Engineering RNA-protein complexes with different shapes for imaging and therapeutic applications

Molecular machines composed of RNA–protein (RNP) complexes may expand the fields of molecular robotics, nanomedicine, and synthetic biology. However, constructing and directly visualizing a functional RNP nanostructure to detect and control living cell function remains a challenge. Here we show that RNP nanostructures with modular functions can be designed and visualized at single-RNP resolution in real time. The RNP structural images collected in solution through high-speed atomic force microscopy showed that a single RNP interaction induces a conformational change in the RNA scaffold, which supports the nanostructure formation designed. The specific RNP interaction also improved RNA nanostructure stability in a serum-containing buffer. We developed and visualized functional RNPs (e.g., to detect human cancer cells or knockdown target genes) by attaching a protein or RNA module to the same RNA scaffold of an optimal size. The synthetic RNP architecture may provide alternative materials to detect and control functions in target mammalian cells.