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    22837 Publications
    3073 Total Profiles
    23 Edited Profiles

    Doudna, Jennifer

    TitleBiologist Faculty
    SchoolLawrence Berkeley National Lab
    DepartmentPhysical Biosciences
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/643-0225

       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can sign in to make corrections and additions, or contact us for help.
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      1. Knight SC, Xie L, Deng W, Guglielmi B, Witkowsky LB, Bosanac L, Zhang ET, El Beheiry M, Masson JB, Dahan M, Liu Z, Doudna JA, Tjian R. Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science. 2015 Nov 13; 350(6262):823-6.
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      2. Redding S, Sternberg SH, Marshall M, Gibb B, Bhat P, Guegler CK, Wiedenheft B, Doudna JA, Greene EC. Surveillance and Processing of Foreign DNA by the Escherichia coli CRISPR-Cas System. Cell. 2015 Nov 5; 163(4):854-65.
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      3. Ma E, Harrington LB, O'Connell MR, Zhou K, Doudna JA. Single-Stranded DNA Cleavage by Divergent CRISPR-Cas9 Enzymes. Mol Cell. 2015 Nov 5; 60(3):398-407.
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      4. Sternberg SH, LaFrance B, Kaplan M, Doudna JA. Conformational control of DNA target cleavage by CRISPR-Cas9. Nature. 2015 Nov 5; 527(7576):110-3.
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      5. Nuñez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA. Foreign DNA capture during CRISPR-Cas adaptive immunity. Nature. 2015 Nov 26; 527(7579):535-8.
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      6. Kranzusch PJ, Wilson SC, Lee AS, Berger JM, Doudna JA, Vance RE. Ancient Origin of cGAS-STING Reveals Mechanism of Universal 2',3' cGAMP Signaling. Mol Cell. 2015 Sep 17; 59(6):891-903.
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      7. Schumann K, Lin S, Boyer E, Simeonov DR, Subramaniam M, Gate RE, Haliburton GE, Ye CJ, Bluestone JA, Doudna JA, Marson A. Generation of knock-in primary human T cells using Cas9 ribonucleoproteins. Proc Natl Acad Sci U S A. 2015 Aug 18; 112(33):10437-42.
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      8. Jiang F, Zhou K, Ma L, Gressel S, Doudna JA. STRUCTURAL BIOLOGY. A Cas9-guide RNA complex preorganized for target DNA recognition. Science. 2015 Jun 26; 348(6242):1477-81.
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      9. Sternberg SH, Doudna JA. Expanding the Biologist's Toolkit with CRISPR-Cas9. Mol Cell. 2015 May 21; 58(4):568-74.
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      10. Bosley KS, Botchan M, Bredenoord AL, Carroll D, Charo RA, Charpentier E, Cohen R, Corn J, Doudna J, Feng G, Greely HT, Isasi R, Ji W, Kim JS, Knoppers B, Lanphier E, Li J, Lovell-Badge R, Martin GS, Moreno J, Naldini L, Pera M, Perry AC, Venter JC, Zhang F, Zhou Q. CRISPR germline engineering-the community speaks. Nat Biotechnol. 2015 May 12; 33(5):478-86.
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      11. Taylor DW, Zhu Y, Staals RH, Kornfeld JE, Shinkai A, van der Oost J, Nogales E, Doudna JA. Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning. Science. 2015 May 1; 348(6234):581-5.
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      12. Baltimore D, Berg P, Botchan M, Carroll D, Charo RA, Church G, Corn JE, Daley GQ, Doudna JA, Fenner M, Greely HT, Jinek M, Martin GS, Penhoet E, Puck J, Sternberg SH, Weissman JS, Yamamoto KR. Biotechnology. A prudent path forward for genomic engineering and germline gene modification. Science. 2015 Apr 3; 348(6230):36-8.
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      13. Doudna JA. Genomic engineering and the future of medicine. JAMA. 2015 Feb 24; 313(8):791-2.
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      14. Jiang F, Doudna JA. The structural biology of CRISPR-Cas systems. Curr Opin Struct Biol. 2015 Feb; 30:100-11.
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      15. Wright AV, Sternberg SH, Taylor DW, Staahl BT, Bardales JA, Kornfeld JE, Doudna JA. Rational design of a split-Cas9 enzyme complex. Proc Natl Acad Sci U S A. 2015 Mar 10; 112(10):2984-9.
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      16. Nuñez JK, Lee AS, Engelman A, Doudna JA. Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity. Nature. 2015 Mar 12; 519(7542):193-8.
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      17. Wilson RC, Tambe A, Kidwell MA, Noland CL, Schneider CP, Doudna JA. Dicer-TRBP Complex Formation Ensures Accurate Mammalian MicroRNA Biogenesis. Mol Cell. 2015 Feb 5; 57(3):397-407.
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      18. Lin S, Staahl BT, Alla RK, Doudna JA. Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. Elife. 2014; 4.
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      19. Doudna JA, Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014 Nov 28; 346(6213):1258096.
