Nucleic Acids Research

Editorial:

EDITORIAL
Nucl. Acids Res. 2003 31: 6381-6382; doi:10.1093/nar/gkg862 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Articles:

Kazuyuki Takai and Shigeyuki Yokoyama

Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons
Nucl. Acids Res. 2003 31: 6383-6391; doi:10.1093/nar/gkg839 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Elizabeth A. Worthey, Achim Schnaufer, I. Saira Mian, Kenneth Stuart, and Reza Salavati

Comparative analysis of editosome proteins in trypanosomatids
Nucl. Acids Res. 2003 31: 6392-6408; doi:10.1093/nar/gkg870 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

A. L. Chambers, A. J. Smith, and N. J. Savery

A DNA translocation motif in the bacterial transcription–repair coupling factor, Mfd
Nucl. Acids Res. 2003 31: 6409-6418; doi:10.1093/nar/gkg868 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nikolai Windbichler, Michael Werner, and Renée Schroeder

Kissing complex-mediated dimerisation of HIV-1 RNA: coupling extended duplex formation to ribozyme cleavage
Nucl. Acids Res. 2003 31: 6419-6427; doi:10.1093/nar/gkg873 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jianxin Wu, Bei-Bei Zhu, Jin Yu, Hong Zhu, Lu Qiu, Mark S. Kindy, Liya Gu, Albrecht Seidel, and Guo-Min Li

In vitro and in vivo modulations of benzo[c]phenanthrene–DNA adducts by DNA mismatch repair system
Nucl. Acids Res. 2003 31: 6428-6434; doi:10.1093/nar/gkg875 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jörg Vogel, Verena Bartels, Thean Hock Tang, Gennady Churakov, Jacoba G. Slagter-Jäger, Alexander Hüttenhofer, and E. Gerhart H. Wagner

RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria
Nucl. Acids Res. 2003 31: 6435-6443; doi:10.1093/nar/gkg867 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Oliver Pusch, Daniel Boden, Rebecca Silbermann, Fred Lee, Lynne Tucker, and Bharat Ramratnam

Nucleotide sequence homology requirements of HIV-1-specific short hairpin RNA
Nucl. Acids Res. 2003 31: 6444-6449; doi:10.1093/nar/gkg876 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Olga Novakova, Jana Kasparkova, Jaroslav Malina, Giovanni Natile, and Viktor Brabec

DNA–protein cross-linking by trans-[PtCl₂(E-iminoether)₂]. A concept for activation of the trans geometry in platinum antitumor complexes
Nucl. Acids Res. 2003 31: 6450-6460; doi:10.1093/nar/gkg863 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

L. David Finger, Lukas Trantirek, Carina Johansson, and Juli Feigon

Solution structures of stem–loop RNAs that bind to the two N-terminal RNA-binding domains of nucleolin
Nucl. Acids Res. 2003 31: 6461-6472; doi:10.1093/nar/gkg866 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Celia Perales, Felipe Cava, Wilfried J. J. Meijer, and José Berenguer

Enhancement of DNA, cDNA synthesis and fidelity at high temperatures by a dimeric single-stranded DNA-binding protein
Nucl. Acids Res. 2003 31: 6473-6480; doi:10.1093/nar/gkg865 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Chun-Chung Wang, Tsung-Cheng Chang, Ching-Wen Lin, Hsiu-Ling Tsui, Page B. C. Chu, Bo-Shun Chen, Zhi-Shun Huang, and Huey-Nan Wu

Nucleic acid binding properties of the nucleic acid chaperone domain of hepatitis delta antigen
Nucl. Acids Res. 2003 31: 6481-6492; doi:10.1093/nar/gkg857 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christopher D. Carvin, Rebecca D. Parr, and Michael P. Kladde

Site-selective in vivo targeting of cytosine-5 DNA methylation by zinc-finger proteins
Nucl. Acids Res. 2003 31: 6493-6501; doi:10.1093/nar/gkg853 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dana Philipps, Alicia M. Celotto, Qiao-Qiao Wang, Rosa S. Tarng, and Brenton R. Graveley

Arginine/serine repeats are sufficient to constitute a splicing activation domain
Nucl. Acids Res. 2003 31: 6502-6508; doi:10.1093/nar/gkg845 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Xiaojun Ren, Gérald Gavory, Haitao Li, Liming Ying, David Klenerman, and Shankar Balasubramanian

Identification of a new RNA·RNA interaction site for human telomerase RNA (hTR): structural implications for hTR accumulation and a dyskeratosis congenita point mutation
Nucl. Acids Res. 2003 31: 6509-6515; doi:10.1093/nar/gkg871 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

