EurekaMag.com logo
+ Site Statistics
References:
53,869,633
Abstracts:
29,686,251
+ Search Articles
+ Subscribe to Site Feeds
EurekaMag Most Shared ContentMost Shared
EurekaMag PDF Full Text ContentPDF Full Text
+ PDF Full Text
Request PDF Full TextRequest PDF Full Text
+ Follow Us
Follow on FacebookFollow on Facebook
Follow on TwitterFollow on Twitter
Follow on LinkedInFollow on LinkedIn

+ Translate

Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer



Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer



Embo Journal 17(8): 2378-2391



The complex formed by the hairpin ribozyme and its substrate consists of two independently folding domains which interact to form a catalytic structure. Fluorescence resonance energy transfer methods permit us to study reversible transitions of the complex between open and closed forms. Results indicate that docking of the domains is required for both the cleavage and ligation reactions. Docking is rate-limiting for ligation (2 min-1) but not for cleavage, where docking (0.5 min-1) precedes a rate-limiting conformational transition or slow-reaction chemistry. Strikingly, most modifications to the RNA (such as a G+1A mutation in the substrate) or reaction conditions (such as omission of divalent metal ion cofactors) which inhibit catalysis do so by preventing docking. This demonstrates directly that mutations and modifications which inhibit a step following substrate binding are not necessarily involved in catalysis. An improved kinetic description of the catalytic cycle is derived, including specific structural transitions.

Accession: 009525393

Download citation: RISBibTeXText

PMID: 9545249

DOI: 10.1093/emboj/17.8.2378

Download PDF Full Text: Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer



Related references

Intracellular ribozyme-catalyzed trans-cleavage of RNA monitored by fluorescence resonance energy transfer. Rna 6(4): 628-637, 2000

Structure of the hammerhead ribozyme from fluorescence resonance energy transfer measurements. FASEB Journal 8(7): A1324, 1994

Nucleotide analog interference mapping of the hairpin ribozyme: implications for secondary and tertiary structure formation. Journal of Molecular Biology 291(2): 295-311, 1999

Assay for glucosamine 6-phosphate using a ligand-activated ribozyme with fluorescence resonance energy transfer or CE-laser-induced fluorescence detection. Analytical Chemistry 80(21): 8195-8201, 2008

Structure-mapping of the hairpin ribozyme. Magnesium-dependent folding and evidence for tertiary interactions within the ribozyme-substrate complex. Journal of Molecular Biology 244(1): 52-63, 1994

Transfer RNA unwinding by the HIV-1 nucleocapsid protein monitored by fluorescence resonance energy transfer. Abstracts of Papers American Chemical Society 216(1-3): BIOL 20, 1998

Using fluorescence resonance energy transfer to investigate hammerhead ribozyme kinetics. Methods in Molecular Biology 74: 241-251, 1997

Ion-induced folding of the hammerhead ribozyme: a fluorescence resonance energy transfer study. Embo Journal 16(24): 7481-7489, 1998

A three-dimensional model for the hammerhead ribozyme from fluorescence resonance energy transfer measurements. Journal of Cellular Biochemistry Supplement 0(19A): 218, 1995

Epidermal growth factor -receptor clustering monitored by fluorescence resonance energy transfer using donor photobleaching and lifetime-resolved fluorescence imaging microscopy. Biophysical Journal 64(2 PART 2): A130, 1993

Fluorescence resonance energy transfer (FRET) to follow ribozyme reactions in real time. Nucleosides and Nucleotides 17(9-11): 1835-1850, 1998

Fluorescence resonance energy transfer analysis of the degradation of an oligonucleotide protected by a very stable hairpin. Journal of Biomolecular Structure & Dynamics 14(3): 365-371, 1996

Self-assembly dynamics of a cylindrical capsule monitored by fluorescence resonance energy transfer. Journal of the American Chemical Society 129(28): 8818-8824, 2007

Assembly and exchange of resorcinarene capsules monitored by fluorescence resonance energy transfer. Journal of the American Chemical Society 129(13): 3818-3819, 2007

Fluorescence resonance energy transfer analysis of ribozyme kinetics reveals the mode of action of a facilitator oligonucleotide. Biochemistry 35(50): 16370-7, 1996