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      20. Hochstrasser ML, Doudna JA. Cutting it close: CRISPR-associated endoribonuclease structure and function. Trends Biochem Sci. 2015 Jan; 40(1):58-66.
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      21. Staals RH, Zhu Y, Taylor DW, Kornfeld JE, Sharma K, Barendregt A, Koehorst JJ, Vlot M, Neupane N, Varossieau K, Sakamoto K, Suzuki T, Dohmae N, Yokoyama S, Schaap PJ, Urlaub H, Heck AJ, Nogales E, Doudna JA, Shinkai A, van der Oost J. RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus. Mol Cell. 2014 Nov 20; 56(4):518-30.
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      22. Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS. New tools provide a second look at HDV ribozyme structure, dynamics and cleavage. Nucleic Acids Res. 2014 Nov 10; 42(20):12833-46.
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      23. O'Connell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature. 2014 Dec 11; 516(7530):263-6.
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      24. Bai Y, Tambe A, Zhou K, Doudna JA. RNA-guided assembly of Rev-RRE nuclear export complexes. Elife. 2014; 3:e03656.
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      25. Kidwell MA, Chan JM, Doudna JA. Evolutionarily conserved roles of the dicer helicase domain in regulating RNA interference processing. J Biol Chem. 2014 Oct 10; 289(41):28352-62.
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      26. Kranzusch PJ, Lee AS, Wilson SC, Solovykh MS, Vance RE, Berger JM, Doudna JA. Structure-Guided Reprogramming of Human cGAS Dinucleotide Linkage Specificity. Cell. 2014 Aug 28; 158(5):1011-21.
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      27. Mortimer SA, Kidwell MA, Doudna JA. Insights into RNA structure and function from genome-wide studies. Nat Rev Genet. 2014 Jul; 15(7):469-79.
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      28. Nuñez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA. Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nat Struct Mol Biol. 2014 Jun; 21(6):528-34.
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      29. Hochstrasser ML, Taylor DW, Bhat P, Guegler CK, Sternberg SH, Nogales E, Doudna JA. CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference. Proc Natl Acad Sci U S A. 2014 May 6; 111(18):6618-23.
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      30. Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Anders C, Hauer M, Zhou K, Lin S, Kaplan M, Iavarone AT, Charpentier E, Nogales E, Doudna JA. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science. 2014 Mar 14; 343(6176):1247997.
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      31. Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature. 2014 Mar 6; 507(7490):62-7.
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      32. Doudna JA, Sontheimer EJ. Preface. Methods Enzymol. 2014; 546:xix-xx.
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      33. Niewoehner O, Jinek M, Doudna JA. Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Nucleic Acids Res. 2014 Jan 1; 42(2):1341-53.
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      34. Staals RH, Agari Y, Maki-Yonekura S, Zhu Y, Taylor DW, van Duijn E, Barendregt A, Vlot M, Koehorst JJ, Sakamoto K, Masuda A, Dohmae N, Schaap PJ, Doudna JA, Heck AJ, Yonekura K, van der Oost J, Shinkai A. Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus. Mol Cell. 2013 Oct 10; 52(1):135-45.
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      35. Cox EM, Sagan SM, Mortimer SA, Doudna JA, Sarnow P. Enhancement of hepatitis C viral RNA abundance by precursor miR-122 molecules. RNA. 2013 Dec; 19(12):1825-32.
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      36. Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol. 2013 Sep; 31(9):839-43.
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      37. Lo TW, Pickle CS, Lin S, Ralston EJ, Gurling M, Schartner CM, Bian Q, Doudna JA, Meyer BJ. Precise and heritable genome editing in evolutionarily diverse nematodes using TALENs and CRISPR/Cas9 to engineer insertions and deletions. Genetics. 2013 Oct; 195(2):331-48.
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      38. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA, Weissman JS, Qi LS. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. 2013 Jul 18; 154(2):442-51.
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      39. Kidwell MA, Doudna JA. Activating silent argonautes. Nat Struct Mol Biol. 2013 Jul; 20(7):769-71.
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      40. Bai Y, Zhou K, Doudna JA. Hepatitis C virus 3'UTR regulates viral translation through direct interactions with the host translation machinery. Nucleic Acids Res. 2013 Sep; 41(16):7861-74.
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      41. Sun C, Querol-Audí J, Mortimer SA, Arias-Palomo E, Doudna JA, Nogales E, Cate JH. Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation. Nucleic Acids Res. 2013 Aug; 41(15):7512-21.
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      42. Kranzusch PJ, Lee AS, Berger JM, Doudna JA. Structure of human cGAS reveals a conserved family of second-messenger enzymes in innate immunity. Cell Rep. 2013 May 30; 3(5):1362-8.
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      43. Lee HY, Zhou K, Smith AM, Noland CL, Doudna JA. Differential roles of human Dicer-binding proteins TRBP and PACT in small RNA processing. Nucleic Acids Res. 2013 Jul; 41(13):6568-76.
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      44. Taylor DW, Ma E, Shigematsu H, Cianfrocco MA, Noland CL, Nagayama K, Nogales E, Doudna JA, Wang HW. Substrate-specific structural rearrangements of human Dicer. Nat Struct Mol Biol. 2013 Jun; 20(6):662-70.
