Materials and Methods

From 2008.igem.org

(Difference between revisions)
(Materials and Methods)
(Materials and Methods)
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'''To make the silencers:'''
'''To make the silencers:'''
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1. pRS315, Adh1P/Adh1t
1. pRS315, Adh1P/Adh1t
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4. pRS305, Ga11P/Adh1t
4. pRS305, Ga11P/Adh1t
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'''To make the reporters:''' (same plasmids as above, with a 5' or 3' 8X LexA operator array.
+
'''To make the reporters:''' (same plasmids as above, with a 5' or 3' 8X LexA operator array)
 +
 
1. pRS315, Adh1P/Adh1t
1. pRS315, Adh1P/Adh1t

Revision as of 16:54, 22 October 2008

Materials and Methods

1. General Cloning/Molecular biology

Constructs were cloned using the AarI method, developed by Sergio Pesajovich for the 2007 iGEM competition. To learn more about AarI cloning:

Everything you ever wanted to know about AarI

In brief: yeast genomic DNA was used as a template to PCR amplify "parts". Parts were TOPO cloned, validated by sequencing, and then combinatorially cloned into the following AarI adapted acceptor vectors:

To make the silencers:

1. pRS315, Adh1P/Adh1t

2. pRS315, Cyc1P/Adh1t

3. pRS315, Fig1P/Adh1t

4. pRS305, Ga11P/Adh1t

To make the reporters: (same plasmids as above, with a 5' or 3' 8X LexA operator array)

1. pRS315, Adh1P/Adh1t

2. pRS315, Cyc1P/Adh1t

3. pRS315, Fig1P/Adh1t

4. pRS305, Ga11P/Adh1t

In some cases, finished constructs were subcloned as cassettes (using Kpn1 or PspOMI and SacI sites) into various pRS3__ series vectors to swap the marker.

Yeast Strains

SF992/W303 or CB008: W303 MATa, Ste5::KanR, bar1::NatR, far1D, his 3, trp1, leu2, ura3 (for pheromone experiments) were transformed with finished plasmids using standard protocols.

2. Silencing Assay In cases where galactose induction was required, yeast were re-streaked to S-Raffinose plates, plus or minus 2% galactose. Overnight cultures in the same media were diluted in the am (typically 1:50 or 1:100), and 3 hours later, at OD600 0.05-0.1 range, flow cytometry measurements were taken using a BD LSR-II flow cytometer (BD Biosciences). For each sample, 10,000 cells were counted, and GFP fluorescence was measured by exciting at 488 nm with a 100 mW Coherent Sapphire laser. For experiments with pheromone-inducible promoters, cultures were grown to early log phase (OD600=0.1-0.3) in complete synthetic dropout media and then treated with 1 μM α-factor (Zymo Research) to activate the pathway. Cultures were analyzed after 3 hours of growth.

Representative flow cytometery plots are shown for all experiments, but each experiment was conducted in triplicate (using different clones) with consistent results.


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