Nucleic Acids Research

Survey and Summary:

Marilyn Kozak

A second look at cellular mRNA sequences said to function as internal ribosome entry sites
Nucl. Acids Res. 2005 33: 6593-6602; doi:10.1093/nar/gki958 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Articles:

Shawn M. Christensen, Arkadiusz Bibillo, and Thomas H. Eickbush

Role of the Bombyx mori R2 element N-terminal domain in the target-primed reverse transcription (TPRT) reaction
Nucl. Acids Res. 2005 33: 6461-6468; doi:10.1093/nar/gki957 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Takao Kasuga, Jeffrey P. Townsend, Chaoguang Tian, Luz B. Gilbert, Gertrud Mannhaupt, John W. Taylor, and N. Louise Glass

Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination
Nucl. Acids Res. 2005 33: 6469-6485; doi:10.1093/nar/gki953 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Nitin Bhardwaj, Robert E. Langlois, Guijun Zhao, and Hui Lu

Kernel-based machine learning protocol for predicting DNA-binding proteins
Nucl. Acids Res. 2005 33: 6486-6493; doi:10.1093/nar/gki949 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alexandre Lomsadze, Vardges Ter-Hovhannisyan, Yury O. Chernoff, and Mark Borodovsky

Gene identification in novel eukaryotic genomes by self-training algorithm
Nucl. Acids Res. 2005 33: 6494-6506; doi:10.1093/nar/gki937 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Sophie Nolivos, Agamemnon J. Carpousis, and Béatrice Clouet-d'Orval

The K-loop, a general feature of the Pyrococcus C/D guide RNAs, is an RNA structural motif related to the K-turn
Nucl. Acids Res. 2005 33: 6507-6514; doi:10.1093/nar/gki962 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alexander Kotlyar, Natalia Borovok, Tatiana Molotsky, Dmitry Klinov, Benjamin Dwir, and Eli Kapon

Synthesis of novel poly(dG)–poly(dG)–poly(dC) triplex structure by Klenow exo^– fragment of DNA polymerase I
Nucl. Acids Res. 2005 33: 6515-6521; doi:10.1093/nar/gki963 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kui Lin and Da-Yong Zhang

The excess of 5' introns in eukaryotic genomes
Nucl. Acids Res. 2005 33: 6522-6527; doi:10.1093/nar/gki970 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Li-Kwan Chang, Jian-Ying Chung, Yi-Ren Hong, Takaya Ichimura, Mitsuyoshi Nakao, and Shih-Tung Liu

Activation of Sp1-mediated transcription by Rta of Epstein–Barr virus via an interaction with MCAF1
Nucl. Acids Res. 2005 33: 6528-6539; doi:10.1093/nar/gki956 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

S. A. Keatch, P. G. Leonard, J. E. Ladbury, and D. T. F. Dryden

StpA protein from Escherichia coli condenses supercoiled DNA in preference to linear DNA and protects it from digestion by DNase I and EcoKI
Nucl. Acids Res. 2005 33: 6540-6546; doi:10.1093/nar/gki951 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jeremy E. Wilusz, Sean C. Devanney, and Massimo Caputi

Chimeric peptide nucleic acid compounds modulate splicing of the bcl-x gene in vitro and in vivo
Nucl. Acids Res. 2005 33: 6547-6554; doi:10.1093/nar/gki960 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chunyu Han, Hao Liu, Jin Liu, Kang Yin, Yi Xie, Xiao Shen, Yong Wang, Jiangang Yuan, Boqing Qiang, Yong-Jian Liu, and Xiaozhong Peng

Human Bex2 interacts with LMO2 and regulates the transcriptional activity of a novel DNA-binding complex
Nucl. Acids Res. 2005 33: 6555-6565; doi:10.1093/nar/gki964 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Cindy Vandewalle, Joke Comijn, Bram De Craene, Petra Vermassen, Erik Bruyneel, Henriette Andersen, Eugene Tulchinsky, Frans Van Roy, and Geert Berx

SIP1/ZEB2 induces EMT by repressing genes of different epithelial cell–cell junctions
Nucl. Acids Res. 2005 33: 6566-6578; doi:10.1093/nar/gki965 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hsien-Tsung Lai, Hsiang Chen, Cheng Li, Kathleen J. McNamara-Schroeder, and William E. Stumph

The PSEA promoter element of the Drosophila U1 snRNA gene is sufficient to bring DmSNAPc into contact with 20 base pairs of downstream DNA
Nucl. Acids Res. 2005 33: 6579-6586; doi:10.1093/nar/gki972 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tomokazu Konishi