A. M. Cerdeño-Tárraga, A. Efstratiou, L. G. Dover, M. T. G. Holden, M. Pallen, S. D. Bentley, G. S. Besra, C. Churcher, K. D. James, A. De Zoysa, T. Chillingworth, A. Cronin, L. Dowd, T. Feltwell, N. Hamlin, S. Holroyd, K. Jagels, S. Moule, M. A. Quail, E. Rabbinowitsch, K. M. Rutherford, N. R. Thomson, L. Unwin, S. Whitehead, B. G. Barrell, and J. Parkhill

The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129
Nucl. Acids Res. 2003 31: 6516-6523; doi:10.1093/nar/gkg874 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Marie-Line Bortolin, Jean-Pierre Bachellerie, and Béatrice Clouet-d’Orval

In vitro RNP assembly and methylation guide activity of an unusual box C/D RNA, cis-acting archaeal pre-tRNA^Trp
Nucl. Acids Res. 2003 31: 6524-6535; doi:10.1093/nar/gkg860 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Silke Dorner, Claudia Panuschka, Walther Schmid, and Andrea Barta

Mononucleotide derivatives as ribosomal P-site substrates reveal an important contribution of the 2'-OH to activity
Nucl. Acids Res. 2003 31: 6536-6542; doi:10.1093/nar/gkg842 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Patrice Vitali, Hélène Royo, Hervé Seitz, Jean-Pierre Bachellerie, Alexander Hüttenhofer, and Jérôme Cavaillé

Identification of 13 novel human modification guide RNAs
Nucl. Acids Res. 2003 31: 6543-6551; doi:10.1093/nar/gkg849 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nikolai V. Ravin, Victor V. Kuprianov, Eddie B. Gilcrease, and Sherwood R. Casjens

Bidirectional replication from an internal ori site of the linear N15 plasmid prophage
Nucl. Acids Res. 2003 31: 6552-6560; doi:10.1093/nar/gkg856 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tina Ruggiero, Martina Olivero, Antonia Follenzi, Luigi Naldini, Raffaele Calogero, and Maria Flavia Di Renzo

Deletion in a (T)₈ microsatellite abrogates expression regulation by 3'-UTR
Nucl. Acids Res. 2003 31: 6561-6569; doi:10.1093/nar/gkg858 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Eduardo P. C. Rocha and Antoine Danchin

Gene essentiality determines chromosome organisation in bacteria
Nucl. Acids Res. 2003 31: 6570-6577; doi:10.1093/nar/gkg859 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Danny Barash

Deleterious mutation prediction in the secondary structure of RNAs
Nucl. Acids Res. 2003 31: 6578-6584; doi:10.1093/nar/gkg872 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kent Søe and Frank Grosse

p53 stimulates human topoisomerase I activity by modulating its DNA binding
Nucl. Acids Res. 2003 31: 6585-6592; doi:10.1093/nar/gkg846 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Eugenia Basyuk, Florence Suavet, Alain Doglio, Rémy Bordonné, and Edouard Bertrand

Human let-7 stem–loop precursors harbor features of RNase III cleavage products
Nucl. Acids Res. 2003 31: 6593-6597; doi:10.1093/nar/gkg855 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Beatriz Galán, Annie Kolb, Jesús M. Sanz, José Luis García, and María A. Prieto

Molecular determinants of the hpa regulatory system of Escherichia coli: the HpaR repressor
Nucl. Acids Res. 2003 31: 6598-6609; doi:10.1093/nar/gkg851 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Carole Lartigue, Alain Blanchard, Joël Renaudin, François Thiaucourt, and Pascal Sirand-Pugnet

Host specificity of mollicutes oriC plasmids: functional analysis of replication origin
Nucl. Acids Res. 2003 31: 6610-6618; doi:10.1093/nar/gkg848 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Akira Goto, Stéphanie Blandin, Julien Royet, Jean-Marc Reichhart, and Elena A. Levashina

Silencing of Toll pathway components by direct injection of double-stranded RNA into Drosophila adult flies
Nucl. Acids Res. 2003 31: 6619-6623; doi:10.1093/nar/gkg852 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mirko Marabese, Faina Vikhanskaya, Cristina Rainelli, Toshiyuki Sakai, and Massimo Broggini

DNA damage induces transcriptional activation of p73 by removing C-EBP repression on E2F1
Nucl. Acids Res. 2003 31: 6624-6632; doi:10.1093/nar/gkg869 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Clotilde Claudel-Renard, Claude Chevalet, Thomas Faraut, and Daniel Kahn

Enzyme-specific profiles for genome annotation: PRIAM
Nucl. Acids Res. 2003 31: 6633-6639; doi:10.1093/nar/gkg847 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jérôme Eeckhoute, Bénédicte Oxombre, Pierre Formstecher, Philippe Lefebvre, and Bernard Laine

