Nucleic Acids Research

Articles:

Marie Phelan, Ryan J. Banks, Graeme Conn, and Vasudevan Ramesh

NMR studies of the structure and Mg²⁺ binding properties of a conserved RNA motif of EMCV picornavirus IRES element
Nucl. Acids Res. 2004 32: 4715-4724; doi:10.1093/nar/gkh805 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Berend Snel, Vera van Noort, and Martijn A. Huynen

Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes
Nucl. Acids Res. 2004 32: 4725-4731; doi:10.1093/nar/gkh815 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Hugh P. Shanahan, Mario A. Garcia, Susan Jones, and Janet M. Thornton

Identifying DNA-binding proteins using structural motifs and the electrostatic potential
Nucl. Acids Res. 2004 32: 4732-4741; doi:10.1093/nar/gkh803 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ángel Baldán, Joana Relat, Pedro F. Marrero, and Diego Haro

Functional interaction between peroxisome proliferator-activated receptors- and Mef-2C on human carnitine palmitoyltransferase 1ß (CPT1ß) gene activation
Nucl. Acids Res. 2004 32: 4742-4749; doi:10.1093/nar/gkh806 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Daniel Braas, Holger Gundelach, and Karl-Heinz Klempnauer

The glioma-amplified sequence 41 gene (GAS41) is a direct Myb target gene
Nucl. Acids Res. 2004 32: 4750-4757; doi:10.1093/nar/gkh808 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Stephen W. Mason, Carol Lawetz, Yvon Gaudette, Florence Dô, Erika Scouten, Lisette Lagacé, Bruno Simoneau, and Michel Liuzzi

Polyadenylation-dependent screening assay for respiratory syncytial virus RNA transcriptase activity and identification of an inhibitor
Nucl. Acids Res. 2004 32: 4758-4767; doi:10.1093/nar/gkh809 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ai-min Li, Claudia A. Vargas, Melissa A. Brykailo, Kimberly K. Openo, Anita H. Corbett, and Judith L. Fridovich-Keil

Both KH and non-KH domain sequences are required for polyribosome association of Scp160p in yeast
Nucl. Acids Res. 2004 32: 4768-4775; doi:10.1093/nar/gkh812 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yan Zeng and Bryan R. Cullen

Structural requirements for pre-microRNA binding and nuclear export by Exportin 5
Nucl. Acids Res. 2004 32: 4776-4785; doi:10.1093/nar/gkh824 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kerri E. Rieger and Gilbert Chu

Portrait of transcriptional responses to ultraviolet and ionizing radiation in human cells
Nucl. Acids Res. 2004 32: 4786-4803; doi:10.1093/nar/gkh783 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Hongchao Lu, Xiaopeng Zhu, Haifeng Liu, Geir Skogerbø, Jingfen Zhang, Yong Zhang, Lun Cai, Yi Zhao, Shiwei Sun, Jingyi Xu, Dongbo Bu, and Runsheng Chen

The interactome as a tree—an attempt to visualize the protein–protein interaction network in yeast
Nucl. Acids Res. 2004 32: 4804-4811; doi:10.1093/nar/gkh814 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Jianjun Chen, Miao Sun, W. James Kent, Xiaoqiu Huang, Hanqing Xie, Wenquan Wang, Guolin Zhou, Run Zhang Shi, and Janet D. Rowley

Over 20% of human transcripts might form sense–antisense pairs
Nucl. Acids Res. 2004 32: 4812-4820; doi:10.1093/nar/gkh818 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Stephanie A. Capaldi and James M. Berger

Biochemical characterization of Cdc6/Orc1 binding to the replication origin of the euryarchaeon Methanothermobacter thermoautotrophicus
Nucl. Acids Res. 2004 32: 4821-4832; doi:10.1093/nar/gkh819 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Michael L. Whitfield, Handan Kaygun, Judith A. Erkmann, W. H. Davin Townley-Tilson, Zbigniew Dominski, and William F. Marzluff

SLBP is associated with histone mRNA on polyribosomes as a component of the histone mRNP
Nucl. Acids Res. 2004 32: 4833-4842; doi:10.1093/nar/gkh798 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Robert Giegerich, Björn Voß, and Marc Rehmsmeier

Abstract shapes of RNA
Nucl. Acids Res. 2004 32: 4843-4851; doi:10.1093/nar/gkh779 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kiran Musunuru and Robert B. Darnell

Determination and augmentation of RNA sequence specificity of the Nova K-homology domains
Nucl. Acids Res. 2004 32: 4852-4861; doi:10.1093/nar/gkh799 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ruchika Kaul-Ghanekar, Archana Jalota, L. Pavithra, Philip Tucker, and Samit Chattopadhyay

SMAR1 and Cux/CDP modulate chromatin and act as negative regulators of the TCRß enhancer (Eß)
Nucl. Acids Res. 2004 32: 4862-4875; doi:10.1093/nar/gkh807 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Bernie D. Sattin, Andrew E. Pelling, and M. Cynthia Goh

DNA base pair resolution by single molecule force spectroscopy
Nucl. Acids Res. 2004 32: 4876-4883; doi:10.1093/nar/gkh826 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Sanghoon Moon, Yanga Byun, Hong-Jin Kim, Sunjoo Jeong, and Kyungsook Han

