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J A Doudna

Publications and source records attributed to J A Doudna.

At least 55 records · Page 3Linked to original sources
PubMed1996

Metal-binding sites in the major groove of a large ribozyme domain.

BACKGROUND: Group I self-splicing introns catalyze sequential transesterification reactions within an RNA transcript to produce the correctly spliced product. Often several hundred nucleotides in size, these ribozymes fold into specific three-dimensional structures that confer activity. The 2.8 A crystal structure of a central component of the Tetrahymena thermophila group I intron, the 160-nucleotide P4-P6 domain, provides the first detailed view of metal binding in an RNA large enough to exhibit side-by-side helical packing. The long-range contacts and bound ligands that stabilize this fold can now be examined in detail. RESULTS: Heavy-atom derivatives used for the structure determination reveal characteristics of some of the metal-binding sites in the P4-P6 domain. Although long-range RNA-RNA contacts within the molecule primarily involve the minor groove, osmium hexammine binds at three locations in the major groove. All three sites involve G and U nucleotides exclusively; two are formed by G.U wobble base pairs. In the native RNA, two of the sites are occupied by fully-hydrated magnesium ions. Samarium binds specifically to the RNA by displacing a magnesium ion in a region critical to the folding of the entire domain. CONCLUSIONS: Bound at specific sites in the P4-P6 domain RNA, osmium (III) hexammine produced the high-quality heavy-atom derivative used for structure determination. These sites can be engineered into other RNAs, providing a rational means of obtaining heavy-atom derivatives with hexammine compounds. The features of the observed metal-binding sites expand the known repertoire of ligand-binding motifs in RNA, and suggest that some of the conserved tandem G.U base pairs in ribosomal RNAs are magnesium-binding sites.

Animals↗
PubMed1996

Crystal structure of a group I ribozyme domain: principles of RNA packing.

Group I self-splicing introns catalyze their own excision from precursor RNAs by way of a two-step transesterification reaction. The catalytic core of these ribozymes is formed by two structural domains. The 2.8-angstrom crystal structure of one of these, the P4-P6 domain of the Tetrahymena thermophila intron, is described. In the 160-nucleotide domain, a sharp bend allows stacked helices of the conserved core to pack alongside helices of an adjacent region. Two specific long-range interactions clamp the two halves of the domain together: a two-Mg2+-coordinated adenosine-rich corkscrew plugs into the minor groove of a helix, and a GAAA hairpin loop binds to a conserved 11-nucleotide internal loop. Metal- and ribose-mediated backbone contacts further stabilize the close side-by-side helical packing. The structure indicates the extent of RNA packing required for the function of large ribozymes, the spliceosome, and the ribosome.

Adenine↗
PubMed1996

RNA tertiary structure mediation by adenosine platforms.

The crystal structure of a group I intron domain reveals an unexpected motif that mediates both intra- and intermolecular interactions. At three separate locations in the 160-nucleotide domain, adjacent adenosines in the sequence lie side-by-side and form a pseudo-base pair within a helix. This adenosine platform opens the minor groove for base stacking or base pairing with nucleotides from a noncontiguous RNA strand. The platform motif has a distinctive chemical modification signature that may enable its detection in other structured RNAs. The ability of this motif to facilitate higher order folding provides one explanation for the abundance of adenosine residues in internal loops of many RNAs.

Adenosine↗
PubMed1996

Preliminary X-ray diffraction studies of an RNA pseudoknot that inhibits HIV-1 reverse transcriptase.

Crystals of a 26-nucleotide pseudoknot RNA, PK26, have been grown. The RNA was produced using phosphoramidite chemistry and was purified by denaturing polyacrylamide electrophoresis. The crystallization was robust with respect to changes in the number of nucleotides and to the salt used as precipitant. The crystals belong to space group P4(1)22 or P4(3)22 with unit-cell dimensions a = b = 61.6, c = 98.9 A. The best crystals diffract X-rays to 2.9 A. Three different sequences incorporating a single 5-bromo-deoxyuridine or 5-bromo-uridine nucleotide were also crystallized. Two of these derivatives are being used to determine the structure by multiple isomorphous replacement.

Journal Article↗
PubMed1995

Selection of an RNA molecule that mimics a major autoantigenic epitope of human insulin receptor.

Autoimmunity often involves the abnormal targeting of self-antigens by antibodies, leading to tissue destruction and other pathologies. This process could potentially be disrupted by small ligands that bind specifically to autoantibodies and inhibit their interaction with the target antigen. Here we report the identification of an RNA sequence that binds a mouse monoclonal antibody specific for an autoantigenic epitope of human insulin receptor. The RNA ligand binds specifically and with high affinity (apparent Kd congruent to 2 nM) to the anti-insulin receptor antibody and not to other mouse IgGs. The RNA can also act as a decoy, blocking the antibody from binding the insulin receptor. Thus, it probably binds near the combining site on the antibody. Strikingly, the RNA cross-reacts with autoantibodies from patients with extreme insulin resistance. One simple explanation is that the selected RNA may structurally mimic the antigenic epitope on the insulin receptor protein. These results suggest that decoy RNAs may be used in the treatment of autoimmune diseases.

