Protein and RNA Engineering

Learning Outcomes

This module explores modern strategies in protein and RNA engineering, spanning rational protein design, directed evolution, and de novo construction of novel biomolecules. It introduces RNA-based regulatory systems, including riboswitches, aptamers, and synthetic RNA logic circuits, highlighting their roles in gene control and biosensing. Students gain foundational understanding of enabling technologies used in synthetic biology and RNA biologics, such as DNA assembly, genome editing, and RNA production/purification. 

Upon completion the students will be able to:

• Understand the scope, evolution, and objectives of protein and RNA engineering within modern biotechnology and synthetic biology.
• Differentiate core engineering strategies—rational design, directed evolution, and de novo biomolecular engineering—and evaluate when to apply each.
• Explain how protein structure, folding, thermodynamics, and kinetics determine stability, function, and misfolding.
• Apply rational protein design principles to predict the functional impact of mutations on binding, catalysis, and stability.
• Assess mutagenesis, screening, and selection strategies used in high‑throughput protein engineering and directed evolution.
• Use computational and in silico tools (including AI‑assisted approaches) to model structures, predict mutations, and guide engineering decisions.
• Explain RNA structure, chemical modifications, and regulatory mechanisms relevant to RNA function and stability.
• Design synthetic RNA regulators (sRNAs, asRNAs, riboswitches) for programmable gene control and synthetic gene circuits.
• Analyze CRISPR‑Cas RNA‑based systems and emerging RNA‑targeting technologies for genome and transcriptome engineering.
• Critically evaluate applications and limitations of engineered proteins and RNAs in therapeutics, diagnostics, and biotechnology.

Module Syllabus

Foundations of Protein Engineering
Principles of Protein Structure and Rational Design
High-throughput Protein Engineering
Protein Structure, Folding and Function
Computational Tools and in silico methods for protein design
RNA Design and Assembly Technologies
Synthetic RNA Modifications
RNA-Based Regulatory Circuits
Riboswitches and RNA-Based Genetic Control
CRISPR-based ribosystems for RNA engineering

Suggested Bibliography

• Relevant literature per lecture, including scientific publications and reviews from international journals, which is available in the course e-class.
• Principles and techniques of Biochemistry and Molecular Biology, 7th edition, Edited by Keith Wilson and John Walker, electronic source
• Laboratory techniques in biochemistry and molecular biology, Elsevier, ScienceDirect, electronic source