February 7

Preculture
We started preculture at 12:10.

February 8

Culture
We start culturing with 300[mL] of LB medium.

time	OD600
12:00	start
14:10	0.019
14:45	0.154
15:05	0.267
15:21	0.64

Making Competent Cell
We made competent cells.

Transformation
pGEM_TAP
Lacp (BBa_R0011)
DT (BBa_B0015)

Making Culture Medium Plates
We made 200mL of ampicillin culture, kanamycin culture, and chloramphenicol culture.

Transformation
GFP(BBa_E0040) in pSB1A2
DT(BBa_B0015) in pSB1AK3
ara(BBa_I0500) in pSB2K3
Lacp(BBa_R0011) in pSB1A2

February 9

transformation
BBa-E0040(GFP)(Mr.Fujita)

Liquid culture
DT.leap colony transformed on February 8
colony of competent cell made on February 8

February 10

Miniprep
DT2 43.9μg/ml(1.34 260/230 1.74 260/280)
lacp1 17.1μg/ml(1.54 260/280 0.83 260/230)
lacp2 18.0μg/ml(1.58 260/280 0.87 260/230)

transformation
B0040 1.4k PsB1A2 B0034 1.2M pSB1A2(from iGEM parts plate)

Competent cell
We did preculture for overnight. We put 1.5mL of preculture on 150mL of LB culture.

time	OD600
11:45	start
13:30	0.048
14:30	0.168
15:03	0.256
15:20	0.405
15:35	0.459
at last	0.576

February 11

Checking Transformation efficiency
Conpetent cell's transformation efficiency is 1.3x10^4colonys/μg

February 13

Transformation
Const promoter J23110,J23109,J23100

DNA	Competent cell	total
1μL	20	21

No colony was there on February 14

Liquid culture
lacP,DT,RBS(BBa_B0034),GFP
start at 20:00
in Plus grow with Ampicilin 3mL

February 14

Miniprep
concentration[μg/μL]

lacP3	39.6
lacP4	40.8
lacP5	28.9
RBS1	28.2
RBS2	57.4
RBS3	13.2
DT3	69.7
DT4	64.4
DT5	61.5
GFP1	64.0
GFP2	50.5
GFP3	66.0

Restriction
Const promoterJ23100

DNA	Spe1	Pst1	Buffer2	BSA	MilliQ	total
20	0.5	0.5	3	0.5	5.5	30

at 37℃ for overnight

February 15

Making gel
1% Agarose gel

Agarose	TAE
1.6g	160mL

Electrophoresis

Gel No.1

Restriction product	loading dye
5μL	1

The marker was 1kb ladder
It seemed that this restriction product was not cut.

Gel No.2
Lane1 : 1kb ladder
Lane2 : J23100 2μL + 6*Loading dye 1μL
Lane3 : J23100(Spe1,Pst1) 5μL
Lane4 : J23100(Spe1,Pst1) 2μL

• There were bands on lane_2 and we cannot identify these bands because the sample of lane_2 was not cut with any restriction enzyme.
  
• There must have been bands at 2100bp and 883bp on lane_3 and lane_4.
  
  

Testing whether restriction enzyme were deactivated or not

DNA(DT)	restriction enzyme	Buffer	BSA	MilliQ	total
10	0.5	3	0.5	16	30

at 37℃ for Oveernight
Restriction enzyme means Spe1(1,2) Pst1(1,2,3) in this time.

February 16

Electrophoresis

1. 1kb ladder
2. DT2
3. DT3
4. DT2 (Spe1-1)
5. DT2 (Spe1-2)
6. DT2 (Pst1-1)
7. DT2 (Pst1-2)
8. DT2 (Pst1-3)
9. DT3 (Pst1-4)
10. 1kb ladder

Pst1-1, Pst1-2, and Pst1-3 did not cut DNAs. They seemed to be deactivated.

Genomic PCR

10*Buffer for KOD Plus	2mM dNTPs	25mM MgSO4	10μM primer-f	10μM primer-r	158ng/μL Genomic DNA	KOD plus	MilliQ	total
5	5	3	1.5	1.5	1	1	32	50

Electrophoresis

1. 1kb ladder
2. tatABCD (2.5kb)
3. TAMO reductase (2.7kb)
4. Negative control
We got bands of tatABCD but there were nonspecific amplification products.
We failed amplification of TAMO reductase.







Transformation
Constitutive promoter (BBa_J23107 , BBA_J23117)
High copy plasmid (pSB1AT3)

DNA	competent cell
1μL	10μL

February 17

PCR
We did PCR to amplify products of PCR that we had done yesterday but we could not amplify tatABCD.

