Bi23 Syllabus

Introduction and Background: biochemistry, molecular biology, and biotechnology

• Engineering across scales – molecules to organisms
• Nucleic acid structure and chemistry.
• Basic molecular biology techniques

Self-replicating molecules and the RNA world

• The prebiotic world and some ideas for the first self replicator
• What the RNA world might have looked like
• The tragedy of the molecular commons - or, the origin of the cell
• The twilight of the RNA empire and the rise of proteins

Evolving molecules in the lab

• Function from random libraries - aptamer selections
• Evolving catalysis - ribozymes
• Evolving catalysis - proteins

Biosensors and detectors

• Diagnostic and forensic PCR, RFLP, microarrays, molecular beacons
• ELISAs and other antibody-based technologies
• Aptamer and ribozyme-based detection
• Interfacing the biomolecular and electronic worlds

Nanomaterials, nanodevices, and biomolecular computation

• DNA as a programmable material
• DNA as a nanomechanical device
• DNA as a computer

Controlling gene expression: natural and engineered systems

• Functional RNA in biology: catalysis, riboswitch, miRNA, RNAi
• siRNA as a research tool and therapeutic
• Programmable gene regulation

Synthetic biology – genetic circuits and control

• Control circuits in biology
• Forward engineering of genetic circuits
• Modeling and standardization of biological parts

Systems biology – biology of complex networks

• Network-scale biology: data, modeling, and theory
• Systems-level properties: information processing, robustness, evolvability

Risk and responsibility in engineering the living world

• Ownership of biological material and knowledge – the intellectual property landscape
• Engineering biology and security issues
• Engineering biology and access to innovation
• Engineering challenges in the future