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  • 1
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    Spatial organization of transcription elongation complex in Escherichia coli (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-07-17
    Description: During RNA synthesis in the ternary elongation complex, RNA polymerase enzyme holds nucleic acids in three contiguous sites: the double-stranded DNA-binding site (DBS) ahead of the transcription bubble, the RNA-DNA heteroduplex-binding site (HBS), and the RNA-binding site (RBS) upstream of HBS. Photochemical cross-linking allowed mapping of the DNA and RNA contacts to specific positions on the amino acid sequence. Unexpectedly, the same protein regions were found to participate in both DBS and RBS. Thus, DNA entry and RNA exit occur close together in the RNA polymerase molecule, suggesting that the three sites constitute a single unit. The results explain how RNA in the integrated unit RBS-HBS-DBS may stabilize the ternary complex, whereas a hairpin in RNA result in its dissociation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nudler, E -- Gusarov, I -- Avetissova, E -- Kozlov, M -- Goldfarb, A -- GM49242/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Jul 17;281(5375):424-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA. evgeny.nudler@med.nyu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9665887" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; DNA, Bacterial/chemistry/*metabolism ; DNA-Directed RNA Polymerases/chemistry/*metabolism ; Escherichia coli/*genetics/metabolism ; Idoxuridine/metabolism ; Models, Genetic ; Nucleic Acid Conformation ; Nucleic Acid Heteroduplexes/*metabolism ; Protein Binding ; RNA, Bacterial/chemistry/*metabolism ; Templates, Genetic ; *Transcription, Genetic ; Ultraviolet Rays
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    A structural model of transcription elongation (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-08-01
    Description: The path of the nucleic acids through a transcription elongation complex was tracked by mapping cross-links between bacterial RNA polymerase (RNAP) and transcript RNA or template DNA onto the x-ray crystal structure. In the resulting model, the downstream duplex DNA is nestled in a trough formed by the beta' subunit and enclosed on top by the beta subunit. In the RNAP channel, the RNA/DNA hybrid extends from the enzyme active site, along a region of the beta subunit harboring rifampicin resistance mutations, to the beta' subunit "rudder." The single-stranded RNA is then extruded through another channel formed by the beta-subunit flap domain. The model provides insight into the functional properties of the transcription complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korzheva, N -- Mustaev, A -- Kozlov, M -- Malhotra, A -- Nikiforov, V -- Goldfarb, A -- Darst, S A -- GM30717/GM/NIGMS NIH HHS/ -- GM49242/GM/NIGMS NIH HHS/ -- GM53759/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Jul 28;289(5479):619-25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Public Health Research Institute, 455 First Avenue, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10915625" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cross-Linking Reagents ; Crystallography, X-Ray ; DNA/chemistry/genetics/*metabolism ; DNA Primers ; DNA-Directed RNA Polymerases/*chemistry/genetics/metabolism ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; Nucleic Acid Hybridization ; Oligodeoxyribonucleotides/chemistry/metabolism ; Oligoribonucleotides/chemistry/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Messenger/chemistry/genetics/*metabolism ; Templates, Genetic ; Thermus/enzymology ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Initiation of mammalian liver development from endoderm by fibroblast growth factors (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-06-18
    Description: The signaling molecules that elicit embryonic induction of the liver from the mammalian gut endoderm or induction of other gut-derived organs are unknown. Close proximity of cardiac mesoderm, which expresses fibroblast growth factors (FGFs) 1, 2, and 8, causes the foregut endoderm to develop into the liver. Treatment of isolated foregut endoderm from mouse embryos with FGF1 or FGF2, but not FGF8, was sufficient to replace cardiac mesoderm as an inducer of the liver gene expression program, the latter being the first step of hepatogenesis. The hepatogenic response was restricted to endoderm tissue, which selectively coexpresses FGF receptors 1 and 4. Further studies with FGFs and their specific inhibitors showed that FGF8 contributes to the morphogenetic outgrowth of the hepatic endoderm. Thus, different FGF signals appear to initiate distinct phases of liver development during mammalian organogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jung, J -- Zheng, M -- Goldfarb, M -- Zaret, K S -- GM36477/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Jun 18;284(5422):1998-2003.