| | Articles SURVEY AND SUMMARY: A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes Richard J. Roberts, Marlene Belfort, Timothy Bestor, Ashok S. Bhagwat, Thomas A. Bickle, Jurate Bitinaite, Robert M. Blumenthal, Sergey Kh. Degtyarev, David T. F. Dryden, Kevin Dybvig, Keith Firman, Elizaveta S. Gromova, Richard I. Gumport, Stephen E. Halford, Stanley Hattman, Joseph Heitman, David P. Hornby, Arvydas Janulaitis, Albert Jeltsch, Jytte Josephsen, Antal Kiss, Todd R. Klaenhammer, Ichizo Kobayashi, Huimin Kong, Detlev H. Krüger, Sanford Lacks, Martin G. Marinus, Michiko Miyahara, Richard D. Morgan, Noreen E. Murray, Valakunja Nagaraja, Andrzej Piekarowicz, Alfred Pingoud, Elisabeth Raleigh, Desirazu N. Rao, Norbert Reich, Vladimir E. Repin, Eric U. Selker, Pang-Chui Shaw, Daniel C. Stein, Barry L. Stoddard, Waclaw Szybalski, Thomas A. Trautner, James L. Van Etten, Jorge M. B. Vitor, Geoffrey G. Wilson, and Shuang-yong Xu PMCID: PMC152790 SURVEY AND SUMMARY: A survey of small RNA-encoding genes in Escherichia coli Ruth Hershberg, Shoshy Altuvia, and Hanah Margalit PMCID: PMC152812 A structural and primary sequence comparison of the viral RNA-dependent RNA polymerases Jeremy A. Bruenn PMCID: PMC152793 Scp160p associates with specific mRNAs in yeast Ai-Min Li, Alice Watson, and Judith L. Fridovich-Keil PMCID: PMC152800 DNA helix: the importance of being GC-rich Alexander E. Vinogradov PMCID: PMC152811 Thyroid-specific transcription factors control Hex promoter activity Cinzia Puppin, Angela V. D'Elia, Lucia Pellizzari, Diego Russo, Franco Arturi, Ivan Presta, Sebastiano Filetti, Clifford W. Bogue, Lee A. Denson, and Giuseppe Damante PMCID: PMC152810 Conditional gene expression by controlling translation with tetracycline-binding aptamers Beatrix Suess, Shane Hanson, Christian Berens, Barbara Fink, Renée Schroeder, and Wolfgang Hillen PMCID: PMC152801 AINTEGUMENTA utilizes a mode of DNA recognition distinct from that used by proteins containing a single AP2 domain Beth A. Krizek PMCID: PMC152808 A non-redundant microarray of genes for two related bacteria Steffen Porwollik, Jonathan Frye, Liliana D. Florea, Felisa Blackmer, and Michael McClelland PMCID: PMC152813 The human Imp3 and Imp4 proteins form a ternary complex with hMpp10, which only interacts with the U3 snoRNA in 60–80S ribonucleoprotein complexes Sander Granneman, Jennifer E. G. Gallagher, Judith Vogelzangs, Wendy Horstman, Walther J. van Venrooij, Susan J. Baserga, and Ger J. M. Pruijn PMCID: PMC152815 Functional cooperation between exonucleases and endonucleases—basis for the evolution of restriction enzymes Nidhanapathi K. Raghavendra and Desirazu N. Rao PMCID: PMC152791 Influence of DNA torsional rigidity on excision of 7,8-dihydro-8-oxo-2′-deoxyguanosine in the presence of opposing abasic sites by human OGG1 protein F. Barone, E. Dogliotti, L. Cellai, C. Giordano, M. Bjørås, and F. Mazzei PMCID: PMC152805 Pathology-related substitutions in human mitochondrial tRNAIle reduce precursor 3′ end processing efficiency in vitro Louis Levinger, Richard Giegé, and Catherine Florentz PMCID: PMC152798 Repair of hydrolytic DNA deamination damage in thermophilic bacteria: cloning and characterization of a Vsr endonuclease homolog from Bacillus stearothermophilus Martin Laging, Eric Lindner, Hans-Joachim Fritz, and Wilfried Kramer PMCID: PMC152792 Molecular recognition properties of IGS-mediated reactions catalyzed by a Pneumocystis carinii group I intron Ashley K. Johnson, Dana A. Baum, Jesse Tye, Michael A. Bell, and Stephen M. Testa PMCID: PMC152796 Inhibition of HCV NS3 protease by RNA aptamers in cells Fumiko Nishikawa, Nobuko Kakiuchi, Kohei Funaji, Kotaro Fukuda, Satoru Sekiya, and Satoshi Nishikawa PMCID: PMC152807 What’s in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence Gertrud Mannhaupt, Corinna Montrone, Dirk Haase, H. Werner Mewes, Verena Aign, Jörg D. Hoheisel, Berthold Fartmann, Gerald Nyakatura, Frank Kempken, Josef Maier, and Ulrich Schulte