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138 results on '"DOUDNA, J. A."'

13. A survey of load control programs for price and system stability

Author

Jazayeri, P., Schellenberg, A., Rosehart, W.D., Doudna, J., Widergren, S., Lawrence, D., Mickey, J., and Jones, S.

Subjects
Electric power systems, Business, Electronics, Electronics and electrical industries
Abstract

Load control and demand side load management programs have been implemented in a large number of competitive power markets. These programs can provide enhanced system security and many benefits to participants. This paper reviews and compares existing economically driven programs. Index Terms--Ancillary services, demand side load management, demand side resources, load control, load participation.

Published
2005

14. Chemical synthesis of oligoribonucleotides containing 2-aminopurine: substrates for the investigation of ribozyme function

Author

Doudna, J. A, Szostak, J. W, Rich, A, and Usman, N

Subjects
Exobiology
Abstract

The chemical synthesis of a fully protected ribonucleoside phosphoramidite, containing 2-aminopurine as the base component, and its incorporation into short oligoribonucleotides as substrates for an engineered ribozyme from Tetrahymena is described.

Published
1990
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17. Self-assembly of a group I intron active site from its component tertiary structural domains

Author

Doudna, J A and Cech, T R

Subjects
Tetrahymena, Animals, Nucleic Acid Conformation, RNA, RNA, Catalytic, Polymerase Chain Reaction, Introns, RNA, Protozoan, Research Article
Abstract

The catalytic core of Group I self-splicing introns has been proposed to consist of two structural domains, P4-P6 and P3-P9. Each contains helical segments and conserved unpaired nucleotides, and the isolated P4-P6 domain has been shown to have substantial native tertiary structure. The proposed tertiary structure domains of the Tetrahymena intron were synthesized separately and shown to self-assemble into a catalytically active complex. Surprisingly, the concentration dependence of these reactions revealed that the domains interact with nanomolar apparent dissociation constants, even though there is no known base pairing between P4-P6 and P3-P9. This suggests that the domains interact through multiple tertiary contacts, the nature of which can now be explored in this system. For example, a circularly permuted version of the P4-P6 domain, which folds similarly to the native P4-P6 molecule, formed a stable but inactive complex. Interestingly, activity was demonstrated with the permuted molecule when nucleotides proposed to form a triple-strand interaction with P4 and P6 were restored as part of the P1-P3 substrate or as part of the P3-P9 RNA. Thus, beyond stabilization of the P4-P6 domain, the triple-strand region may facilitate correct orientation of the RNA domains or participate more directly in catalysis.

Published
1995

30. RNA structure, not sequence, determines the 5' splice-site specificity of a group I intron.

Author

Doudna, J A, Cormack, B P, and Szostak, J W

Abstract

The group I self-splicing introns act at exon-intron junctions without recognizing a particular sequence. In order to understand splice-site selection, we have developed an assay system based on the Tetrahymena ribozyme to allow the study of numerous 5'-splice-site variants. Cleavage at the correct site requires formation of the correct secondary structure and occurs most efficiently within a 3-base-pair window centered on base pair 5 from the bottom of the P1 stem. Within this window the ribozyme recognizes and cleaves at a "wobble" base pair; the base pair above the cleavage site also influences splicing efficiency. The recognition of RNA structure rather than sequence explains the ability of these transposable introns to splice out of a variety of sequence contexts.

Published
1989
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31. Miniribozymes, small derivatives of the sunY intron, are catalytically active

Author

Doudna, J A and Szostak, J W

Abstract

The self-splicing sunY intron from bacteriophage T4 has the smallest conserved core secondary structure of any of the active group I introns. Here we show that several nonconserved regions can be deleted from this intron without complete loss of catalytic activity. The 3' stems P9, P9.1, and P9.2 can be deleted while retaining 5' cleaving activity. Two base-paired stems (P7.1 and P7.2) that are peculiar to the group IA introns can also be deleted; however, the activities of the resulting derivatives depend greatly on the choice of replacement sequences and their lengths. The smallest active derivative is less than 180 nucleotides long. These experiments help to define the minimum structural requirements for catalysis.

Published
1989
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46. Structure of Dicer and Mechanistic Implications for RNAi.

Author

MacRae, I. J., Li, F., Zhou, K., Cande, W. Z., and Doudna, J. A.

