Nucleic Acids Research

Articles:

Mark C. Hall, Polina V. Shcherbakova, John M. Fortune, Christoph H. Borchers, J. Michael Dial, Kenneth B. Tomer, and Thomas A. Kunkel

DNA binding by yeast Mlh1 and Pms1: implications for DNA mismatch repair
Nucl. Acids Res. 2003 31: 2025-2034; doi:10.1093/nar/gkg324 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Soma Ghosh, S. Satish, Sonika Tyagi, Alok Bhattacharya, and Sudha Bhattacharya

Differential use of multiple replication origins in the ribosomal DNA episome of the protozoan parasite Entamoeba histolytica
Nucl. Acids Res. 2003 31: 2035-2044; doi:10.1093/nar/gkg320 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ji Hyung Chung, Eun Kyoung Im, Hyun-Young Park, Jun Hye Kwon, Seahyoung Lee, Jaewon Oh, Ki-Chul Hwang, Jong Ho Lee, and Yangsoo Jang

A novel uracil-DNA glycosylase family related to the helix–hairpin–helix DNA glycosylase superfamily
Nucl. Acids Res. 2003 31: 2045-2055; doi:10.1093/nar/gkg319 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Subhasis B. Biswas, Sujata M. Khopde, Fan xiu Zhu, and Esther E. Biswas

Subunit interactions in the assembly of Saccharomyces cerevisiae DNA polymerase
Nucl. Acids Res. 2003 31: 2056-2065; doi:10.1093/nar/gkg311 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Matjaz Polak, Muthiah Manoharan, Gopal B. Inamati, and Janez Plavec

Tuning of conformational preorganization in model 2',5'- and 3',5'-linked oligonucleotides by 3'- and 2'-O-methoxyethyl modification
Nucl. Acids Res. 2003 31: 2066-2076; doi:10.1093/nar/gkg305 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Norie Fujikawa, Hitoshi Kurumizaka, Osamu Nureki, Takaho Terada, Mikako Shirouzu, Tsutomu Katayama, and Shigeyuki Yokoyama

Structural basis of replication origin recognition by the DnaA protein
Nucl. Acids Res. 2003 31: 2077-2086; doi:10.1093/nar/gkg309 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Patrick Deschênes, Jonathan Ouellet, Jonathan Perreault, and Jean-Pierre Perreault

Formation of the P1.1 pseudoknot is critical for both the cleavage activity and substrate specificity of an antigenomic trans-acting hepatitis delta ribozyme
Nucl. Acids Res. 2003 31: 2087-2096; doi:10.1093/nar/gkg307 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Virna Dapic, Vedra Abdomerovic, Rachel Marrington, Jemma Peberdy, Alison Rodger, John O. Trent, and Paula J. Bates

Biophysical and biological properties of quadruplex oligodeoxyribonucleotides
Nucl. Acids Res. 2003 31: 2097-2107; doi:10.1093/nar/gkg316 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ying Huang, Edward McGillicuddy, Michael Weindel, Steven Dong, and Richard J. Maraia

The fission yeast TFIIB-related factor limits RNA polymerase III to a TATA-dependent pathway of TBP recruitment
Nucl. Acids Res. 2003 31: 2108-2116; doi:10.1093/nar/gkg301 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Maja Hemmings-Mieszczak, Gabriele Dorn, François J. Natt, Jonathan Hall, and William L. Wishart

Independent combinatorial effect of antisense oligonucleotides and RNAi-mediated specific inhibition of the recombinant Rat P2X₃ receptor
Nucl. Acids Res. 2003 31: 2117-2126; doi:10.1093/nar/gkg322 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

T. Ohbayashi, M. Shimada, T. Nakadai, T. Wada, H. Handa, and T. Tamura

Vertebrate TBP-like protein (TLP/TRF2/TLF) stimulates TATA-less terminal deoxynucleotidyl transferase promoters in a transient reporter assay, and TFIIA-binding capacity of TLP is required for this function
Nucl. Acids Res. 2003 31: 2127-2133; doi:10.1093/nar/gkg315 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

T. D. Read, G. S. A. Myers, R. C. Brunham, W. C. Nelson, I. T. Paulsen, J. Heidelberg, E. Holtzapple, H. Khouri, N. B. Federova, H. A. Carty, L. A. Umayam, D. H. Haft, J. Peterson, M. J. Beanan, O. White, S. L. Salzberg, R. -c. Hsia, G. McClarty, R. G. Rank, P. M. Bavoil, and C. M. Fraser

Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae
Nucl. Acids Res. 2003 31: 2134-2147; doi:10.1093/nar/gkg321 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Louis Droogmans, Martine Roovers, Janusz M. Bujnicki, Catherine Tricot, Thomas Hartsch, Victor Stalon, and Henri Grosjean

Cloning and characterization of tRNA (m¹A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures
Nucl. Acids Res. 2003 31: 2148-2156; doi:10.1093/nar/gkg314 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Julianne Smith, Enriqueta Riballo, Boris Kysela, Celine Baldeyron, Kostas Manolis, Christel Masson, Michael R. Lieber, Dora Papadopoulo, and Penny Jeggo

