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61. Full Text dsRNA with 5′ overhangs contributes to endogenous and antiviral RNA silencing pathways in plants
by Fukunaga, Ryuya and Doudna, Jennifer A
The EMBO Journal, ISSN 0261-4189, 03/2009, Volume 28, Issue 5, pp. 545 - 555
In plants, SGS3 and RNA‐dependent RNA polymerase 6 (RDR6) are required to convert single‐ to double‐stranded RNA (dsRNA) in the innate RNAi‐based antiviral... 
dsRNA‐binding | viral suppressor | RNA silencing | overhang | plant | dsRNA-binding | Plant | Overhang | Viral suppressor | SUPPRESSOR | METHYLATION | PROTEIN | RECOGNITION | BIOCHEMISTRY & MOLECULAR BIOLOGY | COILED COILS | CELL BIOLOGY | SMALL INTERFERING RNA | SGS3 | BIOGENESIS | TRANS-ACTING SIRNAS | ARABIDOPSIS | Binding, Competitive | Lycopersicon esculentum - metabolism | Arabidopsis Proteins - genetics | Begomovirus - metabolism | RNA Replicase - genetics | Protein Multimerization | RNA Replicase - metabolism | Substrate Specificity | Viral Proteins - genetics | Viral Proteins - metabolism | Arabidopsis - metabolism | Arabidopsis Proteins - metabolism | Plant Proteins - genetics | Point Mutation | Protein Binding | 5' Flanking Region | Electrophoretic Mobility Shift Assay | Plant Proteins - metabolism | RNA, Double-Stranded - metabolism | RNA Interference - physiology | RNA-Binding Proteins - metabolism | Viruses | RNA polymerase | Catalysis | Molecular biology | Botany
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62. Full Text Generation of knock-in primary human T cells using Cas9 ribonucleoproteins
by Kathrin Schumann and Steven Lin and Eric Boyer and Dimitre R. Simeonov and Meena Subramaniam and Rachel E. Gate and Genevieve E. Haliburton and Chun J. Ye and Jeffrey A. Bluestone and Jennifer A. Doudna and Alexander Marson and Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 8/2015, Volume 112, Issue 33, pp. 10437 - 10442
T-cell genome engineering holds great promise for cell-based therapies for cancer, HIV, primary immune deficiencies, and autoimmune diseases, but genetic... 
Cas9 ribonucleoprotein|RNP | CRISPR/Cas9|genome engineering | Primary human T cells | CRISPR/Cas9 | primary human T cells | MULTIDISCIPLINARY SCIENCES | RECEPTOR | CXCR4 | CANCER | TUMORS | THERAPY | HIV | RNP | 7-TRANSMEMBRANE | CCR5 | genome engineering | Cas9 ribonucleoprotein | ADOPTIVE IMMUNOTHERAPY | HEMATOPOIETIC STEM | Genetic Engineering - methods | Cell Line | Endonucleases - genetics | CD4-Positive T-Lymphocytes - cytology | Humans | Bacterial Proteins - chemistry | Bacterial Proteins - genetics | Electroporation | Endonucleases - chemistry | Gene Knock-In Techniques | Receptors, CXCR4 - metabolism | T-Lymphocytes - cytology | Clustered Regularly Interspaced Short Palindromic Repeats | Leukocytes, Mononuclear - cytology | Ribonucleoproteins - genetics | High-Throughput Nucleotide Sequencing | Ribonucleoproteins - chemistry | Genome | Genetic aspects | T cells | Gene expression | Observations | Health aspects | Ribonucleoproteins | RNP primary | 60 APPLIED LIFE SCIENCES | human T cells | Biological Sciences | CRISPR | Cas9
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63. Cutting it close: CRISPR-associated endoribonuclease structure and function
by Megan L Hochstrasser and Jennifer A Doudna
Trends in Biochemical Sciences, ISSN 0968-0004, 01/2015, Volume 40, Issue 1, p. 58
  Many bacteria and archaea possess an adaptive immune system consisting of repetitive genetic elements known as clustered regularly interspaced short... 
