill Nucleic Acids Res. 2004; 32(10): 3005–3016. Published online 2004 June 1. doi: 10.1093/nar/gkh623.PMCID: PMC434430 Definitions and analysis of DNA Holliday junction geometry Jeffrey Watson, Franklin A. Hays, and P. Shing Ho Nucleic Acids Res. 2004; 32(10): 3017–3027. Published online 2004 June 1. doi: 10.1093/nar/gkh631.PMCID: PMC434437 Interaction of Escherichia coli DbpA with 23S rRNA in different functional states of the enzyme Fedor V. Karginov and Olke C. Uhlenbeck Nucleic Acids Res. 2004; 32(10): 3028–3032. Published online 2004 June 1. doi: 10.1093/nar/gkh640.PMCID: PMC434445 Acetylation of the human DNA glycosylase NEIL2 and inhibition of its activity Kishor K. Bhakat, Tapas K. Hazra, and Sankar Mitra Nucleic Acids Res. 2004; 32(10): 3033–3039. Published online 2004 June 2. doi: 10.1093/nar/gkh632.PMCID: PMC434438 Twinkle and POLG defects enhance age-dependent accumulation of mutations in the control region of mtDNA Sjoerd Wanrooij, Petri Luoma, Gert van Goethem, Christine van Broeckhoven, Anu Suomalainen, and Johannes N. Spelbrink Nucleic Acids Res. 2004; 32(10): 3053–3064. Published online 2004 June 4. doi: 10.1093/nar/gkh634.PMCID: PMC434440 Inhibition of human breast carcinoma proliferation, migration, chemoinvasion and solid tumour growth by DNAzymes targeting the zinc finger transcription factor EGR-1 Ainslie Mitchell, Crispin R. Dass, Lun-Quan Sun, and Levon M. Khachigian Nucleic Acids Res. 2004; 32(10): 3065–3069. Published online 2004 June 4. doi: 10.1093/nar/gkh626.PMCID: PMC434432 The Drosophila Bruno paralogue Bru-3 specifically binds the EDEN translational repression element Jérôme Delaunay, Gwenn Le Mée, Nader Ezzeddine, Gilles Labesse, Christophe Terzian, Michèle Capri, and Ounissa Aït-Ahmed Nucleic Acids Res. 2004; 32(10): 3070–3082. Published online 2004 June 4. doi: 10.1093/nar/gkh627.PMCID: PMC434433 NMR solution structure of a parallel LNA quadruplex Antonio Randazzo, Veronica Esposito, Oliver Ohlenschläger, Ramadurai Ramachandran, and Luciano Mayol Nucleic Acids Res. 2004; 32(10): 3083–3092. Published online 2004 June 4. doi: 10.1093/nar/gkh629.PMCID: PMC434435 Sequence-specific Rho–RNA interactions in transcription termination James E. Graham Nucleic Acids Res. 2004; 32(10): 3093–3100. Published online 2004 June 4. doi: 10.1093/nar/gkh630.PMCID: PMC434436 LNA/DNA chimeric oligomers mimic RNA aptamers targeted to the TAR RNA element of HIV-1 Fabien Darfeuille, Jens Bo Hansen, Henrik Orum, Carmelo Di Primo, and Jean-Jacques Toulmé Nucleic Acids Res. 2004; 32(10): 3101–3107. Published online 2004 June 4. doi: 10.1093/nar/gkh636.PMCID: PMC434442 Genome-wide identification of genes likely to be involved in human genetic disease Núria López-Bigas and Christos A. Ouzounis Nucleic Acids Res. 2004; 32(10): 3108–3114. Published online 2004 June 4. doi: 10.1093/nar/gkh605.PMCID: PMC434425 Demonstration of a universal surface DNA computer Xingping Su and Lloyd M. Smith Nucleic Acids Res. 2004; 32(10): 3115–3123. Published online 2004 June 4. doi: 10.1093/nar/gkh635.PMCID: PMC434441 PeerGAD: a peer-review-based and community-centric web application for viewing and annotating prokaryotic genome sequences Mark D. D’Ascenzo, Alan Collmer, and Gregory B. Martin Nucleic Acids Res. 2004; 32(10): 3124–3135. Published online 2004 June 7. doi: 10.1093/nar/gkh615.PMCID: PMC434426 Recognition of DNA by ω protein from the broad-host range Streptococcus pyogenes plasmid pSM19035: analysis of binding to operator DNA with one to four heptad repeats Ana B. de la Hoz, Florencia Pratto, Rolf Misselwitz, Christian Speck, Wilhelm Weihofen, Karin Welfle, Wolfram Saenger, Heinz Welfle, and Juan C. Alonso Nucleic Acids Res. 2004; 32(10): 3136–3147. Published online 2004 June 9. doi: 10.1093/nar/gkh633.PMCID: PMC434439 KpnI restriction endonuclease and methyltransferase exhibit contrasting mode of sequence recognition Siddamadappa Chandrashekaran, U. H. Manjunatha, and Valakunja Nagaraja Nucleic Acids Res. 2004; 32(10): 3148–3155. Published online 2004 June 10. doi: 10.1093/nar/gkh638.PMCID: PMC434444 Analysis of the LAGLIDADG interface of the monomeric homing endonuclease I-DmoI George H. Silva and Marlene Belfort Nucleic Acids Res. 2004; 32(10): 3156–3168. Published online 2004 June 9. doi: 10.1093/nar/gkh618.PMCID: PMC434427 Altered DNA binding specificity of Arnt by selection of partner bHLH–PAS proteins Koshi Kinoshita, Yasuo Kikuchi, Yukie Sasakura, Masashi Suzuki, Yoshiaki Fujii-Kuriyama, and Kazuhiro Sogawa Nucleic Acids Res. 2004; 32(10): 3169–3179. Published online 2004 June 9. doi: 10.1093/nar/gkh637.PMCID: PMC434443 Direct interaction of NRSF with TBP: chromatin reorganization and core promoter repression for neuron-specific gene transcription Kiyohito Murai, Yoshihisa Naruse, Yosef Shaul, Yasutoshi Agata, and Nozomu Mori Nucleic Acids Res. 2004; 32(10): 3180–3189. Published online 2004 June 14. doi: 10.1093/nar/gkh550.PMCID: PMC434424 Structure-specific DNA binding and bipolar helicase activities of PcrA Syam P. Anand and Saleem A. Khan Nucleic Acids Res. 2004; 32(10): 3190–3197. Published online 2004 June 15. doi: 10.1093/nar/gkh641.PMCID: PMC434446 MUTYH prevents OGG1 or APEX1 from inappropriately processing its substrate or reaction product with its C-terminal domain Yohei Tominaga, Yasuhiro Ushijima, Daisuke Tsuchimoto, Masaki Mishima, Masahiro Shirakawa, Seiki Hirano, Kunihiko Sakumi, and Yusaku Nakabeppu Nucleic Acids Res. 2004; 32(10): 3198–3211. Published online 2004 June 15. doi: 10.1093/nar/gkh642.PMCID: PMC434447 Sensing complex regulatory networks by conformationally controlled hairpin ribozymes S. Hani Najafi-Shoushtari, Günter Mayer, and Michael Famulok Nucleic Acids Res. 2004; 32(10): 3212–3219. Published online 2004 June 15. doi: 10.1093/nar/gkh643.PMCID: PMC434448 Thiostrepton-resistant mutants of Thermus thermophilus Dale M. Cameron, Jill Thompson, Steven T. Gregory, Paul E. March, and Albert E. Dahlberg Nucleic Acids Res. 2004; 32(10): 3220–3227. Published online 2004 June 15. doi: 10.1093/nar/gkh644.PMCID: PMC434449 Global structure of a DNA three-way junction