SynBio Project Tutorials

This site is a structured, modular guide for learning to design, execute, and manage synthetic biology experiments. It emphasizes practical skills, design from first principles, and a deep understanding of the molecular biology and chemistry behind each step.

The tutorials are organized into three parts:

• Part A: Wetlab — Step-by-step execution of a cloning experiment, including molecular biology concepts, lab protocols, documentation, and data interpretation.
• Part B: Construction — How to design cloning workflows, simulate outcomes, and represent cloning plans using standardized formats.
• Part C: Project Planning — Strategies for organizing experiments, selecting parts with informatics tools, and managing experimental workflows.

Each tutorial includes embedded quizzes, videos, and progress tracking. This platform supports students, researchers, and anyone seeking a rigorous, hands-on introduction to synthetic biology.

Part A: Wetlab

1. pP6 Experiment Introduction
   Learn the goal of the pP6 library experiment, the concept of consensus promoters, and why randomized promoter libraries are used.

2. Pipetting
   Learn how to use a pipette properly, interpret volume markings, and avoid common errors.

3. Polymerase Chain Reaction
   Instructions for setting up the PCR using degenerate oligos to amplify the pP6 library.

4. Gel Electrophoresis
   Run a gel to verify the PCR product, and interpret results.

5. Zymo Cleanup
   Purify the PCR product to prepare it for assembly.

6. Assembly
   Rejoin ends of the linear DNA to regenerate the plasmid using Golden Gate assembly.

7. Transformation
   Transform E. coli with your assembled DNA and plate colonies.

8. Colony Picking
   Pick colonies and grow liquid cultures from selected transformants.

9. Miniprep
   Purify plasmid DNA from the cultures using a miniprep protocol.

10. Cycle Sequencing
    Submit DNA for sequencing and interpret results to identify strong promoter variants.

11. Measuring Fluorescence
    Quantify promoter activity by measuring amilGFP fluorescence and OD, and calculate Relative Promoter Units (RPUs).

Part B: Construction

1. DNA Basics
   Learn about DNA structure, reverse complement operations, strandedness, plasmids, and genomes.

2. Sequence Editing Tools
   Learn to use a sequence editor (ApE, Benchling, or other tools) for finding subsequences, reverse complementing, and translating DNA.

3. Manual Product Prediction
   Manually predict PCR products using a sequence editor and understand the concept of annealing regions.

4. Simulation Tools
   Use simulation tools to test cloning steps written in Construction File shorthand.

5. Basic Cloning
   Walk through traditional cloning steps.

6. Gibson Assembly
   Introduction to Gibson Assembly for seamless cloning.

7. Golden Gate Assembly
   Learn Golden Gate cloning methods.

8. Site-Directed Mutagenesis
   Constructing and designing short parts and mutagenesis.

9. Sequencing Confirmation
   Learn to analyze sequencing results.

Part C: Project Planning

1. Project Setup and Nomenclature
   Learn how to structure a project, name experiments, and organize your working directory.

2. Experimental Design Principles
   Understand how to think about synthetic biology experiments from the ground up.

3. Sequence Retrieval and Analysis
   Use BLAST and other tools to find, analyze, and align DNA sequences for cloning.

4. Choosing a Fabrication Strategy
   Design primers and synthetic fragments for amplification and cloning.

5. Simulation Tools
   Simulate your cloning designs using the Java-based CFS tool and the web-based C6 Tools platform.

6. Inventory and Labsheets
   Organize your physical inventory and use labsheets to plan and document your experiments.

7. Ortholog Scan Project
   Design an ortholog scan for the complex gene ispA as a capstone project, integrating bioinformatics, cloning strategy, and documentation.

Each tutorial includes step-by-step instructions, videos, and interactive examples.