Nucleic Acids Research

Articles:

Jin Han and Thomas A. Cooper

Identification of CELF splicing activation and repression domains in vivo
Nucl. Acids Res. 2005 33: 2769-2780; doi:10.1093/nar/gki561 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Anthony G. Russell, Yoh-ichi Watanabe, J. Michael Charette, and Michael W. Gray

Unusual features of fibrillarin cDNA and gene structure in Euglena gracilis: evolutionary conservation of core proteins and structural predictions for methylation-guide box C/D snoRNPs throughout the domain Eucarya
Nucl. Acids Res. 2005 33: 2781-2791; doi:10.1093/nar/gki574 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Maria A. Xaplanteri, Alexandros D. Petropoulos, George P. Dinos, and Dimitrios L. Kalpaxis

Localization of spermine binding sites in 23S rRNA by photoaffinity labeling: parsing the spermine contribution to ribosomal 50S subunit functions
Nucl. Acids Res. 2005 33: 2792-2805; doi:10.1093/nar/gki557 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Troy Zerr and Steven Henikoff

Automated band mapping in electrophoretic gel images using background information
Nucl. Acids Res. 2005 33: 2806-2812; doi:10.1093/nar/gki580 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Z. Li, J. Stanelle, C. Leurs, H. Hanenberg, and B. M. Pützer

Selection of novel mediators of E2F1-induced apoptosis through retroviral expression of an antisense cDNA library
Nucl. Acids Res. 2005 33: 2813-2821; doi:10.1093/nar/gki581 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hongwei Wu, Zhengchang Su, Fenglou Mao, Victor Olman, and Ying Xu

Prediction of functional modules based on comparative genome analysis and Gene Ontology application
Nucl. Acids Res. 2005 33: 2822-2837; doi:10.1093/nar/gki573 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zhihong Zhang and Fred S. Dietrich

Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE
Nucl. Acids Res. 2005 33: 2838-2851; doi:10.1093/nar/gki583 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Filomena De Lucia, Jian-Quan Ni, Catherine Vaillant, and Fang-Lin Sun

HP1 modulates the transcription of cell-cycle regulators in Drosophila melanogaster
Nucl. Acids Res. 2005 33: 2852-2858; doi:10.1093/nar/gki584 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

M. L. Rinne, Y. He, B. F. Pachkowski, J. Nakamura, and M. R. Kelley

N-methylpurine DNA glycosylase overexpression increases alkylation sensitivity by rapidly removing non-toxic 7-methylguanine adducts
Nucl. Acids Res. 2005 33: 2859-2867; doi:10.1093/nar/gki601 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Julian Walfridsson, Pernilla Bjerling, Maria Thalen, Eung-Jae Yoo, Sang Dai Park, and Karl Ekwall

The CHD remodeling factor Hrp1 stimulates CENP-A loading to centromeres
Nucl. Acids Res. 2005 33: 2868-2879; doi:10.1093/nar/gki579 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jen Bohon and Carlos R. de los Santos

Effect of 6-thioguanine on the stability of duplex DNA
Nucl. Acids Res. 2005 33: 2880-2886; doi:10.1093/nar/gki572 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Anat Yafe, Shulamit Etzioni, Pnina Weisman-Shomer, and Michael Fry

Formation and properties of hairpin and tetraplex structures of guanine-rich regulatory sequences of muscle-specific genes
Nucl. Acids Res. 2005 33: 2887-2900; doi:10.1093/nar/gki606 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alan K. Todd, Matthew Johnston, and Stephen Neidle

Highly prevalent putative quadruplex sequence motifs in human DNA
Nucl. Acids Res. 2005 33: 2901-2907; doi:10.1093/nar/gki553 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Julian L. Huppert and Shankar Balasubramanian

Prevalence of quadruplexes in the human genome
Nucl. Acids Res. 2005 33: 2908-2916; doi:10.1093/nar/gki609 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Michael J. Law, Eric J. Chambers, Phinikoula S. Katsamba, Ian S. Haworth, and Ite A. Laird-Offringa

Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction
Nucl. Acids Res. 2005 33: 2917-2928; doi:10.1093/nar/gki602 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tara Dobson, Angela Minic, Kirsten Nielsen, Elizabeth Amiott, and Les Krushel

