Intelligent detection of miRNA by competitive strand displacement

Micro-RNAs (miRNAs) represent a major class of small non-coding RNAs (19-25 nucleotides) that regulate gene expression post-transcriptionally. miRNAs generally function through a process known as RNA interference (RNAi), in which miRNAs base pair with messenger RNA (mRNA) in a complementary manner. This results in either mRNA degradation or translation inhibition ultimately silencing gene expression. They control almost one third of all human genome and play an important role in many cellular processes, such as proliferation, apoptosis, differentiation, and stress response. Furthermore, the diversity of miRNAs is remarkable, particularly for their role in malignancy, functioning as a tumor suppressors and oncogenes. Dysregulation (over- or under-expression) of miRNAs has been implicated in a variety devastating diseases, including many cancers. In the majority of these cancers, it is not a single miRNA that gets dysregulated, but rather a combination of multiple miRNAs that may result in or serve as a marker for specific types of cancer. Because of this, novel approaches to miRNA detection have been widely pursued; however, there is currently no technology capable of detecting specific combinations of miRNAs inside cells. The goal of this work is to design a novel platform for fluorescence-based detection of multiple miRNAs using a logic based approach. The initial goal of this work is to design a DNA origami structure capable of detecting pair wise combinations of miRNA in AND and OR logical configurations. Initial proof-of-principle experiments will be performed using DNA targets. We currently have developed an initial design to detect miR-21 and miR-155, which are miRNAs dysregulated in cancer that function as diagnostics and prevention markers in several different diseases, particularly in breast cancer. Our findings will help advance the diagnosis of cancer with novel miRNA detection technology.