Mechanisms of Ribozyme-Mediated RNA Cleavage

Kuimelis, Robert G.; McLaughlin, Larry W.

doi:10.1021/cr960426p

Cited by 72 publications

(62 citation statements)

References 197 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…[31] RNA self-cleavage in both HDV and hammerhead ribozymes proceeds by metal ion dependent mechanisms. [32] Displacement of catalytic metal ions by electrostatically complementary cationic compounds has been suggested as the general principle of aminoglycoside action on these ribozymes. [33,34] …”

Section: Roles Of Rnas In Biological Processesmentioning

confidence: 99%

Strategies for the Design of Drugs Targeting RNA and RNA–Protein Complexes

Hermann

2000

Angew. Chem. Int. Ed.

186

123

View full text Add to dashboard Cite

In many steps of gene replication and expression, RNA molecules participate as key players, which renders them attractive targets for therapeutic intervention. While the function of nucleic acids as carriers of genetic material is based on their sequence, a number of important RNAs are involved in processes that depend on the defined three‐dimensional structures of these molecules. As for proteins, numerous complex folds of RNA exist. The development of drugs that bind specifically to RNA folds opens exciting new ways to expand greatly the existing repertoire of protein‐targeted therapeutics. Most functions of RNAs involve interactions with proteins that contain RNA‐binding domains. Effector molecules targeted at RNA may either alter the functional three‐dimensional structure of the nucleic acid, so the interaction with proteins is thereby inhibited or enhanced, or, as interface inhibitors, they may directly prevent the formation of competent RNA–protein complexes. While the same tools used for the design of protein‐targeted drugs may be considered for studying effectors binding to nucleic acids, the differences between proteins and RNAs in the forces which dominate their three‐dimensional folding call for novel drug design strategies. In the present review, I will outline how our rapidly expanding knowledge of RNA three‐dimensional structure and function facilitates rational approaches to develop RNA‐binding compounds. Putative RNA targets for therapeutic intervention will be discussed along with recent advances in understanding RNA–small molecule and RNA–protein interactions.

show abstract

Section: Roles Of Rnas In Biological Processesmentioning

confidence: 99%

Strategies for the Design of Drugs Targeting RNA and RNA–Protein Complexes

Hermann

2000

Angew. Chem. Int. Ed.

186

123

View full text Add to dashboard Cite

show abstract

“…26 Furthermore, it is still unresolved whether the metal ion also coordinates to the leaving 5Ј-oxygen to facilitate bond breakage. 20,21 Thus there is data on metal ion presence consistent with an active role of the metal ion in catalysis. However, the final proof for such a role is still lacking.…”

Section: Structure and Reaction Mechanismmentioning

confidence: 82%

“…14,20,21 The reaction is sequence specific in that cleavage occurs 3Ј to the triplet of the general formula NUH where N is any nucleotide, U is uridine, and H is any nucleotide except guanosine. The targeting of a particular NUH triplet for cleavage in an RNA is determined by the sequence of the ribozyme binding arms that have to be complementary to the upstream and downstream sequences of the triplet to form the ribozyme-substrate complex.…”

Section: Structure and Reaction Mechanismmentioning

confidence: 99%

The hammerhead ribozyme

Eckstein

Bramlage

1999

Biopolymers

View full text Add to dashboard Cite

“…The heterodimeric maxizyme simultaneously RNAs that can cleave target RNAs at specific sites ( Fig. 1A) cleaved HTV-1 tat mRNA at two independent sites both in (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15). In studies directed towards the development of thervitro and in cultured cells (33,37).…”

mentioning

confidence: 99%

Cleavage of an Inaccessible Site by the Maxizyme with Two Independent Binding Arms: An Alternative Approach to the Recruitment of RNA Helicases

Kuwabara

Warashina

Taira

2002

Journal of Biochemistry

View full text Add to dashboard Cite

To overcome obstacles to target site selection, we recently created a novel hybrid ribozyme that could access any chosen site by the recruitment of intracellular RNA helicases [Warashina et al. (2001) Proc. Natl. Acad. Sci. USA 98, 5572-5577; Kawasaki et al. (2002) Nat. Biotech. 20, 376-380]. We also demonstrated previously that pol III-driven maxizymes with two substrate-binding arms that were directed against two different sites within a target mRNA formed very active heterodimers in vivo [Kuwabara, et al. (2000) Trends Biotechnol. 18, 462-468; Tanabe et al. (2001) Nature 406, 473-474]. Despite the complicated dimerization process, all the maxizymes that we tested in cultured cells had greater catalytic activity than the parental ribozymes. To investigate the action of maxizymes in cells, we designed a specific maxizyme with two substrate-binding arms that was directed against endogenously expressed LTR-luciferase chimeric mRNA, where LTR refers to the long terminal repeat of HIV-1. One substrate-binding arm of the maxizyme was designed to bind to a site within HIV-1 TAR RNA that is known to form a stable stem structure that normally prevents binding of a ribozyme. The other substrate-binding arm was directed against a relatively accessible site within the luciferase gene. As expected, the conventional ribozyme failed to cleave the TAR region in vivo because of the latter's stable secondary structure. However, to our surprise, the maxizyme cleaved the TAR region within the stem with high efficiency in vivo. The enhanced cleavage in vivo by the maxizyme might have resulted from an entropically favorable, intramolecular, second binding process that occurred during the breathing of the stem structure of the target mRNA. Importantly, our data suggest that this maxizyme technology might be used as an alternative approach to the recruitment of RNA helicases in cleaving sites previously found to be inaccessible.

show abstract

Mechanisms of Ribozyme-Mediated RNA Cleavage

Cited by 72 publications

References 197 publications

Strategies for the Design of Drugs Targeting RNA and RNA–Protein Complexes

Strategies for the Design of Drugs Targeting RNA and RNA–Protein Complexes

The hammerhead ribozyme

Cleavage of an Inaccessible Site by the Maxizyme with Two Independent Binding Arms: An Alternative Approach to the Recruitment of RNA Helicases

Contact Info

Product

Resources

About