Sandbox Reserved 1582
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== Background == | == Background == | ||
| - | Natural ribozymes are very rare. There are only 11 distinct classes of ribozymes that have been validated experimentally. Only six of these are self-cleaving. | + | Natural ribozymes are very rare. There are only 11 distinct classes of ribozymes that have been validated experimentally. Only six of these are self-cleaving. <ref name="other"> PMID:26167874</ref> |
== Structure == | == Structure == | ||
| - | Hatchet ribozyme is a self-cleaving enzyme made of RNA. Hatchet ribozyme is composed of four base-paired stems. The self-cleavage site is unique in that it is located on the 5’ end of the first stem.<ref name="keyword"> PMID: 21638687</ref> Hatchet ribozyme exists surprisingly as a dimer. The ribozyme constructs called (HT-GAAA and HT-UUCG) exist as a mixture of monomers and dimers in solution. Two molecules of HT-GAAA form a nearly symmetrical dimer. It is suggested that the hatchet ribozyme does not need to be a dimer but can also be cleavage-active as a monomer when in solution. Both HT-GAAA and HT-UUCG constructs form nearly symmetric and symmetric dimers respectively.<ref name="keyword" /> The size exclusion experiments that have been performed shows that the hatched ribozyme product exists as an equilibrium between monomer and dimer. The nucleotides that surround the active site of the ribozyme vary little, suggesting that the specific nucleotides that are present are important to the functionality of the cleavage reaction catalyzed by the ribozyme. It has been reported that the Mg2+ is required for the hatchet ribozyme to initiate the self-cleavage reaction. It has not been proven that this is required and Mg2+ Ions were not detected in the vicinity of the cleavage site of either HT-GAAA or HT-UUCG.<ref name="keyword" /> | + | Hatchet ribozyme is a self-cleaving enzyme made of RNA. Hatchet ribozyme is composed of four base-paired stems. The self-cleavage site is unique in that it is located on the 5’ end of the first stem.<ref name="keyword"> PMID: 21638687</ref> Hatchet ribozyme exists surprisingly as a dimer. The ribozyme constructs called (HT-GAAA and HT-UUCG) exist as a mixture of monomers and dimers in solution. Two molecules of HT-GAAA form a nearly symmetrical dimer.<ref name="other" /> It is suggested that the hatchet ribozyme does not need to be a dimer but can also be cleavage-active as a monomer when in solution. Both HT-GAAA and HT-UUCG constructs form nearly symmetric and symmetric dimers respectively.<ref name="keyword" /> The size exclusion experiments that have been performed shows that the hatched ribozyme product exists as an equilibrium between monomer and dimer. The nucleotides that surround the active site of the ribozyme vary little, suggesting that the specific nucleotides that are present are important to the functionality of the cleavage reaction catalyzed by the ribozyme. It has been reported that the Mg2+ is required for the hatchet ribozyme to initiate the self-cleavage reaction. It has not been proven that this is required and Mg2+ Ions were not detected in the vicinity of the cleavage site of either HT-GAAA or HT-UUCG.<ref name="keyword" /> |
== Relevance == | == Relevance == | ||
| - | Ribozymes are necessary for protein synthesis and RNA processing. They are used in expression of cleaved RNAs in vivo for various synthetic biological applications. Most self-cleaving ribozymes have unknown utility, as there is much to learn about them. It is largely unknown in what ways hatchet ribozyme is truly useful.<ref name="keyword" /> | + | Ribozymes are necessary for protein synthesis and RNA processing.<ref name="other" /> They are used in expression of cleaved RNAs in vivo for various synthetic biological applications. Most self-cleaving ribozymes have unknown utility, as there is much to learn about them. It is largely unknown in what ways hatchet ribozyme is truly useful.<ref name="keyword" /> |
== Structural highlights == | == Structural highlights == | ||
Current revision
| This Sandbox is Reserved from September 14, 2021, through May 31, 2022, for use in the class Introduction to Biochemistry taught by User:John Means at the University of Rio Grande, Rio Grande, OH, USA. This reservation includes 5 reserved sandboxes (Sandbox Reserved 1590 through Sandbox Reserved 1594). |
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Hatchet Ribozyme
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References
- ↑ 1.0 1.1 1.2 Weinberg Z, Kim PB, Chen TH, Li S, Harris KA, Lunse CE, Breaker RR. New classes of self-cleaving ribozymes revealed by comparative genomics analysis. Nat Chem Biol. 2015 Aug;11(8):606-10. doi: 10.1038/nchembio.1846. Epub 2015 Jul, 13. PMID:26167874 doi:http://dx.doi.org/10.1038/nchembio.1846
- ↑ 2.0 2.1 2.2 2.3 2.4 2.5 Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