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      45. Noland CL, Doudna JA. Multiple sensors ensure guide strand selection in human RNAi pathways. RNA. 2013 May; 19(5):639-48.
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      46. Lee HY, Haurwitz RE, Apffel A, Zhou K, Smart B, Wenger CD, Laderman S, Bruhn L, Doudna JA. RNA-protein analysis using a conditional CRISPR nuclease. Proc Natl Acad Sci U S A. 2013 Apr 2; 110(14):5416-21.
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      47. Charpentier E, Doudna JA. Biotechnology: Rewriting a genome. Nature. 2013 Mar 7; 495(7439):50-1.
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      48. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013 Feb 28; 152(5):1173-83.
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      49. Mortimer SA, Doudna JA. Unconventional miR-122 binding stabilizes the HCV genome by forming a trimolecular RNA structure. Nucleic Acids Res. 2013 Apr; 41(7):4230-40.
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      50. Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J. RNA-programmed genome editing in human cells. Elife. 2013; 2:e00471.
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      51. Wilson RC, Doudna JA. Molecular mechanisms of RNA interference. Annu Rev Biophys. 2013; 42:217-39.
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      52. Koh HR, Kidwell MA, Ragunathan K, Doudna JA, Myong S. ATP-independent diffusion of double-stranded RNA binding proteins. Proc Natl Acad Sci U S A. 2013 Jan 2; 110(1):151-6.
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      53. Lee HY, Doudna JA. TRBP alters human precursor microRNA processing in vitro. RNA. 2012 Nov; 18(11):2012-9.
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      54. Qi L, Haurwitz RE, Shao W, Doudna JA, Arkin AP. RNA processing enables predictable programming of gene expression. Nat Biotechnol. 2012 Oct; 30(10):1002-6.
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      55. van Duijn E, Barbu IM, Barendregt A, Jore MM, Wiedenheft B, Lundgren M, Westra ER, Brouns SJ, Doudna JA, van der Oost J, Heck AJ. Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa. Mol Cell Proteomics. 2012 Nov; 11(11):1430-41.
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      56. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012 Aug 17; 337(6096):816-21.
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      57. Ma E, Zhou K, Kidwell MA, Doudna JA. Coordinated activities of human dicer domains in regulatory RNA processing. J Mol Biol. 2012 Sep 28; 422(4):466-76.
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      58. Kaya E, Doudna JA. Biochemistry. Guided tour to the heart of RISC. Science. 2012 May 25; 336(6084):985-6.
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      59. Haurwitz RE, Sternberg SH, Doudna JA. Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA. EMBO J. 2012 Jun 13; 31(12):2824-32.
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      60. Sashital DG, Wiedenheft B, Doudna JA. Mechanism of foreign DNA selection in a bacterial adaptive immune system. Mol Cell. 2012 Jun 8; 46(5):606-15.
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      61. Sternberg SH, Haurwitz RE, Doudna JA. Mechanism of substrate selection by a highly specific CRISPR endoribonuclease. RNA. 2012 Apr; 18(4):661-72.
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      62. Wiedenheft B, Sternberg SH, Doudna JA. RNA-guided genetic silencing systems in bacteria and archaea. Nature. 2012 Feb 16; 482(7385):331-8.
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      63. Arribere JA, Doudna JA, Gilbert WV. Reconsidering movement of eukaryotic mRNAs between polysomes and P bodies. Mol Cell. 2011 Dec 9; 44(5):745-58.
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      64. Sun C, Todorovic A, Querol-Audí J, Bai Y, Villa N, Snyder M, Ashchyan J, Lewis CS, Hartland A, Gradia S, Fraser CS, Doudna JA, Nogales E, Cate JH. Functional reconstitution of human eukaryotic translation initiation factor 3 (eIF3). Proc Natl Acad Sci U S A. 2011 Dec 20; 108(51):20473-8.
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      65. Mehle A, Dugan VG, Taubenberger JK, Doudna JA. Reassortment and mutation of the avian influenza virus polymerase PA subunit overcome species barriers. J Virol. 2012 Feb; 86(3):1750-7.
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      66. Berry KE, Waghray S, Mortimer SA, Bai Y, Doudna JA. Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning. Structure. 2011 Oct 12; 19(10):1456-66.
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      67. Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJ, van der Oost J, Doudna JA, Nogales E. Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature. 2011 Sep 22; 477(7365):486-9.
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      68. Noland CL, Ma E, Doudna JA. siRNA repositioning for guide strand selection by human Dicer complexes. Mol Cell. 2011 Jul 8; 43(1):110-21.
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      69. Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP. Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci U S A. 2011 Jul 5; 108(27):11063-8.
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      70. Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L. Modeling and automation of sequencing-based characterization of RNA structure. Proc Natl Acad Sci U S A. 2011 Jul 5; 108(27):11069-74.
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      71. Sashital DG, Jinek M, Doudna JA. An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3. Nat Struct Mol Biol. 2011 Jun; 18(6):680-7.
