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    Doudna, Jennifer

    TitleBiologist Faculty
    SchoolLawrence Berkeley National Lab
    DepartmentMolecular Biophys & Integ Bio
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/643-0225
    vCardDownload vCard

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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Knott GJ, East-Seletsky A, Cofsky JC, Holton JM, Charles E, O'Connell MR, Doudna J. Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme. Nat Struct Mol Biol. 2017 Sep 11. PMID: 28892041.
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      2. Harrington LB, Doxzen KW, Ma E, Liu JJ, Knott GJ, Edraki A, Garcia B, Amrani N, Chen JS, Cofsky JC, Kranzusch PJ, Sontheimer EJ, Davidson AR, Maxwell KL, Doudna J. A Broad-Spectrum Inhibitor of CRISPR-Cas9. Cell. 2017 Sep 07; 170(6):1224-1233.e15. PMID: 28844692.
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      3. Dagdas YS, Chen JS, Sternberg SH, Doudna J, Yildiz A. A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9. Sci Adv. 2017 Aug; 3(8):eaao0027. PMID: 28808686.
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      4. Wright AV, Liu JJ, Knott GJ, Doxzen KW, Nogales E, Doudna J. Structures of the CRISPR genome integration complex. Science. 2017 Sep 15; 357(6356):1113-1118. PMID: 28729350.
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      5. Doudna J. Gene editing: CRISPR book review - Doudna responds. Nature. 2017 Jul 12; 547(7662):162. PMID: 28703186.
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      6. Shin J, Jiang F, Liu JJ, Bray NL, Rauch BJ, Baik SH, Nogales E, Bondy-Denomy J, Corn JE, Doudna J. Disabling Cas9 by an anti-CRISPR DNA mimic. Sci Adv. 2017 Jul; 3(7):e1701620. PMID: 28706995.
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      7. Gaj T, Staahl BT, Rodrigues GMC, Limsirichai P, Ekman FK, Doudna J, Schaffer DV. Targeted gene knock-in by homology-directed genome editing using Cas9 ribonucleoprotein and AAV donor delivery. Nucleic Acids Res. 2017 Jun 20; 45(11):e98. PMID: 28334779.
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      8. Doxzen KW, Doudna J. DNA recognition by an RNA-guided bacterial Argonaute. PLoS One. 2017; 12(5):e0177097. PMID: 28520746.
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      9. Boyle EA, Andreasson JOL, Chircus LM, Sternberg SH, Wu MJ, Guegler CK, Doudna J, Greenleaf WJ. High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding. Proc Natl Acad Sci U S A. 2017 May 23; 114(21):5461-5466. PMID: 28495970.
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      10. East-Seletsky A, O'Connell MR, Burstein D, Knott GJ, Doudna J. RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes. Mol Cell. 2017 May 04; 66(3):373-383.e3. PMID: 28475872.
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      11. Jiang F, Doudna J. CRISPR-Cas9 Structures and Mechanisms. Annu Rev Biophys. 2017 May 22; 46:505-529. PMID: 28375731.
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      12. Lintner NG, McClure KF, Petersen D, Londregan AT, Piotrowski DW, Wei L, Xiao J, Bolt M, Loria PM, Maguire B, Geoghegan KF, Huang A, Rolph T, Liras S, Doudna J, Dullea RG, Cate JH. Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain. PLoS Biol. 2017 Mar; 15(3):e2001882. PMID: 28323820.
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      13. Gorski SA, Vogel J, Doudna J. RNA-based recognition and targeting: sowing the seeds of specificity. Nat Rev Mol Cell Biol. 2017 Apr; 18(4):215-228. PMID: 28196981.
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      14. Staahl BT, Benekareddy M, Coulon-Bainier C, Banfal AA, Floor SN, Sabo JK, Urnes C, Munares GA, Ghosh A, Doudna J. Efficient genome editing in the mouse brain by local delivery of engineered Cas9 ribonucleoprotein complexes. Nat Biotechnol. 2017 May; 35(5):431-434. PMID: 28191903.
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      15. Liu TY, Iavarone AT, Doudna J. RNA and DNA Targeting by a Reconstituted Thermus thermophilus Type III-A CRISPR-Cas System. PLoS One. 2017; 12(1):e0170552. PMID: 28114398.
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      16. Koh HR, Kidwell MA, Doudna J, Myong S. RNA Scanning of a Molecular Machine with a Built-in Ruler. J Am Chem Soc. 2017 01 11; 139(1):262-268. PMID: 27958730.
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      17. Fellmann C, Gowen BG, Lin PC, Doudna J, Corn JE. Cornerstones of CRISPR-Cas in drug discovery and therapy. Nat Rev Drug Discov. 2017 02; 16(2):89-100. PMID: 28008168.