Impact of DNA ligase IV on the fidelity of end joining in human cells
Nucl. Acids Res. 2003 31: 2157-2167; doi:10.1093/nar/gkg317 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yuexing Zhang, Nicholas Woodford, Xianmin Xia, and Anne W. Hamburger

Repression of E2F1-mediated transcription by the ErbB3 binding protein Ebp1 involves histone deacetylases
Nucl. Acids Res. 2003 31: 2168-2177; doi:10.1093/nar/gkg318 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Amitava Adhikary, Volker Buschmann, Christian Müller, and Markus Sauer

Ensemble and single-molecule fluorescence spectroscopic study of the binding modes of the bis-benzimidazole derivative Hoechst 33258 with DNA
Nucl. Acids Res. 2003 31: 2178-2186; doi:10.1093/nar/gkg308 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Folker Meyer, Alexander Goesmann, Alice C. McHardy, Daniela Bartels, Thomas Bekel, Jörn Clausen, Jörn Kalinowski, Burkhard Linke, Oliver Rupp, Robert Giegerich, and Alfred Pühler

GenDB—an open source genome annotation system for prokaryote genomes
Nucl. Acids Res. 2003 31: 2187-2195; doi:10.1093/nar/gkg312 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Zhiping Zhang and Christina T. Teng

Phosphorylation of Kruppel-like factor 5 (KLF5/IKLF) at the CBP interaction region enhances its transactivation function
Nucl. Acids Res. 2003 31: 2196-2208; doi:10.1093/nar/gkg310 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yilmaz Niyaz, Irina Frenz, Gabriele Petersen, and Ulrich Gehring

Transcriptional stimulation by the DNA binding protein Hap46/BAG-1M involves hsp70/hsc70 molecular chaperones
Nucl. Acids Res. 2003 31: 2209-2216; doi:10.1093/nar/gkg303 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Per Unneberg, Anders Wennborg, and Magnus Larsson

Transcript identification by analysis of short sequence tags—influence of tag length, restriction site and transcript database
Nucl. Acids Res. 2003 31: 2217-2226; doi:10.1093/nar/gkg313 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Chien-Chung Cheng, Wei-Chun Huang-Fu, Kuo-Chan Hung, Po-Jui Chen, Wen Jwu Wang, and Yu-Ju Chen

Mechanistic aspects of Co^II(HAPP)(TFA)₂ in DNA bulge-specific recognition
Nucl. Acids Res. 2003 31: 2227-2233; doi:10.1093/nar/gkg323 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Karen E. Sandman, Daniel F. Tardiff, Lori A. Neely, and Christopher J. Noren

Revised Escherichia coli selenocysteine insertion requirements determined by in vivo screening of combinatorial libraries of SECIS variants
Nucl. Acids Res. 2003 31: 2234-2241; doi:10.1093/nar/gkg304 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ronald Jansen, Harmen J. Bussemaker, and Mark Gerstein

Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models
Nucl. Acids Res. 2003 31: 2242-2251; doi:10.1093/nar/gkg306 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

NAR Methods Online:

Masahiko Hashimoto, Yan He, and Edward S. Yeung

On-line integration of PCR and cycle sequencing in capillaries: from human genomic DNA directly to called bases
Nucl. Acids Res. 2003 31: e41; doi:10.1093/nar/gng041 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sean D. Mooney, Teri E. Klein, Russ B. Altman, Mark A. Trifiro, and Bruce Gottlieb

A functional analysis of disease-associated mutations in the androgen receptor gene
Nucl. Acids Res. 2003 31: e42; doi:10.1093/nar/gng042 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hongxia Xu, Michael Y. Sha, Edith Y. Wong, Janet Uphoff, Yanzhang Xu, Joseph A. Treadway, Anh Truong, Eamonn O’Brien, Steven Asquith, Michael Stubbins, Nigel K. Spurr, Eric H. Lai, and Walt Mahoney

Multiplexed SNP genotyping using the Qbead^TM system: a quantum dot-encoded microsphere-based assay
Nucl. Acids Res. 2003 31: e43; doi:10.1093/nar/gng043 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Gerhart U. Ryffel, Dagmar Werdien, Gülüzar Turan, Andrea Gerhards, Stefan Gooßes, and Sabine Senkel

Tagging muscle cell lineages in development and tail regeneration using Cre recombinase in transgenic Xenopus
Nucl. Acids Res. 2003 31: e44; doi:10.1093/nar/gng044 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Martin Bengtsson, H. Jonas Karlsson, Gunnar Westman, and Mikael Kubista

A new minor groove binding asymmetric cyanine reporter dye for real-time PCR
Nucl. Acids Res. 2003 31: e45; doi:10.1093/nar/gng045 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Grace T. Y. Chung, Yoshihiro Yamada, Richard Pannell, Alan Forster, and Terence H. Rabbitts

The hepatitis C virus internal ribosome entry site facilitates efficient protein synthesis in blood vessel endothelium during tumour angiogenesis
Nucl. Acids Res. 2003 31: e46; doi:10.1093/nar/gng046 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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