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      72. Wiedenheft B, van Duijn E, Bultema JB, Bultema J, Waghmare SP, Waghmare S, Zhou K, Barendregt A, Westphal W, Heck AJ, Heck A, Boekema EJ, Boekema E, Dickman MJ, Dickman M, Doudna JA. RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proc Natl Acad Sci U S A. 2011 Jun 21; 108(25):10092-7.
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      73. Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders AP, Dickman MJ, Doudna JA, Boekema EJ, Heck AJ, van der Oost J, Brouns SJ. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol. 2011 May; 18(5):529-36.
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      74. Jinek M, Coyle SM, Doudna JA. Coupled 5' nucleotide recognition and processivity in Xrn1-mediated mRNA decay. Mol Cell. 2011 Mar 4; 41(5):600-8.
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      75. Ataide SF, Schmitz N, Shen K, Ke A, Shan SO, Doudna JA, Ban N. The crystal structure of the signal recognition particle in complex with its receptor. Science. 2011 Feb 18; 331(6019):881-6.
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      76. Berry KE, Peng B, Koditek D, Beeman D, Pagratis N, Perry JK, Parrish J, Zhong W, Doudna JA, Shih IH. Optimized high-throughput screen for hepatitis C virus translation inhibitors. J Biomol Screen. 2011 Feb; 16(2):211-20.
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      77. Weeks AM, Coyle SM, Jinek M, Doudna JA, Chang MC. Structural and biochemical studies of a fluoroacetyl-CoA-specific thioesterase reveal a molecular basis for fluorine selectivity. Biochemistry. 2010 Nov 2; 49(43):9269-79.
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      78. Chakravarthy S, Sternberg SH, Kellenberger CA, Doudna JA. Substrate-specific kinetics of Dicer-catalyzed RNA processing. J Mol Biol. 2010 Dec 3; 404(3):392-402.
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      79. Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science. 2010 Sep 10; 329(5997):1355-8.
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      80. Berry KE, Waghray S, Doudna JA. The HCV IRES pseudoknot positions the initiation codon on the 40S ribosomal subunit. RNA. 2010 Aug; 16(8):1559-69.
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      81. Clarkson BK, Gilbert WV, Doudna JA. Functional overlap between eIF4G isoforms in Saccharomyces cerevisiae. PLoS One. 2010; 5(2):e9114.
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      82. Mehle A, Doudna JA. A host of factors regulating influenza virus replication. Viruses. 2010 Feb; 2(2):566-73.
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      83. Jinek M, Fabian MR, Coyle SM, Sonenberg N, Doudna JA. Structural insights into the human GW182-PABC interaction in microRNA-mediated deadenylation. Nat Struct Mol Biol. 2010 Feb; 17(2):238-40.
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      84. Sashital DG, Doudna JA. Structural insights into RNA interference. Curr Opin Struct Biol. 2010 Feb; 20(1):90-7.
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      85. Mehle A, Doudna JA. Adaptive strategies of the influenza virus polymerase for replication in humans. Proc Natl Acad Sci U S A. 2009 Dec 15; 106(50):21312-6.
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      86. Wang HW, Noland C, Siridechadilok B, Taylor DW, Ma E, Felderer K, Doudna JA, Nogales E. Structural insights into RNA processing by the human RISC-loading complex. Nat Struct Mol Biol. 2009 Nov; 16(11):1148-53.
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      87. Fabian MR, Mathonnet G, Sundermeier T, Mathys H, Zipprich JT, Svitkin YV, Rivas F, Jinek M, Wohlschlegel J, Doudna JA, Chen CY, Shyu AB, Yates JR, Hannon GJ, Filipowicz W, Duchaine TF, Sonenberg N. Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol Cell. 2009 Sep 24; 35(6):868-80.
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      88. Wiedenheft B, Zhou K, Jinek M, Coyle SM, Ma W, Doudna JA. Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure. 2009 Jun 10; 17(6):904-12.
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      89. Fraser CS, Hershey JW, Doudna JA. The pathway of hepatitis C virus mRNA recruitment to the human ribosome. Nat Struct Mol Biol. 2009 Apr; 16(4):397-404.
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      90. Jinek M, Doudna JA. A three-dimensional view of the molecular machinery of RNA interference. Nature. 2009 Jan 22; 457(7228):405-12.
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      91. Fukunaga R, Doudna JA. dsRNA with 5' overhangs contributes to endogenous and antiviral RNA silencing pathways in plants. EMBO J. 2009 Mar 4; 28(5):545-55.
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      92. Coyle SM, Gilbert WV, Doudna JA. Direct link between RACK1 function and localization at the ribosome in vivo. Mol Cell Biol. 2009 Mar; 29(6):1626-34.
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      93. Mehle A, Doudna JA. An inhibitory activity in human cells restricts the function of an avian-like influenza virus polymerase. Cell Host Microbe. 2008 Aug 14; 4(2):111-22.