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      18. Heler R, Wright AV, Vucelja M, Bikard D, Doudna J, Marraffini LA. Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response. Mol Cell. 2017 Jan 05; 65(1):168-175. PMID: 28017588.
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      19. Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna J, Banfield JF. New CRISPR-Cas systems from uncultivated microbes. Nature. 2017 02 09; 542(7640):237-241. PMID: 28005056.
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      20. Hultquist JF, Schumann K, Woo JM, Manganaro L, McGregor MJ, Doudna J, Simon V, Krogan NJ, Marson A. A Cas9 Ribonucleoprotein Platform for Functional Genetic Studies of HIV-Host Interactions in Primary Human T Cells. Cell Rep. 2016 Oct 25; 17(5):1438-1452. PMID: 27783955.
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      21. Chen X, Shen Y, Draper W, Buenrostro JD, Litzenburger U, Cho SW, Satpathy AT, Carter AC, Ghosh RP, East-Seletsky A, Doudna J, Greenleaf WJ, Liphardt JT, Chang HY. ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. Nat Methods. 2016 Dec; 13(12):1013-1020. PMID: 27749837.
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      22. Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna J, Zhou Q, Sali A, Hurley JH. Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex. Elife. 2016 Oct 12; 5. PMID: 27731797.
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      23. East-Seletsky A, O'Connell MR, Knight SC, Burstein D, Cate JH, Tjian R, Doudna J. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature. 2016 Oct 13; 538(7624):270-273. PMID: 27669025.
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      24. Singh D, Sternberg SH, Fei J, Doudna J, Ha T. Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9. Nat Commun. 2016 Sep 14; 7:12778. PMID: 27624851; PMCID: PMC5027287.
      25. Barrangou R, Doudna J. Applications of CRISPR technologies in research and beyond. Nat Biotechnol. 2016 Sep 08; 34(9):933-941. PMID: 27606440.
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      26. Wright AV, Doudna J. Protecting genome integrity during CRISPR immune adaptation. Nat Struct Mol Biol. 2016 Oct; 23(10):876-883. PMID: 27595346.
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      27. Hochstrasser ML, Taylor DW, Kornfeld JE, Nogales E, Doudna J. DNA Targeting by a Minimal CRISPR RNA-Guided Cascade. Mol Cell. 2016 Sep 01; 63(5):840-51. PMID: 27588603.
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      28. Lee AS, Kranzusch PJ, Doudna J, Cate JH. eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation. Nature. 2016 08 04; 536(7614):96-9. PMID: 27462815; PMCID: PMC5003174 [Available on 02/04/17].
      29. Carlson LA, Bai Y, Keane SC, Doudna J, Hurley JH. Reconstitution of selective HIV-1 RNA packaging in vitro by membrane-bound Gag assemblies. Elife. 2016 Jun 25; 5. PMID: 27343348; PMCID: PMC4946900.
      30. Nuñez JK, Bai L, Harrington LB, Hinder TL, Doudna J. CRISPR Immunological Memory Requires a Host Factor for Specificity. Mol Cell. 2016 Jun 16; 62(6):824-833. PMID: 27211867.
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      31. Oh S, Flynn RA, Floor SN, Purzner J, Martin L, Do BT, Schubert S, Vaka D, Morrissy S, Li Y, Kool M, Hovestadt V, Jones DT, Northcott PA, Risch T, Warnatz HJ, Yaspo ML, Adams CM, Leib RD, Breese M, Marra MA, Malkin D, Lichter P, Doudna J, Pfister SM, Taylor MD, Chang HY, Cho YJ. Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. Oncotarget. 2016 May 10; 7(19):28169-82. PMID: 27058758.
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      32. Oakes BL, Nadler DC, Flamholz A, Fellmann C, Staahl BT, Doudna J, Savage DF. Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch. Nat Biotechnol. 2016 Jun; 34(6):646-51. PMID: 27136077; PMCID: PMC4900928 [Available on 11/02/16].
      33. Isaac RS, Jiang F, Doudna J, Lim WA, Narlikar GJ, Almeida R. Nucleosome breathing and remodeling constrain CRISPR-Cas9 function. Elife. 2016 Apr 28; 5. PMID: 27130520; PMCID: PMC4880442.
      34. Kaya E, Doxzen KW, Knoll KR, Wilson RC, Strutt SC, Kranzusch PJ, Doudna J. A bacterial Argonaute with noncanonical guide RNA specificity. Proc Natl Acad Sci U S A. 2016 Apr 12; 113(15):4057-62. PMID: 27035975; PMCID: PMC4839417.
