Nucleic Acids Research

Articles:

Paul M. Sharp, Elizabeth Bailes, Russell J. Grocock, John F. Peden, and R. Elizabeth Sockett

Variation in the strength of selected codon usage bias among bacteria
Nucl. Acids Res. 2005 33: 1141-1153; doi:10.1093/nar/gki242 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Darui Xu, Nancy L. Greenbaum, and Marcia O. Fenley

Recognition of the spliceosomal branch site RNA helix on the basis of surface and electrostatic features
Nucl. Acids Res. 2005 33: 1154-1161; doi:10.1093/nar/gki249 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Erez Y. Levanon, Martina Hallegger, Yaron Kinar, Ronen Shemesh, Kristina Djinovic-Carugo, Gideon Rechavi, Michael F. Jantsch, and Eli Eisenberg

Evolutionarily conserved human targets of adenosine to inosine RNA editing
Nucl. Acids Res. 2005 33: 1162-1168; doi:10.1093/nar/gki239 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Augustine Chen, Y. F. Kao, and Chris M. Brown

Translation of the first upstream ORF in the hepatitis B virus pregenomic RNA modulates translation at the core and polymerase initiation codons
Nucl. Acids Res. 2005 33: 1169-1181; doi:10.1093/nar/gki251 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Barbara Saccà, Laurent Lacroix, and Jean-Louis Mergny

The effect of chemical modifications on the thermal stability of different G-quadruplex-forming oligonucleotides
Nucl. Acids Res. 2005 33: 1182-1192; doi:10.1093/nar/gki257 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Melissa A. Calmann, Anetta Nowosielska, and M. G. Marinus

Separation of mutation avoidance and antirecombination functions in an Escherichia coli mutS mutant
Nucl. Acids Res. 2005 33: 1193-1200; doi:10.1093/nar/gki263 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Irina L. Kuznetsova, Marina A. Zenkova, Hans J. Gross, and Valentin V. Vlassov

Enhanced RNA cleavage within bulge-loops by an artificial ribonuclease
Nucl. Acids Res. 2005 33: 1201-1212; doi:10.1093/nar/gki264 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

M. Sidiqi, J. A. Wilce, J. P. Vivian, C. J. Porter, A. Barker, P. J. Leedman, and M. C. J. Wilce

Structure and RNA binding of the third KH domain of poly(C)-binding protein 1
Nucl. Acids Res. 2005 33: 1213-1221; doi:10.1093/nar/gki265 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Maria V. Sukhanova, Svetlana N. Khodyreva, Natalia A. Lebedeva, Rajendra Prasad, Samuel H. Wilson, and Olga I. Lavrik

Human base excision repair enzymes apurinic/apyrimidinic endonuclease1 (APE1), DNA polymerase ß and poly(ADP-ribose) polymerase 1: interplay between strand-displacement DNA synthesis and proofreading exonuclease activity
Nucl. Acids Res. 2005 33: 1222-1229; doi:10.1093/nar/gki266 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Patricia L. Opresko, Jinshui Fan, Shamika Danzy, David M. Wilson, III, and Vilhelm A. Bohr

Oxidative damage in telomeric DNA disrupts recognition by TRF1 and TRF2
Nucl. Acids Res. 2005 33: 1230-1239; doi:10.1093/nar/gki273 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lucien Junior Bergeron and Jean-Pierre Perreault

Target-dependent on/off switch increases ribozyme fidelity
Nucl. Acids Res. 2005 33: 1240-1248; doi:10.1093/nar/gki278 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Scott R. Budihas, Inna Gorshkova, Sergei Gaidamakov, Antony Wamiru, Marion K. Bona, Michael A. Parniak, Robert J. Crouch, James B. McMahon, John A. Beutler, and Stuart F. J. Le Grice

Selective inhibition of HIV-1 reverse transcriptase-associated ribonuclease H activity by hydroxylated tropolones
Nucl. Acids Res. 2005 33: 1249-1256; doi:10.1093/nar/gki268 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kevin Range, Evelyn Mayaan, L. J. Maher, III, and Darrin M. York

