Prof. Friedrich Simmel
TU Munich, TUM School of Natural Sciences, Department of Bioscience
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 (i) complex analyte mixtures for point-of-care biosensing, (ii) implementation of logic or analog circuits as controllers in synthetic cells, and (iii) 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.
The project involves biomolecular design, genetic engineering, fluorescence microscopy, and computational modeling.
Requirements: The ideal candidate has a degree in physics/biophysics, alternatively biochemistry/molecular biology with excellent quantitative bioscience/computational skills.
Planned secondments: Khmelinskaia lab, Ouldrige group, Di Michele lab
Salary: Gross salary € 4,058.12 + € 710.00 mobility allowance (+ €495.00 family allowance, if applicable).
The salary (36 months) is directly based on Marie Sklodowska-Curie Actions (MSCA) Doctoral Network budgeting (including a country-specific living allowance and a fixed mobility allowance for a doctoral candidate, as well as a possible family allowance).