| | Articles In silico identification of transcriptional regulators associated with c-Myc Ran Elkon, Karen I. Zeller, Chaim Linhart, Chi V. Dang, Ron Shamir, and Yosef Shiloh Nucleic Acids Res. 2004; 32(17): 4955–4961. Published online 2004 September 23. doi: 10.1093/nar/gkh816.PMCID: PMC521640 DNA computing using single-molecule hybridization detection Kristiane A. Schmidt, Christiaan V. Henkel, Grzegorz Rozenberg, and Herman P. Spaink Nucleic Acids Res. 2004; 32(17): 4962–4968. Published online 2004 September 23. doi: 10.1093/nar/gkh817.PMCID: PMC521641 Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes Marie Touchon, Alain Arneodo, Yves d'Aubenton-Carafa, and Claude Thermes Nucleic Acids Res. 2004; 32(17): 4969–4978. Published online 2004 September 23. doi: 10.1093/nar/gkh823.PMCID: PMC521644 Bipartite pattern discovery by entropy minimization-based multiple local alignment Chengpeng Bi and Peter K. Rogan Nucleic Acids Res. 2004; 32(17): 4979–4991. Published online 2004 September 23. doi: 10.1093/nar/gkh825.PMCID: PMC521645 DNA-mediated assembly of weakly interacting DNA-binding protein subunits: in vitro recruitment of phage 434 repressor and yeast GCN4 DNA-binding domains Corrado Guarnaccia, Bakthisaran Raman, Sotir Zahariev, András Simoncsits, and Sándor Pongor Nucleic Acids Res. 2004; 32(17): 4992–5002. Published online 2004 September 23. doi: 10.1093/nar/gkh827.PMCID: PMC521646 The post-replication repair RAD18 and RAD6 genes are involved in the prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine in Saccharomyces cerevisiae Marcelo de Padula, Guenaelle Slezak, Patricia Auffret van Der Kemp, and Serge Boiteux Nucleic Acids Res. 2004; 32(17): 5003–5010. Published online 2004 September 23. doi: 10.1093/nar/gkh831.PMCID: PMC521648 Amplification and assembly of chip-eluted DNA (AACED): a method for high-throughput gene synthesis Kathryn E. Richmond, Mo-Huang Li, Matthew J. Rodesch, Madhusudan Patel, Aaron M. Lowe, Changhan Kim, Larry L. Chu, Narasimhar Venkataramaian, Shane F. Flickinger, James Kaysen, Peter J. Belshaw, Michael R. Sussman, and Franco Cerrina Nucleic Acids Res. 2004; 32(17): 5011–5018. Published online 2004 September 24. doi: 10.1093/nar/gkh793.PMCID: PMC521639 Lsh, an epigenetic guardian of repetitive elements Jiaqiang Huang, Tao Fan, Qingsheng Yan, Heming Zhu, Stephen Fox, Haleem J. Issaq, Lionel Best, Lisa Gangi, David Munroe, and Kathrin Muegge Nucleic Acids Res. 2004; 32(17): 5019–5028. Published online 2004 September 24. doi: 10.1093/nar/gkh821.PMCID: PMC521642 Comparative analysis of complete genomes reveals gene loss, acquisition and acceleration of evolutionary rates in Metazoa, suggests a prevalence of evolution via gene acquisition and indicates that the evolutionary rates in animals tend to be conserved Vladimir N. Babenko and Dmitri M. Krylov Nucleic Acids Res. 2004; 32(17): 5029–5035. Published online 2004 September 24. doi: 10.1093/nar/gkh833.PMCID: PMC521649 Solving the riddle of codon usage preferences: a test for translational selection Mario dos Reis, Renos Savva, and Lorenz Wernisch Nucleic Acids Res. 2004; 32(17): 5036–5044. Published online 2004 September 24. doi: 10.1093/nar/gkh834.PMCID: PMC521650 Selection and evolution of NTP-specific aptamers Laure Weill, Dominique Louis, and Bruno Sargueil Nucleic