| | 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 PMCID: PMC521640 DNA computing using single-molecule hybridization detection Kristiane A. Schmidt, Christiaan V. Henkel, Grzegorz Rozenberg, and Herman P. Spaink PMCID: PMC521641 Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes Marie Touchon, Alain Arneodo, Yves d'Aubenton-Carafa, and Claude Thermes PMCID: PMC521644 Bipartite pattern discovery by entropy minimization-based multiple local alignment Chengpeng Bi and Peter K. Rogan 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 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 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 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 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 PMCID: PMC521649 Solving the riddle of codon usage preferences: a test for translational selection Mario dos Reis, Renos Savva, and Lorenz Wernisch PMCID: PMC521650 Selection and evolution of NTP-specific aptamers Laure Weill, Dominique Louis, and Bruno Sargueil 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 PMCID: PMC521652 Pdr3 is required for DNA damage induction of MAG1 and DDI1 via a bi-directional promoter element Yu Zhu and Wei Xiao 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 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 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 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 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 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 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 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 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 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 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 PMCID: PMC521665 Adjust quality scores from alignment and improve sequencing accuracy Ming Li, Magnus Nordborg, and Lei M. Li 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 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 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 PMCID: PMC521669 Biochemical properties of Trypanosoma cruzi telomerase Denise P. Muñoz and Kathleen Collins 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 PMCID: PMC521673 PhyloGenie: automated phylome generation and analysis Tancred Frickey and Andrei N. Lupas 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 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 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 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 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 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 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 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 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 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 PMCID: PMC521679 Protein evolution by codon-based random deletions Joel Osuna, Jorge Yáñez, Xavier Soberón, and Paul Gaytán 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. |