The contribution of phosphate–phosphate repulsions to the free energy of DNA bending
Nucl. Acids Res. 2005 33: 1257-1268; doi:10.1093/nar/gki272 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Chwen-Huey Wu, Chanhyo Lee, Ruopeng Fan, Meghan J. Smith, Yuki Yamaguchi, Hiroshi Handa, and David S. Gilmour

Molecular characterization of Drosophila NELF
Nucl. Acids Res. 2005 33: 1269-1279; doi:10.1093/nar/gki274 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Anna-Laura Ross, Laura J. Simpson, and Julian E. Sale

Vertebrate DNA damage tolerance requires the C-terminus but not BRCT or transferase domains of REV1
Nucl. Acids Res. 2005 33: 1280-1289; doi:10.1093/nar/gki279 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Angie M. Cheng, Mike W. Byrom, Jeffrey Shelton, and Lance P. Ford

Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis
Nucl. Acids Res. 2005 33: 1290-1297; doi:10.1093/nar/gki200 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Elisheva Smith, Todd E. Meyerrose, Thomas Kohler, Malka Namdar-Attar, Natti Bab, Olga Lahat, Tommy Noh, Jingjing Li, Mazen W. Karaman, Joseph G. Hacia, Ting T. Chen, Jan A. Nolta, Ralph Müller, Itai Bab, and Baruch Frenkel

Leaky ribosomal scanning in mammalian genomes: significance of histone H4 alternative translation in vivo
Nucl. Acids Res. 2005 33: 1298-1308; doi:10.1093/nar/gki248 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Steven J. Kavanagh, Thomas C. Schulz, Philippa Davey, Charles Claudianos, Carrie Russell, and Peter D. Rathjen

A family of RS domain proteins with novel subcellular localization and trafficking
Nucl. Acids Res. 2005 33: 1309-1322; doi:10.1093/nar/gki269 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Deepa Alex and Kevin A. W. Lee

RGG-boxes of the EWS oncoprotein repress a range of transcriptional activation domains
Nucl. Acids Res. 2005 33: 1323-1331; doi:10.1093/nar/gki270 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Rajeev Gangal and Pankaj Sharma

Human pol II promoter prediction: time series descriptors and machine learning
Nucl. Acids Res. 2005 33: 1332-1336; doi:10.1093/nar/gki271 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Masatoshi Jinnin, Hironobu Ihn, Kenichi Yamane, Yoshihiro Mimura, Yoshihide Asano, and Kunihiko Tamaki

2(I) collagen gene regulation by protein kinase C signaling in human dermal fibroblasts
Nucl. Acids Res. 2005 33: 1337-1351; doi:10.1093/nar/gki275 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ming-Hon Hou and Andrew H.-J. Wang

Mithramycin forms a stable dimeric complex by chelating with Fe(II): DNA-interacting characteristics, cellular permeation and cytotoxicity
Nucl. Acids Res. 2005 33: 1352-1361; doi:10.1093/nar/gki276 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

John A. Brazier, Takayuki Shibata, John Townsley, Brian F. Taylor, Elaine Frary, Nicholas H. Williams, and David M. Williams

Amino-functionalized DNA: the properties of C5-amino-alkyl substituted 2'-deoxyuridines and their application in DNA triplex formation
Nucl. Acids Res. 2005 33: 1362-1371; doi:10.1093/nar/gki254 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Do-Hyung Kim, Kyoung-Hwa Lee, Jeong-Hoon Kim, Gi-Hyuck Ryu, Sung-Ho Bae, Byung-Chul Lee, Kyeong-Yeop Moon, Si-Myung Byun, Hyeon-Sook Koo, and Yeon-Soo Seo

Enzymatic properties of the Caenorhabditis elegans Dna2 endonuclease/helicase and a species-specific interaction between RPA and Dna2
Nucl. Acids Res. 2005 33: 1372-1383; doi:10.1093/nar/gki255 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Samuela Pasquali, Hin Hark Gan, and Tamar Schlick

Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs
Nucl. Acids Res. 2005 33: 1384-1398; doi:10.1093/nar/gki267 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

John W. Pinney, Martin W. Shirley, Glenn A. McConkey, and David R. Westhead

metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella
Nucl. Acids Res. 2005 33: 1399-1409; doi:10.1093/nar/gki285 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sreeparna Banerjee and Hernan Flores-Rozas

