Week 1 HW: Final Project Ideas

What do you want to make?

DNA/RNA strand-displacement switch

What living system could make it?

. E. Coli
. Cell-free transcription

How could automation help you make it?

STEP 1: AI / algorithm
STEP 2: Design thousands of candidate circuits
STEP 3: Automated DNA/RNA manufacturing
STEP 4: Automated assembly
STEP 5: Robotic testing
STEP 6: Sequencing / fluorescence / MS
STEP 7: Performance data
STEP 8: AI Optimization

What would it take to make it at a meaningful scale?

Target: target as 10⁹–10¹² usable molecular gates per production run
Industrial stack to build:

1. Design
   
2. Biological Production
   
3. Assembly
   
4. Spatial Organization
   
5. Computation
   
6. Readout
   
7. QC
   
8. Automation
   

Week 2 HW: DNA Design

PART I: DESIGN: DEFINITION OF EXPRESSION TARGET

What molecule are you expressing?

What is the sequence?

What host or chassis?

Where does the product need to go?

PART II: DESIGN: DEFINITION OF GENETIC PARTS

Layer 1: Transcription start

. Part Short Name:
. Sequence:
. Origin:
. Justification:

Layer 2: Translation start

. Part Short Name:
. Sequence:
. Origin:
. Justification:

Layer 3: Coding sequence

. Part Short Name:
. Sequence:
. Origin:
. Justification:

Layer 4: Targeting

. Part Short Name:
. Sequence:
. Origin:
. Justification:

Layer 5: Transcription stop

. Part Short Name:
. Sequence:
. Origin:
. Justification:

Layer 6: Vector context

. Part Short Name:
. Sequence:
. Origin:
. Justification:

PART III: DESIGN: CONSTRUCT ASSEMBLY

Kernel Schematic:

Link to Kernel Assembled Construct:

PART IV: DESIGN: OPTIMIZATION & QUALITY CHECK

Codon Optimization:

. BEFORE:
. AFTER:

Sequence Search:

Safety Screen Report:

PART V: FROM DESIGN TO BUILD

How would you build it?

What are your synthesis constrains?

Prototype vs. scale:

Final Project