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      94. Zhou M, Sandercock AM, Fraser CS, Ridlova G, Stephens E, Schenauer MR, Yokoi-Fong T, Barsky D, Leary JA, Hershey JW, Doudna JA, Robinson CV. Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3. Proc Natl Acad Sci U S A. 2008 Nov 25; 105(47):18139-44.
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      95. Puglisi JD, Doudna JA. Nucleic acids and their protein partners. Curr Opin Struct Biol. 2008 Jun; 18(3):279-81.
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      96. Ma E, MacRae IJ, Kirsch JF, Doudna JA. Autoinhibition of human dicer by its internal helicase domain. J Mol Biol. 2008 Jun 27; 380(1):237-43.
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      97. MacRae IJ, Ma E, Zhou M, Robinson CV, Doudna JA. In vitro reconstitution of the human RISC-loading complex. Proc Natl Acad Sci U S A. 2008 Jan 15; 105(2):512-7.
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      98. MacRae IJ, Zhou K, Doudna JA. Structural determinants of RNA recognition and cleavage by Dicer. Nat Struct Mol Biol. 2007 Oct; 14(10):934-40.
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      99. Gilbert WV, Zhou K, Butler TK, Doudna JA. Cap-independent translation is required for starvation-induced differentiation in yeast. Science. 2007 Aug 31; 317(5842):1224-7.
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      100. MacRae IJ, Doudna JA. An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer. Acta Crystallogr D Biol Crystallogr. 2007 Sep; 63(Pt 9):993-9.
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      101. Fraser CS, Berry KE, Hershey JW, Doudna JA. eIF3j is located in the decoding center of the human 40S ribosomal subunit. Mol Cell. 2007 Jun 22; 26(6):811-9.
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      102. Fraser CS, Doudna JA. Quantitative studies of ribosome conformational dynamics. Q Rev Biophys. 2007 May; 40(2):163-89.
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      103. Kiessling LL, Doudna JA, Johnsson K, Mapp AK, Marletta MA, Seeberger PH, Williamson JR, Wedde SG. A higher degree of difficulty. ACS Chem Biol. 2007 Apr 24; 2(4):197-9.
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      104. Ke A, Ding F, Batchelor JD, Doudna JA. Structural roles of monovalent cations in the HDV ribozyme. Structure. 2007 Mar; 15(3):281-7.
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      105. Damoc E, Fraser CS, Zhou M, Videler H, Mayeur GL, Hershey JW, Doudna JA, Robinson CV, Leary JA. Structural characterization of the human eukaryotic initiation factor 3 protein complex by mass spectrometry. Mol Cell Proteomics. 2007 Jul; 6(7):1135-46.
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      106. MacRae IJ, Doudna JA. Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Curr Opin Struct Biol. 2007 Feb; 17(1):138-45.
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      107. Siu FY, Spanggord RJ, Doudna JA. SRP RNA provides the physiologically essential GTPase activation function in cotranslational protein targeting. RNA. 2007 Feb; 13(2):240-50.
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      108. Fraser CS, Doudna JA. Structural and mechanistic insights into hepatitis C viral translation initiation. Nat Rev Microbiol. 2007 Jan; 5(1):29-38.
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      109. Wu S, Ke A, Doudna JA. A fast and efficient procedure to produce scFvs specific for large macromolecular complexes. J Immunol Methods. 2007 Jan 10; 318(1-2):95-101.
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      110. Green R, Doudna JA. RNAs regulate biology. ACS Chem Biol. 2006 Jul 21; 1(6):335-8.
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      111. Chmiel NH, Rio DC, Doudna JA. Distinct contributions of KH domains to substrate binding affinity of Drosophila P-element somatic inhibitor protein. RNA. 2006 Feb; 12(2):283-91.
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      112. Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA. Structural basis for double-stranded RNA processing by Dicer. Science. 2006 Jan 13; 311(5758):195-8.
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      113. Macrae IJ, Li F, Zhou K, Cande WZ, Doudna JA. Structure of Dicer and mechanistic implications for RNAi. Cold Spring Harb Symp Quant Biol. 2006; 71:73-80.
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      114. Karbstein K, Doudna JA. GTP-dependent formation of a ribonucleoprotein subcomplex required for ribosome biogenesis. J Mol Biol. 2006 Feb 17; 356(2):432-43.
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      115. Siridechadilok B, Fraser CS, Hall RJ, Doudna JA, Nogales E. Structural roles for human translation factor eIF3 in initiation of protein synthesis. Science. 2005 Dec 2; 310(5753):1513-5.
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      116. Karbstein K, Jonas S, Doudna JA. An essential GTPase promotes assembly of preribosomal RNA processing complexes. Mol Cell. 2005 Nov 23; 20(4):633-43.
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      117. Spanggord RJ, Siu F, Ke A, Doudna JA. RNA-mediated interaction between the peptide-binding and GTPase domains of the signal recognition particle. Nat Struct Mol Biol. 2005 Dec; 12(12):1116-22.
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      118. Doudna JA. Chemical biology at the crossroads of molecular structure and mechanism. Nat Chem Biol. 2005 Nov; 1(6):300-3.
