2018

Receptor-Mediated Delivery of CRISPR-Cas9 Endonuclease for Cell Type Specific Gene Editing.
Rouet R, Thuma BA, Roy MD, Lintner NG, Rubitski DM, Finley JE, Wisniewska HM, Mendonsa R, Hirsh A, de Oñate L, Compte J, Mclellan TJ, Bellenger J, Feng X, Varghese A, Chrunyk BA, Borzilleri KA, Hesp KD, Zhou K, Ma N, Tu M, Dullea R, Mcclure KF, Wilson RC, Liras S, Mascitti V, Doudna JA.
J Am Chem Soc. 2018 Apr 18. doi: 10.1021/jacs.8b01551. [Epub ahead of print]
Genomes in Focus: Development and Applications of CRISPR-Cas9 Imaging Technologies.
Knight SC, Tjian R, Doudna JA.
Angew Chem Int Ed Engl. 2018 Apr 9;57(16):4329-4337. doi: 10.1002/anie.201709201. Epub 2018 Feb 28.
Lapinaite A, Doudna JA, Cate JHD.
Proc Natl Acad Sci USA. 2018 Mar 12. pii: 201717725. doi: 10.1073/pnas.1717725115. [Epub ahead of print]
Chen JS, Ma E, Harrington LB, Da Costa M, Tian X, Palefsky JM, Doudna JA.
Science. 2018 Feb 15. pii: eaar6245. doi: 10.1126/science.aar6245. [Epub ahead of print]
Strutt SC, Torrez RM, Kaya E, Negrete OA, Doudna JA.
Elife. 2018 Jan 5;7. pii: e32724. doi: 10.7554/eLife.32724.

2017

CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing.
Moreno-Mateos MA, Fernandez JP, Rouet R, Vejnar CE, Lane MA, Mis E, Khokha MK, Doudna JA, Giraldez AJ.
Nat Commun. 2017 Dec 8;8(1):2024. doi: 10.1038/s41467-017-01836-2.

Widespread Translational Remodeling during Human Neuronal Differentiation.
Blair JD, Hockemeyer D, Doudna JA, Bateup HS, Floor SN.
Cell Rep. 2017 Nov 14;21(7):2005-2016. doi: 10.1016/j.celrep.2017.10.095.

A thermostable Cas9 with increased lifetime in human plasma.
Harrington LB, Paez-Espino D, Staahl BT, Chen JS, Ma E, Kyrpides NC, Doudna JA
Nat Commun. 2017 Nov 10;8(1):1424. doi: 10.1038/s41467-017-01408-4.

GENOMES IN FOCUS: DEVELOPMENT AND APPLICATIONS OF CRISPR-CAS9 IMAGING TECHNOLOGIES.
Knight S, Tjian R, Doudna J.
Angew Chem Int Ed Engl. 2017 Oct 27. doi: 10.1002/anie.201709201. [Epub ahead of print]

Enhanced proofreading governs CRISPR-Cas9 targeting accuracy.
Chen JS, Dagdas YS, Kleinstiver BP, Welch MM, Sousa AA, Harrington LB, Sternberg SH, Joung JK, Yildiz A, Doudna JA.
Nature. 2017 Sep 20. doi: 10.1038/nature24268. [Epub ahead of print]

Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme.
Knott GJ, East-Seletsky A, Cofsky JC, Holton JM, Charles E, O’Connell MR, Doudna JA.
Nat Struct Mol Biol. 2017 Sep 11. doi: 10.1038/nsmb.3466. [Epub ahead of print]

A Broad-Spectrum Inhibitor of CRISPR-Cas9.
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 JA.
Cell. 2017 Aug 23. pii: S0092-8674(17)30873-5. doi: 10.1016/j.cell.2017.07.037. [Epub ahead of print]

A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9.
Dagdas YS, Chen JS, Sternberg SH, Doudna JA, Yildiz A.
Sci Adv. 2017 Aug 4;3(8):eaao0027. doi: 10.1126/sciadv.aao0027. eCollection 2017 Aug.

Structures of the CRISPR genome integration complex.
Wright AV, Liu JJ, Knott GJ, Doxzen KW, Nogales E, Doudna JA.
Science. 2017 Jul 20. pii: eaao0679. doi: 10.1126/science.aao0679. [Epub ahead of print]

Disabling Cas9 by an anti-CRISPR DNA mimic.
Shin J, Jiang F, Liu JJ, Bray NL, Rauch BJ, Baik SH, Nogales E, Bondy-Denomy J, Corn JE, Doudna JA.
Science Advances 2017 Jul 12;3(7):e1701620. doi: 10.1126/sciadv.1701620. eCollection 2017 Jul.

DNA recognition by an RNA-guided bacterial Argonaute.
Doxzen KW, Doudna JA.
PLoS One. 2017 May 17;12(5):e0177097. doi: 10.1371/journal.pone.0177097. eCollection 2017.

High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding.
Boyle EA, Andreasson JOL, Chircus LM, Sternberg SH, Wu MJ, Guegler CK, Doudna JA, Greenleaf WJ.
Proc Natl Acad Sci U S A. 2017 May 11. pii: 201700557. doi: 10.1073/pnas.1700557114. [Epub ahead of print]

RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes.
East-Seletsky A, O’Connell MR, Burstein D, Knott GJ, Doudna JA.
Mol Cell. 2017 May 4;66(3):373-383.e3. doi: 10.1016/j.molcel.2017.04.008.

CRISPR-Cas9 Structures and Mechanisms.
Jiang F, Doudna JA.
Annu Rev Biophys. 2017 Mar 30. doi: 10.1146/annurev-biophys-062215-010822. [Epub ahead of print]

Targeted gene knock-in by homology-directed genome editing using Cas9 ribonucleoprotein and AAV donor delivery.
Gaj T, Staahl BT, Rodrigues GM, Limsirichai P, Ekman FK, Doudna JA, Schaffer DV.
Nucleic Acids Res. 2017 Mar 2. doi: 10.1093/nar/gkx154. [Epub ahead of print]

Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain.
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 JA, Dullea RG, Cate JH.
PLoS Biol. 2017 Mar 21;15(3):e2001882. doi: 10.1371/journal.pbio.2001882. eCollection 2017.

RNA-based recognition and targeting: sowing the seeds of specificity.
Gorski SA, Vogel J, Doudna JA.
Nat Rev Mol Cell Biol. 2017 Feb 15. doi: 10.1038/nrm.2016.174. [Epub ahead of print]

Efficient genome editing in the mouse brain by local delivery of engineered Cas9 ribonucleoprotein complexes.
Staahl BT, Benekareddy M, Coulon-Bainier C, Banfal AA, Floor SN, Sabo JK, Urnes C, Munares GA, Ghosh A Doudna JA.
Nat Biotechnol. 2017 Feb 13. doi: 10.1038/nbt.3806. [Epub ahead of print]

RNA and DNA Targeting by a Reconstituted Thermus thermophiles Type III-A CRISPR-Cas System.
Liu TY, Iavarone AT, Doudna JA.
PLoS One. 2017 Jan 23;12(1):e0170552. doi: 10.1371/journal.pone.0170552. eCollection 2017.

Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response.
Heler R, Wright AV, Vucelja M, Bikard D, Doudna JA, Marraffini LA.
Mol Cell. 2017 Jan 5;65(1):168-175. doi: 10.1016/j.molcel.2016.11.031. Epub 2016 Dec 22.

2016

Cornerstones of CRISPR-Cas in drug discovery and therapy.
Fellmann C, Gowen BG, Lin PC, Doudna JA, Corn JE.
Nat Rev Drug Discov. 2016 Dec 23. doi: 10.1038/nrd.2016.238. [Epub ahead of print]

New CRISPR-Cas systems from uncultivated microbes.
Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Banfield JF.
Nature. 2016 Dec 22. doi: 10.1038/nature21059. [Epub ahead of print]

RNA scanning of a molecular machine with a built-in ruler.
Koh HR, Kidwell MA, Doudna JA, Myong S.
J Am Chem Soc. 2016 Dec 13. [Epub ahead of print]

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing.
Chen X, Shen Y, Draper W, Buenrostro JD, Litzenburger U, Cho SW, Satpathy AT, Carter AC, Ghosh RP, East-Seletsky A, Doudna JA, Greenleaf WJ, Liphardt JT, Chang HY.
Nat Methods. 2016 Oct 17. doi: 10.1038/nmeth.4031. [Epub ahead of print]

A Cas9 Ribonucleoprotein Platform for Functional Genetic Studies of HIV-Host Interactions in Primary Human T Cells.
Hultquist JF, Schumann K, Woo JM, Manganaro L, McGregor MJ, Doudna J, Simon V, Krogan NJ, Marson A.
Cell Rep. 2016 Oct 25;17(5):1438-1452. doi: 10.1016/j.celrep.2016.09.080.

Insights into HIV-1 proviral transcription from the structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex.
Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH.
Elife.2016 Oct 12;5. pii: e15910. doi: 10.7554/eLife.15910. [Epub ahead of print]

Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection.
East-Seletsky A, O’Connell MR, Knight SC, Burstein D, Cate JH, Tjian R, Doudna JA.
Nature. 2016 Sep 26. doi: 10.1038/nature19802. [Epub ahead of print]

Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9.
Singh D, Sternberg SH, Fei J, Doudna JA, Ha T.
Nat Commun. 2016 Sep 14;7:12778. doi: 10.1038/ncomms12778.

Applications of CRISPR technologies in research and beyond.
Barrangou R, Doudna JA.
Nat Biotechnol. 2016 Sep 8:933-941. doi: 10.1038/nbt.3659. [Epub ahead of print]

Protecting genome integrity during CRISPR immune adaptation.
Wright AV, Doudna JA.
Nat Struct Mol Biol.2016 Sep 5. doi: 10.1038/nsmb.3289. [Epub ahead of print]

DNA Targeting by a Minimal CRISPR RNA-Guided Cascade.
Hochstrasser ML, Taylor DW, Kornfeld JE, Nogales E, Doudna JA.
Mol Cell. 2016 Sep 1;63(5):840-51. doi: 10.1016/j.molcel.2016.07.027.

eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation.
Lee AS, Kranzusch PJ, Doudna JA, Cate JH.
Nature. 2016 Jul 27. doi: 10.1038/nature18954. [Epub ahead of print]

Reconstitution of selective HIV-1 RNA packaging in vitro by membrane-bound Gag assemblies.
Carlson LA, Bai Y, Keane SC, Doudna JA, Hurley JH.
Elife 2016 Jun 25;pii: e14663. doi: 10.7554/eLife.14663. [Epub ahead of print]

CRISPR Immunological Memory Requires a Host Factor for Specificity.
Nuñez JK, Bai L, Harrington LB, Hinder TL, Doudna JA.
Mol Cell 2016 Jun 16;62(6):824-33.

Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch.
Oakes BL, Nadler DC, Flamholz A, Fellmann C, Staahl BT, Doudna JA Savage DF.
Nat Biotechnol. 2016 Jun;34(6):646-51.

Nucleosome breathing and remodeling constrain CRISPR-Cas9 function.
Isaac RS, Jiang F, Doudna JA, Lim WA, Narlikar GJ, Almeida RA
Elife 2016 Apr 28;5. pii: e13450.

Programmable RNA Tracking in Live Cells with CRISPR/Cas9.
Nelles DA, Fang MY, O’Connell MR, Xu JL, Markmiller SJ, Doudna JA, Yeo GW
Cell 2016 Apr 7;165(2):488-96.

Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress.
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 JA, Pfister SM, Taylor MD, Chang HY, Cho YJ.
Oncotarget 2016 Apr 5

A bacterial Argonaute with noncanonical guide RNA specificity.
Kaya E, Doxzen KW, Knoll KR, Wilson RC, Strutt SC, Kranzusch PJ, Doudna JA.
Proc Natl Acad Sci U S A 2016 Mar 30

Programmable RNA Tracking in Live Cells with CRISPR/Cas9.
Nelles DA, Fang MY, O’Connell MR, Xu JL, Markmiller SJ, Doudna JA, Yeo GW.
Cell 2016 Mar 16

Chemical and Biophysical Modulation of Cas9 for Tunable Genome Engineering.
Nuñez JK, Harrington LB, Doudna JA.
ACS Chem Biol 2016 Feb 9

Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage.
Jiang F, Taylor DW, Chen JS, Kornfeld JE, Zhou K, Thompson AJ, Nogales E, Doudna JA
Science 2016 Jan 14. pii: aad8282.

Biology and Applications of CRISPR Systems: Harnessing Nature’s Toolbox for Genome Engineering.
Wright AV, Nuñez JK, Doudna JA
Cell 2016 Jan 14;164(1-2):29-44.

Tunable protein synthesis by transcript isoforms in human cells.
Floor SN, Doudna JA
eLife 2016 Jan 6;5. pii: e10921

2015

Genome-editing revolution: My whirlwind year with CRISPR.
Doudna JA
Nature 2015 Dec 24;528(7583):469-71

Genome editing: the end of the beginning.
Doudna JA, Gersbach CA
Genome Biol 2015 Dec 23;16(1):292

Analog sensitive chemical inhibition of the DEAD-box protein DDX3.
Floor SN, Barkovich KJ, Condon KJ, Shokat KM, Doudna JA
Protein Sci 2015 Dec 9;

Get in LINE: Competition for Newly Minted Retrotransposon Proteins at the Ribosome.
Floor SN, Doudna JA
Mol Cell 2015 Dec 3;60(5):712-4

Perspective: Embryo editing needs scrutiny.
Doudna J
Nature 2015 Dec 3;528(7580):S6

Autoinhibitory Interdomain Interactions and Subfamily-Specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3.
Floor SN, Condon KJ, Sharma D, Jankowsky E, Doudna JA
J Biol Chem 2015 Nov 23;

Dynamics of CRISPR-Cas9 genome interrogation in living cells.
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
Science 2015 Nov 13;350(6262):823-6

Single-Stranded DNA Cleavage by Divergent CRISPR-Cas9 Enzymes.
Ma E, Harrington LB, O’Connell MR, Zhou K, Doudna JA
Mol Cell 2015 Nov 5;60(3):398-407 PMCID: PMC4636735

Conformational control of DNA target cleavage by CRISPR-Cas9.
Sternberg SH, LaFrance B, Kaplan M, Doudna JA
Nature 2015 Nov 5;527(7576):110-3

