Nucleic Acids Research

Editorial:

EDITORIAL
Nucl. Acids Res. 2003 31: 6063; doi:10.1093/nar/gkg843 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Articles:

Taco G. Uil, Hidde J. Haisma, and Marianne G. Rots

Therapeutic modulation of endogenous gene function by agents with designed DNA-sequence specificities
Nucl. Acids Res. 2003 31: 6064-6078; doi:10.1093/nar/gkg815 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Merlind Mucke, Detlev H. Kruger, and Monika Reuter

Diversity of Type II restriction endonucleases that require two DNA recognition sites
Nucl. Acids Res. 2003 31: 6079-6084; doi:10.1093/nar/gkg836 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Pawel Jaloszynski, Chikahide Masutani, Fumio Hanaoka, Ana Blanco Perez, and Susumu Nishimura

8-Hydroxyguanine in a mutational hotspot of the c-Ha-ras gene causes misreplication, ‘action-at-a-distance’ mutagenesis and inhibition of replication
Nucl. Acids Res. 2003 31: 6085-6095; doi:10.1093/nar/gkg829 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Bernard de Bono and Cyrus Chothia

Exegesis: a procedure to improve gene predictions and its use to find immunoglobulin superfamily proteins in the human and mouse genomes
Nucl. Acids Res. 2003 31: 6096-6103; doi:10.1093/nar/gkg828 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Paul Ajuh and Angus I. Lamond

Identification of peptide inhibitors of pre-mRNA splicing derived from the essential interaction domains of CDC5L and PLRG1
Nucl. Acids Res. 2003 31: 6104-6116; doi:10.1093/nar/gkg817 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mineaki Seki, Federica Marini, and Richard D. Wood

POLQ (Pol ), a DNA polymerase and DNA-dependent ATPase in human cells
Nucl. Acids Res. 2003 31: 6117-6126; doi:10.1093/nar/gkg814 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Vincenzo Salerno, Alessandra Napoli, Malcolm F. White, Mosè Rossi, and Maria Ciaramella

Transcriptional response to DNA damage in the archaeon Sulfolobus solfataricus
Nucl. Acids Res. 2003 31: 6127-6138; doi:10.1093/nar/gkg831 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Milko B. Kermekchiev, Anatoly Tzekov, and Wayne M. Barnes

Cold-sensitive mutants of Taq DNA polymerase provide a hot start for PCR
Nucl. Acids Res. 2003 31: 6139-6147; doi:10.1093/nar/gkg813 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Isabel Schlosser, Michael Hölzel, Marlies Mürnseer, Helmut Burtscher, Ulrich H. Weidle, and Dirk Eick

A role for c-Myc in the regulation of ribosomal RNA processing
Nucl. Acids Res. 2003 31: 6148-6156; doi:10.1093/nar/gkg794 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sandra Carriero and Masad J. Damha

Inhibition of pre-mRNA splicing by synthetic branched nucleic acids
Nucl. Acids Res. 2003 31: 6157-6167; doi:10.1093/nar/gkg824 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Apolinar Maya-Mendoza, Rolando Hernández-Muñoz, Patricio Gariglio, and Armando Aranda-Anzaldo

Gene positional changes relative to the nuclear substructure correlate with the proliferating status of hepatocytes during liver regeneration
Nucl. Acids Res. 2003 31: 6168-6179; doi:10.1093/nar/gkg825 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Chia-Lun Tsai, Monalisa Chatterji, and David G. Schatz

DNA mismatches and GC-rich motifs target transposition by the RAG1/RAG2 transposase
Nucl. Acids Res. 2003 31: 6180-6190; doi:10.1093/nar/gkg819 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Fenfei Leng, Jonathan B. Chaires, and Michael J. Waring

Energetics of echinomycin binding to DNA
Nucl. Acids Res. 2003 31: 6191-6197; doi:10.1093/nar/gkg826 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Satoshi Ishizuka, Kareen Martin, Catherine Booth, Christopher S. Potten, Gilbert de Murcia, Alexander Bürkle, and Thomas B. L. Kirkwood

Poly(ADP-ribose) polymerase-1 is a survival factor for radiation-exposed intestinal epithelial stem cells in vivo
Nucl. Acids Res. 2003 31: 6198-6205; doi:10.1093/nar/gkg840 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Regine Heilbronn, Markus Engstler, Stefan Weger, Antje Krahn, Christian Schetter, and Michael Boshart

ssDNA-dependent colocalization of adeno-associated virus Rep and herpes simplex virus ICP8 in nuclear replication domains
Nucl. Acids Res. 2003 31: 6206-6213; doi:10.1093/nar/gkg827 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Lirong Zhang and Liaofu Luo