PMCID: PMC152809 Specific SR protein-dependent splicing substrates identified through genomic SELEX Soyoun Kim, Hua Shi, Dong-ki Lee, and John T. Lis PMCID: PMC152802 Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays Doeke Hekstra, Alexander R. Taussig, Marcelo Magnasco, and Felix Naef PMCID: PMC152799 Transcription of genes encoding trans-acting factors required for rRNA maturation/ribosomal subunit assembly is coordinately regulated with ribosomal protein genes and involves Rap1 in Saccharomyces cerevisiae Keita Miyoshi, Chiharu Shirai, and Keiko Mizuta PMCID: PMC152794 Conserved sequence elements associated with exon skipping Elana Miriami, Hanah Margalit, and Ruth Sperling PMCID: PMC152795 3′-Exonuclease resistance of DNA oligodeoxynucleotides containing O6-[4-oxo-4-(3-pyridyl)butyl]guanine Soobong Park, Mahadevan Seetharaman, Alexis Ogdie, David Ferguson, and Natalia Tretyakova PMCID: PMC152814 An approach to identify over-represented cis-elements in related sequences Jiashun Zheng, Jiajin Wu, and Zhirong Sun PMCID: PMC152803 Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures Junji Kitagawa, Yasuhiro Futamura, and Kenji Yamamoto PMCID: PMC152804 Self-association and conformational properties of RAG1: implications for formation of the V(D)J recombinase LeAnn J. Godderz, Negar S. Rahman, George M. Risinger, Janeen L. Arbuckle, and Karla K. Rodgers PMCID: PMC152797 NAR Methods Online Bypassing antibiotic selection: positive screening of genetically modified cells with an antigen-dependent proliferation switch Masahiro Kawahara, Hiroshi Ueda, Sumiyo Morita, Kouhei Tsumoto, Izumi Kumagai, and Teruyuki Nagamune PMCID: PMC152817 Amplification of repeat-containing transcribed sequences (ARTS): a transcriptome fingerprinting strategy to detect functionally relevant microsatellite mutations in cancer Martina Olivero, Tina Ruggiero, Nadia Coltella, Antonella Maffe’, Raffaele Calogero, Enzo Medico, and Maria Flavia Di Renzo PMCID: PMC152818 Internal 32P-labeling of l-deoxyoligonucleotides Christian Frauendorf, Felix Hausch, Ingo Röhl, Andrea Lichte, Stefan Vonhoff, and Sven Klussmann PMCID: PMC152819 Light-directed 5′→3′ synthesis of complex oligonucleotide microarrays Thomas J. Albert, Jason Norton, Markus Ott, Todd Richmond, Kate Nuwaysir, Emile F. Nuwaysir, Klaus-Peter Stengele, and Roland D. Green PMCID: PMC152820 Data extraction from composite oligonucleotide microarrays Ilya Shmulevich, Jaakko Astola, David Cogdell, Stanley R. Hamilton, and Wei Zhang PMCID: PMC152821 RNaseCut: a MALDI mass spectrometry-based method for SNP discovery Stefan Krebs, Ivica Međugorac, Doris Seichter, and Martin Förster PMCID: PMC152822 A simple and cost-effective method for producing small interfering RNAs with high efficacy Muhammad Sohail, Graeme Doran, Johann Riedemann, Val Macaulay, and Edwin M. Southern PMCID: PMC152823 Mechanisms underlying the impact of humic acids on DNA quantification by SYBR Green I and consequences for the analysis of soils and aquatic sediments Hubert Zipper, Christiane Buta, Katrin Lämmle, Herwig Brunner, Jürgen Bernhagen, and Frank Vitzthum PMCID: PMC152824 Construction and purification of site-specifically modified DNA templates for transcription assays Rebecca A. Perlow, Thomas M. Schinecker, Se Jun Kim, Nicholas E. Geacintov, and David A. Scicchitano PMCID: PMC152825 Corrigenda Nucleic Acids Res. 2003 April 1; 31(7): 2024. PMCID: PMC152806 Corrects: Paul D. Thomas, et al. PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res. 2003 January 1; 31(1): 334–341. Nucleic Acids Res. 2003 April 1; 31(7): 2024. PMCID: PMC152816 Corrects: Adrian M. Davies, et al. A Ca2+-induced mitochondrial permeability transition causes complete release of rat liver endonuclease G activity from its exclusive location within the mitochondrial intermembrane space. Identification of a novel endo-exonuclease activity residing within the mitochondrial matrix. Nucleic Acids Res. 2003 February 15; 31(4): 1364–1373. |
