| | Articles Nucleic Acids Res. 2003 July 15; 31(14): 3869–3871. PMCID: PMC165949 A Hox gene mutation that triggers nonsense-mediated RNA decay and affects alternative splicing during Drosophila development Claudio R. Alonso and Michael Akam PMCID: PMC167643 Replication of damaged DNA in vitro is blocked by p53 Jianmin Zhou and Carol Prives PMCID: PMC165982 Incision at hypoxanthine residues in DNA by a mammalian homologue of the Escherichia coli antimutator enzyme endonuclease V Ane Moe, Jeanette Ringvoll, Line M. Nordstrand, Lars Eide, Magnar Bjørås, Erling Seeberg, Torbjørn Rognes, and Arne Klungland PMCID: PMC167633 Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction Mu Xiao, Michael J. Leibowitz, and Yi Zhang PMCID: PMC165970 Mitochondria-mediated nuclear mutator phenotype in Saccharomyces cerevisiae Anne Karin Rasmussen, Aditi Chatterjee, Lene Juel Rasmussen, and Keshav K. Singh PMCID: PMC165961 Bacteriophage P1 Ban protein is a hexameric DNA helicase that interacts with and substitutes for Escherichia coli DnaB Marc Lemonnier, Günter Ziegelin, Tobias Reick, Ana Muñoz Gómez, Ramón Díaz-Orejas, and Erich Lanka PMCID: PMC165978 Pseudocomplementary PNAs as selective modifiers of protein activity on duplex DNA: the case of type IIs restriction enzymes Ekaterina Protozanova, Vadim V. Demidov, Peter E. Nielsen, and Maxim D. Frank-Kamenetskii PMCID: PMC165965 The role of the yeast cleavage and polyadenylation factor subunit Ydh1p/Cft2p in pre-mRNA 3′-end formation Andrea Kyburz, Martin Sadowski, Bernhard Dichtl, and Walter Keller PMCID: PMC167639 Importance of the reverse Hoogsteen base pair 54-58 for tRNA function Ekaterina I. Zagryadskaya, Felix R. Doyon, and Sergey V. Steinberg PMCID: PMC165963 Transient recruitment of the hnRNP K protein to inducibly transcribed gene loci Jerzy Ostrowski, Yasunobu Kawata, Daniel S. Schullery, Oleg N. Denisenko, and Karol Bomsztyk PMCID: PMC165967 The cationic porphyrin TMPyP4 destabilizes the tetraplex form of the fragile X syndrome expanded sequence d(CGG)n Pnina Weisman-Shomer, Esther Cohen, Inbal Hershco, Samer Khateb, Orit Wolfovitz-Barchad, Laurence H. Hurley, and Michael Fry PMCID: PMC165968 Histone deacetylases in fungi: novel members, new facts Patrick Trojer, Eva M. Brandtner, Gerald Brosch, Peter Loidl, Johannes Galehr, Roland Linzmaier, Hubertus Haas, Karin Mair, Martin Tribus, and Stefan Graessle PMCID: PMC167634 Comparative protein structure modeling by iterative alignment, model building and model assessment Bino John and Andrej Sali PMCID: PMC165975 The frequency of gene targeting in Trypanosoma brucei is independent of target site copy number Bill Wickstead, Klaus Ersfeld, and Keith Gull PMCID: PMC165960 Direct real-time molecular scale visualisation of the degradation of condensed DNA complexes exposed to DNase I Hosam G. Abdelhady, Stephanie Allen, Martyn C. Davies, Clive J. Roberts, Saul J. B. Tendler, and Philip M. Williams PMCID: PMC165977 Initiation-mediated mRNA decay in yeast affects heat-shock mRNAs, and works through decapping and 5′-to-3′ hydrolysis Heather L. Heikkinen, Sara A. Llewellyn, and Christine A. Barnes PMCID: PMC167635 Hfq affects the length and the frequency of short oligo(A) tails at the 3′ end of Escherichia coli rpsO mRNAs Jacques Le Derout, Marc Folichon, Federica Briani, Gianni Dehò, Philippe Régnier, and Eliane Hajnsdorf PMCID: PMC165971 Processing of DNA lesions by archaeal DNA polymerases from Sulfolobus solfataricus Petr Grúz, Masatomi Shimizu, Francesca M. Pisani, Mariarita De Felice, Yusuke Kanke, and Takehiko Nohmi PMCID: PMC165962 Spatial organization of topoisomerase I-mediated DNA cleavage induced by