Splice site prediction with quadratic discriminant analysis using diversity measure
Nucl. Acids Res. 2003 31: 6214-6220; doi:10.1093/nar/gkg805 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Veerle Kempeneers, Karen Vastmans, Jef Rozenski, and Piet Herdewijn

Recognition of threosyl nucleotides by DNA and RNA polymerases
Nucl. Acids Res. 2003 31: 6221-6226; doi:10.1093/nar/gkg833 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

H. Jonas Karlsson, Maja Eriksson, Erik Perzon, Björn Åkerman, Per Lincoln, and Gunnar Westman

Groove-binding unsymmetrical cyanine dyes for staining of DNA: syntheses and characterization of the DNA-binding
Nucl. Acids Res. 2003 31: 6227-6234; doi:10.1093/nar/gkg821 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Maja Eriksson, H. Jonas Karlsson, Gunnar Westman, and Björn Åkerman

Groove-binding unsymmetrical cyanine dyes for staining of DNA: dissociation rates in free solution and electrophoresis gels
Nucl. Acids Res. 2003 31: 6235-6242; doi:10.1093/nar/gkg822 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Vaishali Handa, Tapas Saha, and Karen Usdin

The fragile X syndrome repeats form RNA hairpins that do not activate the interferon-inducible protein kinase, PKR, but are cut by Dicer
Nucl. Acids Res. 2003 31: 6243-6248; doi:10.1093/nar/gkg818 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Eli Hershkovitz, Emmanuel Tannenbaum, Shelley B. Howerton, Ajay Sheth, Allen Tannenbaum, and Loren Dean Williams

Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA
Nucl. Acids Res. 2003 31: 6249-6257; doi:10.1093/nar/gkg835 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

J. R. Milligan, J. A. Aguilera, A. Ly, N. Q. Tran, O. Hoang, and J. F. Ward

Repair of oxidative DNA damage by amino acids
Nucl. Acids Res. 2003 31: 6258-6263; doi:10.1093/nar/gkg816 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Haidong Gu and Daniel R. Schoenberg

U2AF modulates poly(A) length control by the poly(A)-limiting element
Nucl. Acids Res. 2003 31: 6264-6271; doi:10.1093/nar/gkg823 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Rosine Onclercq-Delic, Patrick Calsou, Christine Delteil, Bernard Salles, Dora Papadopoulo, and Mounira Amor-Guéret

Possible anti-recombinogenic role of Bloom’s syndrome helicase in double-strand break processing
Nucl. Acids Res. 2003 31: 6272-6282; doi:10.1093/nar/gkg834 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Sabine Tornow and H. W. Mewes

Functional modules by relating protein interaction networks and gene expression
Nucl. Acids Res. 2003 31: 6283-6289; doi:10.1093/nar/gkg838 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Patricia Giraldo, Antonio Martínez, Lucía Regales, Alfonso Lavado, Angel García-Díaz, Ángel Alonso, Ana Busturia, and Lluís Montoliu

Functional dissection of the mouse tyrosinase locus control region identifies a new putative boundary activity
Nucl. Acids Res. 2003 31: 6290-6305; doi:10.1093/nar/gkg793 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

J. Weiner III, C.-U. Zimmerman, H. W. H. Göhlmann, and R. Herrmann

Transcription profiles of the bacterium Mycoplasma pneumoniae grown at different temperatures
Nucl. Acids Res. 2003 31: 6306-6320; doi:10.1093/nar/gkg841 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Xavier Roca, Ravi Sachidanandam, and Adrian R. Krainer

Intrinsic differences between authentic and cryptic 5' splice sites
Nucl. Acids Res. 2003 31: 6321-6333; doi:10.1093/nar/gkg830 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Aaron M. Bellows, Margaret A. Kenna, Lynne Cassimeris, and Robert V. Skibbens

Human EFO1p exhibits acetyltransferase activity and is a unique combination of linker histone and Ctf7p/Eco1p chromatid cohesion establishment domains
Nucl. Acids Res. 2003 31: 6334-6343; doi:10.1093/nar/gkg811 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Alexander A. Ishchenko, Guenhaël Sanz, Cyril V. Privezentzev, Andrei V. Maksimenko, and Murat Saparbaev

