General acid-base catalysis mediated by nucleobases in the hairpin ribozyme. [PDF]
J Am Chem Soc, 2012 The catalytic mechanism by which the hairpin ribozyme accelerates cleavage or ligation of the phosphodiester backbone of RNA has been incompletely understood.
Kath-Schorr S +5 more
europepmc +7 more sources
Equilibrium properties and force-driven unfolding pathways of RNA molecules [PDF]
Phys. Rev. Lett. 103: 188102 (2009), 2009 The mechanical unfolding of a simple RNA hairpin and of a 236--bases portion of the Tetrahymena thermophila ribozyme is studied by means of an Ising--like model.
A. Imparato +3 more
core +2 more sources
Mechanical unfolding of RNA: From hairpins to structures with internal multiloops [PDF]
Biophys. J. vol 92 (2007) 731-743, 2006 Mechanical unfolding of RNA structures, ranging from hairpins to ribozymes, using laser optical tweezer (LOT) experiments have begun to reveal the features of the energy landscape that cannot be easily explored using conventional experiments.
Bokinsky +45 more
core +3 more sources
Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins [PDF]
Structure (2006) vol 14. 1633-1645, 2006 Using self-organized polymer models, we predict mechanical unfolding and refolding pathways of ribo-zymes, and the green fluorescent protein. In agreement with experiments, there are between six and eight unfolding transitions in the Tetrahymena ribozyme.
Dima, Ruxandra I +2 more
core +3 more sources
Nucleobase catalysis in the hairpin ribozyme [PDF]
RNA, 2006 RNA catalysis is important in the processing and translation of RNA molecules, yet the mechanisms of catalysis are still unclear in most cases. We have studied the role of nucleobase catalysis in the hairpin ribozyme, where the scissile phosphate is juxtaposed between guanine and adenine bases.
Lisa Araki +6 more
openaire +4 more sources
A comparative survey of the influence of small self-cleaving ribozymes on gene expression in human cell culture [PDF]
RNA BiologySelf-cleaving ribozymes are versatile tools for synthetic biologists when it comes to controlling gene expression. Up to date, 12 different classes are known, and over the past decades more and more details about their structure, cleavage mechanisms and ...
Dennis Kläge +2 more
doaj +2 more sources
Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme. [PDF]
Biophys Chem, 2017 White NA, Hoogstraten CG.
europepmc +3 more sources
The folding of the hairpin ribozyme: Dependence on the loops and the junction [PDF]
RNA, 2000 In its natural context, the hairpin ribozyme is constructed around a four-way helical junction. This presents the two loops that interact to form the active site on adjacent arms, requiring rotation into an antiparallel structure to bring them into proximity.
Kaera Maxwell +3 more
openaire +5 more sources
A triplex ribozyme expression system based on a single hairpin ribozyme. [PDF]
Oligonucleotides, 2008 Triplex ribozyme (RZ) configurations allow for the individual activity of trans-acting RZs in multiple expression cassettes (multiplex), thereby increasing target cleavage relative to conventionally expressed RZs. Although hairpin RZs have been advantageously compared to hammerhead RZs, their longer size and structural features complicated triplex ...
Aquino-Jarquin G +3 more
europepmc +5 more sources
Dual Promoters Improve the Rescue of Recombinant Measles Virus in Human Cells
Viruses, 2021 Reverse genetics is a technology that allows the production of a virus from its complementary DNA (cDNA). It is a powerful tool for analyzing viral genes, the development of novel vaccines, and gene delivery vectors.
Soroth Chey +3 more
doaj +1 more source