Proteins | Enzymes | Eukaryotes | Bacteria | Ribonucleic acid--RNA | Deoxyribonucleic acid--DNA
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64. Full Text Expanding the Biologist’s Toolkit with CRISPR-Cas9
by Sternberg, Samuel H and Doudna, Jennifer A
Molecular Cell, ISSN 1097-2765, 05/2015, Volume 58, Issue 4, pp. 568 - 574
Few discoveries transform a discipline overnight, but biologists today can manipulate cells in ways never possible before, thanks to a peculiar form of... 
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65. Full Text Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage
by Jiang, Fuguo and Taylor, David W and Chen, Janice S and Kornfeld, Jack E and Zhou, Kaihong and Thompson, Aubri J and Nogales, Eva and Doudna, Jennifer A
Clinical Rheumatology, ISSN 0770-3198, 02/2016, Volume 351, Issue 6275, pp. 867 - 871
Bacterial adaptive immunity and genome engineering involving the CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) protein... 
ADAPTIVE IMMUNITY | BACTERIA | ENDONUCLEASE | RNA | RECOGNITION | CRYSTAL-STRUCTURE | MULTIDISCIPLINARY SCIENCES | TARGET DNA | CASCADE | CAS SYSTEMS | PROKARYOTES | Catalytic Domain | Crystallography, X-Ray | RNA - chemistry | Endonucleases - chemistry | DNA - chemistry | Endonucleases - ultrastructure | Genetic Engineering | Streptococcus pyogenes - enzymology | CRISPR-Cas Systems | Clustered Regularly Interspaced Short Palindromic Repeats | Protein Conformation | RNA, Guide | Genome | Nucleic Acid Conformation | DNA Cleavage | Nucleotide sequencing | Observations | DNA damage | Methods | DNA sequencing | Proteins | Bacteria | Ribonucleic acid--RNA | Deoxyribonucleic acid--DNA
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66. Full Text DNA recognition by an RNA-guided bacterial Argonaute
by Doxzen, Kevin W and Doudna, Jennifer A
PLoS ONE, ISSN 1932-6203, 05/2017, Volume 12, Issue 5, p. e0177097
Argonaute (Ago) proteins are widespread in prokaryotes and eukaryotes and share a four-domain architecture capable of RNA-or DNA-guided nucleic acid... 
TARGET RECOGNITION | COMPLEX | PROTEINS | CRYSTAL-STRUCTURE | MULTIDISCIPLINARY SCIENCES | INSIGHTS | Argonaute Proteins - chemistry | Argonaute Proteins - metabolism | Bacteria - metabolism | DNA, Bacterial - metabolism | Models, Biological | Molecular Conformation | RNA, Bacterial - chemistry | Protein Binding | DNA, Bacterial - chemistry | Protein Interaction Domains and Motifs | Bacteria - genetics | RNA, Bacterial - metabolism | RNA | DNA | Analysis | Crystals | Gram-positive bacteria | Genetic aspects | Research | Structure | DNA structure | Phosphates | Residues | Target recognition | Transcription | Microbiology | Defensive behavior | Gene regulation | Biochemistry | Biology | Crystallography | Proteins | Degradation | Thermodynamics | Engineering | E coli | Cleavage | Deoxyribonucleic acid--DNA | Crystal structure | Biodegradation | Enzymes | Alanine | Translation | Degradation products | Nucleotide sequence | Prokaryotes | Base pairs | Crystallization | Unwinding | Biophysics | Argonaute 2 protein | Gene expression | Immunological tolerance | Substrates | Mode of action | MicroRNAs | Kinetics | Gene mapping | Molecular biology | Protein structure | Deoxyribonucleic acid
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67. Full Text Unconventional miR-122 binding stabilizes the HCV genome by forming a trimolecular RNA structure
by Mortimer, Stefanie A and Doudna, Jennifer A
Nucleic Acids Research, ISSN 0305-1048, 04/2013, Volume 41, Issue 7, pp. 4230 - 4240
MicroRNAs (miRNAs) typically downregulate protein expression from target mRNAs through limited base-pairing interactions between the 5' 'seed' region of the... 
