Nucleic Acids Research

Editorial:

EDITORIAL
Nucl. Acids Res. 2004 32: 3513; doi:10.1093/nar/gkh704 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Articles:

Denis E. Kainov, Jirí Lísal, Dennis H. Bamford, and Roman Tuma

Packaging motor from double-stranded RNA bacteriophage 12 acts as an obligatory passive conduit during transcription
Nucl. Acids Res. 2004 32: 3515-3521; doi:10.1093/nar/gkh680 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jinfeng Liu and Burkhard Rost

Sequence-based prediction of protein domains
Nucl. Acids Res. 2004 32: 3522-3530; doi:10.1093/nar/gkh684 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jason L. Parsons, Irina I. Dianova, and Grigory L. Dianov

APE1 is the major 3'-phosphoglycolate activity in human cell extracts
Nucl. Acids Res. 2004 32: 3531-3536; doi:10.1093/nar/gkh676 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Martin Kampmann and Daniela Stock

Reverse gyrase has heat-protective DNA chaperone activity independent of supercoiling
Nucl. Acids Res. 2004 32: 3537-3545; doi:10.1093/nar/gkh683 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Mustafa Erayman, Devinder Sandhu, Deepak Sidhu, Muharrem Dilbirligi, P. S. Baenziger, and Kulvinder S. Gill

Demarcating the gene-rich regions of the wheat genome
Nucl. Acids Res. 2004 32: 3546-3565; doi:10.1093/nar/gkh639 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Stanislav Zelivianski, Richard Glowacki, and Ming-Fong Lin

Transcriptional activation of the human prostatic acid phosphatase gene by NF-B via a novel hexanucleotide-binding site
Nucl. Acids Res. 2004 32: 3566-3580; doi:10.1093/nar/gkh677 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Roland Barriot, Jérôme Poix, Alexis Groppi, Aurélien Barré, Nicolas Goffard, David Sherman, Isabelle Dutour, and Antoine de Daruvar

New strategy for the representation and the integration of biomolecular knowledge at a cellular scale
Nucl. Acids Res. 2004 32: 3581-3589; doi:10.1093/nar/gkh681 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Naglis Malys, Kathleen Carroll, Jaleel Miyan, David Tollervey, and John E. G. McCarthy

The ‘scavenger’ m⁷GpppX pyrophosphatase activity of Dcs1 modulates nutrient-induced responses in yeast
Nucl. Acids Res. 2004 32: 3590-3600; doi:10.1093/nar/gkh687 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Petr Svoboda, Paula Stein, Witold Filipowicz, and Richard M. Schultz

Lack of homologous sequence-specific DNA methylation in response to stable dsRNA expression in mouse oocytes
Nucl. Acids Res. 2004 32: 3601-3606; doi:10.1093/nar/gkh697 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

José Gallego

Sequence-dependent nucleotide dynamics revealed by intercalated ring rotation in DNA–bisnaphthalimide complexes
Nucl. Acids Res. 2004 32: 3607-3614; doi:10.1093/nar/gkh693 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Andreas Fiebig, Sandra Stegemann, and Ralph Bock

Rapid evolution of RNA editing sites in a small non-essential plastid gene
Nucl. Acids Res. 2004 32: 3615-3622; doi:10.1093/nar/gkh695 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Matthew D. Simon, Ken Sato, Gregory A. Weiss, and Kevan M. Shokat

A phage display selection of engrailed homeodomain mutants and the importance of residue Q50
Nucl. Acids Res. 2004 32: 3623-3631; doi:10.1093/nar/gkh690 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Chandrani Chattopadhyay, David Hawke, Ryuji Kobayashi, and Sankar N. Maity

Human p32, interacts with B subunit of the CCAAT-binding factor, CBF/NF-Y, and inhibits CBF-mediated transcription activation in vitro
Nucl. Acids Res. 2004 32: 3632-3641; doi:10.1093/nar/gkh692 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Martin A. Maier, Yongseok Choi, Hans Gaus, Joseph J. Barchi, Jr, Victor E. Marquez, and Muthiah Manoharan