Animals↗
PubMed1995

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

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.

Animals↗
PubMed1993

Crystallization of ribozymes and small RNA motifs by a sparse matrix approach.

The three-dimensional structures of RNA enzymes form catalytic centers that include specific substrate binding sites. High-resolution determination of these and other RNA structures is essential for a detailed understanding of the function of RNA in biological systems. The crystal structures of only a few RNA molecules are currently known. These include tRNAs, which were produced in vivo and contained modified bases, and short oligonucleotide duplexes lacking tertiary interactions. Here we report that a number of different RNA molecules of 4-50 kDa, all synthesized in vitro, have been crystallized. A highly successful method for the growth of RNA crystals based on previously reported conditions for tRNA crystallization is presented. This method is rapid and economical, typically requiring 1.1 mg of RNA to set up an experiment and 2 weeks to complete the observations. Using this technique, we have obtained crystals of 8 of 10 different RNA molecules tested, ranging in size from a dodecamer duplex to a 208-nucleotide catalytic intron. Several of these crystal forms diffract to high resolution; in one case, we have collected a 2.8-A native data set for a 160-nucleotide domain of the group I self-splicing intron from Tetrahymena thermophila. The solution of these RNA structures should reveal aspects of tertiary structure that relate to RNA function and catalytic mechanisms.

Animals↗
PubMed1993

Ribozyme-catalyzed primer extension by trinucleotides: a model for the RNA-catalyzed replication of RNA.

The existence of RNA enzymes that catalyze phosphodiester transfer reactions suggests that RNA-catalyzed RNA replication might be possible. Indeed, it has been shown that the Tetrahymena and sunY self-splicing introns will catalyze the template-directed ligation of RNA oligonucleotides (Doudna et al., 1989, 1991). We have sought to develop a more general RNA replication system in which arbitrary template sequences could be copied by the assembly of a limited set of short oligonucleotides. Here we examine the use of tetranucleotides as substrates for a primer-extension reaction in which the 5'-nucleoside of the tetranucleotide is the leaving group, and the primer is extended by the remaining three nucleotides. When the 5'-nucleoside is guanosine, the reaction is quite efficient, but a number of competing side reactions occur, in which inappropriate guanosine residues in the primer or the template occupy the guanosine binding site of the ribozyme. We have blocked these side reactions by using the guanosine analogue 2-aminopurine riboside (2AP) as the leaving group, in a reaction catalyzed by a mutant sunY ribozyme that binds efficiently to 2AP and not to guanosine. We have begun to address the issue of the fidelity of the primer-extension reaction by measuring reaction rates with a number of different triplet/template combinations. Our results provide the basis for the further development of an RNA-catalyzed RNA replication system using short oligonucleotide substrates with novel leaving groups.

Animals↗
PubMed1991

A multisubunit ribozyme that is a catalyst of and template for complementary strand RNA synthesis.

Derivatives of the sunY self-splicing intron efficiently catalyzed the synthesis of complementary strand RNA by template-directed assembly of oligonucleotides. These ribozymes were separated into three short RNA fragments that formed active catalytic complexes. One of the multisubunit sunY derivatives catalyzed the synthesis of a strand of RNA complementary to one of its own subunits. These results suggest that prebiotically synthesized oligonucleotides might have been able to assemble into a complex capable of self-replication.

Animals↗
PubMed1991

Template-directed primer extension catalyzed by the Tetrahymena ribozyme.

The Tetrahymena ribozyme has been shown to catalyze an RNA polymerase-like reaction in which an RNA primer is extended by the sequential addition of pN nucleotides derived from GpN dinucleotides, where N = A, C, or U. Here, we show that this reaction is influenced by the presence of a template; bases that can form Watson-Crick base pairs with a template add as much as 25-fold more efficiently than mismatched bases. A mutant enzyme with an altered guanosine binding site can catalyze template-directed primer extension with all four bases when supplied with dinucleotides of the form 2-aminopurine-pN.

Animals↗
PubMed1990

Mutational analysis of conserved nucleotides in a self-splicing group I intron.

We have constructed all single base substitutions in almost all of the highly conserved residues of the Tetrahymena self-splicing intron. Mutation of highly conserved residues almost invariably leads to loss of enzymatic activity. In many cases, activity could be regained by making additional mutations that restored predicted base-pairings; these second site suppressors in general confirm the secondary structure derived from phylogenetic data. At several positions, our suppression data can be most readily explained by assuming non-Watson-Crick base-pairings. In addition to the requirements imposed by the secondary structure, the sequence of the intron is constrained by "negative interactions", the exclusion of particular nucleotide sequences that would form undesirable secondary structures. A comparison of genetic and phylogenetic data suggests sites that may be involved in tertiary structural interactions.

Animals↗
PubMed1989

RNA-catalysed synthesis of complementary-strand RNA.

The Tetrahymena ribozyme can splice together multiple oligonucleotides aligned on a template strand to yield a fully complementary product strand. This reaction demonstrates the feasibility of RNA-catalysed RNA replications.

Animals↗