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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 2011

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 lectures.

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 MAIN resource.

Day 1 Basic DNA manipulations: Tues., 18 October

Pre-Lab		Experimental Procedures
Wiring parts to function collectively		plasmid DNA mini prep
Registry of Standard Biological Parts		restriction enzyme (RE) digests
BioBrick Standard Assembly		phosphatase treatment of vector

Day 2 Basic DNA manipulations: Thurs., 20 October

Pre-Lab		Experimental Procedures
A genetic switch		agarose gel analysis of digests
Primer design (HW assignment)		gel purification of insert and vector DNA
		DNA ligation
		bacterial transformation and selection

Day 3 PCR: colony screen; fragment amplification for isothermal assembly: Tues., 25 October

Pre-Lab		Experimental Procedures
Matt Bennett (Invited Speaker)		PCR colony screen
		PCR amplification of fragments for assembly
		preparation of vector for assembly

Day 4 Isothermal assembly of vectors: Thurs., 27 October

Pre-Lab		Experimental Procedures
Christian Ray (Invited Speaker)		agarose gel analysis of PCR: size & yield
		purification of DNA fragments for assembly
		isothermal assembly of vectors

Day 5 Transformation with assembled vector: Tues., 1 November

Pre-Lab		Experimental Procedures
Student presentations		agarose gel analysis of assembly reaction
Promoter regulation		transformation with assembled vector
		fluorescent plate reader training

Day 6 Functional analysis of simple circuit; transformation with two plasmids: Thurs., 3 November

Pre-Lab		Experimental Procedures
Student presentations		fluorescence analysis of pTetR-GFP
		transformation with two plasmids
		exp. design: choose REs to confirm ITA tsfmn. (Homework)

Day 7 Confirmation of ITA transformation: Tues., 8 November

Pre-Lab		Experimental Procedures
Student presentations		mini prep/RE digests to confirm ITA plasmid
		exp. design: growth conditions to test circuit (in-lab)

Day 8 Functional analysis of complex circuit: Thurs., 10 November

Pre-Lab		Experimental Procedures
Student presentations		fluorescence analysis of pVenus-Grx/pTara

POST-LAB DUE DATES

Final notebook pages (including data analysis/conclusions and Table of Contents) are due by 4 p.m. on Tues., 15 November (Dr. Beason's inbox, ABL 326)
Brainstorming document is due by 11:55 PM on Thurs., 17 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., 22 November (submit as TEAM assignment in OWL-Space)
Project proposal is due by 4 p.m. on Fri., 2 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 3 November 2011