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Observing Putative RNA Structures That Resist XRN1 Degradation

A critical aspect of RNA biology is observing and experimenting with secondary and tertiary RNA structures that provide unique functions within the cell. One of these RNA structures is the pseudoknot. Specifically, this research will be aimed to test in-vitro transcribed putative XRN1-resistant xrRNA structures known as pseudoknots within mRNA transcripts. This study will utilize the enzyme XRN-1 and the complementary DNA to produce the mRNA transcript. The pseudoknots ability to stop degradation of the mRNA transcript will be assessed through denaturing polyacrylamide gel electrophoresis (dPAGE) analysis. Even though, the results of this experiment have not yet manifested. There are a few possibilities of what the results of the experiment might be: 1) Definitive proof of the RNA transcripts resisting XRN1 degradation 2) XRN1 completely degrades the RNA transcripts and there is no sign of 5’ truncated products. Understanding and researching such structures could reveal an unexplored facet of gene expression/regulation.

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