      35. Nelles DA, Fang MY, O'Connell MR, Xu JL, Markmiller SJ, Doudna J, Yeo GW. Programmable RNA Tracking in Live Cells with CRISPR/Cas9. Cell. 2016 Apr 07; 165(2):488-96. PMID: 26997482; PMCID: PMC4826288 [Available on 04/07/17].
      36. Amit I, Baker D, Barker R, Berger B, Bertozzi C, Bhatia S, Biffi A, Demichelis F, Doudna J, Dowdy SF, Endy D, Helmstaedter M, Junca H, June C, Kamb S, Khvorova A, Kim DH, Kim JS, Krishnan Y, Lakadamyali M, Lappalainen T, Lewin S, Liao J, Loman N, Lundberg E, Lynd L, Martin C, Mellman I, Miyawaki A, Mummery C, Nelson K, Paz J, Peralta-Yahya P, Picotti P, Polyak K, Prather K, Qin J, Quake S, Regev A, Rogers JA, Shetty R, Sommer M, Stevens M, Stolovitzky G, Takahashi M, Tang F, Teichmann S, Torres-Padilla ME, Tripathi L, Vemula P, Verdine G, Vollmer F, Wang J, Ying JY, Zhang F, Zhang T. Voices of biotech. Nat Biotechnol. 2016 Mar; 34(3):270-5. PMID: 26963549.
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      37. Nuñez JK, Harrington LB, Doudna J. Chemical and Biophysical Modulation of Cas9 for Tunable Genome Engineering. ACS Chem Biol. 2016 Mar 18; 11(3):681-8. PMID: 26857072.
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      38. Jiang F, Taylor DW, Chen JS, Kornfeld JE, Zhou K, Thompson AJ, Nogales E, Doudna J. Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage. Science. 2016 Feb 19; 351(6275):867-71. PMID: 26841432.
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      39. Wright AV, Nuñez JK, Doudna J. Biology and Applications of CRISPR Systems: Harnessing Nature's Toolbox for Genome Engineering. Cell. 2016 Jan 14; 164(1-2):29-44. PMID: 26771484.
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      40. Floor SN, Doudna J. Tunable protein synthesis by transcript isoforms in human cells. Elife. 2016 Jan 06; 5. PMID: 26735365; PMCID: PMC4764583.
      41. Floor SN, Barkovich KJ, Condon KJ, Shokat KM, Doudna J. Analog sensitive chemical inhibition of the DEAD-box protein DDX3. Protein Sci. 2016 Mar; 25(3):638-49. PMID: 26650549; PMCID: PMC4815421 [Available on 03/01/17].
      42. Doudna J. Genome-editing revolution: My whirlwind year with CRISPR. Nature. 2015 Dec 24; 528(7583):469-71. PMID: 26701037.
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      43. Doudna J, Gersbach CA. Genome editing: the end of the beginning. Genome Biol. 2015 Dec 23; 16:292. PMID: 26700220; PMCID: PMC4699356.
      44. Floor SN, Doudna J. Get in LINE: Competition for Newly Minted Retrotransposon Proteins at the Ribosome. Mol Cell. 2015 Dec 03; 60(5):712-714. PMID: 26638173.
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      45. Doudna J. Perspective: Embryo editing needs scrutiny. Nature. 2015 Dec 03; 528(7580):S6. PMID: 26630598.
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      46. Floor SN, Condon KJ, Sharma D, Jankowsky E, Doudna J. Autoinhibitory Interdomain Interactions and Subfamily-specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3. J Biol Chem. 2016 Jan 29; 291(5):2412-21. PMID: 26598523; PMCID: PMC4732223 [Available on 01/29/17].
      47. Knight SC, Xie L, Deng W, Guglielmi B, Witkowsky LB, Bosanac L, Zhang ET, El Beheiry M, Masson JB, Dahan M, Liu Z, Doudna J, Tjian R. Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science. 2015 Nov 13; 350(6262):823-6. PMID: 26564855.
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      48. Redding S, Sternberg SH, Marshall M, Gibb B, Bhat P, Guegler CK, Wiedenheft B, Doudna J, Greene EC. Surveillance and Processing of Foreign DNA by the Escherichia coli CRISPR-Cas System. Cell. 2015 Nov 05; 163(4):854-65. PMID: 26522594; PMCID: PMC4636941 [Available on 11/05/16].
      49. Ma E, Harrington LB, O'Connell MR, Zhou K, Doudna J. Single-Stranded DNA Cleavage by Divergent CRISPR-Cas9 Enzymes. Mol Cell. 2015 Nov 05; 60(3):398-407. PMID: 26545076; PMCID: PMC4636735 [Available on 11/05/16].
      50. Sternberg SH, LaFrance B, Kaplan M, Doudna J. Conformational control of DNA target cleavage by CRISPR-Cas9. Nature. 2015 Nov 05; 527(7576):110-3. PMID: 26524520; PMCID: PMC4859810.
