Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes
- 23 October 2005
- journal article
- research article
- Published by Springer Nature in Nature Biotechnology
- Vol. 23 (11) , 1424-1433
- https://doi.org/10.1038/nbt1155
Abstract
Allosteric RNAs operate as molecular switches that alter folding and function in response to ligand binding. A common type of natural allosteric RNAs is the riboswitch; designer RNAs with similar properties can be created by RNA engineering. We describe a computational approach for designing allosteric ribozymes triggered by binding oligonucleotides. Four universal types of RNA switches possessing AND, OR, YES and NOT Boolean logic functions were created in modular form, which allows ligand specificity to be changed without altering the catalytic core of the ribozyme. All computationally designed allosteric ribozymes were synthesized and experimentally tested in vitro. Engineered ribozymes exhibit >1,000-fold activation, demonstrate precise ligand specificity and function in molecular circuits in which the self-cleavage product of one RNA triggers the action of a second. This engineering approach provides a rapid and inexpensive way to create allosteric RNAs for constructing complex molecular circuits, nucleic acid detection systems and gene control elements.Keywords
This publication has 61 references indexed in Scilit:
- Characterization of a native hammerhead ribozyme derived from schistosomesRNA, 2005
- ADP-Specific Sensors Enable Universal Assay of Protein Kinase ActivityChemistry & Biology, 2004
- In vitro selection of ribozymes dependent on peptides for activityRNA, 2003
- Genetic Control by Metabolite‐Binding RiboswitchesChemBioChem, 2003
- DNA Library Design for Molecular ComputationJournal of Computational Biology, 2003
- Folding mechanisms of group I ribozymes: role of stability and contact orderBiochemical Society Transactions, 2002
- Allosteric Hammerhead Ribozyme TRAPsBiochemistry, 2002
- Construction of new ribozymes requiring short regulator oligonucleotides as a cofactorJournal of Molecular Biology, 2000
- Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structureJournal of Molecular Biology, 1999
- The equilibrium partition function and base pair binding probabilities for RNA secondary structureBiopolymers, 1990