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Box G-J363, Providence, RI 02912, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10373120" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Culture Techniques ; Digestive System/embryology ; *Embryonic Induction ; Endoderm/metabolism/*physiology ; Fibroblast Growth Factor 1 ; Fibroblast Growth Factor 2/genetics/pharmacology/physiology ; Fibroblast Growth Factor 8 ; Fibroblast Growth Factors/genetics/pharmacology/*physiology ; Gene Expression ; Heart/embryology ; Heparitin Sulfate/pharmacology ; Liver/*embryology/metabolism ; Mesoderm/metabolism ; Mice ; Mice, Inbred C3H ; Morphogenesis ; Organ Specificity ; Prealbumin/genetics ; Receptors, Fibroblast Growth Factor/physiology ; Recombinant Fusion Proteins ; Serum Albumin/genetics ; Signal Transduction ; alpha-Fetoproteins/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Direct measurement of the reaction front in chemically amplified photoresists (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-07-20
    Description: The continuing drive by the semiconductor industry to fabricate smaller structures using photolithography will soon require dimensional control at length scales comparable to the size of the polymeric molecules in the materials used to pattern them. The current technology, chemically amplified photoresists, uses a complex reaction-diffusion process to delineate patterned areas with high spatial resolution. However, nanometer-level control of this critical process is limited by the lack of direct measurements of the reaction front. We demonstrate the use of x-ray and neutron reflectometry as a general method to measure the spatial evolution of the reaction-diffusion process with nanometer resolution. Measuring compositional profiles, provided by deuterium-labeled reactant groups for neutron scattering contrast, we show that the reaction front within the material is broad rather than sharply defined and the compositional profile is altered during development. Measuring the density profile, we directly correlate the developed film structure with that of the reaction front.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, Eric K -- Soles, Christopher L -- Goldfarb, Dario L -- Trinque, Brian C -- Burns, Sean D -- Jones, Ronald L -- Lenhart, Joseph L -- Angelopoulos, Marie -- Willson, C Grant -- Satija, Sushil K -- Wu, Wen-Li -- New York, N.Y. -- Science. 2002 Jul 19;297(5580):372-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Polymers Division and, Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-8541, USA. eric.lin@nist.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12130778" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Blocking of the initiation-to-elongation transition by a transdominant RNA polymerase mutation (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-05-25
    Description: RNA polymerase, the principal enzyme of gene expression, possesses structural features conserved in evolution. A substitution of an evolutionarily invariant amino acid (Lys1065----Arg) in the beta subunit of Escherichia coli RNA polymerase apparently disrupts its catalytic center. The mutant protein inhibited cell growth when expressed from an inducible promoter. The assembled holoenzyme carrying the mutant subunit formed stable promoter complexes that continuously synthesized promoter-specific dinucleotides but that did not enter the elongation step. The mutant polymerase inhibited transcription by blocking the access of the wild-type enzyme to promoters.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kashlev, M -- Lee, J -- Zalenskaya, K -- Nikiforov, V -- Goldfarb, A -- GM30717/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 May 25;248(4958):1006-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Genetics, U.S.S.R. Academy of Sciences, Moscow.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1693014" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; DNA Mutational Analysis ; DNA-Directed RNA Polymerases/*genetics/metabolism ; Escherichia coli/enzymology/genetics ; Genes, Dominant ; Molecular Sequence Data ; Promoter Regions, Genetic ; RNA/biosynthesis ; Structure-Activity Relationship
