Nucleic Acids Research

Articles:

Weimei Sun, Alexandre Pertzev, and Allen W. Nicholson

Catalytic mechanism of Escherichia coli ribonuclease III: kinetic and inhibitor evidence for the involvement of two magnesium ions in RNA phosphodiester hydrolysis
Nucl. Acids Res. 2005 33: 807-815; doi:10.1093/nar/gki197 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

V. A. Simossis, J. Kleinjung, and J. Heringa

Homology-extended sequence alignment
Nucl. Acids Res. 2005 33: 816-824; doi:10.1093/nar/gki233 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jens Bohne, Harald Wodrich, and Hans-Georg Kräusslich

Splicing of human immunodeficiency virus RNA is position-dependent suggesting sequential removal of introns from the 5' end
Nucl. Acids Res. 2005 33: 825-837; doi:10.1093/nar/gki185 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Xiaochun Fan, Hua Shi, and John T. Lis

Distinct transcriptional responses of RNA polymerases I, II and III to aptamers that bind TBP
Nucl. Acids Res. 2005 33: 838-845; doi:10.1093/nar/gki212 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Harris S. Soifer, Adriana Zaragoza, Maany Peyvan, Mark A. Behlke, and John J. Rossi

A potential role for RNA interference in controlling the activity of the human LINE-1 retrotransposon
Nucl. Acids Res. 2005 33: 846-856; doi:10.1093/nar/gki223 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Prasad N. Kuduvalli, Rupak Mitra, and Nancy L. Craig

Site-specific Tn7 transposition into the human genome
Nucl. Acids Res. 2005 33: 857-863; doi:10.1093/nar/gki227 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

S. Döhr, A. Klingenhoff, H. Maier, M. Hrabé de Angelis, T. Werner, and R. Schneider

Linking disease-associated genes to regulatory networks via promoter organization
Nucl. Acids Res. 2005 33: 864-872; doi:10.1093/nar/gki230 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Suhasini Modem, Kameswara R. Badri, Thomas C. Holland, and Thipparthi R. Reddy

Sam68 is absolutely required for Rev function and HIV-1 production
Nucl. Acids Res. 2005 33: 873-879; doi:10.1093/nar/gki231 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Morgan N. Price, Katherine H. Huang, Eric J. Alm, and Adam P. Arkin

A novel method for accurate operon predictions in all sequenced prokaryotes
Nucl. Acids Res. 2005 33: 880-892; doi:10.1093/nar/gki232 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Michael J. Poderycki, Leonard H. Rome, Lea Harrington, and Valerie A. Kickhoefer

The p80 homology region of TEP1 is sufficient for its association with the telomerase and vault RNAs, and the vault particle
Nucl. Acids Res. 2005 33: 893-902; doi:10.1093/nar/gki234 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, and Azuma Ohuchi

Design of nucleic acid sequences for DNA computing based on a thermodynamic approach
Nucl. Acids Res. 2005 33: 903-911; doi:10.1093/nar/gki235 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Karen L. Buchmueller, Andrew M. Staples, Peter B. Uthe, Cameron M. Howard, Kimberly A. O. Pacheco, Kari K. Cox, James A. Henry, Suzanna L. Bailey, Sarah M. Horick, Binh Nguyen, W. David Wilson, and Moses Lee

Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides
Nucl. Acids Res. 2005 33: 912-921; doi:10.1093/nar/gki238 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Aristotelis Tsirigos and Isidore Rigoutsos

A new computational method for the detection of horizontal gene transfer events
Nucl. Acids Res. 2005 33: 922-933; doi:10.1093/nar/gki187 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Yamini Dalal, Tomara J. Fleury, Alfred Cioffi, and Arnold Stein

Long-range oscillation in a periodic DNA sequence motif may influence nucleosome array formation
Nucl. Acids Res. 2005 33: 934-945; doi:10.1093/nar/gki224 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Evgeny M. Zdobnov, Mónica Campillos, Eoghan D. Harrington, David Torrents, and Peer Bork

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes
Nucl. Acids Res. 2005 33: 946-954; doi:10.1093/nar/gki236 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Riki Kawaguchi and Julia Bailey-Serres

mRNA sequence features that contribute to translational regulation in Arabidopsis
Nucl. Acids Res. 2005 33: 955-965; doi:10.1093/nar/gki240 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Deo Prakash Pandey and Kenn Gerdes

