| | Articles Electron transfer in DNA duplexes containing 2-methyl-1,4-naphthoquinone François Bergeron, Daniel Houde, Darel J. Hunting, and J. Richard Wagner PMCID: PMC535664 Diversity-oriented solid-phase synthesis and biological evaluation of oligonucleotide hairpins as HIV-1 RT RNase H inhibitors Rami N. Hannoush, Kyung-Lyum Min, and Masad J. Damha PMCID: PMC535663 A novel nuclease-ATPase (Nar71) from archaea is part of a proposed thermophilic DNA repair system Colin P. Guy, Alan I. Majerník, James P. J. Chong, and Edward L. Bolt PMCID: PMC535669 Cloning of CviPII nicking and modification system from chlorella virus NYs-1 and application of Nt.CviPII in random DNA amplification Siu-hong Chan, Zhenyu Zhu, James L. Van Etten, and Shuang-yong Xu PMCID: PMC535667 Complete set of orthogonal 21st aminoacyl-tRNA synthetase-amber, ochre and opal suppressor tRNA pairs: concomitant suppression of three different termination codons in an mRNA in mammalian cells Caroline Köhrer, Eric L. Sullivan, and Uttam L. RajBhandary PMCID: PMC535668 Computational method for discovery of estrogen responsive genes Suisheng Tang, Sin Lam Tan, Suresh Kumar Ramadoss, Arun Prashanth Kumar, Man-Hung Eric Tang, and Vladimir B. Bajic PMCID: PMC535661 NFI and Oct-1 bend the Ad5 origin in the same direction leading to optimal DNA replication Monika E. Mysiak, Claire Wyman, P. Elly Holthuizen, and Peter C. van der Vliet PMCID: PMC535662 EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference Weidong Tian, Adrian K. Arakaki, and Jeffrey Skolnick PMCID: PMC535665 The role of phosphate groups in the VS ribozyme–substrate interaction Yana S. Kovacheva, Svetomir B. Tzokov, Iain A. Murray, and Jane A. Grasby PMCID: PMC535666 DmGEN, a novel RAD2 family endo-exonuclease from Drosophila melanogaster Gen Ishikawa, Yoshihiro Kanai, Kei-ichi Takata, Ryo Takeuchi, Kaori Shimanouchi, Tatsushi Ruike, Tomoyuki Furukawa, Seisuke Kimura, and Kengo Sakaguchi PMCID: PMC535671 Repair of 3-methylthymine and 1-methylguanine lesions by bacterial and human AlkB proteins Pål Ø. Falnes PMCID: PMC535673 DNA polymerase δ, RFC and PCNA are required for repair synthesis of large looped heteroduplexes in Saccharomyces cerevisiae Stephanie E. Corrette-Bennett, Claudia Borgeson, Debbie Sommer, Peter M. J. Burgers, and Robert S. Lahue PMCID: PMC535674 Analysis of transcription asymmetries along the tRNAE-COB operon: evidence for transcription attenuation and rapid RNA degradation between coding sequences Kirsten Krause and Carol L. Dieckmann PMCID: PMC535675 Substrate requirements for let-7 function in the developing zebrafish embryo Wigard P. Kloosterman, Erno Wienholds, René F. Ketting, and Ronald H.A. Plasterk PMCID: PMC535676 Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus Hideto Takami, Yoshihiro Takaki, Gab-Joo Chee, Shinro Nishi, Shigeru Shimamura, Hiroko Suzuki, Satomi Matsui, and Ikuo Uchiyama PMCID: PMC535678 Influence of a fluorobenzene nucleobase analogue on the conformational flexibility of RNA studied by molecular dynamics simulations Martin Zacharias and Joachim W. Engels PMCID: PMC535679 PreSPI: a domain combination based prediction system for protein–protein interaction Dong-Soo Han, Hong-Soog Kim, Woo-Hyuk Jang, Sung-Doke Lee, and Jung-Keun Suh PMCID: PMC535680 Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes Tobias Doerks, Christian von Mering, and Peer Bork PMCID: PMC535681 Paradoxical homozygous expression from heterozygotes and heterozygous expression from homozygotes as a consequence of transcriptional infidelity through a polyadenine tract in the AP3B1 gene responsible for canine cyclic neutropenia Kathleen F. Benson, Richard E. Person, Feng-Qian Li, Kayleen Williams, and Marshall Horwitz PMCID: PMC535682 Chemotherapeutic deletion of CTG repeats in lymphoblast cells from DM1 patients Vera I. Hashem, Malgorzata J. Pytlos, Elzbieta A. Klysik, Kuniko Tsuji, Merhdad Khajav, Tetsuo Ashizawa, and Richard R. Sinden PMCID: PMC535684 Identification of genes with fast-evolving regions in microbial genomes Yu Zheng, Richard J. Roberts, and