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    Fatal familial insomnia and familial Creutzfeldt-Jakob disease: disease phenotype determined by a DNA polymorphism (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-10-30
    Description: Fatal familial insomnia (FFI) and a subtype of familial Creutzfeldt-Jakob disease (CJD), two clinically and pathologically distinct diseases, are linked to the same mutation at codon 178 (Asn178) of the prion protein gene. The possibility that a second genetic component modified the phenotypic expression of the Asn178 mutation was investigated. FFI and the familial CJD subtype segregated with different genotypes determined by the Asn178 mutation and the methionine-valine polymorphism at codon 129. The Met129, Asn178 allele segregated with FFI in all 15 affected members of five kindreds whereas the Val129, Asn178 allele segregated with the familial CJD subtype in all 15 affected members of six kindreds. Thus, two distinct disease phenotypes linked to a single pathogenic mutation can be determined by a common polymorphism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goldfarb, L G -- Petersen, R B -- Tabaton, M -- Brown, P -- LeBlanc, A C -- Montagna, P -- Cortelli, P -- Julien, J -- Vital, C -- Pendelbury, W W -- 1 R01 AGNS08155-02/AG/NIA NIH HHS/ -- AG-08012-02/AG/NIA NIH HHS/ -- NS 14509-13/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1992 Oct 30;258(5083):806-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Central Nervous System Studies, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, Maryland 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1439789" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Asparagine/genetics ; Chromosomes, Human, Pair 20 ; Codon ; Creutzfeldt-Jakob Syndrome/*genetics ; DNA/*genetics ; Genotype ; Humans ; Middle Aged ; *Mutation ; *Phenotype ; *Polymorphism, Genetic ; Prion Diseases/*genetics ; Prions/genetics ; Valine/genetics
    Print ISSN: 0036-8075
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  • 7
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    Whose finger is on the switch? (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-06-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goldfarb, D S -- New York, N.Y. -- Science. 1997 Jun 20;276(5320):1814-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Rochester, Rochester, NY 14627, USA. Goldfarb@nucleus.biology.rochester.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9206840" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Transport ; Cell Nucleus/*metabolism ; Cytoplasm/metabolism ; GTP Phosphohydrolases/*metabolism ; GTP-Binding Proteins/metabolism ; Guanosine Triphosphate/metabolism ; Nuclear Envelope/metabolism ; Nuclear Localization Signals ; Nuclear Proteins/*metabolism ; RNA/metabolism ; Vesicular stomatitis Indiana virus/*metabolism ; Viral Matrix Proteins/*metabolism ; ran GTP-Binding Protein
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Requirement of FGF-4 for postimplantation mouse development (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-01-13
    Description: Fibroblast growth factors (FGFs) are thought to influence many processes in vertebrate development because of their diverse sites of expression and wide range of biological activities in in vitro culture systems. As a means of elucidating embryonic functions of FGF-4, gene targeting was used to generate mice harboring a disrupted Fgf4 gene. Embryos homozygous for the null allele underwent uterine implantation and induced uterine decidualization but did not develop substantially thereafter. As was consistent with their behavior in vivo, Fgf4 null embryos cultured in vitro displayed severely impaired proliferation of the inner cell mass, whereas growth and differentiation of the inner cell mass were rescued when null embryos were cultured in the presence of FGF-4 protein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feldman, B -- Poueymirou, W -- Papaioannou, V E -- DeChiara, T M -- Goldfarb, M -- HD21988/HD/NICHD NIH HHS/ -- HD27198/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 1995 Jan 13;267(5195):246-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Integrated Program in Cellular, Molecular, and Biophysical Studies, Columbia University College of Physicians and Surgeons, New York, NY 10032.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7809630" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Blastocyst/cytology/physiology ; Crosses, Genetic ; Culture Techniques ; Embryonic Development/*physiology ; Embryonic and Fetal Development/*physiology ; Female ; Fibroblast Growth Factor 4 ; Fibroblast Growth Factors/genetics/pharmacology/*physiology ; Gene Targeting ; Heterozygote ; Male ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Morula/drug effects/physiology ; Phenotype ; Pregnancy ; Proto-Oncogene Proteins/genetics/pharmacology/*physiology ; Recombinant Proteins/pharmacology