Genomic PCR

Buffer	dNTPs	MgSO4	primer-f	primer-r	genomic DNA	KOD plus	MilliQ	total
2.5	2.5	5	0.75	0.75	0.5	0.5	16	50

Predenature 94℃, 2min
Denature 98℃, 10sec
Annealing 57℃, 30sec
Extension 68℃, 2.5min
(30cycles)

Electrophoresis

1. 1kb ladder
2. TAMO reductase
3. Negative control

Restriction

J23100	Spe1	Pst1	Buffer2	BSA	MilliQ	total
10	0.5	0.5	3	0.5	15.5	30

Genomic PCR

	Buffer	dNTPs	MgSO4	primer-f	primer-r	genomic DNA	KOD plus	MilliQ	total
TMAO reductase	2.5	2.5	3	0.75	0.75	0.5	0.5	15.5	25
tatABCD	2.5	2.5	2	0.75	0.75	0.5	0.5	15.5	25
tatABCD	2.5	2.5	2	0.75	0.75	5	0.5	10.5	25

Electrophoresis

1. 1kb ladder
2.3. TAMO reductase
4. tatABCD
5. tatABCD(10 times amount of genome)

Checking of restriction enzyme

DT	enzyme	Buffer	BSA	MilliQ	total
2	0.5	3	0.5	24	30

at 37℃ for overnight
We checked EcoR1 and Xba1.

February 18

Miniprep

	μg/mL	260/280	230/260
JS3117-1	135	1.5	2.06
JS3117-2	75	1.6	1.63
JS3109-1	115	1.5	1.88
JS3109-2	75	1.65	1.71
pSBIAT3-1	70	1.66	1.83
pSBIAT3-2	100	1.52	1.54

diluted to 25 times

Liquid culture
Competent cell
We put 3mL of preculture product on yesterday onto 300mL of LB medium

time	OD600
10:30	start
12:10	0.118
13:00	0.270
13:30	0.502

Transformation

pSB1AT3-2	competent cell	MilliQ	total
0	20	10	30
2	20	8	30
10	20	0	30

• Results(2/19)
  

number of colony 　0 177 590
Transformation efficiency 7.4x10^4 colonys/μg

February 20

Restriction
sample 1

DT plasmid	EcoR1	Xba1	Buffer	BSA	MilliQ	total
7.5	0.5	0.5	3	0.5	18	30

sample2

GFP plasmid	EcoR1	Spe1	Buffer	BSA	MilliQ	total
10	0.5	0.5	3	0.5	15.5	30

Electrophoresis

• sample1
  

a. sample1 2μL + MilliQ 3μL + 6×Loading Dye 1μL
b. sample1 5μL + 6×Loading Dye 1μL
lane_1 1kb ladder
lane_2 a
lane_3 b
lane_4 a
lane_5 b
lane_6 a
lane_7 b
lane_8 1kb ladder

• sample2
  

c. sample2 2μL + MilliQ 3μL + 6×Loading Dye 1μL
d. sample2 5μL + 6×Loading Dye 1μL
lane_1 1kb ladder
lane_2 c
lane_3 d
lane_4 1kb ladder

PCR

	Buffer	dNTPs	MgSO4	primer-f	primer-r	genomic DNA	KOD plus	MilliQ	total
tatABCD1	2.5	2.5	1.5	0.75	0.75	0.5	0.5	16	25
tatABCD2	2.5	2.5	1.5	0.75	0.75	0.5	0.5	16	25
TMAO reductase1	2.5	2.5	2	0.75	0.75	0.5	0.5	15.5	25
TMAO reductase2	2.5	2.5	2	0.75	0.75	5	0.5	10.5	25

Predenature 94℃ 2min
Denature 98℃ 10sec
Annealing 59℃ 30sec
Extension 68℃ 2.5min
→30cycles

	Buffer	dNTPs	MgSO4	primer-f	primer-r	PCR products	genomic DNA	KOD plus	MilliQ	total
tatABCD1	2.5	2.5	1.5	0.75	0.75	0	0.5	0.5	16	25
tatABCD2	2.5	2.5	1.5	0.75	0.75	1	0	0.5	15.5	25
TMAO reductase1	2.5	2.5	2	0.75	0.75	0	0	0.5	16	25
TMAO reductase2	2.5	2.5	2	0.75	0.75	0	0	0.5	16	25

Predenature 94℃ 2min
Denature 98℃ 10sec
Annealing 59℃ 30sec
Extension 68℃ 2.5min
→35cycles

Electrophoresis

lane_1.1kb ladder
lane_2.tatABCD
lane_3.tatABCD
lane_4.TAMO1
lane_5.TAMO2
lane_6.1kb ladder

lane_1.1kb ladder
lane_2.tatABCD1
lane_3.tatABCD2
lane_4.TAMO
lane_5.TAMO
lane_6.1kb ladder

February 21

PCR (Advantage HF protocol)

	buffer	dNTPs	primer-f	primer-r	gDNA	PCR products	DW	polymerase	total
tatABCD	2.5	2.5	0.75	0.75	1	0	17	0.5	25
TMAO	2.5	2.5	0.75	0.75	0	1	17	0.5	25

Predenature 94℃ 1min
Denature 94℃ 30sec
Annealing 58℃ 30sec
Extension 68℃ 3min
→25cycles

Electrophoresis
1. 1kb ladder 2μL
2. tatABCD 5μL + 6×Loading Buffer 1μL
3. TAMO 5μL + 6×Loading Buffer 1μL
4. 1kb ladder 2μL