      51. Nuñez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna J. Foreign DNA capture during CRISPR-Cas adaptive immunity. Nature. 2015 Nov 26; 527(7579):535-8. PMID: 26503043; PMCID: PMC4662619.
      52. Kranzusch PJ, Wilson SC, Lee AS, Berger JM, Doudna J, Vance RE. Ancient Origin of cGAS-STING Reveals Mechanism of Universal 2',3' cGAMP Signaling. Mol Cell. 2015 Sep 17; 59(6):891-903. PMID: 26300263; PMCID: PMC4575873.
      53. Schumann K, Lin S, Boyer E, Simeonov DR, Subramaniam M, Gate RE, Haliburton GE, Ye CJ, Bluestone JA, Doudna J, 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. PMID: 26216948; PMCID: PMC4547290.
      54. Jiang F, Zhou K, Ma L, Gressel S, Doudna J. STRUCTURAL BIOLOGY. A Cas9-guide RNA complex preorganized for target DNA recognition. Science. 2015 Jun 26; 348(6242):1477-81. PMID: 26113724.
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      55. Sternberg SH, Doudna J. Expanding the Biologist's Toolkit with CRISPR-Cas9. Mol Cell. 2015 May 21; 58(4):568-74. PMID: 26000842.
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      56. 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; 33(5):478-86. PMID: 25965754.
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      57. Taylor DW, Zhu Y, Staals RH, Kornfeld JE, Shinkai A, van der Oost J, Nogales E, Doudna J. Structural biology. Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning. Science. 2015 May 01; 348(6234):581-5. PMID: 25837515; PMCID: PMC4582657.
      58. Baltimore D, Berg P, Botchan M, Carroll D, Charo RA, Church G, Corn JE, Daley GQ, Doudna J, 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 03; 348(6230):36-8. PMID: 25791083; PMCID: PMC4394183.
      59. Doudna J. Genomic engineering and the future of medicine. JAMA. 2015 Feb 24; 313(8):791-2. PMID: 25710652.
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      60. Jiang F, Doudna J. The structural biology of CRISPR-Cas systems. Curr Opin Struct Biol. 2015 Feb; 30:100-11. PMID: 25723899; PMCID: PMC4417044.
      61. Wright AV, Sternberg SH, Taylor DW, Staahl BT, Bardales JA, Kornfeld JE, Doudna J. Rational design of a split-Cas9 enzyme complex. Proc Natl Acad Sci U S A. 2015 Mar 10; 112(10):2984-9. PMID: 25713377; PMCID: PMC4364227.
      62. Nuñez JK, Lee AS, Engelman A, Doudna J. Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity. Nature. 2015 Mar 12; 519(7542):193-8. PMID: 25707795; PMCID: PMC4359072.
      63. Wilson RC, Tambe A, Kidwell MA, Noland CL, Schneider CP, Doudna J. Dicer-TRBP complex formation ensures accurate mammalian microRNA biogenesis. Mol Cell. 2015 Feb 05; 57(3):397-407. PMID: 25557550; PMCID: PMC4320653.
      64. Lin S, Staahl BT, Alla RK, Doudna J. Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. Elife. 2014 Dec 15; 3:e04766. PMID: 25497837; PMCID: PMC4383097.
      65. Doudna J, Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014 Nov 28; 346(6213):1258096. PMID: 25430774.
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      66. Hochstrasser ML, Doudna J. Cutting it close: CRISPR-associated endoribonuclease structure and function. Trends Biochem Sci. 2015 Jan; 40(1):58-66. PMID: 25468820.
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      67. 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 J, 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. PMID: 25457165; PMCID: PMC4342149.
      68. Kapral GJ, Jain S, Noeske J, Doudna J, 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. PMID: 25326328; PMCID: PMC4227795.
      69. O'Connell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna J. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature. 2014 Dec 11; 516(7530):263-6. PMID: 25274302; PMCID: PMC4268322.
      70. Bai Y, Tambe A, Zhou K, Doudna J. RNA-guided assembly of Rev-RRE nuclear export complexes. Elife. 2014 Aug 27; 3:e03656. PMID: 25163983; PMCID: PMC4142337.
      71. Kidwell MA, Chan JM, Doudna J. Evolutionarily conserved roles of the dicer helicase domain in regulating RNA interference processing. J Biol Chem. 2014 Oct 10; 289(41):28352-62. PMID: 25135636; PMCID: PMC4192488.
      72. Kranzusch PJ, Lee ASY, Wilson SC, Solovykh MS, Vance RE, Berger JM, Doudna J. Structure-guided reprogramming of human cGAS dinucleotide linkage specificity. Cell. 2014 Aug 28; 158(5):1011-1021. PMID: 25131990; PMCID: PMC4157622.