Toxin–antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes
Nucl. Acids Res. 2005 33: 966-976; doi:10.1093/nar/gki201 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Aurélie Faure, Christina Calmels, Cécile Desjobert, Michel Castroviejo, Anne Caumont-Sarcos, Laura Tarrago-Litvak, Simon Litvak, and Vincent Parissi

HIV-1 integrase crosslinked oligomers are active in vitro
Nucl. Acids Res. 2005 33: 977-986; doi:10.1093/nar/gki241 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lothar Vassen, Katharina Fiolka, Stefan Mahlmann, and Tarik Möröy

Direct transcriptional repression of the genes encoding the zinc-finger proteins Gfi1b and Gfi1 by Gfi1b
Nucl. Acids Res. 2005 33: 987-998; doi:10.1093/nar/gki243 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sanda Rocak, Bertrand Emery, N. Kyle Tanner, and Patrick Linder

Characterization of the ATPase and unwinding activities of the yeast DEAD-box protein Has1p and the analysis of the roles of the conserved motifs
Nucl. Acids Res. 2005 33: 999-1009; doi:10.1093/nar/gki244 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mythily Sachchithananthan, Stan J. Stasinopoulos, Jeffrey Wilusz, and Robert L. Medcalf

The relationship between the prothrombin upstream sequence element and the G20210A polymorphism: the influence of a competitive environment for mRNA 3'-end formation
Nucl. Acids Res. 2005 33: 1010-1020; doi:10.1093/nar/gki245 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

E. L. Baldwin, A. C. Berger, A. H. Corbett, and N. Osheroff

Mms22p protects Saccharomyces cerevisiae from DNA damage induced by topoisomerase II
Nucl. Acids Res. 2005 33: 1021-1030; doi:10.1093/nar/gki246 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nouha Ben Gaied, Nicole Glasser, Nick Ramalanjaona, Hervé Beltz, Philippe Wolff, Roland Marquet, Alain Burger, and Yves Mély

8-vinyl-deoxyadenosine, an alternative fluorescent nucleoside analog to 2'-deoxyribosyl-2-aminopurine with improved properties
Nucl. Acids Res. 2005 33: 1031-1039; doi:10.1093/nar/gki253 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Mitsuoki Kawano, April A. Reynolds, Juan Miranda-Rios, and Gisela Storz

Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli
Nucl. Acids Res. 2005 33: 1040-1050; doi:10.1093/nar/gki256 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Gila Lithwick and Hanah Margalit

Relative predicted protein levels of functionally associated proteins are conserved across organisms
Nucl. Acids Res. 2005 33: 1051-1057; doi:10.1093/nar/gki261 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Emily J. Borda and Snorri Th. Sigurdsson

Investigation of Mg²⁺- and temperature-dependent folding of the hairpin ribozyme by photo-crosslinking: effects of photo-crosslinker tether length and chemistry
Nucl. Acids Res. 2005 33: 1058-1068; doi:10.1093/nar/gki237 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

I. A. Shahmuradov, V. V. Solovyev, and A. J. Gammerman

Plant promoter prediction with confidence estimation
Nucl. Acids Res. 2005 33: 1069-1076; doi:10.1093/nar/gki247 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kimberly D. Dyer and Helene F. Rosenberg

The mouse RNase 4 and RNase 5/ang 1 locus utilizes dual promoters for tissue-specific expression
Nucl. Acids Res. 2005 33: 1077-1086; doi:10.1093/nar/gki250 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Thomas Göhler, Stefan Jäger, Gabriele Warnecke, Hideyo Yasuda, Ella Kim, and Wolfgang Deppert

Mutant p53 proteins bind DNA in a DNA structure-selective mode
Nucl. Acids Res. 2005 33: 1087-1100; doi:10.1093/nar/gki252 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Friederike Böhm, Ferdinand Kappes, Ingo Scholten, Nicole Richter, Hiroshi Matsuo, Rolf Knippers, and Tanja Waldmann

The SAF-box domain of chromatin protein DEK
Nucl. Acids Res. 2005 33: 1101-1110; doi:10.1093/nar/gki258 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Luisa M. Figueiredo, Eduardo P. C. Rocha, Liliana Mancio-Silva, Christine Prevost, Danièle Hernandez-Verdun, and Artur Scherf