Liquid culture
pSB3C5-1,2
pSB4K5-1,2

February 22

Gel extraction
lane 1 of the gel 45.0μg/mL

PCR purification
product 38.2μg/mL

PCR
TMAO reductase

	Buffer	dNTPs	MgSO4	prefix primer-f	suffix primer-r	product of gel extract	product of PCR purification(1ng/μL)	KOD plus	MilliQ	total
1	5	5	4	1.5	1.5	0.5	0	1	32.5	50
2	5	5	4	1.5	1.5	1	0	1	32.5	50
3	5	5	4	1.5	1.5	0	0.5	1	32.5	50
4	5	5	4	1.5	1.5	0	1	1	32.5	50

94℃, 2min
98℃, 10sec
59℃, 30sec
68℃, 3min
→25cycles

Electrophoresis

1. 1kb ladder
2. TAMO1
3. TAMO2
4. TAMO3
5. TAMO4
6. constructive promoter 1-18C
7. constructive promoter Spe1
8. constructive promoter Pst1
9. 1kb ladder
PCR

	Buffer	dNTPs	MgSO4	prefix primer-f	suffix primer-r	product of PCR purification(1ng/μL)	KOD plus	MilliQ	total
1	5	5	3	1.5	1.5	0.5	1	32.5	50
2	5	5	3	1.5	1.5	1	1	32	50
3	5	5	3	1.5	1.5	2	1	31	50
4	5	5	3	1.5	1.5	3	1	30	50
5	5	5	3	1.5	1.5	10	1	29	50
6	5	5	3	1.5	1.5	0	1	33	50

94℃, 2min
98℃, 10sec
59℃, 30sec
68℃, 3min
→25cycles

Electrophoresis

Checking Dpn1

Buffer	lacp(28.7ng/μL)	Dpn1	MilliQ	total
2	10	0.5	7.5	20
2	10	0	5	17

February 23

Colony PCR
tatABCD(2 samples)

Buffer	dNTPs	MgSO4	primer-f	primer-r	KOD plus	MilliQ	total
5	5	3	1.5	1.5	1	33	50

Predenature 94℃ 1min
Denature 98℃ 10sec
Annealing 59℃ 30sec
Extension 68℃ 3min
→25cycles

Electrophoresis

1. 1kb ladder 2μL
2. tatABCD 1 5μL + 6×Loading Buffer 1μL
3. tatABCD 2 5μL + 6×Loading Buffer 1μL
4. 1kb ladder 2μL

Miniprep
pSB4K5 and pSB3C5
deluted it to 25 times and then measured it
pSB4K5 1 : 60.0 μg/ml 1.67(260/280) 1.98(260/230)
pSB4K5 2 : 55.0 μg/ml 1.49(260/280) 1.62(260/230)
pSB3C5-3 : 3.6 μg/ml 1.57(260/280) 3.00(260/230)
pSB3C5-4 : 1.3 μg/ml 1.44(260/280) 1.04(260/230)

Liquid culture
pSB3C5-3,4

Electrophoresis

1. 1kb ladder 2μL
2. pSB3C5-3 5μL, 6×loading dye 1μL
3. pSB3C5-4 5μL, 6×loading dye 1μL
4. 1kb ladder 2μL

February 27

Test of Dpn1

Buffer2	GFP2	BSA	MilliQ	Dpn1
3	3	0.3	23	1

Colony PCR

	buffer	dNTPs	MgSO4	Primer-f	Primer-r	MilliQ	KOD Plus	total
Colony PCR(2 samples)	5	5	3	1.5	1.5	33	1	50
Negative control	5	5	3	1.5	1.5	34	0	50

Predenature 94℃,2min
Denature 98℃,10sec
Annealing 59℃,30sec
Extension 68℃,3min
→25cycles

Electrophoresis

	sample	Loading Dye	MilliQ
1.1kb ladder	2	0	0
2.product of PCR1	5	1	0
3.product of PCR2	5	1	0
4.product of PCR(Negative control)	5	1	0
5.product of PCR(2/23)	5	1	0
6.GFP2(DPN1)	10	2	0
7.GFP2	3	2	7
8.1kb ladder	2	0	0

Results of liquid culture
We measure this after dilute it to 10 times.

pSB3C5-5	pSB3C5-6	pSB3C5-5(1% glucose)	pSB3C5-6(1% glucose)
8.5[µg/ml]	-1.8	-17.9	-18.2

PCR

	buffer	dNTPs	MgSO4	Primer-f(prefix)	Primer-r(suffix)	PCR purification product(1ng/µL)	MilliQ	KOD Plus	total
1	5	5	3	1.5	1.5	0.2	32.8	1	50
2	5	5	3	1.5	1.5	0.5	32.5	1	50

• PCR purification product was that purification product(75ng/µL) of electrophoresis-3 deluted to 1ng/µL
  

Predenature 94℃,2min
Denature 98℃,10sec
Annealing 59℃,30sec
Extension 68℃,3min
→25cycles