A thermodynamic model of transcriptome formation
Nucl. Acids Res. 2005 33: 6587-6592; doi:10.1093/nar/gki967 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Teca Calcagno Galvão and Jean O. Thomas

Structure-specific binding of MeCP2 to four-way junction DNA through its methyl CpG-binding domain
Nucl. Acids Res. 2005 33: 6603-6609; doi:10.1093/nar/gki971 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Catherine Cifuentes-Rojas, Kari Halbig, Anastasia Sacharidou, Monica De Nova-Ocampo, and Jorge Cruz-Reyes

Minimal pre-mRNA substrates with natural and converted sites for full-round U insertion and U deletion RNA editing in trypanosomes
Nucl. Acids Res. 2005 33: 6610-6620; doi:10.1093/nar/gki943 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Levent Sari and Ioan Andricioaei

Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation
Nucl. Acids Res. 2005 33: 6621-6634; doi:10.1093/nar/gki935 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

G. Mercier, N. Berthault, N. Touleimat, F. Képès, G. Fourel, E. Gilson, and M. Dutreix

A haploid-specific transcriptional response to irradiation in Saccharomyces cerevisiae
Nucl. Acids Res. 2005 33: 6635-6643; doi:10.1093/nar/gki959 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ken Dornfeld and Monika Johnson

AP endonuclease deficiency results in extreme sensitivity to thymidine deprivation
Nucl. Acids Res. 2005 33: 6644-6653; doi:10.1093/nar/gki975 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Aleksey N. Krasnov, Maria M. Kurshakova, Vasily E. Ramensky, Pavel V. Mardanov, Elena N. Nabirochkina, and Sofia G. Georgieva

A retrocopy of a gene can functionally displace the source gene in evolution
Nucl. Acids Res. 2005 33: 6654-6661; doi:10.1093/nar/gki969 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jennifer A. Roberts and Malcolm F. White

DNA end-directed and processive nuclease activities of the archaeal XPF enzyme
Nucl. Acids Res. 2005 33: 6662-6670; doi:10.1093/nar/gki974 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Erratum:

Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids
Nucl. Acids Res. 2005 33: 6671; doi:10.1093/nar/gki955 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Hiroshi Sakamoto, Sabine Thiberge, Susan Akerman, Chris J. Janse, Teresa Gil Carvalho, and Robert Ménard

Towards systematic identification of Plasmodium essential genes by transposon shuttle mutagenesis
Nucl. Acids Res. 2005 33: e174; doi:10.1093/nar/gni173 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Manhong Dai, Pinglang Wang, Andrew D. Boyd, Georgi Kostov, Brian Athey, Edward G. Jones, William E. Bunney, Richard M. Myers, Terry P. Speed, Huda Akil, Stanley J. Watson, and Fan Meng

Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data
Nucl. Acids Res. 2005 33: e175; doi:10.1093/nar/gni179 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mehrnaz Fatemi, Martha M. Pao, Shinwu Jeong, Einav Nili Gal-Yam, Gerda Egger, Daniel J. Weisenberger, and Peter A. Jones

Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level
Nucl. Acids Res. 2005 33: e176; doi:10.1093/nar/gni180 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Suhyung Cho, Ji-Eun Kim, Bo-Rahm Lee, June-Hyung Kim, and Byung-Gee Kim

Bis-aptazyme sensors for hepatitis C virus replicase and helicase without blank signal
Nucl. Acids Res. 2005 33: e177; doi:10.1093/nar/gni174 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Patrick Chames, Jean-Charles Epinat, Sophie Guillier, Amélie Patin, Emmanuel Lacroix, and Frédéric Pâques

In vivo selection of engineered homing endonucleases using double-strand break induced homologous recombination
Nucl. Acids Res. 2005 33: e178; doi:10.1093/nar/gni175 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Caifu Chen, Dana A. Ridzon, Adam J. Broomer, Zhaohui Zhou, Danny H. Lee, Julie T. Nguyen, Maura Barbisin, Nan Lan Xu, Vikram R. Mahuvakar, Mark R. Andersen, Kai Qin Lao, Kenneth J. Livak, and Karl J. Guegler

Real-time quantification of microRNAs by stem–loop RT–PCR
Nucl. Acids Res. 2005 33: e179; doi:10.1093/nar/gni178 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Keith K. Stanley and Elektra Szewczuk

Multiplexed tandem PCR: gene profiling from small amounts of RNA using SYBR Green detection
Nucl. Acids Res. 2005 33: e180; doi:10.1093/nar/gni182 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Oleg Suslov and Dennis A. Steindler

PCR inhibition by reverse transcriptase leads to an overestimation of amplification efficiency
Nucl. Acids Res. 2005 33: e181; doi:10.1093/nar/gni176 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

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