Nucleic Acids Research

Survey and Summary:

Paul F. Agris

Decoding the genome: a modified view
Nucl. Acids Res. 2004 32: 223-238; doi:10.1093/nar/gkh185 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Articles:

Suisheng Zhang, Bernhard Schlott, Matthias Görlach, and Frank Grosse

DNA-dependent protein kinase (DNA-PK) phosphorylates nuclear DNA helicase II/RNA helicase A and hnRNP proteins in an RNA-dependent manner
Nucl. Acids Res. 2004 32: 1-10; doi:10.1093/nar/gkg933 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dean Laslett and Bjorn Canback

ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
Nucl. Acids Res. 2004 32: 11-16; doi:10.1093/nar/gkh152 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nouri Ben Zakour, Michel Gautier, Rumen Andonov, Dominique Lavenier, Marie-Françoise Cochet, Philippe Veber, Alexei Sorokin, and Yves Le Loir

GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification
Nucl. Acids Res. 2004 32: 17-24; doi:10.1093/nar/gkg928 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Emily E. Bosco, Christopher N. Mayhew, Robert F. Hennigan, Julien Sage, Tyler Jacks, and Erik S. Knudsen

RB signaling prevents replication-dependent DNA double-strand breaks following genotoxic insult
Nucl. Acids Res. 2004 32: 25-34; doi:10.1093/nar/gkg919 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Rob D. Chapman, Benoit Palancade, Andreas Lang, Olivier Bensaude, and Dirk Eick

The last CTD repeat of the mammalian RNA polymerase II large subunit is important for its stability
Nucl. Acids Res. 2004 32: 35-44; doi:10.1093/nar/gkh172 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Claire Checroun, Patricia Bordes, Olivier Leroy, Annie Kolb, and Claude Gutierrez

Interactions between the 2.4 and 4.2 regions of ^S, the stress-specific factor of Escherichia coli, and the –10 and –35 promoter elements
Nucl. Acids Res. 2004 32: 45-53; doi:10.1093/nar/gkh155 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Arthur Liberzon, Gabriela Ridner, and Michael D. Walker

Role of intrinsic DNA binding specificity in defining target genes of the mammalian transcription factor PDX1
Nucl. Acids Res. 2004 32: 54-64; doi:10.1093/nar/gkh156 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Laurence G. May, Mark A. Madine, and Michael J. Waring

Echinomycin inhibits chromosomal DNA replication and embryonic development in vertebrates
Nucl. Acids Res. 2004 32: 65-72; doi:10.1093/nar/gkh166 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Laurent Gros, Alexander A. Ishchenko, Hiroshi Ide, Rhoderick H. Elder, and Murat K. Saparbaev

The major human AP endonuclease (Ape1) is involved in the nucleotide incision repair pathway
Nucl. Acids Res. 2004 32: 73-81; doi:10.1093/nar/gkh165 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Norie Fujikawa, Hitoshi Kurumizaka, Osamu Nureki, Yoshinori Tanaka, Mitsuyoshi Yamazoe, Sota Hiraga, and Shigeyuki Yokoyama

Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein
Nucl. Acids Res. 2004 32: 82-92; doi:10.1093/nar/gkh173 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dimitry Bosoy and Neal F. Lue

Yeast telomerase is capable of limited repeat addition processivity
Nucl. Acids Res. 2004 32: 93-101; doi:10.1093/nar/gkg943 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jacob Giehm Mikkelsen, Søren Vestergaard Rasmussen, and Finn Skou Pedersen

Complementarity-directed RNA dimer-linkage promotes retroviral recombination in vivo
Nucl. Acids Res. 2004 32: 102-114; doi:10.1093/nar/gkh159 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Balazs Ribar, Tadahide Izumi, and Sankar Mitra

The major role of human AP-endonuclease homolog Apn2 in repair of abasic sites in Schizosaccharomyces pombe
Nucl. Acids Res. 2004 32: 115-126; doi:10.1093/nar/gkh151 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Veena Vijayanathan, Thresia Thomas, Thomas Antony, Akira Shirahata, and T. J. Thomas