February 28

Electrophoresis
1. 1kb ladder
2. PCR1 →Product of gel extraction : tatABCD with prefix and suffix 105[ng/µL]
3. PCR2

Restriction

Buffer2	plasmid(?)	enzyme	MilliQ	total
2	2	0.2	15.8	20

incubate 1 hour at 37℃

Electrophoresis
1. 1kb ladder
2. Control (without enzymes)
3. EcoR1
4. Xba1 (crystallized)
5. Xba1 (with seal)
6. Spe1
7. Pst1
8. 1kb ladder

PCR and Electrophoresis

Quick Taq Dye Mix	primer-f	primer-r	template	MilliQ	total
25	1.0	1.0	0.5	22.5	50

Predenature 94℃,2min
Denature 94℃,30sec
Annealing 59℃,30sec
Extension 68℃,3min
→25cycles

Restriction

BufferH	tatABCD	EcoR1	Spe1	MilliQ	total
2	5	0.2	0.2	12.6	20

PCR purification
We eluted the product for 30µL MilliQ

Ligation

Insert(tatABCD)	Vector(pSB1C3)	Ligation High	total
10	1	5	16

4℃, overnight

February 29

Transformation

tatABCD	competent cell	total
1	10	11

Checking Restriction enzyme

plasmid seems to be 1-18C promoter	Enzyme	Buffer	MilliQ	total
2	0.2	2	15.8	20

Checking tatABCD

tatABCD	Hind3	Buffer	MilliQ	total
5	0.2	2	12.8	20

PCR

	buffer	dNTPs	MgSO4	Primer-f	Primer-r	ColE1(6.5ng/µL) / TMAO	MilliQ	KOD Plus Neo	total
Kil	2.5	2.5	1.5	0.75	0.75	0.5	16	0.5	25
TMAO	2.5	2.5	1.5	0.75	0.75	0.5	16	0.5	25

Predenature 94℃,2min
Denature 98℃,10sec
Annealing 60℃,30sec
Extension 68℃,3min
→30cycles

Electrophoresis
1. 1kb ladder
2. Kil (649bp)
3. TMAO (2720bp)
4. TMAO (Quick Taq)
5. tatABCD (Quick Taq)
6. tatABCD (Hind3)
7. 1kb ladder

March 1

PCR

• TMAO
  

Template is gDNA and product of colony PCR gel extraction

	Buffer	gNTPs	MgSO4	Primer-f	Primer-r	KOD Plus Neo	Template gDNA	product of gel extraction	DW	total
1	2.5	2.5	1.5	0.75	0.75	0.5	0.5	0	16	25
2	2.5	2.5	1.5	0.75	0.75	0.5	0	2	14.5	25

94℃, 2min
98℃, 10sec
60℃, 30sec
68℃, 1.5min
→25cycles

• Kil

Buffer	dNTPs	MgSO4	primer-f	primer-r	colE1(6.5ng/µL)	KOD Plus Neo	MilliQ	total
2.5	2.5	1.5	0.75	0.75	0.5	16	0.5	25

94℃, 2min
98℃, 10sec
61℃, 30sec
68℃, 1min
→20cycles

Electrophoresis
1. 1kb ladder
2. TMAO1 (gDNA)
3. TMAO2 (product of gel extraction)
4. Kil

PCR

Buffer	dNTPs	MgSO4	primer-f	primer-r	Product of Purification	KOD Plus Neo	MilliQ	total
5	5	3	1.5	1.5	1	32	1	50

94℃, 2min
98℃, 10sec
61℃, 30sec
68℃, 30sec
20cycles
→Purification 230ng/µL

Restriction

Kil	EcoR1	Spe1	BufferH	MilliQ	total
5	0.2	0.2	2	12.6	20

incubate at 37℃, for 1.5 hours

PCR Purification

Ligation

Kil	pSB1C3	Ligation High	total
5	1	3	9

at 4℃, for overnight

March 2

Ligation

Kil	pSB1C3	Ligation High Ver.2	total
5	1	3	9

tatABCD	pSB1C3	Ligation	total
10	1	5	16

at 16℃ for 1 hour

Transformation

Kil	Kil(3/1,Ligation)	tatABCD	competet cell	total
1	0	0	10	11
0	1	0	10	11
0	0	1	10	11

PCR

Quick Taq	primer-r	primer-f	template	MilliQ	total
25	1	1	0.5	22.5	50

Electrophoresis (27)

Restriction

pSB3C5-5	EcoR1	Pst1	BufferH	BSA	MilliQ	total
20	0.5	0.5	3	0.5	5.5	30

at 37℃, for 2 hour

Electrophoresis
1. 1kb ladder 2µL
2. pSB3C5 5µL + 6×Loading Buffer 1µL
・product of gel extraction(about 2700bp)
－30.9µg/mL

