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Formal Lab Session - 1st September 2009

Overview

• Stochastic Switch Team - analysed cut pSB1AT3 plasmid (successful) and also cleaned up ssbp PCR product. Also froze down strains of transformant E. coli containing BioBricks

• Metal Sensor Team - prepared the newly arrive pMA1 and pMA2 primers and then used these primers to amplify czrA from B. subtilis genome (PCR). Also used PCR to amplify sac, ara and sspb for Stochastic Switch team.

• Promoter Library Sub-Project - attempted to amplify the three sets of sigA promoter using PCR

Stochastic Switch Team

Today we run the gel for pSB1AT3 plasmid backbone purified last week from the gel. It was cut with EcoRI and SpeI sites. The length of the band confirmed that we have the right product.

We also used PCR clean-up kit to extract sspB from last week's PCR. We used sigma-d's PCR clean-up protocol. The final volume was measured as 48ul. We measured the concentration and run it on the gel using 5ul of sspb + 4ul of water + 1ul of the loading buffer. The band confirmed that we had the right product after the clean-up process.

The concentration of sspB was 37.5ng/ul

Today we also made ON cultures of the following strains in order to freeze them down into the TPA collection. First the TPA book had to be filled out to record the strains:

• 2489- BBa_CO178
• 2490- BBa_ROO62
• 2491- BBa_CO161
• 2492- BBa_CO179
• 2493- BBa_ROO79
• 2494- BBa_J44000

These will be frozen down in DMSO tomorrow.

Metal Sensor Team

Introduction

So far, the Metal Sensing Team have successfully digested the pSB1A2 plasmid (which contains the BBa_J33206 BioBrick - the arsR gene and binding site) so that the plasmid has had it's promoter removed. With this linearised fragment we hope to insert the czrA gene along with the cadA promoter; these genes will be extracted from the genome of Bacillus subtilis via PCR reactions. The primers capable of this are pMA1 and pMA2 (designed by Mathew and Arun).

Today we will carry out PCR in order to amplify czrA gene for our team and sac, ara and sspb genes for the stochastic switch team. However we must first of all hydrate and prepare the primers which have just arrived (i.e. pMA1 and pMA2). We will also need to prepare for the possibility of the PCR reactions not working - overnight cultures of B. subtilis in LB medium will be prepared for a possible PCR tomorrow.

Practical Outline

These are the three things which the Metal Sensing Team need to have accomplished by today:

1. Hydrate the newly-arrived primers pMA1 and pMA2, adding water according to their concentrations (in nMoles); then dilute them to 10x dilution.
2. Using the 10x hydrated primers, carry out a czrA amplification PCR reaction on cells taken from a plate containing wild type Bacillus subtilis
3. Inoculate LB cultures with B. subtilis cells and grow overnight - this is for if the PCR reactions today don't work

Procedure

1) Preparing primers pMA1 and pMA2

pMA1 and pMA2 need to be rehydrated by adding sterile distilled water. The volume of water to be added is simply (the concentration (in nMoles) of the primers multiplied by 5) ul. The concentrations of the primers are as follows

• pMA1 = 30.6 nMoles
• pMA2 = 31.3 nMoles

Therefore the amount of water to be added to each of the primers is:

• pMA1 = (30.6 x 5) = 153ul
• pMA2 = (31.3 x 5) = 156.5ul

The next thing to do is make 10x dilutions by extracting 50ul of each of these hydrated primers and adding them to 450ul of sterile distilled water.

2) PCR

We carried out PCR reactions in the same way as described on 21/08/2009 along with the stochastic switch team. It must be noted that the annealing temperatures for pMA1 and pMA2 are 63.1°C and 62.9°C respectively.