by solution NMR: towards prediction of 3H fold Bin Wu, Frederic Girard, Bernd van Buuren, Jürgen Schleucher, Marco Tessari, and Sybren Wijmenga Nucleic Acids Res. 2004; 32(10): 3228–3239. Published online 2004 June 15. doi: 10.1093/nar/gkh645.PMCID: PMC434450 Endonuclease III and endonuclease VIII conditionally targeted into mitochondria enhance mitochondrial DNA repair and cell survival following oxidative stress Lyudmila I. Rachek, Valentina I. Grishko, Mikhail F. Alexeyev, Viktoriya V. Pastukh, Susan P. LeDoux, and Glenn L. Wilson Nucleic Acids Res. 2004; 32(10): 3240–3247. Published online 2004 June 15. doi: 10.1093/nar/gkh648.PMCID: PMC434452 A Rad50-dependent pathway of DNA repair is deficient in Fanconi anemia fibroblasts Sarah L. Donahue and Colin Campbell Nucleic Acids Res. 2004; 32(10): 3248–3257. Published online 2004 June 15. doi: 10.1093/nar/gkh649.PMCID: PMC434453 RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences Giulio Pavesi, Giancarlo Mauri, Marco Stefani, and Graziano Pesole Nucleic Acids Res. 2004; 32(10): 3258–3269. Published online 2004 June 15. doi: 10.1093/nar/gkh650.PMCID: PMC434454 NAR Methods Online High-throughput polyribosome fractionation Yipeng Wang, Steven Ringquist, Ann H. Cho, Gaelle Rondeau, and John Welsh Nucleic Acids Res. 2004; 32(10): e79. Published online 2004 June 1. doi: 10.1093/nar/gnh077.PMCID: PMC434456 Construction of oligonucleotide arrays on a glass surface using a heterobifunctional reagent, N-(2-trifluoroethanesulfonatoethyl)-N-(methyl)-triethoxysilylpropyl-3-amine (NTMTA) P. Kumar, Jyoti Choithani, and K. C. Gupta Nucleic Acids Res. 2004; 32(10): e80. Published online 2004 June 2. doi: 10.1093/nar/gnh075.PMCID: PMC434455 Genomic DNA as a cohybridization standard for mammalian microarray measurements Brian A. Williams, Richele M. Gwirtz, and Barbara J. Wold Nucleic Acids Res. 2004; 32(10): e81. Published online 2004 June 9. doi: 10.1093/nar/gnh078.PMCID: PMC434457 The recognition and modification sites for the bacterial type I restriction systems KpnAI, StySEAI, StySENI and StySGI Julie K. A. Kasarjian, Masumi Hidaka, Takashi Horiuchi, Masatake Iida, and Junichi Ryu Nucleic Acids Res. 2004; 32(10): e82. Published online 2004 June 15. doi: 10.1093/nar/gnh079.PMCID: PMC434458 A high-throughput assay for Tn5 Tnp-induced DNA cleavage Brandon Ason and William S. Reznikoff Nucleic Acids Res. 2004; 32(10): e83. Published online 2004 June 16. doi: 10.1093/nar/gnh080.PMCID: PMC434459 Rapid preparation of RNA samples for NMR spectroscopy and X-ray crystallography Hae-Kap Cheong, Eunha Hwang, Chulhyun Lee, Byong-Seok Choi, and Chaejoon Cheong Nucleic Acids Res. 2004; 32(10): e84. Published online 2004 June 15. doi: 10.1093/nar/gnh081.PMCID: PMC434460 Inducible suppression of Fgfr2 and Survivin in ES cells using a combination of the RNA interference (RNAi) and the Cre–LoxP system Xavier Coumoul, Wenmei Li, Rui-Hong Wang, and Chuxia Deng Nucleic Acids Res. 2004; 32(10): e85. Published online 2004 June 15. doi: 10.1093/nar/gnh083.PMCID: PMC434461 |