Predicting genes expressed via –1 and +1 frameshifts
Nucl. Acids Res. 2004 32: 4884-4892; doi:10.1093/nar/gkh829 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Takehiko Shiraishi and Peter E. Nielsen

Down-regulation of MDM2 and activation of p53 in human cancer cells by antisense 9-aminoacridine–PNA (peptide nucleic acid) conjugates
Nucl. Acids Res. 2004 32: 4893-4902; doi:10.1093/nar/gkh820 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hui Zhao and Ann Dean

An insulator blocks spreading of histone acetylation and interferes with RNA polymerase II transfer between an enhancer and gene
Nucl. Acids Res. 2004 32: 4903-4919; doi:10.1093/nar/gkh832 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Laurent Huck, Anne Scherrer, Lionel Terzi, Arthur E. Johnson, Harris D. Bernstein, Stephen Cusack, Oliver Weichenrieder, and Katharina Strub

Conserved tertiary base pairing ensures proper RNA folding and efficient assembly of the signal recognition particle Alu domain
Nucl. Acids Res. 2004 32: 4915-4924; doi:10.1093/nar/gkh837 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jakob Skou Pedersen, Irmtraud Margret Meyer, Roald Forsberg, Peter Simmonds, and Jotun Hein

A comparative method for finding and folding RNA secondary structures within protein-coding regions
Nucl. Acids Res. 2004 32: 4925-4936; doi:10.1093/nar/gkh839 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Kenji Ueda, Atsushi Yamashita, Jun Ishikawa, Masafumi Shimada, Tomo-o Watsuji, Kohji Morimura, Haruo Ikeda, Masahira Hattori, and Teruhiko Beppu

Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism
Nucl. Acids Res. 2004 32: 4937-4944; doi:10.1093/nar/gkh830 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Maria-Grazia Spiga and Gennaro D'Urso

Identification and cloning of two putative subunits of DNA polymerase epsilon in fission yeast
Nucl. Acids Res. 2004 32: 4945-4953; doi:10.1093/nar/gkh811 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Corrigenda:

Christopher J. Nulf and David Corey

Intracellular inhibition of hepatitis C virus (HCV) internal ribosomal entry site (IRES)-dependent translation by peptide nucleic acids (PNAs) and locked nucleic acids (LNAs)
Nucl. Acids Res. 2004 32: 4954; doi:10.1093/nar/gkh840 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Methods Online:

Michael Zeschnigk, Stefan Böhringer, Elizabeth Ann Price, Zerrin Onadim, Lars Maßhöfer, and Dietmar R. Lohmann

A novel real-time PCR assay for quantitative analysis of methylated alleles (QAMA): analysis of the retinoblastoma locus
Nucl. Acids Res. 2004 32: e125; doi:10.1093/nar/gnh122 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Huan Tian, Liching Cao, Yuping Tan, Stephen Williams, Lili Chen, Tracy Matray, Ahmed Chenna, Sean Moore, Vincent Hernandez, Vivian Xiao, Mengxiang Tang, and Sharat Singh

Multiplex mRNA assay using electrophoretic tags for high-throughput gene expression analysis
Nucl. Acids Res. 2004 32: e126; doi:10.1093/nar/gnh119 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Ats Metsis, Ulf Andersson, Göran Baurén, Patrik Ernfors, Peter Lönnerberg, Andreas Montelius, Mats Oldin, Arno Pihlak, and Sten Linnarsson

Whole-genome expression profiling through fragment display and combinatorial gene identification
Nucl. Acids Res. 2004 32: e127; doi:10.1093/nar/gnh126 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Dewang Zhou, Jin-Xiang Ren, Thomas M. Ryan, N. Patrick Higgins, and Tim M. Townes

Rapid tagging of endogenous mouse genes by recombineering and ES cell complementation of tetraploid blastocysts
Nucl. Acids Res. 2004 32: e128; doi:10.1093/nar/gnh128 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Michael J. Molloy, Valerie S. Hall, Susannah I. Bailey, Katharine J. Griffin, Jim Faulkner, and Mark Uden

Effective and robust plasmid topology analysis and the subsequent characterization of the plasmid isoforms thereby observed
Nucl. Acids Res. 2004 32: e129; doi:10.1093/nar/gnh124 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tatyana Chalaya, Elena Gogvadze, Anton Buzdin, Elena Kovalskaya, and Eugene D. Sverdlov

Improving specificity of DNA hybridization-based methods
Nucl. Acids Res. 2004 32: e130; doi:10.1093/nar/gnh125 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Anna M. Heidenblut, Jutta Lüttges, Malte Buchholz, Christian Heinitz, Jeppe Emmersen, Kåre Lehmann Nielsen, Pat Schreiter, Manfred Souquet, Sandra Nowacki, Ulrike Herbrand, Günter Klöppel, Wolff Schmiegel, Thomas Gress, and Stephan A. Hahn

aRNA-longSAGE: a new approach to generate SAGE libraries from microdissected cells
Nucl. Acids Res. 2004 32: e131; doi:10.1093/nar/gnh130 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Hildegard Geyer, Rudolf Geyer, and Vera Pingoud

A novel strategy for the identification of protein–DNA contacts by photocrosslinking and mass spectrometry
Nucl. Acids Res. 2004 32: e132; doi:10.1093/nar/gnh131 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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