Restriction
GFP1,2,3

GFP	EcoR1	Pst1	Buffer	BSA	MilliQ	total
10	0.5	0.5	3	0.5	15.5	30

at 37℃, for 2.5 hours

Restriction

DT	EcoR1	Xba1	BufferM	BSA	MilliQ	total
10	0.2	0.2	3	0.3	16.3	30

Constitutive Promoter	Spe1	Pst1	BufferM	BSA	MilliQ	total
15	0.2	0.2	3	0.3	11.3	30

at 37℃, 2 hours

• J23117-1:135ng/µL, J23107-1:115ng/µL
  
• DT3→PCR Purification
  
• Promoter→Gel Extraction
  
  

Checking TMAO

something seems to be TMAO	Buffer2	EcoR1	MilliQ	total
10	2	0.5	7.5	20

at 37℃, for 1 hour

Electrophoresis
1. 1kb ladder
2. GFP1 that had been cut by restriction enzyme
3. GFP2 that had been cut by restriction enzyme
4. GFP3 that had been cut by restriction enzyme
5. GFP1
6. GFP2
7. GFP3
8. TMAO (control)
9. TMAO (EcoR1)
10. DT (control)
11. DT (EcoR1, Xba1)
12. 1kb ladder

Checking tatABCD

Quick Taq	primer-f	primer-r	MilliQ	total
25	1	1	23	50

Electrophoresis
(28)

March 3

PCR

	template	buffer	dNTPs	MgSO4	VF	VR	KOD plus	MilliQ	total
1	1	5	5	3	1.5	1.5	1	32	50
2	2	5	5	3	1.5	1.5	1	31	50

94℃, 2min
98℃, 10sec
50℃, 30sec
68℃, 1min
→30cycles

Miniprep

March 4

Sequence of tatABCD

Quick Taq	primer-f	promer-r sequence	template	MilliQ	total
25	1	1	1	23	50

Quick Taq	primer-f sequence	primer-r	template	MilliQ	total
25	1	1	1	23	50

Colony PCR of TMAO

buffer	dNTPs	NgSO4	primer-f	primerr-r	KOD plus	MilliQ	total
5	5	4	1.5	1.5	1	32	50

→ethanol precipitation

94℃, 2min
94℃, 30sec
55℃, 30sec
68℃, 2.5min
→25cycles

Electrophoresis

1. 1kb ladder
2. tatABCD1
3. tatABCD2
4. TMAO
5. 1kb ladder

Restriction

TMAO	EcoR1	BufferH	BSA	MilliQ	total
10	0.2	3	0.3	16.5	30

TMAO	Xba1	Pst1	BudderM	BSA	MilliQ	total
10	0.2	0.2	3	0.3	16.3	30

at 37℃ for 1 hour

Electrophoresis

Transformation

pSB1C3	competent cell(made at 2/8)	total
5	100	105

March 5

Restriction

pSB1C3(Xba1, Spe1)	Pst1	BufferH	BSA	MilliQ	total
10	0.2	2	0.2	7.6	20
pSB1C3(Xba1, Spe1)	EcoR1	BufferH	BSA	MilliQ	total
10	0.2	2	0.2	7.6	20

at 37℃ for 1 hour
→Then we did ethanol precipitation

Ligation

Kil(EcoR1, Spe1)	pSB1C3(EcoR1)	Ligation High	total
5	1	3	9

at 16℃ for 1 hour

Transformation

Kil	competent cell	total
1	10	11

We used commercially available competent cells in this time.

PCR

TMAO

buffer	dNTPs	MgSO4	Primer-f	Primer-r	Template	KOD plus	MilliQ	total
5	5	3	1.5	1.5	1	1	32	50

Electrophoresis

(31)

Restriction

	Lacp	pSB3C5	EcoR1	Pst1	BufferH	BSA	MilliQ	total
1	20	0	0.5	0.5	3	0.5	5.5	30
2	0	20	0.5	0.5	3	0.5	5.5	30

at 37℃ for 1 hour
1→Ethanol precipitation　45.4µg/mL
2→Gel extraction　38.7µg/mL

Ligation

LacP	pSB3C5	Ligation High	total
10	2	6	18

at 4℃ for overnight

Transformation

Lacp+pSB3C5	competent cell	total
1	10	11

on ice for 30 mins.
heat shock at 42℃ for 60secs
on ice for 2 mins.
After we incubate with 200µL of SOC culture for 1 hour, we did plating on LB culture with CP

Restriction

GFP Plasmid	EcoR1	Spe1	Buffer2	BSA	MilliQ	total
10	0.5	0.5	3	0.5	15.5	30

at 37℃ for 2 hours

Electrophoresis

1. Ladder 2µL
2. GFP Plasmid (already restricted) 2µL + Loading Dye 2µL + MilliQ 8µL
3. Ladder 2µL

PCR

torA signal and pspA pspAはコロニーPCR

Buffer	dNTPs	MgSO4	Primer-f	Primer-r	template(TMAO)	KOD plus	MilliQ	total
2.5	2.5	1.5	0.75	0.75	0.5	0.5	16	25

94℃, 2min
98℃, 10sec
60℃, 30sec
68℃, 30sec

electrophoresis

1. 100bp Ladder
2. torA signal (272bp)
3. pspA (969bp)
4. 100bp Ladder

March 6

Restriction

GFP	EcoR1	Spe1	BufferM	BSA	MilliQ	total
12	0.5	0.5	3	0.5	13.5	30

We did incubate at 37℃ for 1.5hours.
And we did gel extraction on 3/7 and get 40.0μg/mL GFP.