DOMAIN | SHAPE | CODON | HEPATITIS-C VIRUS | RECOGNITION | BIOCHEMISTRY & MOLECULAR BIOLOGY | IN-VIVO | TRANSLATION | MICRORNA-122 | REVEALS | Genome, Viral | RNA, Viral - chemistry | Base Pairing | 5' Untranslated Regions | Base Sequence | Humans | Hepacivirus - genetics | Molecular Sequence Data | MicroRNAs - metabolism | RNA, Viral - metabolism | Binding Sites | Exoribonucleases - metabolism | RNA
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68. Full Text Structures of Cas9 endonucleases reveal RNA-mediated conformational activation
by Jinek, Martin and Jiang, Fuguo and Taylor, David W and Sternberg, Samuel H and Kaya, Emine and Ma, Enbo and Anders, Carolin and Hauer, Michael and Zhou, Kaihong and Lin, Steven and Kaplan, Matias and Iavarone, Anthony T and Charpentier, Emmanuelle and Nogales, Eva and Doudna, Jennifer A and Medicinska fakulteten and Umeå universitet and Molekylär Infektionsmedicin, Sverige (MIMS)
Science, ISSN 0036-8075, 2014, Volume 343, Issue 6176, pp. 1247997 - 1215
Type II CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to... 
Protein Structure, Tertiary | Amino Acid Sequence | Protein Structure, Secondary | Bacterial Proteins - chemistry | Molecular Sequence Data | Crystallography, X-Ray | RNA - chemistry | Endonucleases - chemistry | Streptococcus pyogenes - enzymology | Clustered Regularly Interspaced Short Palindromic Repeats | Nucleic Acid Conformation | Actinomyces - enzymology | DNA Cleavage | MULTIDISCIPLINARY SCIENCES | Medical and Health Sciences | Medicin och hälsovetenskap
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69. Full Text Rational design of a split-Cas9 enzyme complex
by Addison V. Wright and Samuel H. Sternberg and David W. Taylor and Brett T. Staahl and Jorge A. Bardales and Jack E. Kornfeld and Jennifer A. Doudna and Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 3/2015, Volume 112, Issue 10, pp. 2984 - 2989
Cas9, an RNA-guided DNA endonuclease found in clustered regularly interspaced short palindromic repeats (CRISPR) bacterial immune systems, is a versatile tool... 
Genome engineering | Split enzyme | CRISPR-Cas9 | RNA | CRYSTAL-STRUCTURE | MULTIDISCIPLINARY SCIENCES | GUIDED SURVEILLANCE COMPLEX | SYSTEMS | CAS9 | genome engineering | split enzyme | Hydrolysis | Streptococcus pyogenes - enzymology | Clustered Regularly Interspaced Short Palindromic Repeats | Transcription, Genetic | Electrophoretic Mobility Shift Assay | DNA - metabolism | Nucleic Acid Conformation | DNA polymerases | Physiological aspects | Genetic aspects | Streptococcus | Gene expression | Observations | BASIC BIOLOGICAL SCIENCES | Biological Sciences
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70. Full Text EIF3d is an mRNA cap-binding protein that is required for specialized translation initiation
by Lee, Amy S.Y and Kranzusch, Philip J and Doudna, Jennifer A and Cate, Jamie H.D
Nature, ISSN 0028-0836, 07/2016, Volume 536, Issue 7614, pp. 96 - 99
Eukaryotic mRNAs contain a 5' cap structure that is crucial for recruitment of the translation machinery and initiation of protein synthesis. mRNA recognition... 
