The aim of this project is to design and operate DNA- and RNA-based strand displacement circuits with predictable kinetics in complex environments. These environments involve competing molecular interactions, crowding effects, and the presence of nucleic acid-binding proteins. Achieving precise control over such reactions will enable the use of such circuits for biosensing in analyte samples, synthetic cell models, and within living cells. We will design a range of nucleic acid circuits that respond to biologically relevant inputs such as RNA, proteins, small biomolecules, or combinations thereof. These circuits will span from simple sensors to logic functions and multilayered networks. Potential application scenarios include:

• complex analyte mixtures for point-of-care biosensing,
• implementation of logic or analog circuits as controllers in synthetic cells, and
• in vivo operation targeting endogenous RNA or proteins.

Each of these environments presents distinct challenges in terms of molecular concentrations, competing interactions, crowding, and degradation. To tackle these challenges, strategies such as molecular amplification (feedback circuits), protection against degradation through secondary structures, protein binding, and spatial control via compartmentalization or co-localization will be pursued.