J A Doudna

Summary

Affiliation: Yale University
Country: USA

Publications

  1. ncbi request reprint RNA folds: insights from recent crystal structures
    A R Ferré-D'amaré
    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520 8114, USA
    Annu Rev Biophys Biomol Struct 28:57-73. 1999
  2. ncbi request reprint Crystal structure of a group I ribozyme domain: principles of RNA packing
    J H Cate
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Science 273:1678-85. 1996
  3. ncbi request reprint The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold
    J S Kieft
    Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520 8114, USA
    J Mol Biol 292:513-29. 1999
  4. ncbi request reprint Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle
    R T Batey
    Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, P O Box 208114, New Haven, CT 06520 8814, USA
    J Mol Biol 307:229-46. 2001
  5. ncbi request reprint Direct pK(a) measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme
    A Luptak
    Department of Chemistry, Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA
    J Am Chem Soc 123:8447-52. 2001
  6. ncbi request reprint A universal mode of helix packing in RNA
    E A Doherty
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Nat Struct Biol 8:339-43. 2001
  7. ncbi request reprint Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit
    C M Spahn
    Howard Hughes Medical Institute, Health Research Inc. at the, Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA
    Science 291:1959-62. 2001
  8. ncbi request reprint Ribozyme structures and mechanisms
    E A Doherty
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Annu Rev Biochem 69:597-615. 2000
  9. ncbi request reprint Ribozyme structures and mechanisms
    E A Doherty
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Annu Rev Biophys Biomol Struct 30:457-75. 2001
  10. ncbi request reprint RNA structure: crystal clear?
    J A Doudna
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    Curr Opin Struct Biol 7:310-6. 1997

Collaborators

Detail Information

Publications20

  1. ncbi request reprint RNA folds: insights from recent crystal structures
    A R Ferré-D'amaré
    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520 8114, USA
    Annu Rev Biophys Biomol Struct 28:57-73. 1999
    ..These structures illustrate, to varying degrees, three modes of fold stabilization: association of complementary molecular surfaces, stabilization of close RNA packing by binding of cations, and stabilization through pseudoknotting...
  2. ncbi request reprint Crystal structure of a group I ribozyme domain: principles of RNA packing
    J H Cate
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Science 273:1678-85. 1996
    ..Metal- and ribose-mediated backbone contacts further stabilize the close side-by-side helical packing. The structure indicates the extent of RNA packing required for the function of large ribozymes, the spliceosome, and the ribosome...
  3. ncbi request reprint The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold
    J S Kieft
    Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520 8114, USA
    J Mol Biol 292:513-29. 1999
    ..These results suggest that the 40 S ribosomal subunit and eIF3 bind an HCV IRES that is prefolded to spatially organize recognition domains...
  4. ncbi request reprint Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle
    R T Batey
    Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, P O Box 208114, New Haven, CT 06520 8814, USA
    J Mol Biol 307:229-46. 2001
    ..This analysis reveals how conserved nucleotides within the two internal loop motifs establish the architecture of the macromolecular interface and position essential functional groups for direct recognition by the protein...
  5. ncbi request reprint Direct pK(a) measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme
    A Luptak
    Department of Chemistry, Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA
    J Am Chem Soc 123:8447-52. 2001
    ..While additional results suggest that the pK(a) is not shifted in the reactant state of the ribozyme, these data cannot rule out elevation of the C75 pK(a) in an intermediate state of the transesterification reaction...
  6. ncbi request reprint A universal mode of helix packing in RNA
    E A Doherty
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Nat Struct Biol 8:339-43. 2001
    ..These results provide a thermodynamic explanation for the noted abundance of conserved adenosines within the unpaired regions of RNA secondary structures...
  7. ncbi request reprint Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit
    C M Spahn
    Howard Hughes Medical Institute, Health Research Inc. at the, Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA
    Science 291:1959-62. 2001
    ..IRES binding induces a pronounced conformational change in the 40S subunit and closes the mRNA binding cleft, suggesting a mechanism for IRES-mediated positioning of mRNA in the ribosomal decoding center...
  8. ncbi request reprint Ribozyme structures and mechanisms
    E A Doherty
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Annu Rev Biochem 69:597-615. 2000
    ..The organization of these small catalysts is contrasted to that of larger ribozymes, such as the group I intron...
  9. ncbi request reprint Ribozyme structures and mechanisms
    E A Doherty
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Annu Rev Biophys Biomol Struct 30:457-75. 2001
    ..The organization of these small catalysts is contrasted to that of larger ribozymes, such as the group I intron...
  10. ncbi request reprint RNA structure: crystal clear?
    J A Doudna
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    Curr Opin Struct Biol 7:310-6. 1997
    ..Recent crystal structures of hammerhead ribozymes, a group I intron domain, and RNA duplexes provide new insights into the principles of RNA folding and function...
  11. pmc The stem-loop binding protein forms a highly stable and specific complex with the 3' stem-loop of histone mRNAs
    D J Battle
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    RNA 7:123-32. 2001
    ..Together, these results suggest a novel mode of protein-RNA recognition that forms the core of a ribonucleoprotein complex central to the regulation of histone gene expression...
  12. ncbi request reprint Structural genomics of RNA
    J A Doudna
    Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Nat Struct Biol 7:954-6. 2000
    ....
  13. ncbi request reprint Crystal structure of the ribonucleoprotein core of the signal recognition particle
    R T Batey
    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA
    Science 287:1232-9. 2000
    ..The structure explains why the conserved residues in the protein and RNA are required for SRP assembly and defines a signal sequence recognition surface composed of both protein and RNA...
  14. ncbi request reprint Crystal structure of a hepatitis delta virus ribozyme
    A R Ferré-D'amaré
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    Nature 395:567-74. 1998
    ....
  15. ncbi request reprint Emerging themes in RNA folding
    J A Doudna
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    Fold Des 2:R65-70. 1997
    ....
  16. pmc Mechanism of ribosome recruitment by hepatitis C IRES RNA
    J S Kieft
    Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8114, USA
    RNA 7:194-206. 2001
    ....
  17. ncbi request reprint Metal ions in ribozyme folding and catalysis
    R Hanna
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Curr Opin Chem Biol 4:166-70. 2000
    ..Similarly, reaction conditions can allow different folding pathways to predominate, with divalent cations sometimes playing opposing roles...
  18. ncbi request reprint Ribozymes: the hammerhead swings into action
    J A Doudna
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    Curr Biol 8:R495-7. 1998
    ..A new crystal structure of a modified hammerhead ribozyme reveals an intermediate conformation that may explain discrepancies between previous structures and the required orientation of the labile bond in the ribozyme's active site...
  19. ncbi request reprint Structure of Dicer and mechanistic implications for RNAi
    I J MacRae
    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
    Cold Spring Harb Symp Quant Biol 71:73-80. 2006
    ..Finally, we combine the structure of Dicer with published biochemical data to propose a model for the architecture of the RNA-induced silencing complex (RISC)-loading complex...
  20. ncbi request reprint Large-scale purification of a stable form of recombinant tobacco etch virus protease
    L J Lucast
    Yale University, New Haven, CT, USA
    Biotechniques 30:544-6, 548, 550 passim. 2001
    ..5 mg enzyme per liter of bacterial cell culture. NIa-Pro purified according to this protocol has been used for quantitative removal of fusion domains from a variety of proteins prepared for crystallization and biochemical analysis...