PCR

buffer	dNTPs	MgSO4	Primer-f	Primer-r	template	KOD plus neo	MilliQ	total
5	5	3	1.5	1.5	0.5	1	32.5	50

94℃　2min
98℃　10sec
60℃　30sec
68℃　(torA 10sec / pspA 30sec) 25 cycles
We used product of PCR on 3/5 of torA and pspA as template.

Restriction

Kil	EcoR1	Spe1	BufferM	BSA	MilliQ	total
10	0.3	0.3	3	0.3	16.1	30

DT	EcoR1	Xba1	Buffer2	BSA	MilliQ	total
10	0.5	0.5	3	0.5	15.5	30

at 37℃ for 2 hours
→ purification 37.7ng/μL

Ligation

Kil	pSB1C3	Ligation High Ver.2	total
4	2	3	9

• Kil : 350fmol
  
• pSB1C3 : 29fmol
  

at 16℃ for overnight

March 7

Electrophoresis

1. 1kb ladder 2µL
2. pspA (PCR product)2.5µL + Loading Dye 0.5µL
3. GFP 30µL + Loading Dye 6µL
4. 1kb ladder 2µL

• The GFP was gel extracted on 3/6 and concentrated by Vacuum in 150µg/mL
  
  

Ligation

VectorDNA	GFP	Ligation High Ver.2	total
5	15	10	30

Restriction

torA	EcoR1	Spe1	bufferM	BSA	MilliQ	total
10	0.3	0.3	3	0.3	16.1	30

pspA	EcoR1	Spe1	bufferM	BSA	MilliQ	total
5	0.3	0.3	3	0.3	21.1	30

at 37℃ for 1.5 hours

Purification

torA→31.8ng/µL
pspA→49.3ng/µL

Ligation

torA	pSB1C3	Ligation High Ver.2	total
3	3	3	9

pspA	pSB1C3	Ligation High Ver.2	total
4	2	3	9

at 4℃, for overnight

• torA→31.8ng/µL×3µL=95.4ng=0.529pmol
  
• pSB1C3→19.4ng/µL×3µL=58.2ng=0.042pmol
  
• pspA→49.3ng/µL×4µL=197.2ng=0.308pmol
  
• pSB1C3→19.4ng/µL×2µL=38.8ng=0.029pmol
  

March 8

Restriction

pSB4K5	EcoR1	Spe1	BufferM	BSA	MilliQ	total
20	0.2	0.2	3	0.2	6.4	30

at 37℃ for 1 hour.
→Purification : 36.6ng/µL

Ligation

Kil	pSB4K5	Ligation High Ver.2	total
10	1	5	16

at 4℃ for overnight

• Kil→37.7ng/µL×10µL=377ng=879fmol
  
• pSB4K5→36.6ng/µL×1µL=36.6ng=86fmol
  
  

Liquid culture

Lacp + pSB3C5 -1, 2

Transformation

torA	pspA	competent cell	total
1	0	10	11
0	1	10	11

We use commercially available competent cells in this time.

March 9

Restriction

tatABCD	Xba1	Pst1	BufferM	BSA	MilliQ	total
10	0.2	0.2	3	0.3	16.3	30

at 37℃ for 1hour
→purification : 75.0μg/mL (1.11 260/280 , 0.81 260/230)

Miniprep

lacP + pSB3C5 1 80.5μg/mL (1.78 260/280 , 2.00 260/230)
lacP + pSB3C5 2 107.2μg/mL (1.83 260/280 , 1.90 260/230)

Colony PCR

Quick Taq	VF	VR	MilliQ	total
25	1	1	23	50

94℃ 2min
94℃ 30sec
55℃ 30sec
68℃ 6sec
25cycles

Ligation

tatABCD	constP J23107	Ligation High Ver.2	total
5	1	3	9

tatABCD : 227fmol
constP J23107 : 21fmol

Transformation

	pspA	torA	Kil	competent cell
1	1	0	0	10
2	0	1	0	10
3	0	0	1	10

Miniprep

4mL of plusgrow which had been cultured for overnight.
pSB4K5 : 80.5μg/mL

March 10

Screening PCR

Quick Taq	VF	VR	MilliQ	total
25	1	1	23	50

Then we did electrophoresis to confirm.
1.1kb ladder
2.kil (649bp)
3,4,5, pspA (969bp)
6,1kb ladder

1, 100bp ladder
2,3,4, torA signal

Restriction

LacP-pSB3C5	Spe1	Pst1	BufferM	BSA	MilliQ	total
10	0.2	0.2	2	0.2	7.4	20

for 2.5 hours at 37℃
→purification 29.0ng/μL

torA	Xba1	Pst1	BufferM	BSA	MilliQ	total
10	0.2	0.2	2	0.2	7.4	20

for 2.5 hours at 37℃
→purification 91.8ng/μL

Ligation

torA	Lacp-pSB3C5	Ligation High Ver.2	total
4	2	3	9

torA : 929fmol
Lacp-pSB3C5 : 284fmol
for overnight at 4℃

March 11

Miniprep

We used 3μL of plus grow that we had cultured for overnight.
torA : 62.8ng/μL

Screening PCR

Quick Taq	VF	VR	MilliQ	total
25	1	1	23	50

Electrophoresis

1. 1kb ladder
2〜11. pspA (969bp)
12. 1kb ladder

The results were shown as photograph in the right.

