scholarly journals Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme

2017 ◽  
Vol 228 ◽  
pp. 62-68
Author(s):  
Neil A. White ◽  
Charles G. Hoogstraten
Keyword(s):  
Structure Formation ◽  
Tertiary Structure ◽  
Hairpin Ribozyme ◽  
Thermodynamics And Kinetics ◽  
Rna Tertiary Structure ◽  
Kinetics Of

scholarly journals Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation

2019 ◽  
Vol 116 (34) ◽  
pp. 16847-16855 ◽  
Author(s):  
Joseph D. Yesselman ◽  
Sarah K. Denny ◽  
Namita Bisaria ◽  
Daniel Herschlag ◽  
William J. Greenleaf ◽  
...  
Keyword(s):  
Structure Formation ◽  
Rna Structure ◽  
Tertiary Structure ◽  
Protein Translation ◽  
Detailed Comparison ◽  
Structure Stability ◽  
Control Of Gene Expression ◽  
Conformational Preferences ◽  
Rna Tertiary Structure ◽  
Length Changes

Structured RNAs and RNA complexes underlie biological processes ranging from control of gene expression to protein translation. Approximately 50% of nucleotides within known structured RNAs are folded into Watson–Crick (WC) base pairs, and sequence changes that preserve these pairs are typically assumed to preserve higher-order RNA structure and binding of macromolecule partners. Here, we report that indirect effects of the helix sequence on RNA tertiary stability are, in fact, significant but are nevertheless predictable from a simple computational model called RNAMake-∆∆G. When tested through the RNA on a massively parallel array (RNA-MaP) experimental platform, blind predictions for >1500 variants of the tectoRNA heterodimer model system achieve high accuracy (rmsd 0.34 and 0.77 kcal/mol for sequence and length changes, respectively). Detailed comparison of predictions to experiments support a microscopic picture of how helix sequence changes subtly modulate conformational fluctuations at each base-pair step, which accumulate to impact RNA tertiary structure stability. Our study reveals a previously overlooked phenomenon in RNA structure formation and provides a framework of computation and experiment for understanding helix conformational preferences and their impact across biological RNA and RNA-protein assemblies.

Irradiation behavior of pyrolytic silicon carbide

1983 ◽  
Vol 41 ◽  
pp. 72-73
Author(s):  
R. J. Lauf
Keyword(s):  
Silicon Carbide ◽  
Fission Products ◽  
Thermodynamics And Kinetics ◽  
Neutron Fluences ◽  
Fuel Particles ◽  
Sic Coatings ◽  
Irradiation Behavior ◽  
Kinetics Of ◽  
Htgr Fuel

Fuel particles for the High-Temperature Gas-Cooled Reactor (HTGR) contain a layer of pyrolytic silicon carbide to act as a miniature pressure vessel and primary fission product barrier. Optimization of the SiC with respect to fuel performance involves four areas of study: (a) characterization of as-deposited SiC coatings; (b) thermodynamics and kinetics of chemical reactions between SiC and fission products; (c) irradiation behavior of SiC in the absence of fission products; and (d) combined effects of irradiation and fission products. This paper reports the behavior of SiC deposited on inert microspheres and irradiated to fast neutron fluences typical of HTGR fuel at end-of-life.

Thermodynamics and kinetics of hydriding of the Zr(Ni0.75V0.25)2 laves phase

2004 ◽  
Vol 29 (2) ◽  
pp. 1-9
Author(s):  
Mustapha Boulghallat ◽  
Ahmed Jouaiti ◽  
Norbert Gérard
Keyword(s):  
Laves Phase ◽  
Thermodynamics And Kinetics ◽  
Kinetics Of
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