Internal initiation of translation of the TrkB mRNA is mediated by multiple regions within the 5' leader
Nucl. Acids Res. 2005 33: 2929-2941; doi:10.1093/nar/gki605 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yuka Kato, Noriaki Minakawa, Yasuo Komatsu, Hiroyuki Kamiya, Naoki Ogawa, Hideyoshi Harashima, and Akira Matsuda

New NTP analogs: the synthesis of 4'-thioUTP and 4'-thioCTP and their utility for SELEX
Nucl. Acids Res. 2005 33: 2942-2951; doi:10.1093/nar/gki578 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Lawrence E. Heisler, Dax Torti, Paul C. Boutros, John Watson, Charles Chan, Neil Winegarden, Mark Takahashi, Patrick Yau, Tim H.-M. Huang, Peggy J. Farnham, Igor Jurisica, James R. Woodgett, Rod Bremner, Linda Z. Penn, and Sandy D. Der

CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome
Nucl. Acids Res. 2005 33: 2952-2961; doi:10.1093/nar/gki582 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zheng Meng, Peter H. King, L. Burt Nabors, Nateka L. Jackson, Ching-Yi Chen, Peter D. Emanuel, and Scott W. Blume

The ELAV RNA-stability factor HuR binds the 5'-untranslated region of the human IGF-IR transcript and differentially represses cap-dependent and IRES-mediated translation
Nucl. Acids Res. 2005 33: 2962-2979; doi:10.1093/nar/gki603 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Asis Khan, Sonya Taylor, Chunlei Su, Aaron J. Mackey, Jon Boyle, Robert Cole, Darius Glover, Keliang Tang, Ian T. Paulsen, Matt Berriman, John C. Boothroyd, Elmer R. Pfefferkorn, J. P. Dubey, James W. Ajioka, David S. Roos, John C. Wootton, and L. David Sibley

Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii
Nucl. Acids Res. 2005 33: 2980-2992; doi:10.1093/nar/gki604 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Brian S. Thoma, Mitsuo Wakasugi, Jesper Christensen, Madhava C. Reddy, and Karen M. Vasquez

Human XPC-hHR23B interacts with XPA-RPA in the recognition of triplex-directed psoralen DNA interstrand crosslinks
Nucl. Acids Res. 2005 33: 2993-3001; doi:10.1093/nar/gki610 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Catherine L. Bladen, Wai K. Lam, William S. Dynan, and David J. Kozlowski

DNA damage response and Ku80 function in the vertebrate embryo
Nucl. Acids Res. 2005 33: 3002-3010; doi:10.1093/nar/gki613 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sebastian Jayaraj, Ralph Reid, and Daniel V. Santi

GeMS: an advanced software package for designing synthetic genes
Nucl. Acids Res. 2005 33: 3011-3016; doi:10.1093/nar/gki614 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Shigeki Arai, Toshiyuki Chatake, Takashi Ohhara, Kazuo Kurihara, Ichiro Tanaka, Nobuhiro Suzuki, Zui Fujimoto, Hiroshi Mizuno, and Nobuo Niimura

Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)₂ observed by neutron diffraction measurements
Nucl. Acids Res. 2005 33: 3017-3024; doi:10.1093/nar/gki616 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

David A. Rusling, Vicki E. C. Powers, Rohan T. Ranasinghe, Yang Wang, Sadie D. Osborne, Tom Brown, and Keith R. Fox

Four base recognition by triplex-forming oligonucleotides at physiological pH
Nucl. Acids Res. 2005 33: 3025-3032; doi:10.1093/nar/gki625 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zhiying You and Hisao Masai

DNA binding and helicase actions of mouse MCM4/6/7 helicase
Nucl. Acids Res. 2005 33: 3033-3047; doi:10.1093/nar/gki607 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shawna L. Hiley, Tomas Babak, and Timothy R. Hughes

Global analysis of yeast RNA processing identifies new targets of RNase III and uncovers a link between tRNA 5' end processing and tRNA splicing
Nucl. Acids Res. 2005 33: 3048-3056; doi:10.1093/nar/gki608 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Victoria Valinluck, Pingfang Liu, Joseph I. Kang, Jr, Artur Burdzy, and Lawrence C. Sowers