Formation of DNA nanoparticles in the presence of novel polyamine analogues: a laser light scattering and atomic force microscopic study
Nucl. Acids Res. 2004 32: 127-134; doi:10.1093/nar/gkg936 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dietrich Rebholz-Schuhmann, Stephane Marcel, Sylvie Albert, Ralf Tolle, Georg Casari, and Harald Kirsch

Automatic extraction of mutations from Medline and cross-validation with OMIM
Nucl. Acids Res. 2004 32: 135-142; doi:10.1093/nar/gkh162 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ali Nahvi, Jeffrey E. Barrick, and Ronald R. Breaker

Coenzyme B₁₂ riboswitches are widespread genetic control elements in prokaryotes
Nucl. Acids Res. 2004 32: 143-150; doi:10.1093/nar/gkh167 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sandra Fouace, Cyril Gaudin, Sylvie Picard, Sophie Corvaisier, Jacques Renault, Bertrand Carboni, and Brice Felden

Polyamine derivatives as selective RNaseA mimics
Nucl. Acids Res. 2004 32: 151-157; doi:10.1093/nar/gkh157 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Yulong Shen, Xiao-Feng Tang, Hideshi Yokoyama, Eriko Matsui, and Ikuo Matsui

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
Nucl. Acids Res. 2004 32: 158-168; doi:10.1093/nar/gkh153 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kristi A. Miller, Dorota Sawicka, Daniel Barsky, and Joanna S. Albala

Domain mapping of the Rad51 paralog protein complexes
Nucl. Acids Res. 2004 32: 169-178; doi:10.1093/nar/gkg925 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Peter M. Haverty, Ulla Hansen, and Zhiping Weng

Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification
Nucl. Acids Res. 2004 32: 179-188; doi:10.1093/nar/gkh183 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Martin C. Frith, Ulla Hansen, John L. Spouge, and Zhiping Weng

Finding functional sequence elements by multiple local alignment
Nucl. Acids Res. 2004 32: 189-200; doi:10.1093/nar/gkh169 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Sunanda R. Singh, Nambudiry Rekha, Beena Pillai, Vijender Singh, Aruna Naorem, Vinaya Sampath, N. Srinivasan, and Parag P. Sadhale

Domainal organization of the lower eukaryotic homologs of the yeast RNA polymerase II core subunit Rpb7 reflects functional conservation
Nucl. Acids Res. 2004 32: 201-210; doi:10.1093/nar/gkh163 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hein J. Boot and Sylvia B. E. Pritz-Verschuren

Modifications of the 3'-UTR stem–loop of infectious bursal disease virus are allowed without influencing replication or virulence
Nucl. Acids Res. 2004 32: 211-222; doi:10.1093/nar/gkh177 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

R. Zh. Akbergenov, S. Sh. Zhanybekova, R. V. Kryldakov, A. Zhigailov, N. S. Polimbetova, T. Hohn, and B. K. Iskakov

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
Nucl. Acids Res. 2004 32: 239-247; doi:10.1093/nar/gkh176 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Eriks Rozners and Janelle Moulder

Hydration of short DNA, RNA and 2'-OMe oligonucleotides determined by osmotic stressing
Nucl. Acids Res. 2004 32: 248-254; doi:10.1093/nar/gkh175 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Edward B. Dubrovsky, Veronica A. Dubrovskaya, Louis Levinger, Steffen Schiffer, and Anita Marchfelder

Drosophila RNase Z processes mitochondrial and nuclear pre-tRNA 3' ends in vivo
Nucl. Acids Res. 2004 32: 255-262; doi:10.1093/nar/gkh182 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Colin G. Pearson, Naoya Shikazono, John Thacker, and Peter O’Neill

Enhanced mutagenic potential of 8-oxo-7,8-dihydroguanine when present within a clustered DNA damage site
Nucl. Acids Res. 2004 32: 263-270; doi:10.1093/nar/gkh150 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Fu-Ming Chen, Feng Sha, Ko-Hsin Chin, and Shan-Ho Chou