    Print ISSN: 0036-8075
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  • 9
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    Transcription processivity: protein-DNA interactions holding together the elongation complex (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-07-12
    Description: The elongation of RNA chains during transcription occurs in a ternary complex containing RNA polymerase (RNAP), DNA template, and nascent RNA. It is shown here that elongating RNAP from Escherichia coli can switch DNA templates by means of end-to-end transposition without loss of the transcript. After the switch, transcription continues on the new template. With the use of defined short DNA fragments as switching templates, RNAP-DNA interactions were dissected into two spatially distinct components, each contributing to the stability of the elongating complex. The front (F) interaction occurs ahead of the growing end of RNA. This interaction is non-ionic and requires 7 to 9 base pairs of intact DNA duplex. The rear (R) interaction is ionic and requires approximately six nucleotides of the template DNA strand behind the active site and one nucleotide ahead of it. The nontemplate strand is not involved. With the use of protein-DNA crosslinking, the F interaction was mapped to the conserved zinc finger motif in the NH2-terminus of the beta' subunit and the R interaction, to the COOH-terminal catalytic domain of the beta subunit. Mutational disruption of the zinc finger selectively destroyed the F interaction and produced a salt-sensitive ternary complex with diminished processivity. A model of the ternary complex is proposed here that suggests that trilateral contacts in the active center maintain the nonprocessive complex, whereas a front-end domain including the zinc finger ensures processivity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nudler, E -- Avetissova, E -- Markovtsov, V -- Goldfarb, A -- GM49242/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jul 12;273(5272):211-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Public Health Research Institute, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8662499" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; DNA/chemistry/*metabolism ; DNA, Single-Stranded/metabolism ; DNA-Directed RNA Polymerases/chemistry/genetics/*metabolism ; Escherichia coli/enzymology ; Models, Genetic ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Nucleic Acid Conformation ; Promoter Regions, Genetic ; Protein Binding ; RNA, Messenger/metabolism ; Sodium Chloride/pharmacology ; Templates, Genetic ; *Transcription, Genetic ; Zinc Fingers/genetics/physiology
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    Mapping of catalytic residues in the RNA polymerase active center (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-07-05
    Description: When the Mg2+ ion in the catalytic center of Escherichia coli RNA polymerase (RNAP) is replaced with Fe2+, hydroxyl radicals are generated. In the promoter complex, such radicals cleave template DNA near the transcription start site, whereas the beta' subunit is cleaved at a conserved motif NADFDGD (Asn-Ala-Asp-Phe-Asp-Gly-Asp). Substitution of the three aspartate residues with alanine creates a dominant lethal mutation. The mutant RNAP is catalytically inactive but can bind promoters and form an open complex. The mutant fails to support Fe2+-induced cleavage of DNA or protein. Thus, the NAD-FDGD motif is involved in chelation of the active center Mg2+.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zaychikov, E -- Martin, E -- Denissova, L -- Kozlov, M -- Markovtsov, V -- Kashlev, M -- Heumann, H -- Nikiforov, V -- Goldfarb, A -- Mustaev, A -- New York, N.Y. -- Science. 1996 Jul 5;273(5271):107-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Limnological Institute, Russian Academy of Sciences, Irkutsk, Russia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8658176" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Aspartic Acid/metabolism ; Binding Sites ; DNA/metabolism ; DNA-Directed RNA Polymerases/*chemistry/genetics/*metabolism ; Dithiothreitol/pharmacology ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/*enzymology ; Ferrous Compounds/metabolism ; Hydroxyl Radical ; Magnesium/metabolism ; Molecular Sequence Data ; Mutagenesis ; Promoter Regions, Genetic
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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