Designing Transcription factor (TF) decoys for regulating gene expression using DNA Nanotechnology

TF decoys are short ds DNA sequences that can act like a sponge to soak up free transcription factors in the cell and divert them from their native binding site. This can be harnessed to alter the protein expression and regulate immunological pathways. However, transfecting unmodified transcription factors (TFs) into cells is challenging because the negative charge of DNA causes repulsion at the cell membrane. Additionally, if they do enter, these oligonucleotides are rapidly degraded by nucleases and other enzymes within the cell. This issue can be solved by using DNA-based nanostructures. DNA can fold into different polyhedra due to its flexible nature and the turns of double-stranded DNA, which are also quite stable in the cellular environment, unlike double-stranded DNA-based circuits. 

We are currently focused on building a DNA-based Tetrahedron that can mimic transcription factor binding sites, functioning as a decoy that can bind to transcription factors and regulate gene expression. We are currently testing the transfection and interaction of the TF decoy in E coli, which binds to the Lac repressor, and can regulate GFP expression.