Acids Res. 2004; 32(17): 5045–5058. Published online 2004 September 27. doi: 10.1093/nar/gkh835.PMCID: PMC521651 HYPROSP: a hybrid protein secondary structure prediction algorithm—a knowledge-based approach Kuen-Pin Wu, Hsin-Nan Lin, Jia-Ming Chang, Ting-Yi Sung, and Wen-Lian Hsu Nucleic Acids Res. 2004; 32(17): 5059–5065. Published online 2004 September 24. doi: 10.1093/nar/gkh836.PMCID: PMC521652 Pdr3 is required for DNA damage induction of MAG1 and DDI1 via a bi-directional promoter element Yu Zhu and Wei Xiao Nucleic Acids Res. 2004; 32(17): 5066–5075. Published online 2004 September 27. doi: 10.1093/nar/gkh838.PMCID: PMC521653 A yeast arginine specific tRNA is a remnant aspartate acceptor Aurélie Fender, Renaud Geslain, Gilbert Eriani, Richard Giegé, Marie Sissler, and Catherine Florentz Nucleic Acids Res. 2004; 32(17): 5076–5086. Published online 2004 September 27. doi: 10.1093/nar/gkh843.PMCID: PMC521656 DNA adopts normal B-form upon incorporation of highly fluorescent DNA base analogue tC: NMR structure and UV-Vis spectroscopy characterization K. Cecilia Engman, Peter Sandin, Sadie Osborne, Tom Brown, Martin Billeter, Per Lincoln, Bengt Nordén, Bo Albinsson, and L. Marcus Wilhelmsson Nucleic Acids Res. 2004; 32(17): 5087–5095. Published online 2004 September 27. doi: 10.1093/nar/gkh844.PMCID: PMC521657 Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences Kei Iida, Motoaki Seki, Tetsuya Sakurai, Masakazu Satou, Kenji Akiyama, Tetsuro Toyoda, Akihiko Konagaya, and Kazuo Shinozaki Nucleic Acids Res. 2004; 32(17): 5096–5103. Published online 2004 September 27. doi: 10.1093/nar/gkh845.PMCID: PMC521658 DNA polymerase β overexpression stimulates the Rad51-dependent homologous recombination in mammalian cells Yvan Canitrot, Jean-Pascal Capp, Nadine Puget, Anne Bieth, Bernard Lopez, Jean-Sébastien Hoffmann, and Christophe Cazaux Nucleic Acids Res. 2004; 32(17): 5104–5112. Published online 2004 September 27. doi: 10.1093/nar/gkh848.PMCID: PMC521661 Method for direct discrimination of intra- and intermolecular hydrogen bonds, and characterization of the G(:A):G(:A):G(:A):G heptad, with scalar couplings across hydrogen bonds Hidetsugu Sotoya, Akimasa Matsugami, Tetsuro Ikeda, Kiyoshi Ouhashi, Seiichi Uesugi, and Masato Katahira Nucleic Acids Res. 2004; 32(17): 5113–5118. Published online 2004 September 27. doi: 10.1093/nar/gkh849.PMCID: PMC521662 A general role of the DNA glycosylase Nth1 in the abasic sites cleavage step of base excision repair in Schizosaccharomyces pombe Ingrun Alseth, Hanne Korvald, Fekret Osman, Erling Seeberg, and Magnar Bjørås Nucleic Acids Res. 2004; 32(17): 5119–5125. Published online 2004 September 27. doi: 10.1093/nar/gkh851.PMCID: PMC521664 Determination of thermodynamic parameters for HIV DIS type loop–loop kissing complexes Albert Weixlbaumer, Andreas Werner, Christoph Flamm, Eric Westhof, and Renée Schroeder Nucleic Acids Res. 2004; 32(17): 5126–5133. Published online 2004 September 30. doi: 10.1093/nar/gkh841.PMCID: PMC521654 Thermodynamic, kinetic and structural basis for recognition and repair of abasic sites in DNA by apurinic/apyrimidinic endonuclease from human placenta Natalia G. Beloglazova, Oleg O. Kirpota, Konstantin V. Starostin, Alexander A. Ishchenko, Vitaly I. Yamkovoy, Dmitry O. Zharkov, Kenneth T. Douglas, and