Exp.No.3 PCR experiment plan

No.	Water (ul)	PCR Mix (ul)	Forward Primer (ul)	Reverse Primer (ul)	Template (ul)	Polymerase used (ul)	Total Volume (ul)
1	24	15	pMA1 2.5ul	pMA2 2.5ul	168 DNA 5ul	MolTaq (1ul)	50
2	29	15	pMA1 2.5ul	pMA2 2.5ul	0	MolTaq (1ul)	50
3	24	15	sac_forward 2.5ul	sac_reverse 2.5ul	168 DNA 5ul	MolTaq (1ul)	50
4	29	15	sac_forward 2.5ul	sac_reverse 2.5ul	0	MolTaq (1ul)	50
5	24	15	araR_forward 2.5ul	araR_reverse 2.5ul	168 DNA 5ul	MolTaq (1ul)	50
6	29	15	araR_forward 2.5ul	araR_reverse 2.5ul	0	MolTaq (1ul)	50
7	24	15	sspb_forward 2.5ul	sspb_reverse 2.5ul	168 DNA 5ul	MolTaq (1ul)	50
8	29	15	sspb_forward2.5	sspb_reverse 2.5	0	MolTaq (1ul)	50

PCR conditions:

For sample 1 and 2:

1- 95C for 2min
2- 95C for 30sec
3- 63C for 1min 
4- 75C for 2min
    Step 2-3-4 x 30
5- 75C for 5min
6- 4C Pause

For sample 3, 4, 7 and 8:

1- 95C for 2min
2- 95C for 30sec
3- 57C for 1min 
4- 75C for 2min
    Step 2-3-4 x 30
5- 75C for 5min
6- 4C Pause

For sample 5 and 6:

1- 95C for 2min
2- 95C for 30sec
3- 59C for 1min 
4- 75C for 2min
    Step 2-3-4 x 30
5- 75C for 5min
6- 4C Pause

Tomorrow the team will run the products on the gel and analyse them.

3) Inoculating LB with wt B. subtilis

We added 3ml of LB to a test-tube and, under aseptic conditions, inoculated it with a colony taken from a plate containing wild type Bacillus subtilis. The tube was then transferred to the orbital incubator (37°C) and allowed to grow overnight.

Promoter Library Sub-Project

Introduction

Up until now, this sub-project has seen the pGFP-rrnB plasmid backbone digested and linearised with restriction enzymes EcoRI and NheI. The resulting 8kb fragment (which is the plasmid backbone) has been successfully excised from agarose gel and purified; it is into this plasmid backbone in which we will place our sigA promoters.

Today's work involves the amplification of the promoter library (a collection of sigA promoters specified by degenerate sequences) using PCR.

Preparing the Primers

The first task carried out was the rehydration of the primers involved with this sub-project. A final concentration of 200uM is the desired value and to get this for each primer, the following calculation was observed:

Amount of water to be added (ul) = amount of primer (nMoles) x 5

The table below shows the oligos involved in this practical along with the primer amounts (in nMoles) and the amount of PCR water needed (in ul) to make the primers at a concentration of 200uM

A table showing the oligos with the amount of water needed

Oligo	Purpose	Amount (nMoles)	PCR Water added (ul)
IDT 60396420	Forward Primer	19.6	98.0
IDT 60396419	Reverse Primer	21.9	109.5
alta D68423AW	Control (C0)	0.06	300
alta D68425AW	Variant 2 (V2)	0.06	300
alta D68424AW	Variant 3 (V3)	0.06	300
alta D68426AW	Variant 1 (V1)	0.06	300
alta D68427AW	19mer Primer	0.08	400

All of these oligos were then aliquoted and further diluted 1:100 with PCR water and stored in the -20C freezer. The primer stocks are kept in Neil's yellow box whereas the dilutions in enzymes are kept in the a separate box.

Preparing the PCR

The table below shows the amounts of substances added to each PCR reaction:

PCR Reaction Table

Sample	No.	Water (ul)	PCR Mix (ul)	Forward Primer (ul)	Reverse Primer (ul)	Template (ul)	Polymerase used (ul)	Total Volume (ul)
C0	1	31	15	1	1	200uM (1ul)	Taq (1ul)	50
V1	2	31	15	1	1	200uM (1ul)	Taq (1ul)	50
V2	3	31	15	1	1	200uM (1ul)	Taq (1ul)	50
V3	4	31	15	1	1	200uM (1ul)	Taq (1ul)	50

The PCR Mix was composed of the following substances:

• 30ul dNTP's (6 x 5ul)
• 30ul Buffer (6 x 5ul)
• 30ul DMSO (6 x 5ul)

The Taq polymerase used needed to be prepared too. 6ul of pure Taq enzyme was taken and 1ul was diluted in 5ul of PCR water. 1ul of this diluted Taq was used per tube.