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      119. Chen L, Lullo DJ, Ma E, Celniker SE, Rio DC, Doudna JA. Identification and analysis of U5 snRNA variants in Drosophila. RNA. 2005 Oct; 11(10):1473-7.
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      120. Macrae IJ, Doudna JA. Ro's role in RNA reconnaissance. Cell. 2005 May 20; 121(4):495-6.
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      121. Yu Y, Ji H, Doudna JA, Leary JA. Mass spectrometric analysis of the human 40S ribosomal subunit: native and HCV IRES-bound complexes. Protein Sci. 2005 Jun; 14(6):1438-46.
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      122. Doudna JA, Lorsch JR. Ribozyme catalysis: not different, just worse. Nat Struct Mol Biol. 2005 May; 12(5):395-402.
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      123. Ji H, Fraser CS, Yu Y, Leary J, Doudna JA. Coordinated assembly of human translation initiation complexes by the hepatitis C virus internal ribosome entry site RNA. Proc Natl Acad Sci U S A. 2004 Dec 7; 101(49):16990-5.
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      124. Ke A, Doudna JA. Crystallization of RNA and RNA-protein complexes. Methods. 2004 Nov; 34(3):408-14.
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      125. Rambo RP, Doudna JA. Assembly of an active group II intron-maturase complex by protein dimerization. Biochemistry. 2004 Jun 1; 43(21):6486-97.
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      126. Ke A, Zhou K, Ding F, Cate JH, Doudna JA. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature. 2004 May 13; 429(6988):201-5.
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      127. Sagar MB, Lucast L, Doudna JA. Conserved but nonessential interaction of SRP RNA with translation factor EF-G. RNA. 2004 May; 10(5):772-8.
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      128. Lupták A, Doudna JA. Distinct sites of phosphorothioate substitution interfere with folding and splicing of the Anabaena group I intron. Nucleic Acids Res. 2004; 32(7):2272-80.
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      129. Karbstein K, Doudna JA. RNA: primed for packing? Chem Biol. 2004 Feb; 11(2):149-51.
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      130. Doudna JA, Batey RT. Structural insights into the signal recognition particle. Annu Rev Biochem. 2004; 73:539-57.
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      131. Fraser CS, Lee JY, Mayeur GL, Bushell M, Doudna JA, Hershey JW. The j-subunit of human translation initiation factor eIF3 is required for the stable binding of eIF3 and its subcomplexes to 40 S ribosomal subunits in vitro. J Biol Chem. 2004 Mar 5; 279(10):8946-56.
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      132. Batey RT, Doudna JA. Structural and energetic analysis of metal ions essential to SRP signal recognition domain assembly. Biochemistry. 2002 Oct 1; 41(39):11703-10.
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      133. Battle DJ, Doudna JA. Specificity of RNA-RNA helix recognition. Proc Natl Acad Sci U S A. 2002 Sep 3; 99(18):11676-81.
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      134. Doudna JA, Cech TR. The chemical repertoire of natural ribozymes. Nature. 2002 Jul 11; 418(6894):222-8.
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      135. Kieft JS, Zhou K, Grech A, Jubin R, Doudna JA. Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation. Nat Struct Biol. 2002 May; 9(5):370-4.
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      136. Doudna JA, Rath VL. Structure and function of the eukaryotic ribosome: the next frontier. Cell. 2002 Apr 19; 109(2):153-6.
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      137. Zhang L, Doudna JA. Structural insights into group II intron catalysis and branch-site selection. Science. 2002 Mar 15; 295(5562):2084-8.
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      138. Murray JM, Doudna JA. Creative catalysis: pieces of the RNA world jigsaw. Trends Biochem Sci. 2001 Dec; 26(12):699-701.
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      139. Lupták A, Ferré-D'Amaré AR, Zhou K, Zilm KW, Doudna JA. Direct pK(a) measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme. J Am Chem Soc. 2001 Sep 5; 123(35):8447-52.
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      140. Ferré-D'Amaré AR, Doudna JA. Methods to crystallize RNA. Curr Protoc Nucleic Acid Chem. 2001 May; Chapter 7:Unit 7.6.
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      141. Doherty EA, Batey RT, Masquida B, Doudna JA. A universal mode of helix packing in RNA. Nat Struct Biol. 2001 Apr; 8(4):339-43.
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      142. Batey RT, Sagar MB, Doudna JA. Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle. J Mol Biol. 2001 Mar 16; 307(1):229-46.
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      143. Spahn CM, Kieft JS, Grassucci RA, Penczek PA, Zhou K, Doudna JA, Frank J. Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit. Science. 2001 Mar 9; 291(5510):1959-62.
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      144. Lucast LJ, Batey RT, Doudna JA. Large-scale purification of a stable form of recombinant tobacco etch virus protease. Biotechniques. 2001 Mar; 30(3):544-6, 548, 550 passim.
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      145. Kieft JS, Zhou K, Jubin R, Doudna JA. Mechanism of ribosome recruitment by hepatitis C IRES RNA. RNA. 2001 Feb; 7(2):194-206.