Georgy A. Nevinsky Nucleic Acids Res. 2004; 32(17): 5134–5146. Published online 2004 September 30. doi: 10.1093/nar/gkh846.PMCID: PMC521659 A new hydrogen-bonding potential for the design of protein–RNA interactions predicts specific contacts and discriminates decoys Yu Chen, Tanja Kortemme, Tim Robertson, David Baker, and Gabriele Varani Nucleic Acids Res. 2004; 32(17): 5147–5162. Published online 2004 September 30. doi: 10.1093/nar/gkh785.PMCID: PMC521638 Position- and orientation-specific enhancement of topoisomerase I cleavage complexes by triplex DNA structures Smitha Antony, Paola B. Arimondo, Jian-Sheng Sun, and Yves Pommier Nucleic Acids Res. 2004; 32(17): 5163–5173. Published online 2004 October 4. doi: 10.1093/nar/gkh847.PMCID: PMC521660 AtmtPNPase is required for multiple aspects of the 18S rRNA metabolism in Arabidopsis thaliana mitochondria Romary Perrin, Heike Lange, Jean-Michel Grienenberger, and Dominique Gagliardi Nucleic Acids Res. 2004; 32(17): 5174–5182. Published online 2004 September 30. doi: 10.1093/nar/gkh852.PMCID: PMC521665 Adjust quality scores from alignment and improve sequencing accuracy Ming Li, Magnus Nordborg, and Lei M. Li Nucleic Acids Res. 2004; 32(17): 5183–5191. Published online 2004 September 30. doi: 10.1093/nar/gkh850.PMCID: PMC521663 DNA-binding domain of GCN4 induces bending of both the ATF/CREB and AP-1 binding sites of DNA Anatoly I. Dragan, Yingyun Liu, Elena N. Makeyeva, and Peter L. Privalov Nucleic Acids Res. 2004; 32(17): 5192–5197. Published online 2004 September 30. doi: 10.1093/nar/gkh854.PMCID: PMC521666 A codon window in mRNA downstream of the initiation codon where NGG codons give strongly reduced gene expression in Escherichia coli Ernesto I. Gonzalez de Valdivia and Leif A. Isaksson Nucleic Acids Res. 2004; 32(17): 5198–5205. Published online 2004 September 30. doi: 10.1093/nar/gkh857.PMCID: PMC521668 The Saccharomyces cerevisiae TRT2 tRNAThr gene upstream of STE6 is a barrier to repression in MATα cells and exerts a potential tRNA position effect in MATa cells Tiffany A. Simms, Elsy C. Miller, Nicolas P. Buisson, Nithya Jambunathan, and David Donze Nucleic Acids Res. 2004; 32(17): 5206–5213. Published online 2004 September 30. doi: 10.1093/nar/gkh858.PMCID: PMC521669 Biochemical properties of Trypanosoma cruzi telomerase Denise P. Muñoz and Kathleen Collins Nucleic Acids Res. 2004; 32(17): 5214–5222. Published online 2004 September 30. doi: 10.1093/nar/gkh864.PMCID: PMC521672 The DNA primase of Sulfolobus solfataricus is activated by substrates containing a thymine-rich bubble and has a 3′-terminal nucleotidyl-transferase activity Mariarosaria De Falco, Alessandra Fusco, Mariarita De Felice, Mosè Rossi, and Francesca M. Pisani Nucleic Acids Res. 2004; 32(17): 5223–5230. Published online 2004 September 30. doi: 10.1093/nar/gkh865.PMCID: PMC521673 PhyloGenie: automated phylome generation and analysis Tancred Frickey and Andrei N. Lupas Nucleic Acids Res. 2004; 32(17): 5231–5238. Published online 2004 September 30. doi: 10.1093/nar/gkh867.PMCID: PMC521674 Camptothecin enhances the frequency of oligonucleotide-directed gene repair in mammalian cells by inducing DNA damage and activating homologous recombination Luciana Ferrara and Eric B. Kmiec Nucleic Acids Res. 2004; 32(17): 5239–5248. Published online 