Gerald F Joyce

Summary

Affiliation: The Scripps Research Institute
Country: USA

Publications

  1. ncbi request reprint The antiquity of RNA-based evolution
    Gerald F Joyce
    Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Nature 418:214-21. 2002
  2. pmc Deep sequencing analysis of mutations resulting from the incorporation of dNTP analogs
    Katherine L Petrie
    Department of Chemistry, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA 92037, USA
    Nucleic Acids Res 38:8095-104. 2010
  3. pmc Autocatalytic aptazymes enable ligand-dependent exponential amplification of RNA
    Bianca J Lam
    Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Nat Biotechnol 27:288-92. 2009
  4. pmc Bit by bit: the Darwinian basis of life
    Gerald F Joyce
    Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
    PLoS Biol 10:e1001323. 2012
  5. pmc A complex ligase ribozyme evolved in vitro from a group I ribozyme domain
    L Jaeger
    Institut de Biologie Moleculaire et Cellulaire du Centre National de la Recherche Scientifique, 15 rue Descartes, 67084 Strasbourg, France
    Proc Natl Acad Sci U S A 96:14712-7. 1999
  6. ncbi request reprint Structural biology. A glimpse of biology's first enzyme
    Gerald F Joyce
    Departments of Chemistry and of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
    Science 315:1507-8. 2007
  7. pmc The implausibility of metabolic cycles on the prebiotic Earth
    Leslie E Orgel
    The Salk Institute for BiologicalStudies, San Diego, California, United States ofAmerica
    PLoS Biol 6:e18. 2008
  8. ncbi request reprint Directed evolution of nucleic acid enzymes
    Gerald F Joyce
    Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Annu Rev Biochem 73:791-836. 2004
  9. ncbi request reprint The promise and peril of continuous in vitro evolution
    Glenn C Johns
    Departments of Chemistry and Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Evol 61:253-63. 2005
  10. ncbi request reprint Forty years of in vitro evolution
    Gerald F Joyce
    Department of Chemistry and Molecular Biology, La Jolla, CA 92037, USA
    Angew Chem Int Ed Engl 46:6420-36. 2007

Research Grants

  1. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2002
  2. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2007
  3. Directed Evolution of Nucleic Acid Enzymes
    Gerald F Joyce; Fiscal Year: 2010
  4. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2003
  5. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2004
  6. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2005
  7. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2009