Simon Kasif PMCID: PMC535660 Change of RNase P RNA function by single base mutation correlates with perturbation of metal ion binding in P4 as determined by NMR spectroscopy Michael Schmitz PMCID: PMC535670 Genetics of lagging strand DNA synthesis and maturation in fission yeast: suppression analysis links the Dna2–Cdc24 complex to DNA polymerase δ Hiroyuki Tanaka, Gi-Hyuck Ryu, Yeon-Soo Seo, and Stuart A. MacNeill PMCID: PMC535672 PriA helicase and SSB interact physically and functionally Chris J. Cadman and Peter McGlynn PMCID: PMC535688 Evolution of dnmt-2 and mbd-2-like genes in the free-living nematodes Pristionchus pacificus, Caenorhabditis elegans and Caenorhabditis briggsae Arturo Gutierrez and Ralf J. Sommer PMCID: PMC535690 Different patterns in the recognition of editing sites in plant mitochondria David Choury, Jean-Claude Farré, Xavier Jordana, and Alejandro Araya PMCID: PMC535677 Predicting oligonucleotide-directed mutagenesis failures in protein engineering Christopher D. Wassman, Phillip Y. Tam, Richard H. Lathrop, and Gregory A. Weiss PMCID: PMC535685 Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae Yu Chen and Dong Xu PMCID: PMC535686 Basic helix–loop–helix transcription factor Tcfl5 interacts with the Calmegin gene promoter in mouse spermatogenesis Michel Siep, Esther Sleddens-Linkels, Sabine Mulders, Hans van Eenennaam, Evelyne Wassenaar, Wiggert A. Van Cappellen, Jos Hoogerbrugge, J. Anton Grootegoed, and Willy M. Baarends PMCID: PMC535687 Predicting functional family of novel enzymes irrespective of sequence similarity: a statistical learning approach L. Y. Han, C. Z. Cai, Z. L. Ji, Z. W. Cao, J. Cui, and Y. Z. Chen PMCID: PMC535691 DNA footprinting and biophysical characterization of the controller protein C.AhdI suggests the basis of a genetic switch S. D. Streeter, I. Papapanagiotou, J. E. McGeehan, and G. G. Kneale PMCID: PMC535683 A novel E2 box-GATA element modulates Cdc6 transcription during human cells polyploidization Nuria Vilaboa, Rodrigo Bermejo, Pilar Martinez, Rafael Bornstein, and Carmela Calés PMCID: PMC535689 NAR Methods Online A multi-enzyme model for pyrosequencing Ali Agah, Mariam Aghajan, Foad Mashayekhi, Sasan Amini, Ronald W. Davis, James D. Plummer, Mostafa Ronaghi, and Peter B. Griffin PMCID: PMC535692 Rapid analysis of CpG methylation patterns using RNase T1 cleavage and MALDI-TOF Philipp Schatz, Dimo Dietrich, and Matthias Schuster PMCID: PMC535694 MethylQuant: a sensitive method for quantifying methylation of specific cytosines within the genome Hélène Thomassin, Clémence Kress, and Thierry Grange PMCID: PMC535695 In vitro selection of Jun-associated proteins using mRNA display Kenichi Horisawa, Seiji Tateyama, Masamichi Ishizaka, Nobutaka Matsumura, Hideaki Takashima, Etsuko Miyamoto-Sato, Nobuhide Doi, and Hiroshi Yanagawa PMCID: PMC535696 Quantitative detection of siRNA and single-stranded oligonucleotides: relationship between uptake and biological activity of siRNA Marita Overhoff, Winfried Wünsche, and Georg Sczakiel PMCID: PMC535697 RNA silencing in plants by the expression of siRNA duplexes Shanfa Lu, Rui Shi, Cheng-Chung Tsao, Xiaoping Yi, Laigeng Li, and Vincent L. Chiang PMCID: PMC535699 A mammalian artificial chromosome engineering system (ACE System) applicable to biopharmaceutical protein production, transgenesis and gene-based cell therapy Michael Lindenbaum, Ed Perkins, Erika Csonka, Elena Fleming, Lisa Garcia, Amy Greene, Lindsay Gung, Gyula Hadlaczky, Edmond Lee, Josephine Leung, Neil MacDonald, Alexisann Maxwell, Kathleen Mills, Diane Monteith, Carl F. Perez, Joan Shellard, Sandy Stewart, Tom Stodola, Dana Vandenborre, Sandy Vanderbyl, and Harry C. Ledebur, Jr PMCID: PMC535698 Synthesis of unimolecularly circular G-quadruplexes as prospective molecular probes Tianyan Zhou, Guoshu Chen, Yifan Wang, Qiang Zhang, Ming Yang, and Tianhu Li PMCID: PMC535693 Site-directed, Ligase-Independent Mutagenesis (SLIM): a single-tube methodology approaching 100% efficiency in 4 h Joyce Chiu, Paul E. March, Ryan Lee, and Daniel Tillett PMCID: PMC535700 |