Synthesis and characterization of oligonucleotides containing conformationally constrained bicyclo[3.1.0]hexane pseudosugar analogs
Nucl. Acids Res. 2004 32: 3642-3650; doi:10.1093/nar/gkh667 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Martin Krzywinski, Ian Bosdet, Duane Smailus, Readman Chiu, Carrie Mathewson, Natasja Wye, Sarah Barber, Mabel Brown-John, Susanna Chan, Steve Chand, Alison Cloutier, Noreen Girn, Darlene Lee, Amara Masson, Michael Mayo, Teika Olson, Pawan Pandoh, Anna-Liisa Prabhu, Eric Schoenmakers, Miranda Tsai, Donna Albertson, Wan Lam, Chik-On Choy, Kazutoyo Osoegawa, Shaying Zhao, Pieter J. de Jong, Jacqueline Schein, Steven Jones, and Marco A. Marra

A set of BAC clones spanning the human genome
Nucl. Acids Res. 2004 32: 3651-3660; doi:10.1093/nar/gkh700 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

James C. Samuelson, Zhenyu Zhu, and Shuang-yong Xu

The isolation of strand-specific nicking endonucleases from a randomized SapI expression library
Nucl. Acids Res. 2004 32: 3661-3671; doi:10.1093/nar/gkh674 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Avanti Kulkarni and Douglas A. Julin

Specific inhibition of the E.coli RecBCD enzyme by Chi sequences in single-stranded oligodeoxyribonucleotides
Nucl. Acids Res. 2004 32: 3672-3682; doi:10.1093/nar/gkh675 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nasrollah Saleh-Gohari and Thomas Helleday

Conservative homologous recombination preferentially repairs DNA double-strand breaks in the S phase of the cell cycle in human cells
Nucl. Acids Res. 2004 32: 3683-3688; doi:10.1093/nar/gkh703 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Liangsu Wang, John D. Trawick, Robert Yamamoto, and Carlos Zamudio

Genome-wide operon prediction in Staphylococcus aureus
Nucl. Acids Res. 2004 32: 3689-3702; doi:10.1093/nar/gkh694 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Xing Li, Sephorah Zaman, Yvette Langdon, Janice M. Zengel, and Lasse Lindahl

Identification of a functional core in the RNA component of RNase MRP of budding yeasts
Nucl. Acids Res. 2004 32: 3703-3711; doi:10.1093/nar/gkh689 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tiffany B. Salmon, Barbara A. Evert, Binwei Song, and Paul W. Doetsch

Biological consequences of oxidative stress-induced DNA damage in Saccharomyces cerevisiae
Nucl. Acids Res. 2004 32: 3712-3723; doi:10.1093/nar/gkh696 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Vladimir N. Babenko, Igor B. Rogozin, Sergei L. Mekhedov, and Eugene V. Koonin

Prevalence of intron gain over intron loss in the evolution of paralogous gene families
Nucl. Acids Res. 2004 32: 3724-3733; doi:10.1093/nar/gkh686 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Yoon-Jeong Choi, Tae-Young Choi, Masamitsu Yamaguchi, Akio Matsukage, Young-Shin Kim, and Mi-Ae Yoo

Transcriptional regulation of the Drosophila caudal homeobox gene by DRE/DREF
Nucl. Acids Res. 2004 32: 3734-3742; doi:10.1093/nar/gkh688 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Susan M. Bailey, Mark A. Brenneman, and Edwin H. Goodwin

Frequent recombination in telomeric DNA may extend the proliferative life of telomerase-negative cells
Nucl. Acids Res. 2004 32: 3743-3751; doi:10.1093/nar/gkh691 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Songkai Liu, Maria Asparuhova, Vincent Brondani, Ingrid Ziekau, Thomas Klimkait, and Daniel Schümperli

Inhibition of HIV-1 multiplication by antisense U7 snRNAs and siRNAs targeting cyclophilin A
Nucl. Acids Res. 2004 32: 3752-3759; doi:10.1093/nar/gkh715 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ashley Eversole Hesslein, Vladimir I. Katunin, Malte Beringer, Anne B. Kosek, Marina V. Rodnina, and Scott A. Strobel

Exploration of the conserved A+C wobble pair within the ribosomal peptidyl transferase center using affinity purified mutant ribosomes
Nucl. Acids Res. 2004 32: 3760-3770; doi:10.1093/nar/gkh672 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Patrick L. Garcia, Glyn Bradley, Christopher J. Hayes, Sussie Krintel, Panos Soultanas, and Pavel Janscak

