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If we knew what it was we were doing, it would not be called research, would it?
Albert Einstein

Construction and Functional Analysis of Genetic Circuits

BIOC 313 Introductory Synthetic Biology FALL 2013

You must come to lab prepared--this requires you to read the experimental protocols, not just print a copy of them. Bring whatever information you need to perform the experiments. The procedures for each day are available here and you will be given any additional information in the pre-lab discussions.

SPECIAL NOTE: Record enough procedure details in your notebook during each day of lab so that you can repeat these procedures using your notebook as the primary resource.

Pre-lab: Workshop on Journal Article Presentations, Center for Written, Oral, and Visual Communication, Thurs., 17 Oct., 1-2:30 pm, in ABL B03 (Biology basement classroom)

Day 1 DNA manipulation: Tues., 22 October

Discussion		Experimental Procedures
Introduction to Synthetic Biology		plasmid DNA mini prep
Registry of Standard Biological Parts		restriction enzyme (RE) digests
		phosphatase treatment of vector

Day 2 DNA verification and DNA assembly: Thurs., 24 October

Discussion		Experimental Procedures
Matt Bennett (Invited Speaker)		agarose gel analysis of digests
BioBricks		gel purification of insert and vector DNA
		DNA ligation
		bacterial transformation and selection

Day 3 DNA verification and DNA design: Tues., 29 October

Discussion		Experimental Procedures
PCR		PCR colony screen
ApE: A plasmid Editor		PCR primer design
Ribosomal binding sites (RBS)

Day 4 DNA verification: Thurs., 31 October

Discussion		Experimental Procedures
Joff Silberg (Invited Speaker)		agarose gel analysis of PCR
The Secret Life of Lines & Circles		plasmid DNA mini prep of transformed colony

Day 5 DNA design: Tues., 5 November

Discussion		Experimental Procedures
Student presentations		PCR to mutate RBS
*Team Brainstorming Session*

Day 6 DNA verification and DNA manipulation: Thurs., 7 November

Discussion		Experimental Procedures
Student presentations		agarose gel analysis of PCR
Experimental Design:		DpnI digestion
Do mutations in the RBS affect GFP production?
*Team Brainstorming Session*

Day 7 DNA assembly and DNA design: Tues., 12 November

Discussion		Experimental Procedures
Student presentations		transformation with mutated plasmid
Fluorescence Measurements		plate reader training (purified GFP and bacterial cells)

Day 8 DNA design: Thurs., 14 November

Discussion		Experimental Procedures
*Team Project Presentations*		fluorescence measurements of GFP mutants
Fluorescence Analysis

POST-LAB DUE DATES

Final notebook pages (including data analysis/conclusions and Table of Contents) are due by 3 p.m. on Thurs., 21 November (Dr. Beason's inbox, ABL 326)
Brainstorming document is due by 11:55 PM on Sun., 10 November (submit as TEAM assignment as .doc or .docx in OWL-Space)
Functional Analysis of Circuits document is due by 11:55 PM on Tues., 26 November (submit as TEAM assignment in OWL-Space)
Project proposal is due by 4 p.m. on Fri., 6 December (Dr. Beason's inbox, ABL 326)

We would like to thank New England Biolabs for their generous support of this laboratory course

Copyright, Acknowledgements, and Intended Use
Created by B. Beason (bbeason@rice.edu), Rice University, 4 January 2008
Updated 31 October 2013