Carrying out the PCR

The cycle for the PCR was as follows:

One cycle involving the reverse primer pGFGrrnBrev only with the large degenerate oligo as a template - this is to convert the single-stranded oligo into double stranded DNA. To denature the oligo 90C was needed, to anneal the oligo 60C was needed and to extend the oligo 72C was needed.

The forward primer should then be added and the mixture given 30 cycles (each cycle lasting 1 minute) of 90C denaturing, 54C annealing and 72C extending.

July M T W T F S S     [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/1_July_2009&action=edit 1] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/2_July_2009&action=edit 2] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/3_July_2009&action=edit 3] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/4_July_2009&action=edit 4] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/5_July_2009&action=edit 5] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/6_July_2009&action=edit 6] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/7_July_2009&action=edit 7] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/8_July_2009&action=edit 8] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/9_July_2009&action=edit 9] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/10_July_2009&action=edit 10] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/11_July_2009&action=edit 11] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/12_July_2009&action=edit 12] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/13_July_2009&action=edit 13] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/14_July_2009&action=edit 14] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/15_July_2009&action=edit 15] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/16_July_2009&action=edit 16] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/17_July_2009&action=edit 17] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/18_July_2009&action=edit 18] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/19_July_2009&action=edit 19] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/20_July_2009&action=edit 20] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/21_July_2009&action=edit 21] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/22_July_2009&action=edit 22] [http://2009.igem.org/Team:Newcastle/Labwork/23_July_2009 23] [http://2009.igem.org/Team:Newcastle/Labwork/24_July_2009 24] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/25_July_2009&action=edit 25] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/26_July_2009&action=edit 26] [http://2009.igem.org/Team:Newcastle/Labwork/27_July_2009 27] [http://2009.igem.org/Team:Newcastle/Labwork/28_July_2009 28] [http://2009.igem.org/Team:Newcastle/Labwork/29_July_2009 29] [http://2009.igem.org/Team:Newcastle/Labwork/30_July_2009 30] [http://2009.igem.org/Team:Newcastle/Labwork/31_July_2009 31]

August M T W T F S S           [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/1_August_2009&action=edit 1] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/2_August_2009&action=edit 2] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/3_August_2009&action=edit 3] [http://2009.igem.org/Team:Newcastle/Labwork/4_August_2009 4] [http://2009.igem.org/Team:Newcastle/Labwork/5_August_2009 5] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/6_August_2009&action=edit 6] [http://2009.igem.org/Team:Newcastle/Labwork/7_August_2009 7] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/8_August_2009&action=edit 8] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/9_August_2009&action=edit 9] [http://2009.igem.org/Team:Newcastle/Labwork/10_August_2009 10] [http://2009.igem.org/Team:Newcastle/Labwork/11_August_2009 11] [http://2009.igem.org/Team:Newcastle/Labwork/12_August_2009 12] [http://2009.igem.org/Team:Newcastle/Labwork/13_August_2009 13] [http://2009.igem.org/Team:Newcastle/Labwork/14_August_2009 14] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/15_August_2009&action=edit 15] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/16_August_2009&action=edit 16] [http://2009.igem.org/Team:Newcastle/Labwork/17_August_2009 17] [http://2009.igem.org/Team:Newcastle/Labwork/18_August_2009 18] [http://2009.igem.org/Team:Newcastle/Labwork/19_August_2009 19] [http://2009.igem.org/Team:Newcastle/Labwork/20_August_2009 20] [http://2009.igem.org/Team:Newcastle/Labwork/21_August_2009 21] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/22_August_2009&action=edit 22] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/23_August_2009&action=edit 23] [http://2009.igem.org/Team:Newcastle/Labwork/24_August_2009 24] [http://2009.igem.org/Team:Newcastle/Labwork/25_August_2009 25] [http://2009.igem.org/Team:Newcastle/Labwork/26_August_2009 26] [http://2009.igem.org/Team:Newcastle/Labwork/27_August_2009 27] [http://2009.igem.org/Team:Newcastle/Labwork/28_August_2009 28] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/29_August_2009&action=edit 29] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/30_August_2009&action=edit 30] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/31_August_2009&action=edit 31]

