FLUORESCENT ASSAY FOR THE ANALYSIS OF RNA MATURATION

Rebecca Basch,¹ Nicole Abedrabbo,¹ Carly Mitchell² and Yulia Gerasimova¹

1, Chemistry Department, University of Central Florida, Orlando FL 32816, USA
2, Oviedo High School, Oviedo, FL 32765

 The majority of non-coding RNAs are first transcribed are primary transcripts, which need to undergo several processing steps to yield the mature RNA sequences. One of the steps in RNA maturation is shortening of a primary transcript from one or both ends, sometimes with the formation of several truncated intermediates. For example, bacterial rRNAs are transcribed as a single primary transcript containing the sequences of 5S, 16S and 23S rRNA, which is then cleaved into three individual rRNA precursors. 23S pre-rRNA is then shorten to produce processing intermediates containing ether 3 (M+3 intermediate) or 7 (M+7 intermediate) extra nucleotides at the 5’-end and 7-9 nucleotide at the 3’-end. Here we report on the design and implementation of an array of split deoxyribozyme (sDz) sensors, which can differentiate between M+3 and M+7 intermediates of E. coli 23S rRNA processing. The fluorescent assay offer a time- and cost-efficient alternative to the primer extension assay, which is traditionally used for the analysis of RNA structure.