Collaborators

Detail Information

Publications40

  1. ncbi request reprint The antiquity of RNA-based evolution
    Gerald F Joyce
    Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Nature 418:214-21. 2002
    ..This earlier era is referred to as the 'RNA world', during which the genetic information resided in the sequence of RNA molecules and the phenotype derived from the catalytic properties of RNA...
  2. pmc Deep sequencing analysis of mutations resulting from the incorporation of dNTP analogs
    Katherine L Petrie
    Department of Chemistry, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA 92037, USA
    Nucleic Acids Res 38:8095-104. 2010
    ..Most of the variation appears to result from idiosyncratic features that derive from local sequence context, demonstrating how different genetic sequences have different chemical phenotypes...
  3. pmc Autocatalytic aptazymes enable ligand-dependent exponential amplification of RNA
    Bianca J Lam
    Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Nat Biotechnol 27:288-92. 2009
    ..This process is analogous to quantitative PCR (qPCR) but can be generalized to a wide variety of targets, including proteins and small molecules that are relevant to medical diagnostics and environmental monitoring...
  4. pmc Bit by bit: the Darwinian basis of life
    Gerald F Joyce
    Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
    PLoS Biol 10:e1001323. 2012
    ....
  5. pmc A complex ligase ribozyme evolved in vitro from a group I ribozyme domain
    L Jaeger
    Institut de Biologie Moleculaire et Cellulaire du Centre National de la Recherche Scientifique, 15 rue Descartes, 67084 Strasbourg, France
    Proc Natl Acad Sci U S A 96:14712-7. 1999
    ..This work demonstrates that complex RNA molecules, like their protein counterparts, can share common structural domains while exhibiting distinct catalytic functions...
  6. ncbi request reprint Structural biology. A glimpse of biology's first enzyme
    Gerald F Joyce
    Departments of Chemistry and of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
    Science 315:1507-8. 2007
  7. pmc The implausibility of metabolic cycles on the prebiotic Earth
    Leslie E Orgel
    The Salk Institute for BiologicalStudies, San Diego, California, United States ofAmerica
    PLoS Biol 6:e18. 2008
  8. ncbi request reprint Directed evolution of nucleic acid enzymes
    Gerald F Joyce
    Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Annu Rev Biochem 73:791-836. 2004
    ..The difficulty of this reaction, and therefore the complexity of the corresponding DNA enzyme, depends on whether a catalytic cofactor, such as a divalent metal cation or small molecule, is present in the reaction mixture...
  9. ncbi request reprint The promise and peril of continuous in vitro evolution
    Glenn C Johns
    Departments of Chemistry and Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Evol 61:253-63. 2005
    ..It offers a candid appraisal of both the strengths and the limitations of these systems...
  10. ncbi request reprint Forty years of in vitro evolution
    Gerald F Joyce
    Department of Chemistry and Molecular Biology, La Jolla, CA 92037, USA
    Angew Chem Int Ed Engl 46:6420-36. 2007
    ..This Review summarizes the concepts and methods for the directed evolution of RNA molecules in vitro...
  11. ncbi request reprint Self-replication
    Natasha Paul
    Department of Chemistry, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, 92037, La Jolla, CA, USA
    Curr Biol 13:R46. 2003
  12. pmc Evolution in an RNA world
    G F Joyce
    Departments of Chemistry and Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Cold Spring Harb Symp Quant Biol 74:17-23. 2009
    ..This is the first example, outside of biology, of evolutionary adaptation in a molecular genetic system...
  13. ncbi request reprint RNA structure. Ribozyme evolution at the crossroads
    G F Joyce
    Department of Chemistry, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Science 289:401-2. 2000
    ..In a remarkable study (Schultes and Bartel), an RNA sequence has been designed that can adopt two different structures, each with a different catalytic function. Joyce details how this study sheds light on the evolution of enzymes...
  14. ncbi request reprint Continuous in vitro evolution of a ribozyme that catalyzes three successive nucleotidyl addition reactions
    Kathleen E McGinness
    Department of Chemistry and The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Chem Biol 9:585-96. 2002
    ..This purely chemical system provides a functional model of a multi-step reaction pathway that is undergoing Darwinian evolution...
  15. ncbi request reprint A ribozyme composed of only two different nucleotides
    John S Reader
    Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Nature 420:841-4. 2002
    ..This ribozyme is specific for the formation of biologically relevant 3',5'-phosphodiester linkages...
  16. pmc Emergence of a fast-reacting ribozyme that is capable of undergoing continuous evolution
    Sarah B Voytek
    Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 104:15288-93. 2007
    ..Now that two distinct species of continuously evolving enzymes have been established, it is possible to conduct molecular ecology experiments in which the two are made to compete for limited resources within a common environment...
  17. pmc Niche partitioning in the coevolution of 2 distinct RNA enzymes
    Sarah B Voytek
    Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 106:7780-5. 2009
    ....
  18. pmc Self-sustained replication of an RNA enzyme
    Tracey A Lincoln
    Department of Chemistry and Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA 92037, USA
    Science 323:1229-32. 2009
    ..These replicating RNA enzymes can serve as an experimental model of a genetic system. Many such model systems could be constructed, allowing different selective outcomes to be related to the underlying properties of the genetic system...
  19. ncbi request reprint Minimal self-replicating systems
    Natasha Paul
    Departments of Chemistry and Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA 92037, USA
    Curr Opin Chem Biol 8:634-9. 2004
    ..This review analyzes chemical self-replicating systems that have been developed to date and discusses ongoing challenges in this area of research...
  20. pmc A self-replicating ligase ribozyme
    Natasha Paul
    Departments of Chemistry and Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 99:12733-40. 2002
    ..Further optimization of the system may lead to the sustained exponential growth of ribozymes that undergo self-replication...
  21. pmc A modular, bifunctional RNA that integrates itself into a target RNA
    Roshan M Kumar
    Department of Chemistry, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 100:9738-43. 2003
    ..These molecules also may be useful as tools for the insertional mutagenesis of target mRNAs...
  22. ncbi request reprint RNA-cleaving DNA enzymes with altered regio- or enantioselectivity
    Phillip Ordoukhanian
    Departments of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    J Am Chem Soc 124:12499-506. 2002
    ..These molecules demonstrate how in vitro evolution can be used to obtain regio- and enantioselective catalysts that exhibit specificities for nonnatural analogues of biological compounds...
  23. ncbi request reprint Conversion of a ribozyme to a deoxyribozyme through in vitro evolution
    Natasha Paul
    Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Chem Biol 13:329-38. 2006
