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  • 1
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    Template-directed synthesis of a genetic polymer in a model protocell (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-06-06
    Description: Contemporary phospholipid-based cell membranes are formidable barriers to the uptake of polar and charged molecules ranging from metal ions to complex nutrients. Modern cells therefore require sophisticated protein channels and pumps to mediate the exchange of molecules with their environment. The strong barrier function of membranes has made it difficult to understand the origin of cellular life and has been thought to preclude a heterotrophic lifestyle for primitive cells. Although nucleotides can cross dimyristoyl phosphatidylcholine membranes through defects formed at the gel-to-liquid transition temperature, phospholipid membranes lack the dynamic properties required for membrane growth. Fatty acids and their corresponding alcohols and glycerol monoesters are attractive candidates for the components of protocell membranes because they are simple amphiphiles that form bilayer membrane vesicles that retain encapsulated oligonucleotides and are capable of growth and division. Here we show that such membranes allow the passage of charged molecules such as nucleotides, so that activated nucleotides added to the outside of a model protocell spontaneously cross the membrane and take part in efficient template copying in the protocell interior. The permeability properties of prebiotically plausible membranes suggest that primitive protocells could have acquired complex nutrients from their environment in the absence of any macromolecular transport machinery; that is, they could have been obligate heterotrophs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743009/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743009/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mansy, Sheref S -- Schrum, Jason P -- Krishnamurthy, Mathangi -- Tobe, Sylvia -- Treco, Douglas A -- Szostak, Jack W -- F32 GM074506-01/GM/NIGMS NIH HHS/ -- F32 GM07450601/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Jul 3;454(7200):122-5. doi: 10.1038/nature07018. Epub 2008 Jun 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Molecular Biology and the Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18528332" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Transport ; Cell Membrane/chemistry/*metabolism ; Cell Membrane Permeability/physiology ; *Cell Physiological Phenomena ; Fatty Acids/metabolism ; Heterotrophic Processes ; *Models, Biological ; Nucleotides/metabolism ; Oligonucleotides/*metabolism ; Ribose/metabolism ; Templates, Genetic ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Origins of life: Systems chemistry on early Earth (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-05-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Szostak, Jack W -- England -- Nature. 2009 May 14;459(7244):171-2. doi: 10.1038/459171a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19444196" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; *Models, Chemical ; *Origin of Life ; Oxazoles/chemical synthesis/chemistry ; Phosphates/chemistry ; Pyrimidines/*chemical synthesis/chemistry ; Ribonucleotides/*chemical synthesis/chemistry
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    A multisubunit ribozyme that is a catalyst of and template for complementary strand RNA synthesis (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-03-29
    Description: Derivatives of the sunY self-splicing intron efficiently catalyzed the synthesis of complementary strand RNA by template-directed assembly of oligonucleotides. These ribozymes were separated into three short RNA fragments that formed active catalytic complexes. One of the multisubunit sunY derivatives catalyzed the synthesis of a strand of RNA complementary to one of its own subunits. These results suggest that prebiotically synthesized oligonucleotides might have been able to assemble into a complex capable of self-replication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Doudna, J A -- Couture, S -- Szostak, J W -- New York, N.Y. -- Science. 1991 Mar 29;251(5001):1605-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Massachusetts General Hospital, Boston 02114.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1707185" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Composition ; Base Sequence ; *Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligoribonucleotides/metabolism ; RNA/*biosynthesis/genetics ; RNA Splicing ; RNA, Catalytic/*metabolism ; Templates, Genetic ; Tetrahymena/*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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    Stereochemical course of catalysis by the Tetrahymena ribozyme (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-05-12
    Description: The group I intron from Tetrahymena catalyzes phosphodiester transfer reactions on various RNA substrates. A modified RNA substrate with a phosphorothioate group in one stereoisomeric form at the site of reaction was synthesized in order to determine the stereochemical course of an RNA-catalyzed reaction. The reaction product was digested with a stereospecific nuclease to determine the configuration of the product phosphorothioate. The reaction occurs with inversion of configuration at phosphorus, implying an in-line pathway for the reaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rajagopal, J -- Doudna, J A -- Szostak, J W -- New York, N.Y. -- Science. 1989 May 12;244(4905):692-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Massachusetts General Hospital, Boston 02114.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2470151" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Catalysis ; DNA-Directed RNA Polymerases/metabolism ; Exons ; Guanosine/metabolism ; Introns ; Molecular Conformation ; Oligonucleotides/metabolism ; Phosphorus ; RNA/chemical synthesis/metabolism ; RNA Precursors/metabolism ; RNA Splicing ; RNA, Catalytic ; RNA, Ribosomal/*metabolism ; Ribonucleases/metabolism ; Structure-Activity Relationship ; T-Phages/enzymology ; Templates, Genetic ; Tetrahymena/*genetics ; Thionucleotides/metabolism