Subjects
*PROTEINS, *RNA, *DOUBLE-stranded RNA, *DNA helicases, *GENETIC engineering
Abstract

The article discusses research on the structure of dicer proteins and its mechanistic implications for ribonucleic acid interference (RNAi). Dicer proteins act on double-stranded RNAs that contain even noncanonical base-pairings and minor deviations in duplex structure. It notes that the dicer helicase is responsible for a critical step in the process such as unwinding of the short interfering RNA (siRNA) duplex. Removal of the helicase domain from human Dicer does not impair dicing activity.

Published
2006
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47. CRISPR germline engineering—the community speaks

Author

G. Steven Martin, Michael R. Botchan, Annelien L. Bredenoord, R. Alta Charo, Robin Lovell-Badge, Emmanuelle Charpentier, Dana Carroll, Jin-Soo Kim, Rosario Isasi, Qi Zhou, Anthony C.F. Perry, Weihzi Ji, Bartha Maria Knoppers, Ronald A. Cohen, Martin F. Pera, Luigi Naldini, J. Craig Venter, Jennifer A. Doudna, Henry T. Greely, Jinsong Li, Katrine Bosley, Jonathan D. Moreno, Jacob E. Corn, Edward Lanphier, Guoping Feng, Feng Zhang, Bosley, K, 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, J, Knoppers, B, Lanphier, E, Li, J, Lovell Badge, R, Martin, G, Moreno, J, Naldini, Luigi, Pera, M, Perry, Ac, Venter, Jc, Zhang, F, and Zhou, Q.

Subjects
Genetics, Ethical issues, Genome, Human, Genetic enhancement, education, Biomedical Engineering, MEDLINE, International community, Bioengineering, Computational biology, Biology, Applied Microbiology and Biotechnology, Genome, Germline, Germ Cells, RNA editing, Journal Article, Humans, Molecular Medicine, CRISPR, RNA Editing, CRISPR-Cas Systems, Genetic Engineering, Biotechnology
Abstract

Nature Biotechnology asks selected members of the international community to comment on the ethical issues raised by the prospect of CRISPR-Cas9 engineering of the human germline.

Published
2015
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49. Creative catalysis: pieces of the RNA world jigsaw.

Author

Murray JM and Doudna JA

Subjects
Amino Acyl-tRNA Synthetases metabolism, Animals, Biological Evolution, Catalysis, Directed Molecular Evolution, Enzymes chemistry, Enzymes physiology, RNA metabolism, RNA, Catalytic chemistry, RNA, Catalytic physiology, Models, Chemical, Protein Biosynthesis, RNA, Catalytic metabolism
Published
2001
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50. Direct pK(a) measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme.

Author

Lupták A, Ferré-D'Amaré AR, Zhou K, Zilm KW, and Doudna JA

Subjects
Base Sequence, Binding Sites, Carbon Isotopes, Cytosine chemistry, Hepatitis Delta Virus genetics, Kinetics, Molecular Sequence Data, Nuclear Magnetic Resonance, Biomolecular, Nucleic Acid Conformation, RNA, Catalytic chemistry, RNA, Catalytic genetics, Substrate Specificity, Cytosine metabolism, Hepatitis Delta Virus enzymology, RNA, Catalytic metabolism
Abstract

Hepatitis delta virus ribozymes have been proposed to perform self-cleavage via a general acid/base mechanism involving an active-site cytosine, based on evidence from both a crystal structure of the cleavage product and kinetic measurements. To determine whether this cytosine (C75) in the genomic ribozyme has an altered pK(a) consistent with its role as a general acid or base, we used (13)C NMR to determine its microscopic pK(a) in the product form of the ribozyme. The measured pK(a) is moderately shifted from that of a free nucleoside or a base-paired cytosine and has the same divalent metal ion dependence as the apparent reaction pK(a)'s measured kinetically. However, under all conditions tested, the microscopic pK(a) is lower than the apparent reaction pK(a), supporting a model in which C75 is deprotonated in the product form of the ribozyme at physiological pH. While additional results suggest that the pK(a) is not shifted in the reactant state of the ribozyme, these data cannot rule out elevation of the C75 pK(a) in an intermediate state of the transesterification reaction.

Published
2001
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