APTAFRAME · DNA-origami frame platform for co-evolution ligand selection

DNA-origami frame platform for co-evolution ligand selection

The humoral immune system is a key aspect of human biology in fighting off diseases and eliminating pathogens. Furthermore, engineered antibodies can fight an increasing number of diseases including cancer and autoimmune conditions. Therefore, strategies to systematically and efficiently generate high-affinity antibodies are important parts of modern biotechnology. However, methods of rapidly creating antibodies binding to a very specific region of a target remains challenging and a major unmet goal. New methods of selection, based on spatial control over affinity reagent discovery process should therefore accelerate and increase efficiency of antibody discovery. The overall aim of APTAFRAME was to build a novel technology platform for the systematic discovery of ligands leveraging cooperative binding effects in the context of spatially configurable DNA origami frameworks and to initially demonstrate this in the context of nucleic acid aptamer libraries. As a next step, APTAFRAME envisaged to evolve aptamers composed of macrocyclic peptides (MCP) and antibodies against proteins of interest using co-evolution as a driver for cooperative binding. The best method to display peptides on the DNA origami frames is through ribosome display. Protein discovery through ribosome display relies on the reading of a messenger RNA (mRNA) that also serves as sequence-to-protein connector during high-throughput readout. Unfortunately, the chemical (and biological) degradability of RNA poses a challenge for the development of this, and similar methodologies. Xenonucleic acids (XNAs) are alternative informational polymers largely resistant to chemical and biological degradation. Unfortunately, current ribosomes cannot efficiently translate peptides and proteins from mXNAs. We have therefore focused part of our efforts trying to circumvent this problem by creating ribosomes that can read genetic information encoded in mXNAs. Our hope is that by producing mXNA dependent ribosomes we will create a robust system for the decoration of DNA nano-objects with translated peptides and proteins utilised as a framework for cooperative evolution.

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