Surveillance and Processing of Foreign DNA by the Escherichia coli CRISPR-Cas System.
Redding S, Sternberg SH, Marshall M, Gibb B, Bhat P, Guegler CK, Wiedenheft B, Doudna JA, Greene EC
Cell 2015 Nov 5;163(4):854-65 PMCID: PMC4636941

Foreign DNA capture during CRISPR-Cas adaptive immunity.
Nuñez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA
Nature 2015 Nov 26;527(7579):535-8 PMCID: PMC4662619

Ancient Origin of cGAS-STING Reveals Mechanism of Universal 2′,3′ cGAMP Signaling.
Kranzusch PJ, Wilson SC, Lee AS, Berger JM, Doudna JA, Vance RE
Mol Cell 2015 Sep 17;59(6):891-903 PMCID: PMC4575873

Generation of knock-in primary human T cells using Cas9 ribonucleoproteins.
Schumann K, Lin S, Boyer E, Simeonov DR, Subramaniam M, Gate RE, Haliburton GE, Ye CJ, Bluestone JA, Doudna JA, Marson A
Proc Natl Acad Sci U S A 2015 Aug 18;112(33):10437-42 PMCID: PMC4547290

STRUCTURAL BIOLOGY. A Cas9-guide RNA complex preorganized for target DNA recognition.
Jiang F, Zhou K, Ma L, Gressel S, Doudna JA
Science 2015 Jun 26;348(6242):1477-81

Expanding the Biologist’s Toolkit with CRISPR-Cas9.
Sternberg SH, Doudna JA
Mol Cell 2015 May 21;58(4):568-74

CRISPR germline engineering–the community speaks.
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
Nat Biotechnol 2015 May;33(5):478-86

Structural biology. Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning.
Taylor DW, Zhu Y, Staals RH, Kornfeld JE, Shinkai A, van der Oost J, Nogales E, Doudna JA
Science 2015 May 1;348(6234):581-5 PMCID: PMC4582657

Biotechnology. A prudent path forward for genomic engineering and germline gene modification. (Free Full Text) (Free PDF)
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
Science 2015 Apr 3;348(6230):36-8 PMCID: PMC4394183

The structural biology of CRISPR-Cas systems.
Jiang F, Doudna JA
Curr Opin Struct Biol 2015 Feb;30:100-11 PMCID: PMC4417044

Rational design of a split-Cas9 enzyme complex.
Wright AV, Sternberg SH, Taylor DW, Staahl BT, Bardales JA, Kornfeld JE, Doudna JA
Proc Natl Acad Sci U S A 2015 Mar 10;112(10):2984-9 PMCID: PMC4364227

Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity.
Nuñez JK, Lee AS, Engelman A, Doudna JA
Nature 2015 Mar 12;519(7542):193-8 PMCID: PMC4359072

Dicer-TRBP complex formation ensures accurate mammalian microRNA biogenesis.
Wilson RC, Tambe A, Kidwell MA, Noland CL, Schneider CP, Doudna JA
Mol Cell 2015 Feb 5;57(3):397-407 PMCID: PMC4320653

Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery.
Lin S, Staahl BT, Alla RK, Doudna JA
Elife 2014 Dec 15;3:e04766 PMCID: PMC4383097

Cutting it close: CRISPR-associated endoribonuclease structure and function.
Hochstrasser ML, Doudna JA
Trends Biochem Sci 2015 Jan;40(1):58-66

2014

RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus.
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
Mol Cell 2014 Nov 20;56(4):518-30 PMCID: PMC4342149

Genome editing. The new frontier of genome engineering with CRISPR-Cas9. (Free Full Text)
Doudna JA, Charpentier E
Science 2014 Nov 28;346(6213):1258096

New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.
Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS
Nucleic Acids Res 2014 Nov 10;42(20):12833-46 PMCID: PMC4227795

Programmable RNA recognition and cleavage by CRISPR/Cas9.
O’Connell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA
Nature 2014 Dec 11;516(7530):263-6 PMCID: PMC4268322

RNA-guided assembly of Rev-RRE nuclear export complexes.
Bai Y, Tambe A, Zhou K, Doudna JA
Elife 2014 Aug 27;3:e03656 PMCID: PMC4142337

Evolutionarily conserved roles of the dicer helicase domain in regulating RNA interference processing.
Kidwell MA, Chan JM, Doudna JA
J Biol Chem 2014 Oct 10;289(41):28352-62 PMCID: PMC4192488

Structure-guided reprogramming of human cGAS dinucleotide linkage specificity.
Kranzusch PJ, Lee AS, Wilson SC, Solovykh MS, Vance RE, Berger JM, Doudna JA
Cell 2014 Aug 28;158(5):1011-21 PMCID: PMC4157622

Insights into RNA structure and function from genome-wide studies.
Mortimer SA, Kidwell MA, Doudna JA
Nat Rev Genet 2014 Jul;15(7):469-79

Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity.
Nuñez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA
Nat Struct Mol Biol 2014 Jun;21(6):528-34 PMCID: PMC4075942

CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference.
Hochstrasser ML, Taylor DW, Bhat P, Guegler CK, Sternberg SH, Nogales E, Doudna JA
Proc Natl Acad Sci U S A 2014 May 6;111(18):6618-23 PMCID: PMC4020112

Structures of Cas9 endonucleases reveal RNA-mediated conformational activation.
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.
Science 2014 Mar 14;343(6176):1247997. doi: 10.1126/science.1247997. Epub 2014 Feb 6.

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.
Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA
Nature 2014 Mar 6;507(7490):62-7 PMCID: PMC4106473

Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases.
Niewoehner O, Jinek M, Doudna JA
Nucleic Acids Res 2014 Jan;42(2):1341-53 PMCID: PMC3902920

2013

Precise and heritable genome editing in evolutionarily diverse nematodes using TALENs and CRISPR/Cas9 to engineer insertions and deletions.
Lo TW, Pickle CS, Lin S, Ralston EJ, Gurling M, Schartner CM, Bian Q, Doudna JA, Meyer BJ
Genetics 2013 Oct;195(2):331-48 PMCID: PMC3781963

High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity.
Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR
Nat Biotechnol 2013 Sep;31(9):839-43 PMCID: PMC3782611

Molecular mechanisms of RNA interference.
Wilson RC, Doudna JA.
Annu Rev Biophys. 2013;42:217-39. doi: 10.1146/annurev-biophys-083012-130404.

CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes.
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
Cell 2013 Jul 18;154(2):442-51

Hepatitis C virus 3’UTR regulates viral translation through direct interactions with the host translation machinery.
Bai Y, Zhou K, Doudna JA
Nucleic Acids Res 2013 Sep;41(16):7861-74 PMCID: PMC3763534

Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation.
Sun C, Querol-Audí J, Mortimer SA, Arias-Palomo E, Doudna JA, Nogales E, Cate JH
Nucleic Acids Res 2013 Aug;41(15):7512-21 PMCID: PMC3753635

Structure of human cGAS reveals a conserved family of second-messenger enzymes in innate immunity.
Kranzusch PJ, Lee AS, Berger JM, Doudna JA
Cell Rep 2013 May 30;3(5):1362-8 PMCID: PMC3800681

Differential roles of human Dicer-binding proteins TRBP and PACT in small RNA processing.
Lee HY, Zhou K, Smith AM, Noland CL, Doudna JA
Nucleic Acids Res 2013 Jul;41(13):6568-76 PMCID: PMC3711433

Substrate-specific structural rearrangements of human Dicer.
Taylor DW, Ma E, Shigematsu H, Cianfrocco MA, Noland CL, Nagayama K, Nogales E, Doudna JA, Wang HW
Nat Struct Mol Biol 2013 Jun;20(6):662-70 PMCID: PMC3676429

Multiple sensors ensure guide strand selection in human RNAi pathways.
Noland CL, Doudna JA
RNA 2013 May;19(5):639-48 PMCID: PMC3677279

RNA-protein analysis using a conditional CRISPR nuclease.
Lee HY, Haurwitz RE, Apffel A, Zhou K, Smart B, Wenger CD, Laderman S, Bruhn L, Doudna JA
Proc Natl Acad Sci U S A 2013 Apr 2;110(14):5416-21 PMCID: PMC3619310

Unconventional miR-122 binding stabilizes the HCV genome by forming a trimolecular RNA structure.
Mortimer SA, Doudna JA
Nucleic Acids Res 2013 Apr;41(7):4230-40 PMCID: PMC3627571

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression.
Cell.
2013 Feb 28;152(5):1173-83. doi: 10.1016/j.cell.2013.02.022.

RNA-programmed genome editing in human cells.
Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J
Elife 2013 Jan 29;2:e00471 PMCID: PMC3557905

2012

TRBP alters human precursor microRNA processing in vitro.
Lee HY, Doudna JA
RNA 2012 Nov;18(11):2012-9 PMCID: PMC3479391

RNA processing enables predictable programming of gene expression.
Qi L, Haurwitz RE, Shao W, Doudna JA, Arkin AP
Nat Biotechnol 2012 Oct;30(10):1002-6

A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E
Science 2012 Aug 17;337(6096):816-21

Coordinated activities of human dicer domains in regulatory RNA processing.
Ma E, Zhou K, Kidwell MA, Doudna JA
J Mol Biol 2012 Sep 28;422(4):466-76 PMCID: PMC3461841

Biochemistry. Guided tour to the heart of RISC.
Kaya E, Doudna JA
Science 2012 May 25;336(6084):985-6

Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA.
Haurwitz RE, Sternberg SH, Doudna JA
EMBO J 2012 Jun 13;31(12):2824-32 PMCID: PMC3380207

Mechanism of foreign DNA selection in a bacterial adaptive immune system.
Sashital DG, Wiedenheft B, Doudna JA
Mol Cell 2012 Jun 8;46(5):606-15 PMCID: PMC3397241

Mechanism of substrate selection by a highly specific CRISPR endoribonuclease.
Sternberg SH, Haurwitz RE, Doudna JA
RNA 2012 Apr;18(4):661-72 PMCID: PMC3312554

RNA-guided genetic silencing systems in bacteria and archaea.
Wiedenheft B, Sternberg SH, Doudna JA.
Nature. 2012 Feb 15;482(7385):331-8. doi: 10.1038/nature10886.

Reassortment and mutation of the avian influenza virus polymerase PA subunit overcome species barriers.
Mehle A, Dugan VG, Taubenberger JK, Doudna JA
J Virol 2012 Feb;86(3):1750-7 PMCID: PMC3264373

2010 - 2012


Structures of the RNA-guided surveillance complex from a bacterial immune system. Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJ, van der Oost J, Doudna JA, Nogales E. Nature. 2011 Sep 21; 477(7365): 486-9. PMID: 21938068

siRNA repositioning for guide strand selection by human Dicer complexes. Noland CL, Ma E, Doudna JA. Mol. Cell. 2011 July 8; 43(1):110-21. PMCID: PMC3143821.

Modeling and automation of sequencing-based characterization of RNA structure. Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L.Proc. Natl. Acad. Sci. U.S.A. 2011 July 5; 108(27): 11069-74. PMID: 21642536, PMCID: PMC3131376.

Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Lucks, JB, Mortimer, SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP. Proc. Natl. Acad. Sci. U.S.A. 2011 Jul 5; 108(27):11063-8. PMID: 21642531, PMCID: PMC3131332.

An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3. Sashital, DG, Jinek M, Doudna JA. Nat. Struct. Mol. Biol. 2011 Jun; 18(6):680-7. PMID: 21572442.

RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Wiedenheft B, van Duijn E, Bultema JB, Waghmare SP, Zhou K, Barendregt A, Westphal W, Heck AJ, Boekema EJ, Dickman MJ, Doudna JA. Proc. Natl. Acad. Sci. U.S.A. 2011 Jun 21; 108(25):10092-7. Erratum in: Proc. Natl. Acad. Sci. U. S. A. 2011 Sep 6;108(36):15010. PMID: 21536913, PMCID: PMC3121849

Structural basis for CRISPR RNA-guided DNA recognition by Cascade. 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. Nat. Struct. Mol. Biol. 2011 May; 18(5):529-36. PMID: 21460843.

The crystal structure of the signal recognition particle in complex with its receptor. Ataide SF, Schmitz N, Shen K, Ke A, Shan SO, Doudna JA, Ban N. Science. 2011 Feb 18; 331(6019):881-6. PMID: 21330537.

Coupled 5’ nucleotide recognition and processivity in Xrn1-mediated mRNA decay. Jinek M, Coyle SM, Doudna JA. Mol. Cell. 2011 March 4; 41(5):600-8. PMID: 21362555.

Optimized high-throughput screen for hepatitis C virus translation inhibitors. Berry KE, Peng B, Koditek D, Beeman D, Pagratis N, Perry JK, Parrish J, Zhong W, Doudna JA, Shih IH. J. Biomol. Screen. 2011 Feb; 16(2):211-20. PMID: 21297107, PMCID: PMC3260011.

Substrate-Specific Kinetics of Dicer-Catalyzed RNA Processing. Chakravarthy S, Sternberg SH, Kellenberger CA, Doudna JA. J. Mol. Biol. 2010 Dec 3; 404(3):392-402. PMID: 20932845, PMCID: PMC3005596

Structural and biochemical studies of a fluoroacetyl-CoA-specific thioesterase reveal a molecular basis for fluorine selectivity. Weeks AM, Coyle SM, Jinek M, Doudna JA, Chang MC. Biochemistry. 2010 Nov 2; 49(43):9269-79. PMID: 20836570

Sequence-and structure-specific RNA processing by a CRISPR endonuclease. Haurwitz RE, Wiedenheft B, Zhou K, Doudna JA.Science.2010 329(5997):1355-8. PMID: 20829488, PMCID: PMC3133607.

The HCV IRES pseudoknot positions the initiation codon on the 40S ribosomal subunit. Berry KE, Waghray S, Doudna JA. RNA.2010 Aug 16 (8):1559-69. PMID: 20584896, PMCID: PMC2905755.

A Novel miRNA Processing Pathway Independent of Dicer Requires Argonaute2 Catalytic Activity. Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson N, Wolfe N, Giraldez AJ. Science. 2010 Jun 25; 328(5986):1694-8.

