| | Survey and Summary Decoding the genome: a modified view Paul F. Agris PMCID: PMC384350 Articles DNA-dependent protein kinase (DNA-PK) phosphorylates nuclear DNA helicase II/RNA helicase A and hnRNP proteins in an RNA-dependent manner Suisheng Zhang, Bernhard Schlott, Matthias Görlach, and Frank Grosse PMCID: PMC373260 ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Dean Laslett and Bjorn Canback PMCID: PMC373265 GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification Nouri Ben Zakour, Michel Gautier, Rumen Andonov, Dominique Lavenier, Marie-Françoise Cochet, Philippe Veber, Alexei Sorokin, and Yves Le Loir PMCID: PMC373259 RB signaling prevents replication-dependent DNA double-strand breaks following genotoxic insult Emily E. Bosco, Christopher N. Mayhew, Robert F. Hennigan, Julien Sage, Tyler Jacks, and Erik S. Knudsen PMCID: PMC373257 The last CTD repeat of the mammalian RNA polymerase II large subunit is important for its stability Rob D. Chapman, Benoit Palancade, Andreas Lang, Olivier Bensaude, and Dirk Eick PMCID: PMC373282 Interactions between the 2.4 and 4.2 regions of σS, the stress-specific σ factor of Escherichia coli, and the –10 and –35 promoter elements Claire Checroun, Patricia Bordes, Olivier Leroy, Annie Kolb, and Claude Gutierrez PMCID: PMC373267 Role of intrinsic DNA binding specificity in defining target genes of the mammalian transcription factor PDX1 Arthur Liberzon, Gabriela Ridner, and Michael D. Walker PMCID: PMC373268 Echinomycin inhibits chromosomal DNA replication and embryonic development in vertebrates Laurence G. May, Mark A. Madine, and Michael J. Waring PMCID: PMC373276 The major human AP endonuclease (Ape1) is involved in the nucleotide incision repair pathway Laurent Gros, Alexander A. Ishchenko, Hiroshi Ide, Rhoderick H. Elder, and Murat K. Saparbaev PMCID: PMC373275 Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein Norie Fujikawa, Hitoshi Kurumizaka, Osamu Nureki, Yoshinori Tanaka, Mitsuyoshi Yamazoe, Sota Hiraga, and Shigeyuki Yokoyama PMCID: PMC373283 Yeast telomerase is capable of limited repeat addition processivity Dimitry Bosoy and Neal F. Lue PMCID: PMC373262 Complementarity-directed RNA dimer-linkage promotes retroviral recombination in vivo Jacob Giehm Mikkelsen, Søren Vestergaard Rasmussen, and Finn Skou Pedersen PMCID: PMC373270 The major role of human AP-endonuclease homolog Apn2 in repair of abasic sites in Schizosaccharomyces pombe Balazs Ribar, Tadahide Izumi, and Sankar Mitra PMCID: PMC373264 Formation of DNA nanoparticles in the presence of novel polyamine analogues: a laser light scattering and atomic force microscopic study Veena Vijayanathan, Thresia Thomas, Thomas Antony, Akira Shirahata, and T. J. Thomas PMCID: PMC373261 Automatic extraction of mutations from Medline and cross-validation with OMIM Dietrich Rebholz-Schuhmann, Stephane Marcel, Sylvie Albert, Ralf Tolle, Georg Casari, and Harald Kirsch PMCID: PMC373272 Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes Ali Nahvi, Jeffrey E. Barrick, and Ronald R. Breaker PMCID: PMC373277 Polyamine derivatives as selective RNaseA mimics Sandra Fouace, Cyril Gaudin, Sylvie Picard, Sophie Corvaisier, Jacques Renault, Bertrand Carboni, and Brice Felden PMCID: PMC373269 A 21-amino acid peptide from the cysteine cluster II of the family D DNA polymerase from Pyrococcus horikoshii stimulates its nuclease activity which is Mre11-like and prefers manganese ion as the cofactor Yulong Shen, Xiao-Feng Tang, Hideshi Yokoyama, Eriko Matsui, and Ikuo Matsui PMCID: PMC373266 Domain mapping of the Rad51 paralog protein complexes Kristi A. Miller, Dorota Sawicka, Daniel Barsky, and Joanna S. Albala PMCID: PMC373258 Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification Peter M. Haverty, Ulla Hansen, and Zhiping Weng PMCID: PMC373293 Finding functional sequence elements by multiple local alignment Martin C. Frith, Ulla Hansen, John L. Spouge, and Zhiping Weng PMCID: PMC373279 Domainal organization of the lower eukaryotic homologs of the yeast RNA polymerase II core subunit Rpb7 reflects functional conservation Sunanda R. Singh, Nambudiry Rekha, Beena Pillai, Vijender Singh, Aruna Naorem, Vinaya Sampath, N. Srinivasan, and Parag P. Sadhale PMCID: PMC373273 Modifications of the 3′-UTR stem–loop of infectious bursal disease virus are allowed without influencing replication or virulence Hein J. Boot and Sylvia B. E. Pritz-Verschuren PMCID: PMC373287 ARC-1, a sequence element complementary to an internal 18S rRNA segment, enhances translation efficiency in plants when present in the leader or intercistronic region of mRNAs R. Zh. Akbergenov, S. Sh. Zhanybekova, R. V. Kryldakov, A. Zhigailov, N. S. Polimbetova, T. Hohn, and B. K. Iskakov PMCID: PMC373286 Hydration of short DNA, RNA and 2′-OMe oligonucleotides determined by osmotic stressing Eriks Rozners and Janelle Moulder PMCID: PMC373285 Drosophila RNase Z processes mitochondrial and nuclear pre-tRNA 3′ ends in vivo Edward B. Dubrovsky, Veronica A. Dubrovskaya, Louis Levinger, Steffen Schiffer, and Anita Marchfelder PMCID: PMC373292 Enhanced mutagenic potential of 8-oxo-7,8-dihydroguanine when present within a clustered DNA damage site Colin G. Pearson, Naoya Shikazono, John Thacker, and Peter O’Neill PMCID: PMC373263 The nature of actinomycin D binding to d(AACCAXYG) sequence motifs Fu-Ming Chen, Feng Sha, Ko-Hsin Chin, and Shan-Ho Chou PMCID: PMC373288 Detection of guanine–adenine mismatches by surface plasmon resonance sensor carrying naphthyridine–azaquinolone hybrid on the surface Shinya Hagihara, Hiroyuki Kumasawa, Yuki Goto, Gosuke Hayashi, Akio Kobori, Isao Saito, and Kazuhiko Nakatani PMCID: PMC373281 Characterization of cytosine methylated regions and 5-cytosine DNA methyltransferase (Ehmeth) in the protozoan parasite Entamoeba histolytica Ohad Fisher, Rama Siman-Tov, and Serge Ankri PMCID: PMC373271 The guanine-rich fragile X chromosome repeats are reluctant to form tetraplexes Petr Fojtík, Iva Kejnovská, and Michaela Vorlíčková PMCID: PMC373289 Secondary structure models of the nuclear internal transcribed spacer regions and 5.8S rRNA in Calciodinelloideae (Peridiniaceae) and other dinoflagellates Marc Gottschling and Jörg Plötner PMCID: PMC373278 YB-1 promotes strand separation in vitro of duplex DNA containing either mispaired bases or cisplatin modifications, exhibits endonucleolytic activities and binds several DNA repair proteins Isabelle Gaudreault, David Guay, and Michel Lebel PMCID: PMC373280 TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics Haiyuan Yu, Xiaowei Zhu, Dov Greenbaum, John Karro, and Mark Gerstein PMCID: PMC373274 Stereoselective excision of thymine glycol from oxidatively damaged DNA Holly Miller, Andrea S. Fernandes, Elena Zaika, Monica M. McTigue, M. Cecilia Torres, Maryann Wente, Charles R. Iden, and Arthur P. Grollman PMCID: PMC373299 Nuclear antisense effects in cyclophilin A pre-mRNA splicing by oligonucleotides: a comparison of tricyclo-DNA with LNA Damian Ittig, Songkai Liu, Dorte Renneberg, Daniel Schümperli, and Christian J. Leumann PMCID: PMC373297 Triplex-forming oligonucleotide target sequences in the human genome J. Ramon Goñi, Xavier de la Cruz, and Modesto Orozco PMCID: PMC373298 Function of the C-terminus of ![[var phi]](corehtml/pmc/pmcents/x03C6.gif) 29 DNA polymerase in DNA and terminal protein binding Verónica Truniger, José