Results 181 to 190 of about 59,552 (223)

Folding and catalysis of the hairpin ribozyme

Biochemical Society Transactions, 2005
The active form of the hairpin ribozyme is brought about by the interaction of two formally unpaired loops. In a natural molecule, these are present on two adjacent arms of a four-way junction. Although activity can be obtained in molecules lacking this junction, the junction is important in the promotion of the folded state of the ribozyme under ...
Timothy J. Wilson, Taekjip Ha, David M.J. Lilley, Michelle K. Nahas   +3 more
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Intrinsic Base-Pair Rearrangement in the Hairpin Ribozyme Directs RNA Conformational Sampling and Tertiary Interface Formation.

Journal of Physical Chemistry B, 2016
Dynamic fluctuations in RNA structure enable conformational changes that are required for catalysis and recognition. In the hairpin ribozyme, the catalytically active structure is formed as an intricate tertiary interface between two RNA internal loops ...
P. Ochieng, Neil A. White, M. Feig, C. G. Hoogstraten   +3 more
semanticscholar   +1 more source

The hairpin ribozyme

Biopolymers, 2003
AbstractThe hairpin ribozyme is a naturally occurring RNA that catalyzes sequence‐specific cleavage and ligation of RNA. It has been the subject of extensive biochemical and structural studies, perhaps the most detailed for any catalytic RNA to date. Comparison of the structures of its constituent domains free and fully assembled demonstrates that the ...
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Reactive conformation of the active site in the hairpin ribozyme achieved by molecular dynamics simulations with ε/ζ force field reparametrizations.

Journal of Physical Chemistry B, 2015
X-ray crystallography can provide important insights into the structure of RNA enzymes (ribozymes). However, the details of a ribozyme's active site architecture are often altered by the inactivating chemical modifications necessary to inhibit self ...
V. Mlýnský, Petra Kührová, Marie Zgarbová, P. Jurečka, N. Walter, M. Otyepka, J. Šponer, P. Banáš   +7 more
semanticscholar   +1 more source

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme.

Journal of Chemical Theory and Computation, 2014
We have analyzed the capability of state-of-the-art multiscale computational approaches to provide atomic-resolution electronic structure insights into possible catalytic scenarios of the hairpin ribozyme by evaluating potential and free energy surfaces ...
V. Mlýnský, P. Banáš, J. Šponer, M. W. van der Kamp, A. Mulholland, M. Otyepka   +5 more
semanticscholar   +1 more source

Structure and function of the hairpin ribozyme

Journal of Molecular Biology, 2000
The hairpin ribozyme belongs to the family of small catalytic RNAs that cleave RNA substrates in a reversible reaction that generates 2',3'-cyclic phosphate and 5'-hydroxyl termini. The hairpin catalytic motif was discovered in the negative strand of the tobacco ringspot virus satellite RNA, where hairpin ribozyme-mediated self-cleavage and ligation ...
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Crystallization of the Hairpin Ribozyme: Illustrative Protocols

2004
Conditions and techniques that result in successful crystallization differ from RNA to RNA. However, there are some general principles that facilitate crystallization of most RNAs. Three procedures that were instrumental in obtaining well-ordered crystals of the hairpin ribozyme are described in this chapter.
Adrian R. Ferré-D'Amaré, Peter B. Rupert   +1 more
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The catalytic mechanism of the hairpin ribozyme

Biochemical Society Transactions, 2002
Evidence that hairpin ribozymes function in the absence of bivalent cation cofactors suggests that active site nucleobases might participate directly in catalytic chemistry. We have adopted an abasic ribozyme rescue strategy to begin to dissect the roles of specific nucleobases in hairpin ribozyme activity. Loss of one active site nucleobase, G8, could
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ChemInform Abstract: Origins of RNA Catalysis in the Hairpin Ribozyme [PDF]

ChemInform, 2001
AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
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Design and Function of Triplex Hairpin Ribozymes

2010
Triplex ribozymes allow for the individual activity of multiple trans-acting ribozymes producing higher target cleavage relative to tandem-expressed RZs. A triplex expression system based on a single hairpin ribozyme for the multiple expression (multiplex) vectors can be engineered to target RNAs with single or multiple antisense-accessible sites ...
Ramiro Rojas-Hernández, Guillermo Aquino-Jarquin, Luis Marat Alvarez-Salas   +2 more
openaire   +3 more sources