    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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  • 5
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    Selection of a ribozyme that functions as a superior template in a self-copying reaction (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-12-18
    Description: The sunY ribozyme is derived from a self-splicing RNA group I intron. This ribozyme was chosen as a starting point for the design of a self-replicating RNA because of its small size. As a means of facilitating the self-replication process, the size of this ribozyme was decreased by the deletion of nonconserved structural domains; however, when such deletions were made, there were severe losses of enzymatic activity. In vitro genetic selection was used to identify mutations that reactivate a virtually inactive sunY deletion mutant. A selected mutant with five substitution mutations scattered throughout the primary sequence showed greater catalytic activity than the original ribozyme under the selection conditions. The sunY ribozyme and its small selected variant can both catalyze template-directed oligonucleotide assembly. The small size and reduced secondary structure of the selected variant results in an enhancement, relative to that of the original ribozyme, of its rate of self-copying. This engineered ribozyme is able to function effectively both as a catalyst and as a template in self-copying reactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Green, R -- Szostak, J W -- New York, N.Y. -- Science. 1992 Dec 18;258(5090):1910-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Massachusetts General Hospital, Boston 02114.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1470913" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage T4/*genetics ; Base Sequence ; Escherichia coli/*genetics ; Exons ; Introns ; Models, Structural ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Oligodeoxyribonucleotides ; Oligoribonucleotides ; Polymerase Chain Reaction ; RNA, Catalytic/*biosynthesis/chemistry/genetics ; Sequence Deletion ; Templates, 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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  • 6
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    Experimental models of primitive cellular compartments: encapsulation, growth, and division (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-10-25
    Description: The clay montmorillonite is known to catalyze the polymerization of RNA from activated ribonucleotides. Here we report that montmorillonite accelerates the spontaneous conversion of fatty acid micelles into vesicles. Clay particles often become encapsulated in these vesicles, thus providing a pathway for the prebiotic encapsulation of catalytically active surfaces within membrane vesicles. In addition, RNA adsorbed to clay can be encapsulated within vesicles. Once formed, such vesicles can grow by incorporating fatty acid supplied as micelles and can divide without dilution of their contents by extrusion through small pores. These processes mediate vesicle replication through cycles of growth and division. The formation, growth, and division of the earliest cells may have occurred in response to similar interactions with mineral particles and inputs of material and energy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4484575/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4484575/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hanczyc, Martin M -- Fujikawa, Shelly M -- Szostak, Jack W -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2003 Oct 24;302(5645):618-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14576428" target="_blank"〉PubMed〈/a〉
    Keywords: Adsorption ; Aluminum Silicates/chemistry ; Bentonite/*chemistry ; Catalysis ; Ceramics ; Chemistry, Physical ; Fatty Acids/*chemistry ; Fatty Acids, Monounsaturated/chemistry ; Fluoresceins/chemistry ; Fluorescence Resonance Energy Transfer ; Hydrogen-Ion Concentration ; Light ; Lipid Bilayers/*chemistry ; *Micelles ; Microspheres ; Models, Theoretical ; Myristic Acid/chemistry ; Physicochemical Phenomena ; RNA/*chemistry ; Scattering, Radiation ; Surface Properties
    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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  • 7
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    The emergence of competition between model protocells (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-09-09
    Description: The transition from independent molecular entities to cellular structures with integrated behaviors was a crucial aspect of the origin of life. We show that simple physical principles can mediate a coordinated interaction between genome and compartment boundary, independent of any genomic functions beyond self-replication. RNA, encapsulated in fatty acid vesicles, exerts an osmotic pressure on the vesicle membrane that drives the uptake of additional membrane components, leading to membrane growth at the expense of relaxed vesicles, which shrink. Thus, more efficient RNA replication could cause faster cell growth, leading to the emergence of Darwinian evolution at the cellular level.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4484590/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4484590/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Irene A -- Roberts, Richard W -- Szostak, Jack W -- T32 GM007753/GM/NIGMS NIH HHS/ -- T32-GM07753/GM/NIGMS NIH HHS/ -- T32-GM08313/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2004 Sep 3;305(5689):1474-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, and Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15353806" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Evolution ; *Cell Physiological Phenomena ; Fatty Acids ; Fatty Acids, Monounsaturated ; Fluorescence Resonance Energy Transfer ; Genome ; *Liposomes ; Oleic Acid ; *Osmotic Pressure ; *RNA/metabolism ; RNA, Transfer