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      146. Battle DJ, Doudna JA. The stem-loop binding protein forms a highly stable and specific complex with the 3' stem-loop of histone mRNAs. RNA. 2001 Jan; 7(1):123-32.
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      147. Doherty EA, Doudna JA. Ribozyme structures and mechanisms. Annu Rev Biophys Biomol Struct. 2001; 30:457-75.
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      148. Kieft JS, Grech A, Adams P, Doudna JA. Mechanisms of internal ribosome entry in translation initiation. Cold Spring Harb Symp Quant Biol. 2001; 66:277-83.
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      149. Jubin R, Vantuno NE, Kieft JS, Murray MG, Doudna JA, Lau JY, Baroudy BM. Hepatitis C virus internal ribosome entry site (IRES) stem loop IIId contains a phylogenetically conserved GGG triplet essential for translation and IRES folding. J Virol. 2000 Nov; 74(22):10430-7.
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      150. Hanna RL, Gryaznov SM, Doudna JA. A phosphoramidate substrate analog is a competitive inhibitor of the Tetrahymena group I ribozyme. Chem Biol. 2000 Nov; 7(11):845-54.
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      151. Doudna JA. Structural genomics of RNA. Nat Struct Biol. 2000 Nov; 7 Suppl:954-6.
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      152. Jeruzalmi D, Kuriyan J, Doudna J. Paul Sigler (1934-2000). Trends Biochem Sci. 2000 May; 25(5):221-2.
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      153. Hanna R, Doudna JA. Metal ions in ribozyme folding and catalysis. Curr Opin Chem Biol. 2000 Apr; 4(2):166-70.
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      154. Engelhardt MA, Doherty EA, Knitt DS, Doudna JA, Herschlag D. The P5abc peripheral element facilitates preorganization of the tetrahymena group I ribozyme for catalysis. Biochemistry. 2000 Mar 14; 39(10):2639-51.
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      155. Batey RT, Rambo RP, Lucast L, Rha B, Doudna JA. Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science. 2000 Feb 18; 287(5456):1232-9.
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      156. Ferré-D'Amaré AR, Doudna JA. Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module. J Mol Biol. 2000 Jan 21; 295(3):541-56.
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      157. Cate JH, Doudna JA. Solving large RNA structures by X-ray crystallography. Methods Enzymol. 2000; 317:169-80.
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      158. Doherty EA, Doudna JA. Ribozyme structures and mechanisms. Annu Rev Biochem. 2000; 69:597-615.
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      159. Doudna JA. Cashing in on crystals. Curr Biol. 1999 Oct 7; 9(19):R731-4.
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      160. Kieft JS, Zhou K, Jubin R, Murray MG, Lau JY, Doudna JA. The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold. J Mol Biol. 1999 Sep 24; 292(3):513-29.
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      161. Wadkins TS, Perrotta AT, Ferré-D'Amaré AR, Doudna JA, Been MD. A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes. RNA. 1999 Jun; 5(6):720-7.
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      162. Doherty EA, Herschlag D, Doudna JA. Assembly of an exceptionally stable RNA tertiary interface in a group I ribozyme. Biochemistry. 1999 Mar 9; 38(10):2982-90.
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      163. Ferré-D'Amaré AR, Doudna JA. RNA folds: insights from recent crystal structures. Annu Rev Biophys Biomol Struct. 1999; 28:57-73.
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      164. Basu S, Rambo RP, Strauss-Soukup J, Cate JH, Ferré-D'Amaré AR, Strobel SA, Doudna JA. A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nat Struct Biol. 1998 Nov; 5(11):986-92.
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      165. Ferré-D'Amaré AR, Zhou K, Doudna JA. Crystal structure of a hepatitis delta virus ribozyme. Nature. 1998 Oct 8; 395(6702):567-74.
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      166. Doudna JA. Ribozymes: the hammerhead swings into action. Curr Biol. 1998 Jul 2; 8(14):R495-7.
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      167. Ferré-D'Amaré AR, Zhou K, Doudna JA. A general module for RNA crystallization. J Mol Biol. 1998 Jun 12; 279(3):621-31.
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      168. Batey RT, Doudna JA. The parallel universe of RNA folding. Nat Struct Biol. 1998 May; 5(5):337-40.
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      169. Doudna JA. RNA structure. A molecular contortionist. Nature. 1997 Aug 28; 388(6645):830-1.
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      170. Cate JH, Hanna RL, Doudna JA. A magnesium ion core at the heart of a ribozyme domain. Nat Struct Biol. 1997 Jul; 4(7):553-8.
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      171. Strobel SA, Doudna JA. RNA seeing double: close-packing of helices in RNA tertiary structure. Trends Biochem Sci. 1997 Jul; 22(7):262-6.
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      172. Doudna JA, Cate JH. RNA structure: crystal clear? Curr Opin Struct Biol. 1997 Jun; 7(3):310-6.
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      173. Doherty EA, Doudna JA. The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core. Biochemistry. 1997 Mar 18; 36(11):3159-69.