2004 October 5. doi: 10.1093/nar/gkh822.PMCID: PMC521643 DNA double strand break repair in human bladder cancer is error prone and involves microhomology-associated end-joining Johanne Bentley, Christine P. Diggle, Patricia Harnden, Margaret A. Knowles, and Anne E. Kiltie Nucleic Acids Res. 2004; 32(17): 5249–5259. Published online 2004 October 5. doi: 10.1093/nar/gkh842.PMCID: PMC521655 Comparative genomics of the FtsK–HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging Lakshminarayan M. Iyer, Kira S. Makarova, Eugene V. Koonin, and L. Aravind Nucleic Acids Res. 2004; 32(17): 5260–5279. Published online 2004 October 5. doi: 10.1093/nar/gkh828.PMCID: PMC521647 Negative cross-talk between the human orphan nuclear receptor Nur77/NAK-1/TR3 and nuclear factor-κB Hanna Harant and Ivan J. D. Lindley Nucleic Acids Res. 2004; 32(17): 5280–5290. Published online 2004 October 5. doi: 10.1093/nar/gkh856.PMCID: PMC521667 Mutational analysis of the damage-recognition and catalytic mechanism of human SMUG1 DNA glycosylase Mayumi Matsubara, Tamon Tanaka, Hiroaki Terato, Eiji Ohmae, Shunsuke Izumi, Katsuo Katayanagi, and Hiroshi Ide Nucleic Acids Res. 2004; 32(17): 5291–5302. Published online 2004 October 5. doi: 10.1093/nar/gkh859.PMCID: PMC521670 A novel GTPase activated by the small subunit of ribosome Hyouta Himeno, Kyoko Hanawa-Suetsugu, Takatsugu Kimura, Kuniaki Takagi, Wakana Sugiyama, Shinobu Shirata, Tomoyuki Mikami, Fujiko Odagiri, Yukiko Osanai, Daisuke Watanabe, Simon Goto, Liliya Kalachnyuk, Chisato Ushida, and Akira Muto Nucleic Acids Res. 2004; 32(17): 5303–5309. Published online 2004 October 5. doi: 10.1093/nar/gkh861.PMCID: PMC521671 Automated synthesis of new ferrocenyl-modified oligonucleotides: study of their properties in solution Aude-Emmanuelle Navarro, Nicolas Spinelli, Corinne Moustrou, Carole Chaix, Bernard Mandrand, and Hugues Brisset Nucleic Acids Res. 2004; 32(17): 5310–5319. Published online 2004 October 5. doi: 10.1093/nar/gkh874.PMCID: PMC521675 NAR Methods Online Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays Paul M. K. Gordon and Christoph W. Sensen Nucleic Acids Res. 2004; 32(17): e133. Published online 2004 September 29. doi: 10.1093/nar/gnh127.PMCID: PMC521677 Gene silencing in alveolar type II cells using cell-specific promoter in vitro and in vivo Deming Gou, Telugu Narasaraju, Narendranath Reddy Chintagari, Nili Jin, Pengcheng Wang, and Lin Liu Nucleic Acids Res. 2004; 32(17): e134. Published online 2004 September 27. doi: 10.1093/nar/gnh129.PMCID: PMC521678 Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR Brooks E. Miner, Reinhard J. Stöger, Alice F. Burden, Charles D. Laird, and R. Scott Hansen Nucleic Acids Res. 2004; 32(17): e135. Published online 2004 September 30. doi: 10.1093/nar/gnh132.PMCID: PMC521679 Protein evolution by codon-based random deletions Joel Osuna, Jorge Yáñez, Xavier Soberón, and Paul Gaytán Nucleic Acids Res. 2004; 32(17): e136. Published online 2004 September 30. doi: 10.1093/nar/gnh135.PMCID: PMC521680 Corrigendum Nucleic Acids Res. 2004; 32(17): 5320. Published online 2004 October 5. doi: 10.1093/nar/gkh890.PMCID: PMC521676 Corrects: Chengpeng Bi, et al. Bipartite pattern discovery by entropy minimization-based multiple local alignment. Nucleic Acids Res. 2004; 32(17): 4979–4991. |