Combinatorially generated sequenceable DNA nanostructure libraries for one-pot development of high affinity binders via an evolutionary selection process.

DNA nanostructures are uniquely powerful scaffolds for organizing functional molecules at the nanoscale. This has been used to pattern multiple weak binders to achieve drastically stronger net affinity through avidity.

Current techniques allow for programming the patterning through the strand composition in individual assembly reactions limiting most studies to fewer than ten patterns.

I propose developing a new type of DNA nanostructures “Fragmers” that are constructed by ligating small DNA structural fragments in a single-pot library preparation.

A unique feature of the fragmer system is that the 3D structure is determined by a contiguous genome formed by the ligated fragments, and this genome can be read out at scale using high-throughput sequencing, followed by structural reconstruction using DNA simulation techniques.

The fragmer system will allow for simultaneous screening of large libraries of DNA nanostructures displaying aptamers for proteins or virus particles, where the shape of the binding structures can be recovered through sequencing.

Fragmers could complement or replace antibodies and would benefit from simple synthesis and facile addition of functional elements.This grant would enable me to establish as an independent investigator and develop the experimental and computational tools for the fragmer system and the first proof-of-concept development of high avidity binders to proteins and virus particles using established and new aptamers.