5-Halogenated pyrimidine lesions within a CpG sequence context mimic 5-methylcytosine by enhancing the binding of the methyl-CpG-binding domain of methyl-CpG-binding protein 2 (MeCP2)
Nucl. Acids Res. 2005 33: 3057-3064; doi:10.1093/nar/gki612 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Silke Dorner, Walther Schmid, and Andrea Barta

Activity of 3'-thioAMP derivatives as ribosomal P-site substrates
Nucl. Acids Res. 2005 33: 3065-3071; doi:10.1093/nar/gki617 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yin C. Lin and Jay D. Gralla

Stimulation of the XPB ATP-dependent helicase by the beta subunit of TFIIE
Nucl. Acids Res. 2005 33: 3072-3081; doi:10.1093/nar/gki623 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

D. Dafydd Jones

Triplet nucleotide removal at random positions in a target gene: the tolerance of TEM-1 ß-lactamase to an amino acid deletion
Nucl. Acids Res. 2005 33: e80; doi:10.1093/nar/gni077 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Sonia Schoonbroodt, Nicolas Frans, Mark DeSouza, Rachel Eren, Smadar Priel, Naama Brosh, Judith Ben-Porath, Arie Zauberman, Ehud Ilan, Shlomo Dagan, Edward H. Cohen, Hennie R. Hoogenboom, Robert Charles Ladner, and René M. Hoet

Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library
Nucl. Acids Res. 2005 33: e81; doi:10.1093/nar/gni080 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

David A. Rozak and Philip N. Bryan

Offset recombinant PCR: a simple but effective method for shuffling compact heterologous domains
Nucl. Acids Res. 2005 33: e82; doi:10.1093/nar/gni081 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hui Xu, Haiping Wu, Fei Huang, Shiping Song, Wenxin Li, Yong Cao, and Chunhai Fan

Magnetically assisted DNA assays: high selectivity using conjugated polymers for amplified fluorescent transduction
Nucl. Acids Res. 2005 33: e83; doi:10.1093/nar/gni084 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Chunlei Wu, Roberto Carta, and Li Zhang

Sequence dependence of cross-hybridization on short oligo microarrays
Nucl. Acids Res. 2005 33: e84; doi:10.1093/nar/gni082 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Makoto Kakitani, Takeshi Oshima, Kaori Horikoshi, Tetsuo Yoshitome, Akiko Ueda, Miwa Kajikawa, Yumi Iba, Yoshinao Ozone, Yuki Ijima, Tohko Yoshino, Mikiko Itoh, Sachiko Seki, Ayako Aoki, Toshie Ishihara, Michiyo Shionoya, Utako Makino, Rina Kitada, Atsuko Ohguma, Takami Ohta, Yoshimasa Yoshida, Hiroe Kudoh, Kazunori Hanaoka, Kazunori Sibuya, Isao Ishida, Minoru Kakeda, Mikio Yagi, Takashi Yoneya, and Kazuma Tomizuka

A novel transgenic chimaeric mouse system for the rapid functional evaluation of genes encoding secreted proteins
Nucl. Acids Res. 2005 33: e85; doi:10.1093/nar/gni083 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Martin L. Read, Surjeet Singh, Zubair Ahmed, Mark Stevenson, Simon S. Briggs, David Oupicky, Lee B. Barrett, Rachel Spice, Mark Kendall, Martin Berry, Jon A. Preece, Ann Logan, and Leonard W. Seymour

A versatile reducible polycation-based system for efficient delivery of a broad range of nucleic acids
Nucl. Acids Res. 2005 33: e86; doi:10.1093/nar/gni085 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Antonio Rodríguez-García, Patricia Combes, Rosario Pérez-Redondo, Matthew C. A. Smith, and Margaret C. M. Smith

Natural and synthetic tetracycline-inducible promoters for use in the antibiotic-producing bacteria Streptomyces
Nucl. Acids Res. 2005 33: e87; doi:10.1093/nar/gni086 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Masakiyo Sakaguchi, Takamasa Nukui, Hiroyuki Sonegawa, Hitoshi Murata, Junichiro Futami, Hidenori Yamada, and Nam-ho Huh

Targeted disruption of transcriptional regulatory function of p53 by a novel efficient method for introducing a decoy oligonucleotide into nuclei
Nucl. Acids Res. 2005 33: e88; doi:10.1093/nar/gni088 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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