      73. Mortimer SA, Kidwell MA, Doudna J. Insights into RNA structure and function from genome-wide studies. Nat Rev Genet. 2014 Jul; 15(7):469-79. PMID: 24821474.
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      74. Nuñez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna J. Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nat Struct Mol Biol. 2014 Jun; 21(6):528-34. PMID: 24793649; PMCID: PMC4075942.
      75. Hochstrasser ML, Taylor DW, Bhat P, Guegler CK, Sternberg SH, Nogales E, Doudna J. CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference. Proc Natl Acad Sci U S A. 2014 May 06; 111(18):6618-23. PMID: 24748111; PMCID: PMC4020112.
      76. 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 J. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science. 2014 Mar 14; 343(6176):1247997. PMID: 24505130; PMCID: PMC4184034.
      77. Sternberg SH, Redding S, Jinek M, Greene EC, Doudna J. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature. 2014 Mar 06; 507(7490):62-7. PMID: 24476820; PMCID: PMC4106473.
      78. Doudna J, Sontheimer EJ. Methods in Enzymology. The use of CRISPR/Cas9, ZFNs, and TALENs in generating site-specific genome alterations. Preface. Methods Enzymol. 2014; 546:xix-xx. PMID: 25398356.
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      79. Niewoehner O, Jinek M, Doudna J. Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Nucleic Acids Res. 2014 Jan; 42(2):1341-53. PMID: 24150936; PMCID: PMC3902920.
      80. Staals RHJ, 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 J, Heck AJR, 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):135-145. PMID: 24119403; PMCID: PMC4006948.
      81. Cox EM, Sagan SM, Mortimer SA, Doudna J, Sarnow P. Enhancement of hepatitis C viral RNA abundance by precursor miR-122 molecules. RNA. 2013 Dec; 19(12):1825-32. PMID: 24106328; PMCID: PMC3884667.
      82. Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna J, Liu DR. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol. 2013 Sep; 31(9):839-43. PMID: 23934178; PMCID: PMC3782611.
      83. Lo TW, Pickle CS, Lin S, Ralston EJ, Gurling M, Schartner CM, Bian Q, Doudna J, 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. PMID: 23934893; PMCID: PMC3781963.
      84. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna J, Lim WA, Weissman JS, Qi LS. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. 2013 Jul 18; 154(2):442-51. PMID: 23849981; PMCID: PMC3770145.
      85. Kidwell MA, Doudna J. Activating silent argonautes. Nat Struct Mol Biol. 2013 Jul; 20(7):769-71. PMID: 23984440.
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      86. Bai Y, Zhou K, Doudna J. 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. PMID: 23783572; PMCID: PMC3763534.
      87. Sun C, Querol-Audí J, Mortimer SA, Arias-Palomo E, Doudna J, Nogales E, Cate JH. Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation. Nucleic Acids Res. 2013 Aug; 41(15):7512-21. PMID: 23766293; PMCID: PMC3753635.
      88. Kranzusch PJ, Lee AS, Berger JM, Doudna J. Structure of human cGAS reveals a conserved family of second-messenger enzymes in innate immunity. Cell Rep. 2013 May 30; 3(5):1362-8. PMID: 23707061; PMCID: PMC3800681.
      89. Lee HY, Zhou K, Smith AM, Noland CL, Doudna J. Differential roles of human Dicer-binding proteins TRBP and PACT in small RNA processing. Nucleic Acids Res. 2013 Jul; 41(13):6568-76. PMID: 23661684; PMCID: PMC3711433.
      90. Taylor DW, Ma E, Shigematsu H, Cianfrocco MA, Noland CL, Nagayama K, Nogales E, Doudna J, Wang HW. Substrate-specific structural rearrangements of human Dicer. Nat Struct Mol Biol. 2013 Jun; 20(6):662-70. PMID: 23624860; PMCID: PMC3676429.
      91. Noland CL, Doudna J. Multiple sensors ensure guide strand selection in human RNAi pathways. RNA. 2013 May; 19(5):639-48. PMID: 23531496; PMCID: PMC3677279.
      92. Lee HY, Haurwitz RE, Apffel A, Zhou K, Smart B, Wenger CD, Laderman S, Bruhn L, Doudna J. RNA-protein analysis using a conditional CRISPR nuclease. Proc Natl Acad Sci U S A. 2013 Apr 02; 110(14):5416-21. PMID: 23493562; PMCID: PMC3619310.
      93. Charpentier E, Doudna J. Biotechnology: Rewriting a genome. Nature. 2013 Mar 07; 495(7439):50-1. PMID: 23467164.
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      94. Qi LS, Larson MH, Gilbert LA, Doudna J, 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. PMID: 23452860; PMCID: PMC3664290.
