Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme
نویسندگان
چکیده
منابع مشابه
Helical junctions as determinants for RNA folding: origin of tertiary structure stability of the hairpin ribozyme.
Helical junctions are ubiquitous structural elements that govern the folding and tertiary structure of RNAs. The tobacco ringspot virus hairpin ribozyme consists of two helix-loop-helix elements that lie on adjacent arms of a four-way junction. In the active form of the hairpin ribozyme, the loops are in proximity. The nature of the helical junction determines the stability of the hairpin riboz...
متن کاملTertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer.
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. Dockin...
متن کاملThermodynamics and kinetics of the hairpin ribozyme from atomistic folding/unfolding simulations.
We report a set of atomistic folding/unfolding simulations for the hairpin ribozyme using a Monte Carlo algorithm. The hairpin ribozyme folds in solution and catalyzes self-cleavage or ligation via a specific two-domain structure. The minimal active ribozyme has been studied extensively, showing stabilization of the active structure by cations and dynamic motion of the active structure. Here, w...
متن کاملIntracellular RNA cleavage by the hairpin ribozyme.
Studies involving ribozyme-directed inactivation of targeted RNA molecules have met with mixed success, making clear the importance of methods to measure and optimize ribozyme activity within cells. The interpretation of biochemical assays for determining ribozyme activity in the cellular environment have been complicated by recent results indicating that hammerhead and hairpin ribozymes can cl...
متن کاملThermodynamics and Kinetics of Spiro-Heterocycle Formation Mechanism: Computational Study
Reaction mechanism among indoline-2,3-dione, pyrrolidine-2-carboxylic acid and (Z)-2-(1-(2-hydroxynaphthalen-1-yl)ethylidene)hydroxycarboxamide to form 1’-((((aminooxy)carbonyl)amino)methyl)-2’-(1-hydroxynaphthalen-2-yl)-2’-methyl-1’,2’,5’,6’,7’,7a’-hexahydrospiro[indoline-3,3’-pyrrolo[1,2-a]imidazole-2-one was investigated using density functional theory (DFT) at B3LYP basis theory. The three-...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Biophysical Chemistry
سال: 2017
ISSN: 0301-4622
DOI: 10.1016/j.bpc.2017.07.001