It seemed that there were shorter sample than expected sample, so we did electrophoresis with pspA which was product of PCR and pspA which had already cut with EcoR1 and Spe1.

1.1kb ladder
2. pspA (PCR product)
3, pspA (Eco, Spe)
4〜6, pspA (colony PCR)
7,1kb ladder

The results were shown as photograph in the right.

March 12

Transformation

DT(1ng/μL)	DT(0.1ng/μL)	Kil	lacP-torA	MilliQ	competent cell	total
1	0	0	0	0	20	21
0	1	0	0	0	20	21
0	0	5	0	0	50	51
0	0	0	5	0	50	51
0	0	0	0	1	20	21

Restriction

pspA	EcoR1	Spe1	BufferM	BSA	MilliQ	total
10	0.5	0.5	3	0.3	15.7	30

at 37℃ for 4 hours
→ We did purification and got 48.3ng/μL pspA.

Ligation

pspA	pSB1C3	MilliQ	Ligation High Ver.2	total
4	2	0	3	9
2	2	0	2	6
0	2	2	2	6

March 13

Miniprep

pSB1C3 74.2µg/mL 1.65 (260/280) 1.31 (260/230)

March 14

Restriction

pSB1C3	EcoR1	Spe1	BufferM	BSA	MilliQ	total
20	0.2	0.2	4	0.4	15.2	40

We did gel extraction and got 47.2ng/µL pSB1C3 but we did not cut out RFP.

Ligation

torA	pSB1C3	Ligation High Ver.2	total
4	2	3	9
MilliQ	pSB1C3	Ligation High Ver.2	total
4	2	3	9

at 16℃, for 1 hour

• torA : 0.707pmol
  
• pSB1C3 : 0.068pmol
  
  

Liquid culture

We cultured Lacp-pSB3C5 1,2,3,4,5 (CP tolerance)on culture with Amp.
→Only 4 which did not be cultured succeeded.

March 15

Liquid culture

We cultured Lacp-pSB3C5 6,7,8,9,10 on culture with ampicillin.
→6,8,9,10 were succeeded.

Restriction

GFP	EcoR1	Spe1	Buffer2	BSA	MilliQ	total
10	0.5	0.5	3	0.5	15.5	30

DT	EcoR1	Xba1	Buffer2	BSA	MilliQ	total
10	0.5	0.5	3	0.5	15.5	30

for 2 hours at 37℃.

Miniprep

pspA (pSB1C3) 40.5ng/µL

Ligation

pspA	DT	Ligation High Ver.2	total
5	1.5	3	9.5

• pspA : 385fmol
  
• DT : 36fmol
  
  

Transformation

J23107-tatABCD	DT (0.1ng/µL)	DT (0.01ng/µL)	pspA-DT	competent cells on 3/15	total
2	0	0	0	20	22
0	2	0	0	20	22
0	0	2	0	20	22
0	0	0	2	20	22

Screening PCR

Kil, pspA and torA

Quick Taq	Primer-r	Primer-f	MilliQ	total
25	1	1	23	50

March 16

Miniprep

torA (pSB1C3) 68.8ng/µL
Kil (pSB4K5) 92.7ng/µL
torA was red for some reason. We do not know why.

Colony PCR

Quick Taq	Primer-r	Primer-f	MilliQ	total
25	1	1	23	50

94℃, 2min
94℃, 30sec
55℃, 30sec
68℃, 6sec
→25cycles

Electrophoresis

The results were shown as photograph in the right.

Checking Transformation Efficiency

competent cells that were made on March 15.
DNA : 0.02ng → 668 colonies Transformation Efficiency : 3.3×10^7
DNA : 0.2ng → 1739 colonies Transformation Efficiency : 8.7×10^6

Restriction

pSB1C3	EcoR1	Spe1	BSA	BufferM	BufferH	MilliQ	total
20	0.2	0.2	0.3	3	0	6.3	30
5	0.2	0	0.2	0	2	12.6	20

at 37℃, for 2 hours.
We did gel extraction for product with EcoR1, Spe1. We got 46.1ng/µL pSB1C3.

Kil(pSB4K5)	EcoR1	Pst1	BSA	BufferH	MilliQ	total
5	0.2	0.2	0.2	2	12.4	20
5	0.2	0	0.2	2	12.6	20

for overnight at 37℃.
We did this to confirm.

pspA (pSB1C3)	EcoR1	Pst1	BSA	BufferH	MilliQ	total
5	0.2	0.2	0.2	2	12.4	20
5	0.2	0	0.2	2	12.6	20

for overnight at 37℃.
We did this to confirm.