The nature of actinomycin D binding to d(AACCAXYG) sequence motifs
Nucl. Acids Res. 2004 32: 271-277; doi:10.1093/nar/gkh178 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Shinya Hagihara, Hiroyuki Kumasawa, Yuki Goto, Gosuke Hayashi, Akio Kobori, Isao Saito, and Kazuhiko Nakatani

Detection of guanine–adenine mismatches by surface plasmon resonance sensor carrying naphthyridine–azaquinolone hybrid on the surface
Nucl. Acids Res. 2004 32: 278-286; doi:10.1093/nar/gkh171 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Ohad Fisher, Rama Siman-Tov, and Serge Ankri

Characterization of cytosine methylated regions and 5-cytosine DNA methyltransferase (Ehmeth) in the protozoan parasite Entamoeba histolytica
Nucl. Acids Res. 2004 32: 287-297; doi:10.1093/nar/gkh161 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Petr Fojtík, Iva Kejnovská, and Michaela Vorlícková

The guanine-rich fragile X chromosome repeats are reluctant to form tetraplexes
Nucl. Acids Res. 2004 32: 298-306; doi:10.1093/nar/gkh179 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Marc Gottschling and Jörg Plötner

Secondary structure models of the nuclear internal transcribed spacer regions and 5.8S rRNA in Calciodinelloideae (Peridiniaceae) and other dinoflagellates
Nucl. Acids Res. 2004 32: 307-315; doi:10.1093/nar/gkh168 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Isabelle Gaudreault, David Guay, and Michel Lebel

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
Nucl. Acids Res. 2004 32: 316-327; doi:10.1093/nar/gkh170 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Haiyuan Yu, Xiaowei Zhu, Dov Greenbaum, John Karro, and Mark Gerstein

TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics
Nucl. Acids Res. 2004 32: 328-337; doi:10.1093/nar/gkh164 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Holly Miller, Andrea S. Fernandes, Elena Zaika, Monica M. McTigue, M. Cecilia Torres, Maryann Wente, Charles R. Iden, and Arthur P. Grollman

Stereoselective excision of thymine glycol from oxidatively damaged DNA
Nucl. Acids Res. 2004 32: 338-345; doi:10.1093/nar/gkh190 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Damian Ittig, Songkai Liu, Dorte Renneberg, Daniel Schümperli, and Christian J. Leumann

Nuclear antisense effects in cyclophilin A pre-mRNA splicing by oligonucleotides: a comparison of tricyclo-DNA with LNA
Nucl. Acids Res. 2004 32: 346-353; doi:10.1093/nar/gkh187 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

J. Ramon Goñi, Xavier de la Cruz, and Modesto Orozco

Triplex-forming oligonucleotide target sequences in the human genome
Nucl. Acids Res. 2004 32: 354-360; doi:10.1093/nar/gkh188 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Verónica Truniger, José M. Lázaro, and Margarita Salas

Function of the C-terminus of 29 DNA polymerase in DNA and terminal protein binding
Nucl. Acids Res. 2004 32: 361-370; doi:10.1093/nar/gkh184 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dennis Gomez, Thibault Lemarteleur, Laurent Lacroix, Patrick Mailliet, Jean-Louis Mergny, and Jean-François Riou

Telomerase downregulation induced by the G-quadruplex ligand 12459 in A549 cells is mediated by hTERT RNA alternative splicing
Nucl. Acids Res. 2004 32: 371-379; doi:10.1093/nar/gkh181 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Robert C. Edgar

Local homology recognition and distance measures in linear time using compressed amino acid alphabets
Nucl. Acids Res. 2004 32: 380-385; doi:10.1093/nar/gkh180 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Stephanie Jäger, Andreas Jäger, and Gabriele Klug

CIRCE is not involved in heat-dependent transcription of groESL but in stabilization of the mRNA 5'-end in Rhodobacter capsulatus
Nucl. Acids Res. 2004 32: 386-396; doi:10.1093/nar/gkh174 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Maria A. Graziewicz, Jane M. Sayer, Donald M. Jerina, and William C. Copeland

Nucleotide incorporation by human DNA polymerase opposite benzo[a]pyrene and benzo[c]phenanthrene diol epoxide adducts of deoxyguanosine and deoxyadenosine
Nucl. Acids Res. 2004 32: 397-405; doi:10.1093/nar/gkh213 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