M. Lázaro, and Margarita Salas PMCID: PMC373294 Telomerase downregulation induced by the G-quadruplex ligand 12459 in A549 cells is mediated by hTERT RNA alternative splicing Dennis Gomez, Thibault Lemarteleur, Laurent Lacroix, Patrick Mailliet, Jean-Louis Mergny, and Jean-François Riou PMCID: PMC373291 Local homology recognition and distance measures in linear time using compressed amino acid alphabets Robert C. Edgar PMCID: PMC373290 CIRCE is not involved in heat-dependent transcription of groESL but in stabilization of the mRNA 5′-end in Rhodobacter capsulatus Stephanie Jäger, Andreas Jäger, and Gabriele Klug PMCID: PMC373284 Nucleotide incorporation by human DNA polymerase γ opposite benzo[a]pyrene and benzo[c]phenanthrene diol epoxide adducts of deoxyguanosine and deoxyadenosine Maria A. Graziewicz, Jane M. Sayer, Donald M. Jerina, and William C. Copeland PMCID: PMC373300 NAR Methods Online Dual-regulated expression of C/EBP-α and BMP-2 enables differential differentiation of C2C12 cells into adipocytes and osteoblasts Cornelia Fux, Barbara Mitta, Beat P. Kramer, and Martin Fussenegger PMCID: PMC373304 Ligase-mediated construction of branched DNA strands: a novel DNA joining activity catalyzed by T4 DNA ligase Maritha Mendel-Hartvig, Anil Kumar, and Ulf Landegren PMCID: PMC373312 Facile methods for generating human somatic cell gene knockouts using recombinant adeno-associated viruses Manu Kohli, Carlo Rago, Christoph Lengauer, Kenneth W. Kinzler, and Bert Vogelstein PMCID: PMC373311 Specific cleavage of DNA molecules at RecA-mediated triple-strand structure Yasushi Shigemori and Michio Oishi PMCID: PMC373306 SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development Thomas Thiel, Raja Kota, Ivo Grosse, Nils Stein, and Andreas Graner PMCID: PMC373308 Improved full-length cDNA production based on RNA tagging by T4 DNA ligase Christian Clepet, Isabelle Le Clainche, and Michel Caboche PMCID: PMC373303 PCR-based positive hybridization to detect genomic diversity associated with bacterial secondary metabolism Francesco Pomati and Brett A. Neilan PMCID: PMC373313 A novel assay to determine the sequence preference and affinity of DNA minor groove binding compounds Rita Thomas, Carolyn Gonzalez, Christopher Roberts, Janos Botyanszki, Lillian Lou, and Emil F. Michelotti PMCID: PMC373301 Functionalization of poly(methyl methacrylate) (PMMA) as a substrate for DNA microarrays F. Fixe, M. Dufva, P. Telleman, and C. B. V. Christensen PMCID: PMC373302 A real-time PCR assay for DNA-methylation using methylation-specific blockers Susan E. Cottrell, Jürgen Distler, Nancy S. Goodman, Suzanne H. Mooney, Antje Kluth, Alexander Olek, Ina Schwope, Reimo Tetzner, Heike Ziebarth, and Kurt Berlin PMCID: PMC373310 Method to integrate multiple plasmids into the mycobacterial chromosome Beatrice Saviola and William R. Bishai PMCID: PMC373307 Biological detection of low radiation doses by combining results of two microarray analysis methods G. Mercier, N. Berthault, J. Mary, J. Peyre, A. Antoniadis, J.-P. Comet, A. Cornuejols, C. Froidevaux, and M. Dutreix PMCID: PMC373305 Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA Michael J. Cavaluzzi and Philip N. Borer PMCID: PMC373314 Superior 5′ homogeneity of RNA from ATP-initiated transcription under the T7 2.5 promoter Tricia M. Coleman, Guocan Wang, and Faqing Huang PMCID: PMC373309 Corrigendum Nucleic Acids Res. 2004; 32(1): 406. Published online 2004 January 16. doi: 10.1093/nar/gkh186.PMCID: PMC373296 Corrects: Koen Nauwelaerts, et al. Cleavage of DNA without loss of genetic information by incorporation of a disaccharide nucleoside. Nucleic Acids Res. 2003 December 1; 31(23): 6758–6769. |