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      96. Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J. RNA-programmed genome editing in human cells. Elife. 2013 Jan 29; 2:e00471. PMID: 23386978; PMCID: PMC3557905.
      97. Wilson RC, Doudna J. Molecular mechanisms of RNA interference. Annu Rev Biophys. 2013; 42:217-39. PMID: 23654304.
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      98. Koh HR, Kidwell MA, Ragunathan K, Doudna J, Myong S. ATP-independent diffusion of double-stranded RNA binding proteins. Proc Natl Acad Sci U S A. 2013 Jan 02; 110(1):151-6. PMID: 23251028; PMCID: PMC3538233.
      99. Lee HY, Doudna J. TRBP alters human precursor microRNA processing in vitro. RNA. 2012 Nov; 18(11):2012-9. PMID: 23006623; PMCID: PMC3479391.
      100. Qi L, Haurwitz RE, Shao W, Doudna J, Arkin AP. RNA processing enables predictable programming of gene expression. Nat Biotechnol. 2012 Oct; 30(10):1002-6. PMID: 22983090.
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      101. van Duijn E, Barbu IM, Barendregt A, Jore MM, Wiedenheft B, Lundgren M, Westra ER, Brouns SJ, Doudna J, 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. PMID: 22918228; PMCID: PMC3494201.
      102. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna J, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012 Aug 17; 337(6096):816-21. PMID: 22745249.
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      103. Ma E, Zhou K, Kidwell MA, Doudna J. Coordinated activities of human dicer domains in regulatory RNA processing. J Mol Biol. 2012 Sep 28; 422(4):466-76. PMID: 22727743; PMCID: PMC3461841.
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      105. Haurwitz RE, Sternberg SH, Doudna J. Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA. EMBO J. 2012 Jun 13; 31(12):2824-32. PMID: 22522703; PMCID: PMC3380207.
      106. Sashital DG, Wiedenheft B, Doudna J. Mechanism of foreign DNA selection in a bacterial adaptive immune system. Mol Cell. 2012 Jun 08; 46(5):606-15. PMID: 22521690; PMCID: PMC3397241.
      107. Sternberg SH, Haurwitz RE, Doudna J. Mechanism of substrate selection by a highly specific CRISPR endoribonuclease. RNA. 2012 Apr; 18(4):661-72. PMID: 22345129; PMCID: PMC3312554.
      108. Wiedenheft B, Sternberg SH, Doudna J. RNA-guided genetic silencing systems in bacteria and archaea. Nature. 2012 Feb 15; 482(7385):331-8. PMID: 22337052.
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      109. Arribere JA, Doudna J, Gilbert WV. Reconsidering movement of eukaryotic mRNAs between polysomes and P bodies. Mol Cell. 2011 Dec 09; 44(5):745-58. PMID: 22152478; PMCID: PMC3240842.
      110. Sun C, Todorovic A, Querol-Audí J, Bai Y, Villa N, Snyder M, Ashchyan J, Lewis CS, Hartland A, Gradia S, Fraser CS, Doudna J, 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. PMID: 22135459; PMCID: PMC3251073.
      111. Mehle A, Dugan VG, Taubenberger JK, Doudna J. Reassortment and mutation of the avian influenza virus polymerase PA subunit overcome species barriers. J Virol. 2012 Feb; 86(3):1750-7. PMID: 22090127; PMCID: PMC3264373.
      112. Berry KE, Waghray S, Mortimer SA, Bai Y, Doudna J. Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning. Structure. 2011 Oct 12; 19(10):1456-66. PMID: 22000514; PMCID: PMC3209822.
      113. Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJJ, van der Oost J, Doudna J, Nogales E. Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature. 2011 Sep 21; 477(7365):486-489. PMID: 21938068; PMCID: PMC4165517.
      114. Noland CL, Ma E, Doudna J. siRNA repositioning for guide strand selection by human Dicer complexes. Mol Cell. 2011 Jul 08; 43(1):110-21. PMID: 21726814; PMCID: PMC3143821.
      115. Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna J, 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 05; 108(27):11063-8. PMID: 21642531; PMCID: PMC3131332.
      116. Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna J, Arkin AP, Pachter L. Modeling and automation of sequencing-based characterization of RNA structure. Proc Natl Acad Sci U S A. 2011 Jul 05; 108(27):11069-74. PMID: 21642536; PMCID: PMC3131376.
      117. Sashital DG, Jinek M, Doudna J. An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3. Nat Struct Mol Biol. 2011 Jun; 18(6):680-7. PMID: 21572442.
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      118. 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 J. 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. PMID: 21536913; PMCID: PMC3121849.
      119. 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 J, 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. PMID: 21460843.
