| | Articles NMR studies of the structure and Mg2+ binding properties of a conserved RNA motif of EMCV picornavirus IRES element Marie Phelan, Ryan J. Banks, Graeme Conn, and Vasudevan Ramesh PMCID: PMC519103 Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes Berend Snel, Vera van Noort, and Martijn A. Huynen PMCID: PMC519111 Identifying DNA-binding proteins using structural motifs and the electrostatic potential Hugh P. Shanahan, Mario A. Garcia, Susan Jones, and Janet M. Thornton PMCID: PMC519102 Functional interaction between peroxisome proliferator-activated receptors-α and Mef-2C on human carnitine palmitoyltransferase 1β (CPT1β) gene activation Ángel Baldán, Joana Relat, Pedro F. Marrero, and Diego Haro PMCID: PMC519104 The glioma-amplified sequence 41 gene (GAS41) is a direct Myb target gene Daniel Braas, Holger Gundelach, and Karl-Heinz Klempnauer PMCID: PMC519106 Polyadenylation-dependent screening assay for respiratory syncytial virus RNA transcriptase activity and identification of an inhibitor Stephen W. Mason, Carol Lawetz, Yvon Gaudette, Florence Dô, Erika Scouten, Lisette Lagacé, Bruno Simoneau, and Michel Liuzzi PMCID: PMC519107 Both KH and non-KH domain sequences are required for polyribosome association of Scp160p in yeast Ai-min Li, Claudia A. Vargas, Melissa A. Brykailo, Kimberly K. Openo, Anita H. Corbett, and Judith L. Fridovich-Keil PMCID: PMC519109 Structural requirements for pre-microRNA binding and nuclear export by Exportin 5 Yan Zeng and Bryan R. Cullen PMCID: PMC519115 Portrait of transcriptional responses to ultraviolet and ionizing radiation in human cells Kerri E. Rieger and Gilbert Chu PMCID: PMC519099 The interactome as a tree—an attempt to visualize the protein–protein interaction network in yeast 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 PMCID: PMC519110 Over 20% of human transcripts might form sense–antisense pairs Jianjun Chen, Miao Sun, W. James Kent, Xiaoqiu Huang, Hanqing Xie, Wenquan Wang, Guolin Zhou, Run Zhang Shi, and Janet D. Rowley PMCID: PMC519112 Biochemical characterization of Cdc6/Orc1 binding to the replication origin of the euryarchaeon Methanothermobacter thermoautotrophicus Stephanie A. Capaldi and James M. Berger PMCID: PMC519113 SLBP is associated with histone mRNA on polyribosomes as a component of the histone mRNP Michael L. Whitfield, Handan Kaygun, Judith A. Erkmann, W. H. Davin Townley-Tilson, Zbigniew Dominski, and William F. Marzluff PMCID: PMC519100 Abstract shapes of RNA Robert Giegerich, Björn Voß, and Marc Rehmsmeier PMCID: PMC519098 Determination and augmentation of RNA sequence specificity of the Nova K-homology domains Kiran Musunuru and Robert B. Darnell PMCID: PMC519101 SMAR1 and Cux/CDP modulate chromatin and act as negative regulators of the TCRβ enhancer (Eβ) Ruchika Kaul-Ghanekar, Archana Jalota, L. Pavithra, Philip Tucker, and Samit Chattopadhyay PMCID: PMC519105 DNA base pair resolution by single molecule force spectroscopy Bernie D. Sattin, Andrew E. Pelling, and M. Cynthia Goh PMCID: PMC519116 Predicting genes expressed via −1 and +1 frameshifts Sanghoon Moon, Yanga Byun, Hong-Jin Kim, Sunjoo Jeong, and Kyungsook Han PMCID: PMC519117 Down-regulation of MDM2 and activation of p53 in human cancer cells by antisense 9-aminoacridine–PNA (peptide nucleic acid) conjugates Takehiko Shiraishi and Peter E. Nielsen PMCID: PMC519114 An insulator blocks spreading of histone acetylation and interferes with RNA polymerase II transfer between an enhancer and gene Hui Zhao and Ann Dean PMCID: PMC519119 Conserved tertiary base pairing ensures proper RNA folding and efficient assembly of the signal recognition particle Alu domain Laurent Huck, Anne Scherrer, Lionel Terzi, Arthur E. Johnson, Harris D. Bernstein, Stephen Cusack, Oliver Weichenrieder, and Katharina Strub PMCID: PMC519120 A comparative method for finding and folding RNA secondary structures within protein-coding regions Jakob Skou Pedersen, Irmtraud Margret Meyer, Roald Forsberg, Peter Simmonds, and Jotun Hein PMCID: PMC519121 Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism Kenji Ueda, Atsushi Yamashita, Jun Ishikawa, Masafumi Shimada, Tomo-o Watsuji, Kohji Morimura, Haruo Ikeda, Masahira Hattori, and Teruhiko Beppu PMCID: PMC519118 Identification and cloning of two putative subunits of DNA polymerase epsilon in fission yeast Maria-Grazia Spiga and Gennaro D'Urso PMCID: PMC519108 NAR Methods Online A novel real-time PCR assay for quantitative analysis of methylated alleles (QAMA): analysis of the retinoblastoma locus Michael Zeschnigk, Stefan Böhringer, Elizabeth Ann Price, Zerrin Onadim, Lars Maßhöfer, and Dietmar R. Lohmann PMCID: PMC519124 Multiplex mRNA assay using electrophoretic tags for high-throughput gene expression analysis 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 PMCID: PMC519123 Whole-genome expression profiling through fragment display and combinatorial gene identification Ats Metsis, Ulf Andersson, Göran Baurén, Patrik Ernfors, Peter Lönnerberg, Andreas Montelius, Mats Oldin, Arno Pihlak, and Sten Linnarsson PMCID: PMC519127 Rapid tagging of endogenous mouse genes by recombineering and ES cell complementation of tetraploid blastocysts Dewang Zhou, Jin-Xiang Ren, Thomas M. Ryan, N. Patrick Higgins, and Tim M. Townes PMCID: PMC519128 Effective and robust plasmid topology analysis and the subsequent characterization of the plasmid isoforms thereby observed Michael J. Molloy, Valerie S. Hall, Susannah I. Bailey, Katharine J. Griffin, Jim Faulkner, and Mark Uden PMCID: PMC519125 Improving specificity of DNA hybridization-based methods Tatyana Chalaya, Elena Gogvadze, Anton Buzdin, Elena Kovalskaya, and Eugene D. Sverdlov PMCID: PMC519126 aRNA-longSAGE: a new approach to generate SAGE libraries from microdissected cells 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 PMCID: PMC519129 A novel strategy for the identification of protein–DNA contacts by photocrosslinking and mass spectrometry Hildegard Geyer, Rudolf Geyer, and Vera Pingoud PMCID: PMC519130 Corrigendum Nucleic Acids Res. 2004; 32(16): 4954. Published online 2004 September 23. doi: 10.1093/nar/gkh840.PMCID: PMC519122 Corrects: Christopher J. Nulf, et al. Intracellular inhibition of hepatitis C virus (HCV) internal ribosomal entry site (IRES)-dependent translation by peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). Nucleic Acids Res. 2004; 32(13): 3792–3798. |