September M T W T F S S   [http://2009.igem.org/Team:Newcastle/Labwork/1_September_2009 1] [http://2009.igem.org/Team:Newcastle/Labwork/2_September_2009 2] [http://2009.igem.org/Team:Newcastle/Labwork/3_September_2009 3] [http://2009.igem.org/Team:Newcastle/Labwork/4_September_2009 4] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/5_September_2009&action=edit 5] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/6_September_2009&action=edit 6] [http://2009.igem.org/Team:Newcastle/Labwork/7_September_2009 7] [http://2009.igem.org/Team:Newcastle/Labwork/8_September_2009 8] [http://2009.igem.org/Team:Newcastle/Labwork/9_September_2009 9] [http://2009.igem.org/Team:Newcastle/Labwork/10_September_2009 10] [http://2009.igem.org/Team:Newcastle/Labwork/11_September_2009 11] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/12_September_2009&action=edit 12] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/13_September_2009&action=edit 13] [http://2009.igem.org/Team:Newcastle/Labwork/14_September_2009 14] [http://2009.igem.org/Team:Newcastle/Labwork/15_September_2009 15] [http://2009.igem.org/Team:Newcastle/Labwork/16_September_2009 16] [http://2009.igem.org/Team:Newcastle/Labwork/17_September_2009 17] [http://2009.igem.org/Team:Newcastle/Labwork/18_September_2009 18] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/19_September_2009&action=edit 19] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/20_September_2009&action=edit 20] [http://2009.igem.org/Team:Newcastle/Labwork/21_September_2009 21] [http://2009.igem.org/Team:Newcastle/Labwork/22_September_2009 22] [http://2009.igem.org/Team:Newcastle/Labwork/23_September_2009 23] [http://2009.igem.org/Team:Newcastle/Labwork/24_September_2009 24] [http://2009.igem.org/Team:Newcastle/Labwork/25_September_2009 25] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/26_September_2009&action=edit 26] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/27_September_2009&action=edit 27] [http://2009.igem.org/Team:Newcastle/Labwork/28_September_2009 28] [http://2009.igem.org/Team:Newcastle/Labwork/29_September_2009 29] [http://2009.igem.org/Team:Newcastle/Labwork/30_September_2009 30]

October M T W T F S S       [http://2009.igem.org/Team:Newcastle/Labwork/1_October_2009 1] [http://2009.igem.org/Team:Newcastle/Labwork/2_October_2009 2] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/3_October_2009&action=edit 3] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/4_October_2009&action=edit 4] [http://2009.igem.org/Team:Newcastle/Labwork/5_October_2009 5] [http://2009.igem.org/Team:Newcastle/Labwork/6_October_2009 6] [http://2009.igem.org/Team:Newcastle/Labwork/7_October_2009 7] [http://2009.igem.org/Team:Newcastle/Labwork/8_October_2009 8] [http://2009.igem.org/Team:Newcastle/Labwork/9_October_2009 9] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/10_October_2009&action=edit 10] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/11_October_2009&action=edit 11] [http://2009.igem.org/Team:Newcastle/Labwork/12_October_2009 12] [http://2009.igem.org/Team:Newcastle/Labwork/13_October_2009 13] [http://2009.igem.org/Team:Newcastle/Labwork/14_October_2009 14] [http://2009.igem.org/Team:Newcastle/Labwork/15_October_2009 15] [http://2009.igem.org/Team:Newcastle/Labwork/16_October_2009 16] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/17_October_2009&action=edit 17] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/18_October_2009&action=edit 18] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/19_October_2009&action=edit 19] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/20_October_2009&action=edit 20] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/21_October_2009&action=edit 21] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/22_October_2009&action=edit 22] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/23_October_2009&action=edit 23] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/24_October_2009&action=edit 24] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/25_October_2009&action=edit 25] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/26_October_2009&action=edit 26] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/27_October_2009&action=edit 27] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/28_October_2009&action=edit 28] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/29_October_2009&action=edit 29] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/30_October_2009&action=edit 30] [http://2009.igem.org/wiki/index.php?title=Team:Newcastle/Labwork/31_October_2009&action=edit 31]