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      120. Jinek M, Coyle SM, Doudna J. Coupled 5' nucleotide recognition and processivity in Xrn1-mediated mRNA decay. Mol Cell. 2011 Mar 04; 41(5):600-8. PMID: 21362555; PMCID: PMC3090138.
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      122. Berry KE, Peng B, Koditek D, Beeman D, Pagratis N, Perry JK, Parrish J, Zhong W, Doudna J, Shih IH. Optimized high-throughput screen for hepatitis C virus translation inhibitors. J Biomol Screen. 2011 Feb; 16(2):211-20. PMID: 21297107; PMCID: PMC3260011.
      123. Weeks AM, Coyle SM, Jinek M, Doudna J, Chang MC. Structural and biochemical studies of a fluoroacetyl-CoA-specific thioesterase reveal a molecular basis for fluorine selectivity. Biochemistry. 2010 Nov 02; 49(43):9269-79. PMID: 20836570; PMCID: PMC3461317.
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      127. Clarkson BK, Gilbert WV, Doudna J. Functional overlap between eIF4G isoforms in Saccharomyces cerevisiae. PLoS One. 2010 Feb 09; 5(2):e9114. PMID: 20161741; PMCID: PMC2817733.
      128. Mehle A, Doudna J. A host of factors regulating influenza virus replication. Viruses. 2010 Feb; 2(2):566-73. PMID: 21994648; PMCID: PMC3185602.
      129. Jinek M, Fabian MR, Coyle SM, Sonenberg N, Doudna J. Structural insights into the human GW182-PABC interaction in microRNA-mediated deadenylation. Nat Struct Mol Biol. 2010 Feb; 17(2):238-40. PMID: 20098421; PMCID: PMC2920127.
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      133. Fabian MR, Mathonnet G, Sundermeier T, Mathys H, Zipprich JT, Svitkin YV, Rivas F, Jinek M, Wohlschlegel J, Doudna J, 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. PMID: 19716330; PMCID: PMC2803087.
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      157. Chmiel NH, Rio DC, Doudna J. Distinct contributions of KH domains to substrate binding affinity of Drosophila P-element somatic inhibitor protein. RNA. 2006 Feb; 12(2):283-91. PMID: 16428607; PMCID: PMC1370908.
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      166. Macrae IJ, Doudna J. Ro's role in RNA reconnaissance. Cell. 2005 May 20; 121(4):495-6. PMID: 15907458.
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      167. Yu Y, Ji H, Doudna J, 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. PMID: 15883184; PMCID: PMC2253395.
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      171. Rambo RP, Doudna J. Assembly of an active group II intron-maturase complex by protein dimerization. Biochemistry. 2004 Jun 01; 43(21):6486-97. PMID: 15157082.
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      207. Wadkins TS, Perrotta AT, Ferré-D'Amaré AR, Doudna J, 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. PMID: 10376872; PMCID: PMC1369799.
      208. Doherty EA, Herschlag D, Doudna J. Assembly of an exceptionally stable RNA tertiary interface in a group I ribozyme. Biochemistry. 1999 Mar 09; 38(10):2982-90. PMID: 10074350.
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      209. Ferré-D'Amaré AR, Doudna J. RNA folds: insights from recent crystal structures. Annu Rev Biophys Biomol Struct. 1999; 28:57-73. PMID: 10410795.
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      210. Basu S, Rambo RP, Strauss-Soukup J, Cate JH, Ferré-D'Amaré AR, Strobel SA, Doudna J. A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nat Struct Biol. 1998 Nov; 5(11):986-92. PMID: 9808044.
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      211. Ferré-D'Amaré AR, Zhou K, Doudna J. Crystal structure of a hepatitis delta virus ribozyme. Nature. 1998 Oct 08; 395(6702):567-74. PMID: 9783582.
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      212. Doudna J. Ribozymes: the hammerhead swings into action. Curr Biol. 1998 Jul 02; 8(14):R495-7. PMID: 9663384.
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      213. Ferré-D'Amaré AR, Zhou K, Doudna J. A general module for RNA crystallization. J Mol Biol. 1998 Jun 12; 279(3):621-31. PMID: 9641982.
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      214. Batey RT, Doudna J. The parallel universe of RNA folding. Nat Struct Biol. 1998 May; 5(5):337-40. PMID: 9586989.
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      215. Doudna J. RNA structure. A molecular contortionist. Nature. 1997 Aug 28; 388(6645):830-1. PMID: 9278040.
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      216. Cate JH, Hanna RL, Doudna J. A magnesium ion core at the heart of a ribozyme domain. Nat Struct Biol. 1997 Jul; 4(7):553-8. PMID: 9228948.
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      217. Strobel SA, Doudna J. RNA seeing double: close-packing of helices in RNA tertiary structure. Trends Biochem Sci. 1997 Jul; 22(7):262-6. PMID: 9255068.