camptothecin–oligonucleotide conjugates Paola B. Arimondo, Stéphane Angenault, Ludovic Halby, Alexandre Boutorine, Frédéric Schmidt, Claude Monneret, Thérèse Garestier, Jian-Sheng Sun, Christian Bailly, and Claude Hélène PMCID: PMC165972 Region and amino acid residues required for Rad51C binding in the human Xrcc3 protein Hitoshi Kurumizaka, Rima Enomoto, Maki Nakada, Keiko Eda, Shigeyuki Yokoyama, and Takehiko Shibata PMCID: PMC165957 The first completed genome sequence from a teleost fish (Fugu rubripes) adds significant diversity to the nuclear receptor superfamily Jodi M. Maglich, Justin A. Caravella, Millard H. Lambert, Timothy M. Willson, John T. Moore, and Lakshman Ramamurthy PMCID: PMC165959 The C terminus of the human telomerase reverse transcriptase is a determinant of enzyme processivity Sylvain Huard, Tara J. Moriarty, and Chantal Autexier PMCID: PMC165952 CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle Hiroyuki Kurata, Nana Matoba, and Natsumi Shimizu PMCID: PMC165976 Correlation between premeiotic DNA replication and chromatin transition at yeast recombination initiation sites Hajime Murakami, Valerie Borde, Takehiko Shibata, Michael Lichten, and Kunihiro Ohta PMCID: PMC165956 Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli Claude Sauter, Jérôme Basquin, and Dietrich Suck PMCID: PMC167641 Effect of DNA target sequence on triplex formation by oligo-2′-deoxy- and 2′-O-methylribonucleotides Rachel A. Cassidy, Nitin Puri, and Paul S. Miller PMCID: PMC165951 Biochemical properties of phosphonoacetate and thiophosphonoacetate oligodeoxyribonucleotides David Sheehan, Benjamin Lunstad, Christina M. Yamada, Brian G. Stell, Marvin H. Caruthers, and Douglas J. Dellinger PMCID: PMC165954 Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics John P. McCutcheon and Sean R. Eddy PMCID: PMC165953 An error-prone family Y DNA polymerase (DinB homolog from Sulfolobus solfataricus) uses a ‘steric gate’ residue for discrimination against ribonucleotides Angela M. DeLucia, Nigel D. F. Grindley, and Catherine M. Joyce PMCID: PMC165950 Unusual intercalation of acridin-9-ylthiourea into the 5′-GA/TC DNA base step from the minor groove: implications for the covalent DNA adduct profile of a novel platinum–intercalator conjugate Hemanta Baruah and Ulrich Bierbach PMCID: PMC165979 GAGA facilitates binding of Pleiohomeotic to a chromatinized Polycomb response element Tokameh Mahmoudi, Lobke M. P. Zuijderduijn, Adone Mohd-Sarip, and C. Peter Verrijzer PMCID: PMC167640 On the number of protein–protein interactions in the yeast proteome Andrei Grigoriev PMCID: PMC165980 Selective interactions of human kin17 and RPA proteins with chromatin and the nuclear matrix in a DNA damage- and cell cycle-regulated manner Laurent Miccoli, Denis S. F. Biard, Isabelle Frouin, Francis Harper, Giovanni Maga, and Jaime F. Angulo PMCID: PMC165974 Chemical shift changes provide evidence for overlapping single-stranded DNA- and XPA-binding sites on the 70 kDa subunit of human replication protein A Gary W. Daughdrill, Garry W. Buchko, Maria V. Botuyan, Cheryl Arrowsmith, Marc S. Wold, Michael A. Kennedy, and David F. Lowry PMCID: PMC165966 Mycobacterium tuberculosis RecA intein, a LAGLIDADG homing endonuclease, displays Mn2+ and DNA-dependent ATPase activity N. Guhan and K. Muniyappa PMCID: PMC167636 Hidden messages in the nef gene of human immunodeficiency virus type 1 suggest a novel RNA secondary structure Ofer Peleg, Edward N. Trifonov, and Alexander Bolshoy PMCID: PMC165969 Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene E. A. Worthey, Santiago Martinez-Calvillo, Achim Schnaufer, Gautam Aggarwal, Jason