RPA alleviates the inhibitory effect of vinylphosphonate internucleotide linkages on DNA unwinding by BLM and WRN helicases
Nucl. Acids Res. 2004 32: 3771-3778; doi:10.1093/nar/gkh709 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Corrigenda:

Jorge Fernandez-de-Cossio, Luis Javier Gonzalez, Yoshinori Satomi, Lazaro Betancourt, Yassel Ramos, Vivian Huerta, Abel Amaro, Vladimir Besada, Gabriel Padron, Naoto Minamino, and Toshifumi Takao

Isotopica: a tool for the calculation and viewing of complex isotopic envelopes
Nucl. Acids Res. 2004 32: 3779; doi:10.1093/nar/gkh707 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Methods Online:

Ana Paula M. Silva, Jianjun Chen, Dirce M. Carraro, San Ming Wang, and Anamaria A. Camargo

Generation of longer 3' cDNA fragments from massively parallel signature sequencing tags
Nucl. Acids Res. 2004 32: e94; doi:10.1093/nar/gnh095 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Nobuhide Doi, Shin Kumadaki, Yuko Oishi, Nobutaka Matsumura, and Hiroshi Yanagawa

In vitro selection of restriction endonucleases by in vitro compartmentalization
Nucl. Acids Res. 2004 32: e95; doi:10.1093/nar/gnh096 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Austin P. So, Robin F. B. Turner, and Charles A. Haynes

Increasing the efficiency of SAGE adaptor ligation bydirected ligation chemistry
Nucl. Acids Res. 2004 32: e96; doi:10.1093/nar/gnh082 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Beatrice Spottke, Julia Gross, Hans-Joachim Galla, and Franz Hillenkamp

Reverse Sanger sequencing of RNA by MALDI-TOF mass spectrometry after solid phase purification
Nucl. Acids Res. 2004 32: e97; doi:10.1093/nar/gnh089 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ai-Sheng Xiong, Quan-Hong Yao, Ri-He Peng, Xian Li, Hui-Qin Fan, Zong-Ming Cheng, and Yi Li

A simple, rapid, high-fidelity and cost-effective PCR-based two-step DNA synthesis method for long gene sequences
Nucl. Acids Res. 2004 32: e98; doi:10.1093/nar/gnh094 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Cheng-Chung Chou, Chun-Houh Chen, Te-Tsui Lee, and Konan Peck

Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression
Nucl. Acids Res. 2004 32: e99; doi:10.1093/nar/gnh099 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Xiufen Lei, Yong Zhu, Alan Tomkinson, and LuZhe Sun

Measurement of DNA mismatch repair activity in live cells
Nucl. Acids Res. 2004 32: e100; doi:10.1093/nar/gnh098 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yaxin Jiang, Feng Qin, Yiqin Li, Xiaohong Fang, and Chunli Bai

Measuring specific interaction of transcription factor ZmDREB1A with its DNA responsive element at the molecular level
Nucl. Acids Res. 2004 32: e101; doi:10.1093/nar/gnh100 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Philippe-Emmanuel Mangeot, François-Loïc Cosset, Pierre Colas, and Ivan Mikaelian

A universal transgene silencing method based on RNA interference
Nucl. Acids Res. 2004 32: e102; doi:10.1093/nar/gnh105 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hubert Zipper, Herwig Brunner, Jürgen Bernhagen, and Frank Vitzthum

Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications
Nucl. Acids Res. 2004 32: e103; doi:10.1093/nar/gnh101 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Artem Barski and Baruch Frenkel

ChIP Display: novel method for identification of genomic targets of transcription factors
Nucl. Acids Res. 2004 32: e104; doi:10.1093/nar/gnh097 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Toshihiro Ihara, Shojiro Tanaka, Yasushi Chikaura, and Akinori Jyo

Preparation of DNA-modified nanoparticles and preliminary study for colorimetric SNP analysis using their selective aggregations
Nucl. Acids Res. 2004 32: e105; doi:10.1093/nar/gnh106 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Barbara Mitta, Cornelia C. Weber, Markus Rimann, and Martin Fussenegger

Design and in vivo characterization of self-inactivating human and non-human lentiviral expression vectors engineered for streptogramin-adjustable transgene expression
Nucl. Acids Res. 2004 32: e106; doi:10.1093/nar/gnh104 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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