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