| | Articles Nearest neighbor parameters for Watson–Crick complementary heteroduplexes formed between 2′-O-methyl RNA and RNA oligonucleotides Elzbieta Kierzek, David H. Mathews, Anna Ciesielska, Douglas H. Turner, and Ryszard Kierzek PMCID: PMC1540717 Ancient origin, functional conservation and fast evolution of DNA-dependent RNA polymerase III Galina M. Proshkina, Elena K. Shematorova, Sergey A. Proshkin, Cécile Zaros, Pierre Thuriaux, and George V. Shpakovski PMCID: PMC1540719 Genomic scale sub-family assignment of protein domains Julian Gough PMCID: PMC1540727 NMR structure of the three quasi RNA recognition motifs (qRRMs) of human hnRNP F and interaction studies with Bcl-x G-tract RNA: a novel mode of RNA recognition Cyril Dominguez and Frédéric H.-T. Allain PMCID: PMC1540728 Protein structure database search and evolutionary classification Jinn-Moon Yang and Chi-Hua Tung PMCID: PMC1540718 Formation of isodialuric acid lesion within DNA oligomers via one-electron oxidation of 5-hydroxyuracil: characterization, stability and excision repair Philippe Simon, Didier Gasparutto, Serge Gambarelli, Christine Saint-Pierre, Alain Favier, and Jean Cadet PMCID: PMC1540730 Carbon nanotubes selective destabilization of duplex and triplex DNA and inducing B–A transition in solution Xi Li, Yinghua Peng, and Xiaogang Qu PMCID: PMC1540735 Genome-wide screening for cis-regulatory variation using a classical diallel crossing scheme Raphaël Kiekens, Annelies Vercauteren, Beatrijs Moerkerke, Els Goetghebeur, Hilde Van Den Daele, Roel Sterken, Martin Kuiper, Fred van Eeuwijk, and Marnik Vuylsteke PMCID: PMC1540733 The outcomes of pathway database computations depend on pathway ontology M. L. Green and P. D. Karp PMCID: PMC1540720 Protein binding site prediction using an empirical scoring function Shide Liang, Chi Zhang, Song Liu, and Yaoqi Zhou PMCID: PMC1540721 Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III Alexandre V. Pertzev and Allen W. Nicholson PMCID: PMC1540722 The roles of specific glycosylases in determining the mutagenic consequences of clustered DNA base damage Naoya Shikazono, Colin Pearson, Peter O'Neill, and John Thacker PMCID: PMC1557791 Role of ATP hydrolysis in the DNA translocase activity of the bovine papillomavirus (BPV-1) E1 helicase Sandrine Castella, David Burgin, and Cyril M. Sanders PMCID: PMC1557793 Sequence elements critical for efficient RNA editing of a tobacco chloroplast transcript in vivo and in vitro Michael L. Hayes, Martha L. Reed, Carla E. Hegeman, and Maureen R. Hanson PMCID: PMC1557790 An RNA aptamer that interferes with the DNA binding of the HSF transcription activator Xiaoching Zhao, Hua Shi, Aarti Sevilimedu, Nicole Liachko, Hillary C. M. Nelson, and John T. Lis PMCID: PMC1557789 Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI Michael Carpenter, Pradeep Divvela, Vera Pingoud, Janusz Bujnicki, and Ashok S. Bhagwat PMCID: PMC1557792 The Pathway Tools cellular overview diagram and Omics Viewer Suzanne M. Paley and Peter D. Karp PMCID: PMC1557788 Computational detection of allergenic proteins attains a new level of accuracy with in silico variable-length peptide extraction and machine learning D. Soeria-Atmadja, T. Lundell, M. G. Gustafsson, and U. Hammerling PMCID: PMC1540723 Activation of the chicken Ig-β locus by the collaboration of scattered regulatory regions through changes in chromatin structure Naoko Shimada, Hiroki Matsudo, Kyoichi Osano, Hiroshi Arakawa, Jean-Marie Buerstedde, Yasuyuki Matsumoto, Kozue Chayahara, Atsushi Torihata, and Masao Ono PMCID: PMC1540724 Specific and nontoxic silencing in mammalian cells with expressed long dsRNAs Aurel Strat, Lu Gao, Tada Utsuki, Bing Cheng, Sam Nuthalapaty, J. Mike Mathis, Yoshinobu Odaka, and Tony Giordano PMCID: PMC1540741 Identification by Mn2+ rescue of two residues essential for the proton transfer of tRNase Z catalysis Asako Minagawa, Hiroaki Takaku, Ryohei Ishii, Masamichi Takagi, Shigeyuki Yokoyama, and Masayuki Nashimoto PMCID: PMC1540738 Transcriptional regulation of human MAP2 gene in melanoma: role of neuronal bHLH factors and Notch1 signaling Kumar M. R. Bhat, Nityanand Maddodi, Cooduvalli Shashikant, and Vijayasaradhi Setaluri PMCID: PMC1540725 Methods Online Identification of single-point mutations in mycobacterial 16S rRNA sequences by confocal single-molecule fluorescence spectroscopy Nicole Marmé, Achim Friedrich, Matthias Müller, Oliver Nolte, Jürgen Wolfrum, Jörg D. Hoheisel, Markus Sauer, and Jens-Peter Knemeyer PMCID: PMC1540729 De novo assembly of genuine replication forks on an immobilized circular plasmid in Xenopus egg extracts Akiko Zembutsu and Shou Waga PMCID: PMC1540734 RMCE-ASAP: a gene targeting method for ES and somatic cells to accelerate phenotype analyses Franck Toledo, Chung-Wen Liu, Crystal J. Lee, and Geoffrey M. Wahl PMCID: PMC1540739 Real-time detection and continuous monitoring of ER stress in vitro and in vivo by ES-TRAP: evidence for systemic, transient ER stress during endotoxemia Nobuhiko Hiramatsu, Ayumi Kasai, Kunihiro Hayakawa, Jian Yao, and Masanori Kitamura PMCID: PMC1540736 A matrix of 3,4-diaminobenzophenone for the analysis of oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Yu Fu, Songyun Xu, Chensong Pan, Mingliang Ye, Hanfa Zou, and Baochuan Guo PMCID: PMC1540732 Production of transmitochondrial cybrids containing naturally occurring pathogenic mtDNA variants Deborah Pye, Dimitra S. Kyriakouli, Geoffrey A. Taylor, Riem Johnson, Matthias Elstner, Brigitte Meunier, Zofia M. A. Chrzanowska-Lightowlers, Robert W. Taylor, Douglass M. Turnbull, and Robert N. Lightowlers PMCID: PMC1540737 Engineering a high-affinity methyl-CpG-binding protein Helle F. Jørgensen, Karen Adie, Pascal Chaubert, and Adrian P. Bird PMCID: PMC1540740 A RecA-mediated exon profiling method Yuki Hasegawa, Shiro Fukuda, Kazuro Shimokawa, Shinji Kondo, Norihiro Maeda, and Yoshihide Hayashizaki PMCID: PMC1540731 Simultaneous amplification and screening of whole plasmids using the T7 bacteriophage replisome Yan Xu, Hyun-jin Kim, Ann Kays, Jared Rice, and Huimin Kong PMCID: PMC1540742 High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling Bradley J. Till, Troy Zerr, Elisabeth Bowers, Elizabeth A. Greene, Luca Comai, and Steven Henikoff PMCID: PMC1540726 |