Cawthra, Gholam Fazelinia, Chris Fong, Guoliang Fu, Melissa Hassebrock, Greg Hixson, Alasdair C. Ivens, Patti Kiser, Felicia Marsolini, Erica Rickell, Reza Salavati, Ellen Sisk, Susan M. Sunkin, Kenneth D. Stuart, and Peter J. Myler PMCID: PMC167632 Thermodynamic calculations and statistical correlations for oligo-probes design O. V. Matveeva, S. A. Shabalina, V. A. Nemtsov, A. D. Tsodikov, R. F. Gesteland, and J. F. Atkins PMCID: PMC167637 Temperature-sensitive mutation in yeast mitochondrial ribosome recycling factor (RRF) Emeline Teyssier, Go Hirokawa, Anna Tretiakova, Bradford Jameson, Akira Kaji, and Hideko Kaji PMCID: PMC165964 Assessing functional divergence in EF-1α and its paralogs in eukaryotes and archaebacteria Yuji Inagaki, Christian Blouin, Edward Susko, and Andrew J. Roger PMCID: PMC165955 Unique actinomycin D binding to self-complementary d(CXYGGCCY′X′G) sequences: duplex disruption and binding to a nominally base-paired hairpin Fu-Ming Chen, Feng Sha, Ko-Hsin Chin, and Shan-Ho Chou PMCID: PMC167638 The Arabidopsis AtLIG4 gene is required for the repair of DNA damage, but not for the integration of Agrobacterium T-DNA Haico van Attikum, Paul Bundock, René M. Overmeer, Lan-Ying Lee, Stanton B. Gelvin, and Paul J. J. Hooykaas PMCID: PMC165973 Formation of stable triplexes between purine RNA and pyrimidine oligodeoxyxylonucleotides Sergei Ivanov, Yakov Alekseev, Jean-Remi Bertrand, Claude Malvy, and Marina B. Gottikh PMCID: PMC165958 Molecular modeling of the chromatosome particle M. M. Srinivas Bharath, Nagasuma R. Chandra, and M. R. S. Rao PMCID: PMC167642 Molecular dynamics reveals the stabilizing role of loop closing residues in kissing interactions: comparison between TAR–TAR* and TAR–aptamer François Beaurain, Carmelo Di Primo, Jean Jacques Toulmé, and Michel Laguerre PMCID: PMC165981 NAR Methods Online Simultaneously monitoring DNA binding and helicase-catalyzed DNA unwinding by fluorescence polarization H. Q. Xu, A. H. Zhang, C. Auclair, and X. G. Xi PMCID: PMC167644 Streptomyces-derived quorum-sensing systems engineered for adjustable transgene expression in mammalian cells and mice Wilfried Weber, Ronald Schoenmakers, Manuela Spielmann, Marie Daoud El-Baba, Marc Folcher, Bettina Keller, Cornelia C. Weber, Nils Link, Petra van de Wetering, Christoph Heinzen, Benoît Jolivet, Urs Séquin, Dominique Aubel, Charles J. Thompson, and Martin Fussenegger PMCID: PMC167645 mRNA accessible site tagging (MAST): a novel high throughput method for selecting effective antisense oligonucleotides Hong-Yan Zhang, Jianping Mao, Daixing Zhou, Yunhe Xu, Håkan Thonberg, Zicai Liang, and Claes Wahlestedt PMCID: PMC167646 Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis Stuart N. Peirson, Jason N. Butler, and Russell G. Foster PMCID: PMC167648 A new Thermus sp. class-IIS enzyme sub-family: isolation of a ‘twin’ endonuclease TspDTI with a novel specificity 5′-ATGAA(N11/9)-3′, related to TspGWI, TaqII and Tth111II Piotr M. Skowron, Jarosław Majewski, Agnieszka Żylicz-Stachula, Sylwia M. Rutkowska, Izabela Jaworowska, and Renata I. Harasimowicz-Słowińska PMCID: PMC167652 Heteromeric MAPPIT: a novel strategy to study modification-dependent protein–protein interactions in mammalian cells Irma Lemmens, Sven Eyckerman, Lennart Zabeau, Dominiek Catteeuw, Els Vertenten, Kristin Verschueren, Danny Huylebroeck, Joël Vandekerckhove, and Jan Tavernier PMCID: PMC167658 Simultaneous on/off regulation of transgenes located on a mammalian chromosome with Cre-expressing adenovirus and a mutant loxP Saki Kondo, Aya Okuda, Hiromi Sato, Naoto Tachikawa, Miho Terashima, Yumi Kanegae, and Izumu Saito PMCID: PMC167663 |