DEPENDENT TRANSLATION | MODEL | MECHANISM | C-JUN | PHOSPHORYLATION | MULTIDISCIPLINARY SCIENCES | Binding, Competitive | Eukaryotic Initiation Factor-4F - antagonists & inhibitors | Protein Structure, Tertiary | Eukaryotic Initiation Factor-3 - chemistry | Genes, jun - genetics | Humans | RNA-Binding Proteins - chemistry | Eukaryotic Initiation Factor-4E - metabolism | Models, Molecular | Crystallography, X-Ray | Eukaryotic Initiation Factor-3 - metabolism | Peptide Chain Initiation, Translational | Phylogeny | RNA Caps - metabolism | Eukaryotic Initiation Factor-4E - antagonists & inhibitors | Eukaryotic Initiation Factor-4F - metabolism | Protein Subunits - metabolism | Protein Binding | RNA Caps - chemistry | Protein Subunits - chemistry | RNA Caps - genetics | RNA-Binding Proteins - metabolism | Protein biosynthesis | Messenger RNA | Binding proteins | Genetic translation | Analysis | Proteins | Ribonucleic acid--RNA | Cell growth
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71. Full Text siRNA Repositioning for Guide Strand Selection by Human Dicer Complexes
by Noland, Cameron L and Ma, Enbo and Doudna, Jennifer A
Molecular Cell, ISSN 1097-2765, 07/2011, Volume 43, Issue 1, pp. 110 - 121
The human ribonuclease Dicer and its double-stranded RNA (dsRNA)-binding protein (dsRBP) partners TRBP and PACT play important roles in the biogenesis of... 
RISC-LOADING COMPLEX | STRUCTURAL INSIGHTS | IN-VITRO | ARGONAUTE SILENCING COMPLEX | MESSENGER-RNA | INTERFERING RNA | BIOCHEMISTRY & MOLECULAR BIOLOGY | EMBRYONIC STEM-CELLS | PASSENGER-STRAND | DROSOPHILA | RNA-BINDING PROTEIN | CELL BIOLOGY | RNA, Small Interfering - chemistry | Ribonuclease III - physiology | Thermodynamics | Humans | RNA-Induced Silencing Complex - metabolism | Models, Genetic | RNA-Induced Silencing Complex - chemistry | Binding Sites | RNA, Small Interfering - metabolism | Biosynthesis | Ribonuclease | RNA | Protein binding
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72. Full Text Molecular biology: Structural roles for human translation factor elF3 in initiation of protein synthesis
by Siridechadilok, Bunpote and Fraser, Christopher S and Hall, Richard J and Doudna, Jennifer A and Nogales, Eva
Science, ISSN 0036-8075, 12/2005, Volume 310, Issue 5753, pp. 1513 - 1515
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73. Full Text Structural and mechanistic insights into hepatitis C viral translation initiation
by Doudna, Jennifer A and Fraser, Christopher S
Nature Reviews Microbiology, ISSN 1740-1526, 01/2007, Volume 5, Issue 1, pp. 29 - 38
Hepatitis C virus uses an internal ribosome entry site (IRES) to control viral protein synthesis by directly recruiting ribosomes to the translation-start site... 
SWINE-FEVER VIRUS | INTERNAL RIBOSOME ENTRY | MESSENGER-RNA | 5' NONTRANSLATED REGIONS | MEDIATED TRANSLATION | MICROBIOLOGY | EUKARYOTIC TRANSLATION | PROTEIN-SYNTHESIS | MUTATIONAL ANALYSIS | CAP-INDEPENDENT TRANSLATION | 80S RIBOSOME | Protein Biosynthesis | Eukaryotic Initiation Factor-3 - chemistry | RNA, Messenger - genetics | Ribosomes - chemistry | Hepacivirus - genetics | Ribosomes - metabolism | Eukaryotic Initiation Factor-3 - metabolism | RNA Caps - metabolism | RNA, Messenger - metabolism | Hepacivirus - metabolism | RNA, Viral - chemistry | RNA, Viral - genetics | 5' Untranslated Regions | Protein Structure, Quaternary | RNA, Messenger - chemistry | RNA, Viral - metabolism | Nucleic Acid Conformation | Binding Sites | Viral Proteins - biosynthesis | Genetic aspects | Research | RNA processing | Hepatitis C virus | Genetic translation
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