Functional Overlap between eIF4G Isoforms in Saccharomyces cerevisiae. Clarkson, Bryan K., Gilbert, Wendy V., Doudna, Jennifer A. PLOS One. 2010; 5(2): e9114. PMID: 20161741, PMCID: PMC2817733.

A host of factors regulating influenza virus replication.Mehle A, Doudna JA. Viruses. 2010 Feb;2(2):566-73. PMID: 21994648, PMCID: PMC3185602.

Structural insights into RNA interference. Sashital, DG, Doudna, JA. Curr. Opin. Struct. Biol. 2010 Feb; 20(1):90-7. PMID: 20053548.

Structural insights into the human GW182-PABC interaction in microRNA-mediated deadenylation.. Jinek, M., Fabian, M.R., Coyle, S.M., Sonenberg, N, Doudna, JA Nat. Struct. Mol. Biol. 2010 Feb; 17(2):238-40. PMID: 20098421.

2005-2009

Mehle A, Doudna JA.(2009) Adaptive strategies of the influenza virus polymerase for replication in humans. Proc. Natl. Acad. Sci. U S A. 2009 Dec 5; 106(50):21312-6. PMID: 19995968, PMCID: PMC2789757.

Wang, HW; Noland, C; Siridechadilok, B; et al. (2009) Structural insights into RNA processing by the human RISC-loading complex. Nat. Struct. Mol. Biol. 16 (11):1148-U4. PMID: 19820710.

Chen J, Lakshmi GG, Hays DL, McDowell KM, Ma E, Vaughn JC. (2009) Spatial and temporal expression of dADAR mRNA and protein isoforms during embryogenesis in Drosophila melanogaster. Differentiation. 78(5):312-20. PMID: 19720447.

Fabian, M.R., Mathonnet, G., Sundermeier, T., Mathys, H., Zipprich, J.T., Svitkin, Y.V., Rivas, F., Jinek, M., Wohlschlegel, J., Doudna, J.A., Chen, C.Y., Shyu, A.B., Yates, J.R. 3rd, Hannon, G.J., Filipowicz, W., Duchaine, T.F., Sonenberg, N. (2009) Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol. Cell. Biol. 2009 35(6):739-40. PMID:19716330.

Wiedenheft, B., Zhou, K., Jinek, M., Coyle, S.M., Ma, W., Doudna, J.A. (2009) Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure. 17 (6):904-12.

Fraser, C.S., Hershey, J.W., Doudna, J.A. (2009) The pathway of hepatitis C virus mRNA recruitment to the human ribosome. Nat. Struct. Mol. Biol. 16 (4):397-404. PMID: 19287397.

Fukunaga, R., Doudna, J.A. (2009) dsRNA with 5′ overhangs contributes to endogenous and antiviral RNA silencing pathways in plants. EMBO J. 28 (5):545-55. PMID:19165150.

Jinek, M., Doudna, J.A. (2009) A three-dimensional view of the molecular machinery of RNA interference. Nature. 457 (7228):405-12.

Coyle, S.M., Doudna, J.A. (2008) Direct link between RACK1 function and localization at the ribosome in vivo. Mol. Cell Biol. 29(6):1626-34. PMID: 19114558.

Mehle, A. and Doudna, J.A. (2008) An inhibitory activity in human cells restricts the function of an avian-like influenza virus polymerase. Cell Host Microbe. 4, 111-122.

Zhou, M., Sandercock, A.M., Fraser, C.S., Ridlova, G., Stephens, E., Schenauer, M.R., Yokoi-Fong, T., Barsky, D., Leary, J.A., Hershey, J.W., Doudna, J.A. and Robinson, C.V. (2008) Special Feature: Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3. PNAS. (972KB .pdf)

Puglisi, J.D. and Doudna, J.A. (2008) Nucleic acids and their protein partners. Curr. Opin. Struct. Biol. 18, 279-281. (98KB .pdf)

Ma, E., MacRae, I.J., Kirsch, J.F., and Doudna, J.A. (2008) Autoinhibition of human dicer by its internal helicase domain. J. Mol. Biol. 380, 237-243. (360KB .pdf)

MacRae, I.J., Ma, E., Zhou, M., Robinson, C.V. and Doudna, J.A. (2008) In vitro reconstitution of the human RISC-loading complex. PNAS. 105, 512-517. (1.8MB .pdf)

Fraser, C.S. and Doudna, J.A. (2007) Quantitative studies of ribosome conformational dynamics. Q. Rev. Biophys. 40, 163-189. (308KB .pdf)

MacRae, I.J., Zhou, K. and Doudna, J.A. (2007) Structural determinants of RNA recognition and cleavage by Dicer. Nat. Struct. Mol. Biol. 14, 934-940. (488KB .pdf)

Gilbert, W.V., Zhou, K., Butler, T.K. and Doudna, J.A. (2007) Cap-independent translation is required for starvation-induced differentiation in yeast. Science. 317, 1224-1227. (380KB .pdf)

Fraser, C.S., Berry, K.E., Hershey, J.W. and Doudna, J.A. (2007) eIF3j is located in the decoding center of the human 40S ribosomal subunit. Mol. Cell. 26, 811-819. (1.4MB .pdf)

MacRae, I.J. and Doudna, J.A. (2007) An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer. Acta Cryst. D. 63(Part 9), 993-999. (1.4MB .pdf)

Doudna, J.A., Sarnow, P. (2007) Translation initiation by viral internal ribosome entry sites. In Translational Control in Biology and Medicine (Mathews, M.B., Sonenberg, N., Hershey, J.W.B., Eds.), Cold Spring Harbor Monograph 48, 129-153.  (2.8MB .pdf)

Doudna, J.A. (2007) The right chemistry: an updated nucleic acids textbook. ACS Chem. Biol. 2, 211-212. (152KB .pdf)

Kiessling, L.L., Doudna, J.A., Johnsson, K., Mapp, A.K., Marletta, M.A., Seeberger, P.H., Williamson, J.R. and Wedde S.G. (2007) A higher degree of difficulty. ACS Chem. Biol. 2,197-199.  (292KB .pdf)

Ke, A., Ding, F., Batchelor, J.D. and Doudna, J.A. (2007) Structural roles of monovalent cations in the HDV ribozyme. Structure. 15, 281-287. (1.1MB .pdf)

Damoc, E., Fraser, C.S., Zhou, M., Videler, H., Mayeur, G.L., Hershey, J.W., Doudna, J.A., Robinson, C.V. and Leary, J.A. (2007) Structural characterization of the human eukaryotic initiation factor 3 protein complex by mass spectrometry. Mol. Cell. Proteomics. 6, 1135-1146. (604KB .pdf)

MacRae, I.J. and Doudna, J.A. (2007) Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Curr. Opin. Struct. Biol. 17, 1-8. (1.7MB .pdf)

Fraser, C.S. and Doudna, J.A. (2007) Structural and mechanistic insights into hepatitis C viral translation initiation. Nat. Rev. Microbiol. 5, 29-38. (680KB .pdf)

MacRae, I.J., Li, F., Zhou, K., Cande, W.Z. and Doudna, J.A. (2006) Structure of dicer and mechanistic implications for RNAi. Cold Spring Harb. Symp. Quant. Biol. 71, 73-80. (6.8MB .pdf)