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      218. Doudna J, Cate JH. RNA structure: crystal clear? Curr Opin Struct Biol. 1997 Jun; 7(3):310-6. PMID: 9204271.
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      219. Doherty EA, Doudna J. The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core. Biochemistry. 1997 Mar 18; 36(11):3159-69. PMID: 9115992.
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      220. Ferré-d'Amaré AR, Doudna J. Establishing suitability of RNA preparations for crystallization. Determination of polydispersity. Methods Mol Biol. 1997; 74:371-7. PMID: 9204452.
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      221. Doudna J, Doherty EA. Emerging themes in RNA folding. Fold Des. 1997; 2(5):R65-70. PMID: 9377708.
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      222. Doudna J. Preparation of homogeneous ribozyme RNA for crystallization. Methods Mol Biol. 1997; 74:365-70. PMID: 9204451.
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      223. Cate JH, Doudna J. A sparse matrix approach to crystallizing ribozymes and RNA motifs. Methods Mol Biol. 1997; 74:379-86. PMID: 9204453.
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      224. Cate JH, Doudna J. Metal-binding sites in the major groove of a large ribozyme domain. Structure. 1996 Oct 15; 4(10):1221-9. PMID: 8939748.
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      225. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Szewczak AA, Kundrot CE, Cech TR, Doudna J. RNA tertiary structure mediation by adenosine platforms. Science. 1996 Sep 20; 273(5282):1696-9. PMID: 8781229.
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      226. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna J. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 1996 Sep 20; 273(5282):1678-85. PMID: 8781224.
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      227. Jones JT, Barnes CL, Lietzke SE, Weichenrieder O, Doudna J, Kundrot CE. Preliminary X-ray diffraction studies of an RNA pseudoknot that inhibits HIV-1 reverse transcriptase. Acta Crystallogr D Biol Crystallogr. 1996 Sep 01; 52(Pt 5):1018-20. PMID: 15299613.
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      228. Ferré-D'Amaré AR, Doudna J. Use of cis- and trans-ribozymes to remove 5' and 3' heterogeneities from milligrams of in vitro transcribed RNA. Nucleic Acids Res. 1996 Mar 01; 24(5):977-8. PMID: 8600468; PMCID: PMC145725.
      229. Doudna J. Hammerhead ribozyme structure: U-turn for RNA structural biology. Structure. 1995 Aug 15; 3(8):747-50. PMID: 7582890.
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      230. Doudna J, 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. PMID: 7534420; PMCID: PMC42482.
      231. Doudna J, Cech TR. Self-assembly of a group I intron active site from its component tertiary structural domains. RNA. 1995 Mar; 1(1):36-45. PMID: 7489486; PMCID: PMC1369057.
      232. Doudna J. Hammering out the shape of a ribozyme. Structure. 1994 Dec 15; 2(12):1271-2. PMID: 7704535.
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      233. Doudna J, 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. PMID: 8356090; PMCID: PMC47236.
      234. Doudna J, Usman N, Szostak JW. Ribozyme-catalyzed primer extension by trinucleotides: a model for the RNA-catalyzed replication of RNA. Biochemistry. 1993 Mar 02; 32(8):2111-5. PMID: 7680575.
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      235. 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. PMID: 1876835.
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      236. Bartel DP, Doudna J, Usman N, Szostak JW. Template-directed primer extension catalyzed by the Tetrahymena ribozyme. Mol Cell Biol. 1991 Jun; 11(6):3390-4. PMID: 2038341; PMCID: PMC360195.
      237. Doudna J, 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. PMID: 1707185.
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      238. Doudna J, 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. PMID: 11540922.
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      239. Couture S, Ellington AD, Gerber AS, Cherry JM, Doudna J, 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 05; 215(3):345-58. PMID: 1700131.
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      240. Doudna J, Szostak JW. Miniribozymes, small derivatives of the sunY intron, are catalytically active. Mol Cell Biol. 1989 Dec; 9(12):5480-3. PMID: 2685567; PMCID: PMC363717.
      241. Doudna J, 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. PMID: 2678103; PMCID: PMC298070.
      242. Doudna J, Szostak JW. RNA-catalysed synthesis of complementary-strand RNA. Nature. 1989 Jun 15; 339(6225):519-22. PMID: 2660003.
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      243. Rajagopal J, Doudna J, Szostak JW. Stereochemical course of catalysis by the Tetrahymena ribozyme. Science. 1989 May 12; 244(4905):692-4. PMID: 2470151.
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      244. Doudna J, Gerber AS, Cherry JM, Szostak JW. Genetic dissection of an RNA enzyme. Cold Spring Harb Symp Quant Biol. 1987; 52:173-80. PMID: 2456876.
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