NAR Methods Online:

Cornelia Fux, Barbara Mitta, Beat P. Kramer, and Martin Fussenegger

Dual-regulated expression of C/EBP- and BMP-2 enables differential differentiation of C2C12 cells into adipocytes and osteoblasts
Nucl. Acids Res. 2004 32: e1; doi:10.1093/nar/gnh001 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Maritha Mendel-Hartvig, Anil Kumar, and Ulf Landegren

Ligase-mediated construction of branched DNA strands: a novel DNA joining activity catalyzed by T4 DNA ligase
Nucl. Acids Res. 2004 32: e2; doi:10.1093/nar/gnh011 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Manu Kohli, Carlo Rago, Christoph Lengauer, Kenneth W. Kinzler, and Bert Vogelstein

Facile methods for generating human somatic cell gene knockouts using recombinant adeno-associated viruses
Nucl. Acids Res. 2004 32: e3; doi:10.1093/nar/gnh009 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Yasushi Shigemori and Michio Oishi

Specific cleavage of DNA molecules at RecA-mediated triple-strand structure
Nucl. Acids Res. 2004 32: e4; doi:10.1093/nar/gnh004 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Thomas Thiel, Raja Kota, Ivo Grosse, Nils Stein, and Andreas Graner

SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development
Nucl. Acids Res. 2004 32: e5; doi:10.1093/nar/gnh006 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christian Clepet, Isabelle Le Clainche, and Michel Caboche

Improved full-length cDNA production based on RNA tagging by T4 DNA ligase
Nucl. Acids Res. 2004 32: e6; doi:10.1093/nar/gng158 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Francesco Pomati and Brett A. Neilan

PCR-based positive hybridization to detect genomic diversity associated with bacterial secondary metabolism
Nucl. Acids Res. 2004 32: e7; doi:10.1093/nar/gnh012 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Rita Thomas, Carolyn Gonzalez, Christopher Roberts, Janos Botyanszki, Lillian Lou, and Emil F. Michelotti

A novel assay to determine the sequence preference and affinity of DNA minor groove binding compounds
Nucl. Acids Res. 2004 32: e8; doi:10.1093/nar/gng155 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

F. Fixe, M. Dufva, P. Telleman, and C. B. V. Christensen

Functionalization of poly(methyl methacrylate) (PMMA) as a substrate for DNA microarrays
Nucl. Acids Res. 2004 32: e9; doi:10.1093/nar/gng157 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Susan E. Cottrell, Jürgen Distler, Nancy S. Goodman, Suzanne H. Mooney, Antje Kluth, Alexander Olek, Ina Schwope, Reimo Tetzner, Heike Ziebarth, and Kurt Berlin

A real-time PCR assay for DNA-methylation using methylation-specific blockers
Nucl. Acids Res. 2004 32: e10; doi:10.1093/nar/gnh008 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Beatrice Saviola and William R. Bishai

Method to integrate multiple plasmids into the mycobacterial chromosome
Nucl. Acids Res. 2004 32: e11; doi:10.1093/nar/gnh005 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

G. Mercier, N. Berthault, J. Mary, J. Peyre, A. Antoniadis, J.-P. Comet, A. Cornuejols, C. Froidevaux, and M. Dutreix

Biological detection of low radiation doses by combining results of two microarray analysis methods
Nucl. Acids Res. 2004 32: e12; doi:10.1093/nar/gnh002 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Michael J. Cavaluzzi and Philip N. Borer

Revised UV extinction coefficients for nucleoside-5'-monophosphates and unpaired DNA and RNA
Nucl. Acids Res. 2004 32: e13; doi:10.1093/nar/gnh015 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Tricia M. Coleman, Guocan Wang, and Faqing Huang

Superior 5' homogeneity of RNA from ATP-initiated transcription under the T7 2.5 promoter
Nucl. Acids Res. 2004 32: e14; doi:10.1093/nar/gnh007 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Corrigendum:

Corrigendum
Nucl. Acids Res. 2004 32: 406; doi:10.1093/nar/gkh186 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

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