    ..This transfer of both information and function is relevant to the transition between two different genetic systems based on nucleic acid-like molecules, as postulated to have occurred during the early history of life on Earth...
  24. ncbi request reprint A DNA-templated aldol reaction as a model for the formation of pentose sugars in the RNA world
    Michael Oberhuber
    Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
    Angew Chem Int Ed Engl 44:7580-3. 2005
  25. ncbi request reprint RNA-catalyzed RNA ligation on an external RNA template
    Kathleen E McGinness
    Department of Chemistry, The Skaggs Institute for Chemical Biology, La Jolla, CA 92037, USA
    Chem Biol 9:297-307. 2002
    ..The development of ribozymes that catalyze polymerase-type reactions contributes to the notion that an RNA world could have existed during the early history of life on Earth...
  26. ncbi request reprint In search of an RNA replicase ribozyme
    Kathleen E McGinness
    Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Chem Biol 10:5-14. 2003
    ....
  27. ncbi request reprint Perfectly complementary nucleic acid enzymes
    Scott T Kuhns
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Evol 56:711-7. 2003
    ..The ability to generate functional nucleic acids encoded by both strands of a duplex has implications for the evolution of catalytic nucleic acids and the prospects for realizing maximum functionality from a given genetic sequence...
  28. pmc Binding of a structured D-RNA molecule by an L-RNA aptamer
    Jonathan T Sczepanski
    Departments of Chemistry and Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
    J Am Chem Soc 135:13290-3. 2013
    ..This suggests that L-aptamers, which are intrinsically resistant to degradation by ribonucleases, might be pursued as an alternative to antisense oligonucleotides to target structured RNAs of biological or therapeutic interest...
  29. ncbi request reprint Continuous in vitro evolution of ribozymes that operate under conditions of extreme pH
    Henriette Kühne
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Evol 57:292-8. 2003
    ..The results establish continuous in vitro evolution as a useful model system for exploring the evolution of enzymatic function in extreme environments...
  30. pmc An isothermal system that couples ligand-dependent catalysis to ligand-independent exponential amplification
    Bianca J Lam
    Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    J Am Chem Soc 133:3191-7. 2011
    ..This system is analogous to quantitative polymerase chain reaction (PCR), linking rare recognition events to subsequent exponential amplification, but unlike PCR can be applied to the quantitative detection of non-nucleic acid ligands...
  31. pmc Microfluidic compartmentalized directed evolution
    Brian M Paegel
    Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
    Chem Biol 17:717-24. 2010
    ..During five rounds of this procedure, the enzymes acquired mutations that conferred resistance to neomycin and caused some enzymes to become dependent on neomycin for optimal activity...
  32. pmc Kinetic properties of an RNA enzyme that undergoes self-sustained exponential amplification
    Antonio C Ferretti
    Departments of Chemistry and Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Biochemistry 52:1227-35. 2013
    ..An analysis of this and other kinetic properties of the self-replicating RNA enzymes reveals how exponential amplification is achieved and how the rate of amplification might be increased...
  33. ncbi request reprint Substitution of ribonucleotides in the T7 RNA polymerase promoter element
    Kathleen E McGinness
    Department of Chemistry, The Skaggs Institute for Chemical Biology, La Jolla, California 92037, USA
    J Biol Chem 277:2987-91. 2002
    ....
  34. ncbi request reprint A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron
    William M Shih
    Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Nature 427:618-21. 2004
    ..Because the base-pair sequence of individual struts is not repeated in a given octahedron, each strut is uniquely addressable by the appropriate sequence-specific DNA binder...
  35. pmc Synthetic evolving systems that implement a user-specified genetic code of arbitrary design
    Jonathan T Sczepanski
    Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
    Chem Biol 19:1324-32. 2012
    ..This evolutionary outcome was a consequence of the information capacity and fidelity of the genetic code, suggesting how these parameters should be adjusted to implement codes tailored to particular applications...
  36. pmc Ligand-dependent exponential amplification of a self-replicating L-RNA enzyme
    Charles Olea
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
    J Am Chem Soc 134:8050-3. 2012
    ..In addition, this work provides the first demonstration of the self-sustained exponential amplification of nonbiological molecules...
  37. pmc Darwinian evolution on a chip
    Brian M Paegel
    Department of Chemistry, The Scripps Research Institute, La Jolla, California, United States of America
    PLoS Biol 6:e85. 2008
    ..This system reduces evolution to a microfluidic algorithm, allowing the experimenter to observe and manipulate adaptation...
  38. ncbi request reprint Cross-catalytic replication of an RNA ligase ribozyme
    Dong Eun Kim
    Department of Chemistry and Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Chem Biol 11:1505-12. 2004
    ..As the concentration of the two ribozymes increases, the rate of formation of additional ribozyme molecules increases, consistent with the overall autocatalytic behavior of the reaction system...
  39. ncbi request reprint Obituary: Leslie Orgel (1927-2007)
    Gerald F Joyce
    Gerald F Joyce is in the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
    Nature 450:627. 2007
  40. ncbi request reprint Molecular evolution: booting up life
    Gerald F Joyce
    Nature 420:278-9. 2002

Research Grants8

  1. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2002
    ..The adapter will allow the cofactor to be bound readily by the enzyme, allowing evolution to exploit the bound cofactor for use in catalysis. ..
  2. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2007
    ..These decorated nanostructures then will be subject to in vitro evolution, selecting on the basis of both their form and the function of the appended DNAs. ..
  3. Directed Evolution of Nucleic Acid Enzymes
    Gerald F Joyce; Fiscal Year: 2010
    ..These decorated nanostructures then will be subject to in vitro evolution, selecting on the basis of both their form and the function of the appended DNAs. ..
  4. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2003
    ..The adapter will allow the cofactor to be bound readily by the enzyme, allowing evolution to exploit the bound cofactor for use in catalysis. ..
  5. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2004
    ..The adapter will allow the cofactor to be bound readily by the enzyme, allowing evolution to exploit the bound cofactor for use in catalysis. ..
  6. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2005
    ..The adapter will allow the cofactor to be bound readily by the enzyme, allowing evolution to exploit the bound cofactor for use in catalysis. ..
  7. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2009
    ..These decorated nanostructures then will be subject to in vitro evolution, selecting on the basis of both their form and the function of the appended DNAs. ..