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      174. Ferré-d'Amaré AR, Doudna JA. Establishing suitability of RNA preparations for crystallization. Determination of polydispersity. Methods Mol Biol. 1997; 74:371-7.
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      175. Doudna JA, Doherty EA. Emerging themes in RNA folding. Fold Des. 1997; 2(5):R65-70.
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      176. Doudna JA. Preparation of homogeneous ribozyme RNA for crystallization. Methods Mol Biol. 1997; 74:365-70.
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      177. Cate JH, Doudna JA. A sparse matrix approach to crystallizing ribozymes and RNA motifs. Methods Mol Biol. 1997; 74:379-86.
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      178. Cate JH, Doudna JA. Metal-binding sites in the major groove of a large ribozyme domain. Structure. 1996 Oct 15; 4(10):1221-9.
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      179. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Szewczak AA, Kundrot CE, Cech TR, Doudna JA. RNA tertiary structure mediation by adenosine platforms. Science. 1996 Sep 20; 273(5282):1696-9.
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      180. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna JA. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 1996 Sep 20; 273(5282):1678-85.
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      181. Jones JT, Barnes CL, Lietzke SE, Weichenrieder O, Doudna JA, Kundrot CE. Preliminary X-ray diffraction studies of an RNA pseudoknot that inhibits HIV-1 reverse transcriptase. Acta Crystallogr D Biol Crystallogr. 1996 Sep 1; 52(Pt 5):1018-20.
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      182. Ferré-D'Amaré AR, Doudna JA. Use of cis- and trans-ribozymes to remove 5' and 3' heterogeneities from milligrams of in vitro transcribed RNA. Nucleic Acids Res. 1996 Mar 1; 24(5):977-8.
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      183. Doudna JA. Hammerhead ribozyme structure: U-turn for RNA structural biology. Structure. 1995 Aug 15; 3(8):747-50.
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      184. Doudna JA, Cech TR, Sullenger BA. Selection of an RNA molecule that mimics a major autoantigenic epitope of human insulin receptor. Proc Natl Acad Sci U S A. 1995 Mar 14; 92(6):2355-9.
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      185. Doudna JA, Cech TR. Self-assembly of a group I intron active site from its component tertiary structural domains. RNA. 1995 Mar; 1(1):36-45.
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      186. Doudna JA. Hammering out the shape of a ribozyme. Structure. 1994 Dec 15; 2(12):1271-2.
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      187. Doudna JA, Grosshans C, Gooding A, Kundrot CE. Crystallization of ribozymes and small RNA motifs by a sparse matrix approach. Proc Natl Acad Sci U S A. 1993 Aug 15; 90(16):7829-33.
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      188. Doudna JA, Usman N, Szostak JW. Ribozyme-catalyzed primer extension by trinucleotides: a model for the RNA-catalyzed replication of RNA. Biochemistry. 1993 Mar 2; 32(8):2111-5.
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      189. Musier-Forsyth K, Usman N, Scaringe S, Doudna J, Green R, Schimmel P. Specificity for aminoacylation of an RNA helix: an unpaired, exocyclic amino group in the minor groove. Science. 1991 Aug 16; 253(5021):784-6.
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      190. Bartel DP, Doudna JA, Usman N, Szostak JW. Template-directed primer extension catalyzed by the Tetrahymena ribozyme. Mol Cell Biol. 1991 Jun; 11(6):3390-4.
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      191. Doudna JA, Couture S, Szostak JW. A multisubunit ribozyme that is a catalyst of and template for complementary strand RNA synthesis. Science. 1991 Mar 29; 251(5001):1605-8.
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      192. Doudna JA, Szostak JW, Rich A, Usman N. Chemical synthesis of oligoribonucleotides containing 2-aminopurine: substrates for the investigation of ribozyme function. J Org Chem. 1990 Oct 12; 55(21):5547-9.
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      193. Couture S, Ellington AD, Gerber AS, Cherry JM, Doudna JA, Green R, Hanna M, Pace U, Rajagopal J, Szostak JW. Mutational analysis of conserved nucleotides in a self-splicing group I intron. J Mol Biol. 1990 Oct 5; 215(3):345-58.
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      194. Doudna JA, Szostak JW. Miniribozymes, small derivatives of the sunY intron, are catalytically active. Mol Cell Biol. 1989 Dec; 9(12):5480-3.
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      195. Doudna JA, Cormack BP, Szostak JW. RNA structure, not sequence, determines the 5' splice-site specificity of a group I intron. Proc Natl Acad Sci U S A. 1989 Oct; 86(19):7402-6.
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      196. Doudna JA, Szostak JW. RNA-catalysed synthesis of complementary-strand RNA. Nature. 1989 Jun 15; 339(6225):519-22.
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      197. Rajagopal J, Doudna JA, Szostak JW. Stereochemical course of catalysis by the Tetrahymena ribozyme. Science. 1989 May 12; 244(4905):692-4.
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      198. Doudna JA, Gerber AS, Cherry JM, Szostak JW. Genetic dissection of an RNA enzyme. Cold Spring Harb Symp Quant Biol. 1987; 52:173-80.
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