    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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    Isolation of new ribozymes from a large pool of random sequences [see comment] (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-09-10
    Description: An iterative in vitro selection procedure was used to isolate a new class of catalytic RNAs (ribozymes) from a large pool of random-sequence RNA molecules. These ribozymes ligate two RNA molecules that are aligned on a template by catalyzing the attack of a 3'-hydroxyl on an adjacent 5'-triphosphate--a reaction similar to that employed by the familiar protein enzymes that synthesize RNA. The corresponding uncatalyzed reaction also yields a 3',5'-phosphodiester bond. In vitro evolution of the population of new ribozymes led to improvement of the average ligation activity and the emergence of ribozymes with reaction rates 7 million times faster than the uncatalyzed reaction rate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bartel, D P -- Szostak, J W -- New York, N.Y. -- Science. 1993 Sep 10;261(5127):1411-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Massachusetts General Hospital, Boston 02114.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7690155" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Biological Evolution ; Catalysis ; Kinetics ; Magnesium/metabolism ; Molecular Sequence Data ; Mutation ; Oligoribonucleotides/metabolism ; RNA/*metabolism ; RNA Ligase (ATP)/chemistry/isolation & purification/metabolism ; RNA, Catalytic/chemistry/*isolation & purification/metabolism ; Temperature ; Templates, 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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  • 9
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    Structurally complex and highly active RNA ligases derived from random RNA sequences (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-07-21
    Description: Seven families of RNA ligases, previously isolated from random RNA sequences, fall into three classes on the basis of secondary structure and regiospecificity of ligation. Two of the three classes of ribozymes have been engineered to act as true enzymes, catalyzing the multiple-turnover transformation of substrates into products. The most complex of these ribozymes has a minimal catalytic domain of 93 nucleotides. An optimized version of this ribozyme has a kcat exceeding one per second, a value far greater than that of most natural RNA catalysts and approaching that of comparable protein enzymes. The fact that such a large and complex ligase emerged from a very limited sampling of sequence space implies the existence of a large number of distinct RNA structures of equivalent complexity and activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ekland, E H -- Szostak, J W -- Bartel, D P -- New York, N.Y. -- Science. 1995 Jul 21;269(5222):364-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7618102" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Catalysis ; Cloning, Molecular ; Conserved Sequence ; Introns ; Molecular Sequence Data ; Mutagenesis ; *Nucleic Acid Conformation ; Point Mutation ; RNA, Catalytic/*chemistry/classification/*metabolism ; Sequence Deletion
    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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  • 10
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    A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-23
    Description: Ribozymes are thought to have played a pivotal role in the early evolution of life, but relatively few have been identified in modern organisms. We performed an in vitro selection aimed at isolating self-cleaving RNAs from the human genome. The selection yielded several ribozymes, one of which is a conserved mammalian sequence that resides in an intron of the CPEB3 gene, which belongs to a family of genes regulating messenger RNA polyadenylation. The CPEB3 ribozyme is structurally and biochemically related to the human hepatitis delta virus (HDV) ribozymes. The occurrence of this ribozyme exclusively in mammals suggests that it may have evolved as recently as 200 million years ago. We postulate that HDV arose from the human transcriptome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Salehi-Ashtiani, Kourosh -- Luptak, Andrej -- Litovchick, Alexander -- Szostak, Jack W -- GM53936/GM/NIGMS NIH HHS/ -- HL66678/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2006 Sep 22;313(5794):1788-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology (CCIB), 7215 Simches Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16990549" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Base Sequence ; Catalysis ; Cations, Divalent/metabolism ; Conserved Sequence ; *Evolution, Molecular ; Expressed Sequence Tags ; *Genome, Human ; Genomic Library ; Hepatitis Delta Virus/genetics ; Humans ; Hydrogen-Ion Concentration ; *Introns ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Phosphorylation ; RNA, Catalytic/chemistry/genetics/*isolation & purification/*metabolism ; RNA-Binding Proteins/*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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