Critical role of charged residues in helix 7 of the ligand binding domain in Hepatocyte Nuclear Factor 4 dimerisation and transcriptional activity
Nucl. Acids Res. 2003 31: 6640-6650; doi:10.1093/nar/gkg850 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jun-ichi Nishikawa, Miho Amano, Yoshiro Fukue, Shigeo Tanaka, Haruka Kishi, Yoshiko Hirota, Kinya Yoda, and Takashi Ohyama

Left-handedly curved DNA regulates accessibility to cis-DNA elements in chromatin
Nucl. Acids Res. 2003 31: 6651-6662; doi:10.1093/nar/gkg854 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Paul N. Hengen, Ilya G. Lyakhov, Lisa E. Stewart, and Thomas D. Schneider

Molecular flip–flops formed by overlapping Fis sites
Nucl. Acids Res. 2003 31: 6663-6673; doi:10.1093/nar/gkg877 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Xin-tian Li, Nina Costantino, Lin-yu Lu, De-pei Liu, Rory M. Watt, Kathryn S. E. Cheah, Donald L. Court, and Jian-Dong Huang

Identification of factors influencing strand bias in oligonucleotide-mediated recombination in Escherichia coli
Nucl. Acids Res. 2003 31: 6674-6687; doi:10.1093/nar/gkg844 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

NAR Methods Online:

Steven Giglio, Paul T. Monis, and Christopher P. Saint

Demonstration of preferential binding of SYBR Green I to specific DNA fragments in real-time multiplex PCR
Nucl. Acids Res. 2003 31: e136; doi:10.1093/nar/gng135 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Malte Bussiek, Norbert Mücke, and Jörg Langowski

Polylysine-coated mica can be used to observe systematic changes in the supercoiled DNA conformation by scanning force microscopy in solution
Nucl. Acids Res. 2003 31: e137; doi:10.1093/nar/gng137 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Stephan Laib, Michael Rankl, Thomas Ruckstuhl, and Stefan Seeger

Sizing of single fluorescently stained DNA fragments by scanning microscopy
Nucl. Acids Res. 2003 31: e138; doi:10.1093/nar/gng138 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Brenda M. Ogle, Marilia Cascalho, Cristina Joao, William Taylor, Lori J. West, and Jeffrey L. Platt

Direct measurement of lymphocyte receptor diversity
Nucl. Acids Res. 2003 31: e139; doi:10.1093/nar/gng139 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Philipp Oberdoerffer, Kevin L. Otipoby, Mitsuo Maruyama, and Klaus Rajewsky

Unidirectional Cre-mediated genetic inversion in mice using the mutant loxP pair lox66/lox71
Nucl. Acids Res. 2003 31: e140; doi:10.1093/nar/gng140 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Scott D. Drabenstot, Doris M. Kupfer, James D. White, David W. Dyer, Bruce A. Roe, Kent L. Buchanan, and Juneann W. Murphy

FELINES: a utility for extracting and examining EST-defined introns and exons
Nucl. Acids Res. 2003 31: e141; doi:10.1093/nar/gng141 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

L. Petalidis, S. Bhattacharyya, G. A. Morris, V. P. Collins, T. C. Freeman, and P. A. Lyons

Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis
Nucl. Acids Res. 2003 31: e142; doi:10.1093/nar/gng142 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Xinxin Gao, Peggy Yo, Andrew Keith, Timothy J. Ragan, and Thomas K. Harris

Thermodynamically balanced inside-out (TBIO) PCR-based gene synthesis: a novel method of primer design for high-fidelity assembly of longer gene sequences
Nucl. Acids Res. 2003 31: e143; doi:10.1093/nar/gng143 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Sacha A. F. T. van Hijum, Aldert L. Zomer, Oscar P. Kuipers, and Jan Kok

Projector: automatic contig mapping for gap closure purposes
Nucl. Acids Res. 2003 31: e144; doi:10.1093/nar/gng144 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Shinya Kurata, Takashi Ohtsuki, Tsutomu Suzuki, and Kimitsuna Watanabe

Quick two-step RNA ligation employing periodate oxidation
Nucl. Acids Res. 2003 31: e145; doi:10.1093/nar/gng145 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Baback Gharizadeh, Max Käller, Pål Nyrén, Anders Andersson, Mathias Uhlén, Joakim Lundeberg, and Afshin Ahmadian

Viral and microbial genotyping by a combination of multiplex competitive hybridization and specific extension followed by hybridization to generic tag arrays
Nucl. Acids Res. 2003 31: e146; doi:10.1093/nar/gng147 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nijole Jasinskiene, Craig J. Coates, Aurora Ashikyan, and Anthony A. James

High efficiency, site-specific excision of a marker gene by the phage P1 cre–loxP system in the yellow fever mosquito, Aedes aegypti
Nucl. Acids Res. 2003 31: e147; doi:10.1093/nar/gng148 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Errata:

Erratum
Nucl. Acids Res. 2003 31: 6688; doi:10.1093/nar/gkg885 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

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