The unusually large Plasmodium telomerase reverse-transcriptase localizes in a discrete compartment associated with the nucleolus
Nucl. Acids Res. 2005 33: 1111-1122; doi:10.1093/nar/gki260 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ingrun Alseth, Fikret Osman, Hanne Korvald, Irina Tsaneva, Matthew C. Whitby, Erling Seeberg, and Magnar Bjørås

Biochemical characterization and DNA repair pathway interactions of Mag1-mediated base excision repair in Schizosaccharomyces pombe
Nucl. Acids Res. 2005 33: 1123-1131; doi:10.1093/nar/gki259 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hui Zhao, Wie-Yen Young, Qingfeng Yan, Ronghua Li, Juyang Cao, Qiuju Wang, Xiaoming Li, Jennifer L. Peters, Dongyi Han, and Min-Xin Guan

Functional characterization of the mitochondrial 12S rRNA C1494T mutation associated with aminoglycoside-induced and non-syndromic hearing loss
Nucl. Acids Res. 2005 33: 1132-1139; doi:10.1093/nar/gki262 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Chunfang Zhang, Danny Kitsberg, Hun Chy, Qi Zhou, and John R. Morrison

Transposon-mediated generation of targeting vectors for the production of gene knockouts
Nucl. Acids Res. 2005 33: e24; doi:10.1093/nar/gni014 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Claire L. Simpson, Joanne Knight, Lee M. Butcher, Valerie K. Hansen, Emma Meaburn, Leonard C. Schalkwyk, Ian W. Craig, John F. Powell, Pak C. Sham, and Ammar Al-Chalabi

A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays
Nucl. Acids Res. 2005 33: e25; doi:10.1093/nar/gni028 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

S. Dinel, C. Bolduc, P. Belleau, A. Boivin, M. Yoshioka, E. Calvo, B. Piedboeuf, E. E. Snyder, F. Labrie, and J. St-Amand

Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome
Nucl. Acids Res. 2005 33: e26; doi:10.1093/nar/gni025 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Dominic C. Voon, Lily S. Subrata, Svetlana Baltic, Marco P. Leu, Joanna M. Whiteway, Agnes Wong, Samuel A. Knight, Frank T. Christiansen, and John M. Daly

Use of mRNA- and protein-destabilizing elements to develop a highly responsive reporter system
Nucl. Acids Res. 2005 33: e27; doi:10.1093/nar/gni030 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lida K. Gifford, Joanna B. Opalinska, David Jordan, Vikram Pattanayak, Paul Greenham, Anna Kalota, Michelle Robbins, Kathy Vernovsky, Lesbeth C. Rodriguez, Bao T. Do, Ponzy Lu, and Alan M. Gewirtz

Identification of antisense nucleic acid hybridization sites in mRNA molecules with self-quenching fluorescent reporter molecules
Nucl. Acids Res. 2005 33: e28; doi:10.1093/nar/gni024 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Joerg Schlingemann, Olaf Thuerigen, Carina Ittrich, Grischa Toedt, Heidi Kramer, Meinhard Hahn, and Peter Lichter

Effective transcriptome amplification for expression profiling on sense-oriented oligonucleotide microarrays
Nucl. Acids Res. 2005 33: e29; doi:10.1093/nar/gni029 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Bret S. E. Heale, Harris S. Soifer, Chauncey Bowers, and John J. Rossi

siRNA target site secondary structure predictions using local stable substructures
Nucl. Acids Res. 2005 33: e30; doi:10.1093/nar/gni026 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jeremy Harbig, Robert Sprinkle, and Steven A. Enkemann

A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array
Nucl. Acids Res. 2005 33: e31; doi:10.1093/nar/gni027 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Marcus D. Hughes, Zhan-Ren Zhang, Andrew J. Sutherland, Albert F. Santos, and Anna V. Hine

Discovery of active proteins directly from combinatorial randomized protein libraries without display, purification or sequencing: identification of novel zinc finger proteins
Nucl. Acids Res. 2005 33: e32; doi:10.1093/nar/gni031 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mazen W. Karaman, Susan Groshen, Chi-Chiang Lee, Brian L. Pike, and Joseph G. Hacia

Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays
Nucl. Acids Res. 2005 33: e33; doi:10.1093/nar/gni034 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

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