Improved synthetic DNA structures by evolutionary selection – Erik Benson Group

Research description

DNA and RNA is more than an information carrier in cells. Over the last 50 years, the ability to design and produce custom DNA strands has unlocked key methods for biology (PCR, RCA, transcriptomics, etc), and also technology (DNA nanotechnology and DNA data storage). These methods generally rely on software-assisted manual design of several candidates that are then individually tested for their function, limiting their potential.

We are interested in drawing inspiration from biology and combine DNA and RNA design with evolution to select the sequences that perform best from large initial pools of candidate structures. We are interested in performing selection both computationally by high throughput simulation, and experimentally through in vitro selection experiments. We want to use these methods to produce stronger binders for proteins and viruses, and to better understand how DNA and RNA interact with cells.

Publications

Selected publications

Funding

Grants

  • European Research Council
    1 December 2025 - 30 November 2030
  • European innovation council (EIC)
    1 March 2025 - 28 February 2030
  • Swedish Research Council
    1 January 2023 - 31 December 2026
    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.

Staff and contact

Group leader

All members of the group

Keywords:
Biomaterials Science Biophysics Biophysics Nanopore Sequencing Nanotechnology Nanotechnology for/in Life Science and Medicine SELEX Aptamer Technique Show all
Content reviewer:
Sara Lidman
18-03-2026