Siu, F.Y., Spanggord, R.J. and Doudna, J.A. (2006) SRP RNA provides the physiologically essential GTPase activation function in cotranslational protein targeting. RNA. 13, 240-250.  (1.1MB .pdf)

Green, R. and Doudna, J.A. (2006) RNAs regulate biology. ACS Chem. Biol. 1, 335-338. (304KB .pdf)

Wu, S., Ke, A. and Doudna, J.A. (2006) A fast and efficient procedure to produce scFvs specific for large macromolecular complexes. J. Immunol. Methods. 318, 95-101. (876KB .pdf)

Chmiel, N.H., Rio, D.C. and Doudna, J.A. (2006) Distinct contributions of KH domains to substrate binding affinity of Drosophila P-element somatic inhibitor protein. RNA. 12, 283-291. (764KB .pdf)

MacRae, I.J., Zhou, K., Li, F., Repic, A. Brooks, A.N., Cande, W.Z., Adams, P.D. and Doudna, J.A. (2006) Structural basis for double-stranded RNA processing by Dicer. Science. 311, 195-198. (288KB .pdf) (Figure) (Structure)

Karbstein, K. and Doudna, J.A. (2006) GTP-dependent formation of a ribonucleoprotein subcomplex required for ribosome biogenesis. J. Mol. Biol. 356, 432-443.(300KB .pdf)

Doudna, J.A. (2005) Chemical biology at the crossroads of molecular structure and mechanism. Nat. Chem. Biol. 1, 300-303. (428KB .pdf)

Siridechadilok, B., Fraser, C.S., Hall, R.J., Doudna, J.A. and Nogales, E. (2005) Structural roles for human translation factor eIF3 in initiation of protein synthesis. Science. 310,1513-1515. (216KB .pdf) (Supplemental material: 712KB .pdf) (Figure and QuickTime Movies) (Structures)

Karbstein, K., Jonas, S. and Doudna, J.A. (2005) An essential GTPase promotes assembly of preribosomal RNA processing complexes. Mol. Cell. 20, 633-643. (504KB .pdf)

Spanggord, R.J., Siu, F., Ke, A. and Doudna, J.A. (2005) RNA-mediated interaction between the peptide-binding and GTPase domains of the signal recognition particle. Nat. Struct. Mol. Biol. 12, 1116-1122. (484KB .pdf) (Figures)

Chen, L., Lullo, D.J., Ma, E., Celniker, S.E., Rio, D.C. and Doudna, J.A. (2005) Identification and analysis of U5 snRNA variants in Drosophila. RNA. 11, 1473-7. (268KB .pdf)

MacRae, I. J. and Doudna, J.A. (2005) Ro’s Role in RNA Reconnaissance. Cell. 121, 495-496. (80KB .pdf)

Yu, Y., Ji, H., Doudna, J.A. and Leary, J.A. (2005) Mass spectrometric analysis of the human 40S ribosomal subunit: Native and HCV IRES-bound complexes. Protein Sci. 14,1438-1446. (192KB .pdf)

Doudna, J.A. and Lorsch, J.R. (2005) Ribozyme catalysis: not different, just worse. Nat. Struct. Mol. Biol. 12, 395-402. (580KB .pdf)

Aggarwal, A.K. and Doudna, J.A. (2005) Editorial Overview: Protein-nucleic acid interactions: unlocking mysteries old and new. Curr. Opin. Struct. Biol. 15, 65-67. (72KB .pdf)

2000-2004

Ji, H., Fraser, C.S., Yu, Y., Leary, J. and Doudna, J.A. (2004) Coordinated assembly of human translation initiation complexes by the hepatitis C virus internal ribosome entry site RNA. PNAS. 101, 16990-16995. (508KB .pdf) (Figure)

Ke, A. and Doudna, J.A. (2004) Crystallization of RNA and RNA-protein complexes. Methods. 34, 408-414. (376KB .pdf)

Rambo, R.P. and Doudna, J.A. (2004) Assembly of an active group II intron-maturase complex by protein dimerization. Biochemistry. 43, 6486-6497. (396KB .pdf)

Luptak, A. and Doudna, J.A. (2004) Distinct sites of phosphorothioate substitution interfere with folding and splicing of the Anabaena group I intron. Nucleic Acid Res. 32,2272-2280. (312KB .pdf)

Sagar, M.B., Lucast, L. and Doudna, J.A. (2004) Conserved but nonessential interaction of SRP RNA with translation factor EF-G. RNA. 10, 772-778. (136KB .pdf)

Ke, A., Zhou, K., Ding, F., Cate, J.H.D. and Doudna, J.A. (2004) A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature. 429, 201-205. (348KB .pdf) (Figures and QuickTime Movies) (Structures)

Karbstein, K. and Doudna, J.A. (2004) RNA: Primed for Packing? Chemistry and Biology. 11,149-151. (148KB .pdf)

Doudna, J.A. and Batey, R.T. (2003) Structural insights into the signal recognition particle. Ann. Rev. Biochem. 73, 539-557. (680KB .pdf)

Aggarwal, A.K. and Doudna, J.A. (2003) Editorial Overview: Protein-nucleic acid interactions. Curr. Opin. Struct. Biol. 13, 3-5. (56KB .pdf)

Fraser, C.S., Lee, J.Y., Mayeur, G.L., Bushell, M., Doudna, J.A. and Hershey, J.W. (2003) 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. 279,8946-8956.(532KB .pdf)

Doudna, J.A. and Cech, T.R. (2002) The chemical repertoire of natural ribozymes. Nature. 418, 222-228. (244KB .pdf)

Doudna, J.A. and Rath, V.L. (2002) Structure and function of the eukaryotic ribosome: The next frontier. Cell. 109, 153-156. (120KB .pdf)

Kieft, J.S., Zhou, K., Grech, A., Jubin. R. and Doudna, J.A. (2002) Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation. Nat. Struct. Biol. 9, 370-374. (1.3MB .pdf) (Structure)

Batey, R.T. and Doudna, J.A. (2002) Structural and energetic analysis of metal ions essential to SRP signal recognition domain assembly. Biochemistry. 41, 11703-11710. (536KB .pdf)

Battle, D.J. and Doudna, J.A. (2002) Specificity of RNA-RNA helix recognition. PNAS. 99,11676-11681. (576KB .pdf) Erratum: PNAS 99, 15831-15835. (624KB .pdf) (Structure)

Zhang, L. and Doudna, J.A. (2002) Structural insights into group II intron catalysis and branch-site selection. Science. 295, 2084-2088. (352KB .pdf) (Structure)

Murray, J. and Doudna, J.A. (2001) Creative catalysis: pieces of the RNA world jigsaw. Trends Biochem. Sci. 26, 699-701. (44KB .pdf)

Kieft, J.S., Grech, A., Adams, P. and Doudna, J.A. (2001) Mechanisms of internal ribosome entry in translation initiation. Cold Spring Harb. Symp. Quant. Biol. 66, 277-283. (264KB .pdf)

Doudna, J.A. and Richmond, T.J. (2001) Editorial Overview: Protein-nucleic acid interactions. Curr. Opin. Struct. Biol. 11, 11-13. (40KB .pdf)

Luptak, A., Ferré-D’Amaré, A.R., Zhou, K., Zilm, K.W. and Doudna, J.A. (2001) Direct pKameasurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme. J. Am. Chem. Soc. 123, 8447-8452. (88KB .pdf)