Characterisation of new substrate specificities of Escherichia coli and Saccharomyces cerevisiae AP endonucleases
Nucl. Acids Res. 2003 31: 6344-6353; doi:10.1093/nar/gkg812 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jennifer A. Jackson, Alex V. Trevino, Maryanne C. Herzig, Terence S. Herman, and Jan M. Woynarowski

Matrix attachment region (MAR) properties and abnormal expansion of AT island minisatellites in FRA16B fragile sites in leukemic CEM cells
Nucl. Acids Res. 2003 31: 6354-6364; doi:10.1093/nar/gkg832 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Miriam Frieden, Signe M. Christensen, Nikolaj D. Mikkelsen, Christoph Rosenbohm, Charlotte A. Thrue, Majken Westergaard, Henrik F. Hansen, Henrik Ørum, and Troels Koch

Expanding the design horizon of antisense oligonucleotides with alpha-L-LNA
Nucl. Acids Res. 2003 31: 6365-6372; doi:10.1093/nar/gkg820 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Rajendra P. Ojha and Rakesh K. Tiwari

Triplex hydration: nanosecond molecular dynamics simulation of the solvated triplex formed by mixed sequences
Nucl. Acids Res. 2003 31: 6373-6380; doi:10.1093/nar/gkg796 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

NAR Methods Online:

Yasuaki Kawarasaki, Karl E. Griswold, James D. Stevenson, Tzvia Selzer, Stephen J. Benkovic, Brent L. Iverson, and George Georgiou

Enhanced crossover SCRATCHY: construction and high-throughput screening of a combinatorial library containing multiple non-homologous crossovers
Nucl. Acids Res. 2003 31: e126; doi:10.1093/nar/gng126 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Frank Czauderna, Ansgar Santel, Michael Hinz, Melanie Fechtner, Birgit Durieux, Gerald Fisch, Frauke Leenders, Wolfgang Arnold, Klaus Giese, Anke Klippel, and Jörg Kaufmann

Inducible shRNA expression for application in a prostate cancer mouse model
Nucl. Acids Res. 2003 31: e127; doi:10.1093/nar/gng127 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Matt Cotten, Kerstin Stegmueller, Jan Eickhoff, Miriam Hanke, Katrin Herzberger, Thomas Herget, Axel Choidas, Henrik Daub, and Klaus Godl

Exploiting features of adenovirus replication to support mammalian kinase production
Nucl. Acids Res. 2003 31: e128; doi:10.1093/nar/gng128 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Lovisa Lovmar, Mona Fredriksson, Ulrika Liljedahl, Snaevar Sigurdsson, and Ann-Christine Syvänen

Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping of whole genome amplified DNA
Nucl. Acids Res. 2003 31: e129; doi:10.1093/nar/gng129 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Axel Vater, Florian Jarosch, Klaus Buchner, and Sven Klussmann

Short bioactive Spiegelmers to migraine-associated calcitonin gene-related peptide rapidly identified by a novel approach: Tailored-SELEX
Nucl. Acids Res. 2003 31: e130; doi:10.1093/nar/gng130 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nicolas Jullien, François Sampieri, Alain Enjalbert, and Jean-Paul Herman

Regulation of Cre recombinase by ligand-induced complementation of inactive fragments
Nucl. Acids Res. 2003 31: e131; doi:10.1093/nar/gng131 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Matti Kankainen and Garry Wong

DANCER: a program for digital anatomical reconstruction of gene expression data
Nucl. Acids Res. 2003 31: e132; doi:10.1093/nar/gng132 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kenji Tsuge, Kuniko Matsui, and Mitsuhiro Itaya

One step assembly of multiple DNA fragments with a designed order and orientation in Bacillus subtilis plasmid
Nucl. Acids Res. 2003 31: e133; doi:10.1093/nar/gng133 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jeffrey A. Hodson, Julie M. Bailis, and Susan L. Forsburg

Efficient labeling of fission yeast Schizosaccharomyces pombe with thymidine and BUdR
Nucl. Acids Res. 2003 31: e134; doi:10.1093/nar/gng134 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Stacy L. Gelhaus, William R. LaCourse, Nathan A. Hagan, Gaya K. Amarasinghe, and Daniele Fabris

Rapid purification of RNA secondary structures
Nucl. Acids Res. 2003 31: e135; doi:10.1093/nar/gng136 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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