Cadmium inhibits mismatch repair by blocking the ATPase activity of the MSH2–MSH6 complex
Nucl. Acids Res. 2005 33: 1410-1419; doi:10.1093/nar/gki291 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Corrigendum:

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: 1420; doi:10.1093/nar/gki287 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Erratum:

Joydeep Basu, Gregory Stromberg, George Compitello, Huntington F. Willard, and Gil Van Bokkelen

Rapid creation of BAC-based human artifical chromosome vectors by transposition with synthetic alpha-satellite arrays
Nucl. Acids Res. 2005 33: 1421-1422; doi:10.1093/nar/gki277 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Takeaki Ozawa, Kengo Nishitani, Yusuke Sako, and Yoshio Umezawa

A high-throughput screening of genes that encode proteins transported into the endoplasmic reticulum in mammalian cells
Nucl. Acids Res. 2005 33: e34; doi:10.1093/nar/gni032 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Johannes H. Urban, Richard M. Schneider, Marta Compte, Carsten Finger, Klaus Cichutek, Luis Álvarez-Vallina, and Christian J. Buchholz

Selection of functional human antibodies from retroviral display libraries
Nucl. Acids Res. 2005 33: e35; doi:10.1093/nar/gni033 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Søren Warming, Nina Costantino, Donald L. Court, Nancy A. Jenkins, and Neal G. Copeland

Simple and highly efficient BAC recombineering using galK selection
Nucl. Acids Res. 2005 33: e36; doi:10.1093/nar/gni035 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Na Li, Changjun Yu, and Faqing Huang

Novel cyanine-AMP conjugates for efficient 5' RNA fluorescent labeling by one-step transcription and replacement of [-³²P]ATP in RNA structural investigation
Nucl. Acids Res. 2005 33: e37; doi:10.1093/nar/gni036 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mathias Ehrich, Sebastian Böcker, and Dirk van den Boom

Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS
Nucl. Acids Res. 2005 33: e38; doi:10.1093/nar/gni038 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

J. Stitz, P. O. Krutzik, and G. P. Nolan

Screening of retroviral cDNA libraries for factors involved in protein phosphorylation in signaling cascades
Nucl. Acids Res. 2005 33: e39; doi:10.1093/nar/gni039 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Qixin Leng and A. James Mixson

Modified branched peptides with a histidine-rich tail enhance in vitro gene transfection
Nucl. Acids Res. 2005 33: e40; doi:10.1093/nar/gni040 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nathalie Matter and Harald König

Targeted ‘knockdown’ of spliceosome function in mammalian cells
Nucl. Acids Res. 2005 33: e41; doi:10.1093/nar/gni041 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Olli H. Laitinen, Kari J. Airenne, Vesa P. Hytönen, Erik Peltomaa, Anssi J. Mähönen, Thomas Wirth, Miia M. Lind, Kari A. Mäkelä, Pyry I. Toivanen, Diana Schenkwein, Tommi Heikura, Henri R. Nordlund, Markku S. Kulomaa, and Seppo Ylä-Herttuala

A multipurpose vector system for the screening of libraries in bacteria, insect and mammalian cells and expression in vivo
Nucl. Acids Res. 2005 33: e42; doi:10.1093/nar/gni042 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shinji Masui, Daisuke Shimosato, Yayoi Toyooka, Rika Yagi, Kazue Takahashi, and Hitoshi Niwa

An efficient system to establish multiple embryonic stem cell lines carrying an inducible expression unit
Nucl. Acids Res. 2005 33: e43; doi:10.1093/nar/gni043 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gilda Cobellis, Giancarlo Nicolaus, Mariangela Iovino, Antonio Romito, Emanuele Marra, Manlio Barbarisi, Marco Sardiello, Francesco P. Di Giorgio, Nicola Iovino, Massimo Zollo, Andrea Ballabio, and Riccardo Cortese

Tagging genes with cassette-exchange sites
Nucl. Acids Res. 2005 33: e44; doi:10.1093/nar/gni045 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Dirk Eulberg, Klaus Buchner, Christian Maasch, and Sven Klussmann

Development of an automated in vitro selection protocol to obtain RNA-based aptamers: identification of a biostable substance P antagonist
Nucl. Acids Res. 2005 33: e45; doi:10.1093/nar/gni044 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

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