Doherty, E.A. and Doudna, J.A. (2001) Ribozyme Structures and Mechanisms. Ann. Rev. Biophys. Biomol. Struct. 30, 457-475. (316KB .pdf)

Doherty, E.A., Batey, R.T., Masquida, B. and Doudna, J.A. (2001) A universal mode of helix packing in RNA. Nat. Struct. Biol. 8, 339-343. (1.6MB .pdf)

Spahn, C.M.T., Kieft, J.S., Grassucci, R.A., Penczek, P., Zhou, K., Doudna, J.A. and Frank, J. (2001) Hepatitis C virus IRES RNA-induced changes in the conformation of the 40S ribosomal subunit. Science. 291, 1959-1962. (348KB .pdf) (Figure and Movie)

Batey, R.T., Sagar, M.B. and Doudna, J.A. (2001) Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle. J. Mol. Biol. 307, 229-246. (840KB .pdf) (Figure) (Structure)

Lucast, L.J., Batey, R.T. and Doudna, J.A. (2001) Large-scale purification of a stable form of recombinant tobacco etch virus protease. Biotechniques. 30, 544-554. (108KB .pdf)

Kieft, J.S., Zhou, K., Jubin, R. and Doudna, J.A. (2001) Mechanism of ribosome recruitment by hepatitis C IRES RNA. RNA. 7, 194-206. (3.6MB .pdf)

Battle, D.J. and Doudna, J.A. (2001) The stem-loop binding protein forms a highly stable and specific complex with the 3′ stem-loop of histone mRNAs. RNA. 7, 123-132. (452KB .pdf) Erratum: RNA 7, 642-643.

Ferré-D’Amaré, A.R. and Doudna, J.A. (2000) Methods to crystallize RNA. In Current Protocols in Nucleic Acid Chemistry (Beaucage, S.L., Bergstrom, D.E., Glick, G.D. and Jones, R.A., Eds.), pgs. 7.6.1-7.6.13, John Wiley & Sons, New York. (204KB .pdf)

Hanna, R. and Doudna, J.A. (2000) Metal ions in ribozyme folding and catalysis. Curr. Opin. Chem. Biol. 4, 166-170. (228KB .pdf)

Doudna, J.A. (2000) Structural genomics of RNA. Nature Struct. Biol. 7, Suppl., 954-956. (148KB .pdf)

Doherty, E.A. and Doudna, J.A. (2000) Ribozyme Structures and Mechanisms. Ann. Rev. Biochem. 69, 597-615. (2.0MB .pdf)

Cate, J.H. and Doudna, J.A. (2000) Solving large RNA structures by x-ray crystallography. Meth. Enzymol. 317, 169-180. (1.9MB .pdf)

Jeruzalmi D., Kuriyan J., Doudna J. (2000) Paul Sigler (1934-2000). Trends Biochem. Sci. 25, 221-2. (188KB .pdf)

Jubin, R., Vantuno, N.E., Kieft, J.S., Murray, M.G., Doudna, J.A., Lau, J.Y. and Baroudy, B.M. (2000) 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. 22, 10430-10437. (248KB .pdf)

Hanna, R.L., Gryaznov, S.M. and Doudna, J.A. (2000) A phosphoramidate substrate analog is a competitive inhibitor of the Tetrahymena group I ribozyme. Chemistry and Biology. 7,845-854. (524KB .pdf)

Engelhardt, M.A., Doherty, E.A., Knitt, D.S., Doudna, J.A., Herschlag, D. (2000) The P5abc peripheral element facilitates preorganization of the Tetrahymena group I ribozyme for catalysis. Biochemistry. 39, 2639-2651. (296KB .pdf)

Batey, R.T., Rambo, R.P., Lucast, L., Rha, B. and Doudna, J.A. (2000) Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science. 287, 1232-1239. (2.0MB .pdf) (Figure) (Structure) Comment: Science 287, 1212-1213.

Ferré-D’Amaré, A.R. and Doudna, J.A. (2000) Crystallization and structure determination of a hepatitis delta virus ribozyme: Use of the RNA-binding protein U1A as a crystallization module. J. Mol. Biol. 295, 541-556. (900KB .pdf)

1995-1999

Cashing in on Crystals. (1999)Doudna, J.A. Curr. Biol.1999: 9 (19), R731-R734. (76KB .pdf)

Tertiary motifs in RNA structure and folding. Batey, R.T, Rambo, R. and Doudna, J.A. Angewandte Chemie. 1999: 38, 2327-2343. (468KB .pdf)

RNA folds: Insights from recent crystal structures.Ferré-D’Amaré, A.R. and Doudna, J.A. Ann. Rev. Biophys. Biomolec. Struct.1999: 28, 57-73. (648KB .pdf)

The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold. Kieft, J.S., Zhou, K., Jubin, R., Murray, M.G., Johnson, Y.N.L. and Doudna, J.A. J. Mol. Biol.1999: 292, 513-529. (676KB .pdf)

A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes. Wadkins, T.S., Perrotta, A.T., Ferré-D’Amaré, A.R., Doudna, J.A. and Been, M.D. RNA.1999: 5, 720-727. (676KB .pdf)

Assembly of an exceptionally stable RNA tertiary interface in a group I ribozyme. Doherty, E.A., Herschlag, D. and Doudna, J.A.Biochem. 1999:38, 2982-2990. (176KB .pdf)

RNA structures determined by X-ray crystallography. Doudna, J.A. and Cate, J.H. In Comprehensive Natural Products Chemistry(Söll, D., Nishimura, S. and Moore, P.B., Eds.), 1999, Vol. 6, pp. 49-61. (1.5MB .pdf)

Ribozymes: the hammerhead swings into action. Doudna, J.A. Curr. Biol. 1998:8 (14), R495-R497. (136KB .pdf)

The parallel universe of RNA folding. Batey, R.T. and Doudna, J.A. Nat. Struct. Biol.1998:5, 337-340. (1.1MB .pdf)

Crystal structure of a hepatitis delta virus ribozyme. Ferré-D’Amaré, A.R., Zhou, K. and Doudna J.A. Nature . 1998: 395, 567-574. (684KB .pdf) (Figures and QuickTime Movies) (Structures)

A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Basu, S., Rambo, R., Strauss-Soukup, J., Cate, J.H., Ferré-D’Amaré, A.R., Strobel, S.A. and Doudna, J.A.Nature Struc. Biol.1998: 5(11), 986-992. (1.0MB .pdf)

A general module for RNA crystallization. Ferré-D’Amaré, A.R., Zhou, K. and Doudna, J.A. J. Mol. Biol. 1998:279, 621-631. (420KB .pdf)

RNA structure. A molecular contortionist. Doudna, J.A. Nature.1997: 338, 830-831. (268KB .pdf)

Book Review – Catalytic RNA, edited by Fritz Eckstein and David M.J. Lilley. (1997) Doudna, J.A. Nucleic Acids and Molecular Biology, Vol. 10. Heidelberg: Springer-Verlag. 418 pp. RNA.1996: 3, 1083-1084. (360KB .pdf)

Emerging themes in RNA folding. Doudna, J.A. and Doherty, E.A. Folding and Design 1997:. 2, R65-70. (948KB .pdf)

RNA structure: crystal clear? Doudna, J.A. and Cate, J.H. Curr. Opin. Struct. Biol.1997: 7, 310-316. (652KB .pdf)

RNA seeing double: close-packing of helices in RNA tertiary structure.Strobel, S.A. and Doudna, J.A. Trends in Biochem. Sci.1997: 22, 262-266. (1.0MB .pdf)

A Sparse Matrix Approach to Crystallizing Ribozymes and RNA Motifs. Cate, J.H. and Doudna, J.A. In Ribozyme Protocols, Methods in Molecular Biology Series (P. Turner, Ed.), 1997:Vol. 74, pp. 379-386, Humana Press:Totowa, NJ. (732KB .pdf)

Establishing Suitability of RNA Preparations for Crystallization. Determination of Polydispersity. Ferré-D’Amaré, A.R. and Doudna, J.A. In Ribozyme Protocols, Methods in Molecular Biology Series (P. Turner, Ed.),1997 Vol. 74, pp. 371-378, Humana Press:Totowa, NJ. (672KB .pdf)

Preparation of Homogeneous Ribozyme RNA for Crystallization. Doudna, J.A. In < Ribozyme Protocols, Methods in Molecular Biology Series(P. Turner, Ed.),1997 Vol. 74, pp. 365-370, Humana Press:Totowa, NJ. (612KB .pdf)

A magnesium ion core at the heart of a ribozyme domain. Cate, J.H., Hanna, R.H. and Doudna, J.A. Nat. Struct. Biol.1997:4, 553-558. (968KB .pdf) Comment: Nat. Struct. Biol. 4, 509-512. Erratum: Nat. Struct. Biol. 4, 840.

The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core. Doherty, E.A. and Doudna, J.A. Biochemistry. 1997: 36, 3159-69. (392KB .pdf)

Metal-binding sites in the major groove of a large ribozyme domain. Cate, J.H. and Doudna, J.A.Structure. 1996: 4, 1221-29. (1.2MB .pdf)

RNA tertiary structure mediation by adenosine platforms. (1996)Cate, J.H., Gooding, A., Podell, E., Zhou, K., Golden, B., Szewczak, A., Kundrot, C., Cech, T.R. and Doudna, J.A. Science.1996: 273, 1696-99. (156KB .pdf)

Crystal structure of a group I ribozyme domain: Principles of RNA packing. Cate, J.H., Gooding, A., Podell, E., Zhou, K., Golden, B., Kundrot, C., Cech, T.R. and Doudna, J.A. Science. 1996:273, 1678-85. (360KB .pdf) (Figure) (Structure)

Preliminary x-ray diffraction studies of an RNA pseudoknot that inhibits HIV-1 reverse transcriptase. Jones, J.T., Barnes, C.L., Lietzke, S.E., Weichenrieder, O., Doudna, J.A. and Kundrot, C.E.Acta Cryst. D. 1996:52(Part 5), 1018-1020. (840KB .pdf)

Use of cis- and trans-ribozymes to remove 5′ and 3′ heterogeneities from milligrams of in vitro transcribed RNA. Ferré-D’Amaré, A.R. and Doudna, J.A. Nucleic Acids Res.1996: 24,977-78. (40KB .pdf)

Hammerhead ribozyme structure: U-turn for RNA structural biology. Doudna, J.A. Structure. 1995:3, 747-750. (472KB .pdf)

Self-assembly of a group I intron active site from its component tertiary structural domains. Doudna, J.A. and Cech, T.R. RNA . 1995:1, 36-45. (5.7MB .pdf)

Selection of an RNA molecule that mimics a major autoantigenic epitope of human insulin receptor. Doudna, J.A., Cech, T.R. and Sullenger, B.A. PNAS. 1995:92, 2355-59. (1.1MB .pdf)

1987-1994

Doudna, J.A. (1994) Hammering out the shape of a ribozyme. Structure. 2, 1271-72. (292KB .pdf)

Cech, T.R., Bevilacqua, P.C., Doudna, J.A., McConnell, T.S., Strobel, S.A. and Weinstein, L.A. (1993) Mechanism and Structure of a Catalytic RNA Molecule. In Proceedings of The Robert A. Welch Foundation 37th Conference on Chemical Research: 40 Years of the DNA Double Helix, Houston, Texas, pp. 91-110. (2.0MB .pdf)

Doudna, J.A., Grosshans, C., Gooding, A. and Kundrot, C.E. (1993) Crystallization of ribozymes and small RNA folding motifs by a sparse matrix method. PNAS. 90, 7829-33. (1.0MB .pdf)

Doudna, J.A., Usman, N. and Szostak, J.W. (1993) RNA-catalyzed primer extension by tri-nucleotides: a model for the RNA-catalyzed replication of RNA. Biochemistry. 32, 2111-15. (1.6MB .pdf)

Musier-Forsyth, K., Usman, N., Scaringe, S., Doudna, J., Green, R. and Schimmel, P. (1991) Specificity for aminoacylation of an RNA helix: an unpaired, exocyclic amino group in the minor groove. Science. 253, 784-86. (748KB .pdf)

Doudna, J.A., Couture, S. and Szostak, J.W. (1991) A multisubunit ribozyme that is a catalyst of and template for complementary strand RNA synthesis. Science. 251, 1605-1608. (1.3MB .pdf)

Bartel, D.P., Doudna, J.A., Usman, N. and Szostak, J.W. (1991) Template-directed primer extension catalyzed by the Tetrahymena ribozyme. Mol. Cell. Biol. 11, 3390-94. (1.2MB .pdf)

Doudna, J.A., Szostak, J.W., Rich, A. and Usman, N. (1990) Chemical synthesis of oligo-ribonucleotides containing 2-aminopurine: Substrates for the investigation of ribozyme function. J. Org. Chem. 55, 5547-49. (1.3MB .pdf)

Couture, S., Ellington, A.D., Gerber, A.S., Cherry, J.M., Doudna, J.A., Green, R., Hanna, M., Pace, U., Rajagopal, J. and Szostak, J.W. (1990) Mutational analysis of conserved nucleotides in a self-splicing group I intron. J. Mol. Biol. 215, 345-358. (2.1MB .pdf)

Doudna, J.A. and Szostak, J.W. (1989) Mini ribozymes, small derivatives of the sunYintron, are catalytically active. Mol. Cell. Biol. 9, 5480-83. (796KB .pdf)

Doudna, J.A. and Szostak, J.W. (1989) RNA catalyzed synthesis of complementary strand RNA. Nature. 339, 519-22. (444KB .pdf)

Rajagopal, J., Doudna, J.A. and Szostak, J.W. (1989) Stereochemical course of catalysis by the Tetrahymena ribozyme. Science. 244, 692-94. (920KB .pdf)

Doudna, J.A., Cormack, B.P. and Szostak, J.W. (1989) RNA structure, not sequence, determines the 5′ splice-site specificity of a group I intron. PNAS. 86, 7402-7406. (1.0MB .pdf)

Doudna, J.A., Cherry, J.M., Gerber, A.S. and Szostak, J.W. (1987) Genetic dissection of an RNA enzyme. Cold Spring Harb. Symp. Quant. Biol. 52, 173-180. (1.2MB .pdf)