Ligation

torA	pSB1C3	Ligation High Ver.2	total
4	2	3	9

MilliQ	pSB1C3	Ligation High Ver.2	total
4	2	3	9

at 16℃, for overnight

• torA→767fmol
  
• pSB1C3→68fmol
  

March 17

Miniprep

J23107-tatABCD 72.7ng/µL
pspA-DT 50.5ng/µL

Checking the Insert

J21037-tatABCD	EcoR1	Pst1	BSA	BufferH	MilliQ	total
5	0.2	0.2	0.2	2	12.4	20
5	0.2	0	0.2	2	12.6	20

Success.

pspA-DT	EcoR1	Pst1	BSA	BufferH	MilliQ	total
5	0.2	0.2	0.2	2	12.4	20
5	0.2	0	0.2	2	12.6	20

Failed.

March 19

Restriction

DT	EcoR1	Xba1	BSA	BufferM	MilliQ	total
10	0.2	0.2	0.3	3	16.3	30

We did Gel extraction and got 17.2ng/µL of DT.

Ligation

Kil	DT	Ligation High Ver.2	total
10	2	6	18

We did this for an hour at 16℃.

Restriction

GFP	EcoR1	Spe1	BSA	BufferM	MilliQ	total
10	0.5	0.5	0.5	3	15.5	30

We did this for 4 hours at 37℃

Ligation

pspA	DT	Ligation High Ver.2	total
5	5	5	15

pspA	pSB1C3	Ligation High Ver.2	total
4	1	3	8

We did these for an hour at 16℃.

• pspA (5µL)→377fmol
  
• DT→39fmol
  
• pspA (4µL)→339fmol
  
• pSB1C3→34fmol
  
  

Transformation

pspA-DT, pspA (pSB1C3), torA (pSB1C3) and GFP-DT

March 20

Screaning PCR

Quick Taq	Primer-R	Primer-F	MilliQ	total
25	1	1	23	50

• pspA→○
  
• pspA-DT→○
  
• GFP-DT→○
  
• torA→×
  
• Kil-DT 6 of 8 sumples→○
  

Quick Taq	VR	VF	MilliQ	total
25	1	1	23	50

• pspA→○
  
• pspA-DT→×
  
  

Restriction

torA	EcoR1	Spe1	BSA	BufferM	MilliQ	total
10	0.3	0.3	0.3	3	16.1	30

DT	EcoR1	Xba1	BSA	BufferM	MilliQ	total
10	0.2	0.2	0.3	3	16.3	30

We did this for overnight at 37℃. And we did purification.
torA 34.2ng/µL
DT 28.0ng/µL

March 21

Miniprep

GFP-DT-1 : 77.7ng/µL
GFP-DT-2 : 67.6ng/µL

Restriction

pSB1C3	EcoR1	Spe1	BSA	BufferM	MilliQ	total
10	0.2	0.2	0.3	3	16.3	30
5	0.2	0	0.2	2	12.6	20

We did this for 3 hours at 37℃, and then we did gel extraction. We got 25.1ng/µL pSB1C3

GFP-DT	EcoR1	Pst1	Xba1	BSA	BufferM	MilliQ	total
5	0.2	0.2	0	0.2	2	12.4	20
5	0.2	0	0	0.2	2	12.6	20
10	0.2	0	0.2	0.3	3	16.3	30

We did this for 3 hours at 37℃, and then we did Purification. We got 30.7ng/µL GFP-DT.

Ligation

	torA	pSB1C3	pspA	DT	GFP-DT	Ligation High Ver.2	total
1	4	1	0	0	0	3	8
2	0	1	7	0	0	4	12
3	0	0	5	3	0	4	12
4	3	0	0	0	5	4	12

We did this for an hour at16℃.

March 22

PCR

We did PCR to amplify torA_signal that was product of PCR at March 5 with redesigned primers.

Buffer	dNTPs	MgSO4	Primer-F	Primer-R	Template	MilliQ	KOD plus neo	total
5	5	3	1.5	1.5	0.5	32.5	1	50

94℃, 2min
98℃, 10sec
60℃, 30sec
68℃, 10sec
→30cycles
→Purification 110.7ng/µL

Restriction

torA	EcoR1	Spe1	BSA	BufferM	MilliQ	total
10	0.2	0.2	0.3	3	16.3	30

Ligation

	torA	pSSB1C3	pspA	DT	GFP-DT	Ligation high	total
1	4	3	0	0	0	4	11
2	3	0	0	0	3	3	9
3	0	0	5	5	0	5	15

• torA (4µL)→512fmol
  
• pSB1C3→54fmol
  
• torA (3µL)→384fmol
  
• GFP-DT→36fmol
  
• pspA→377fmol
  
• DT→65fmol
  
  

March 23

Screening PCR

torA (pSB1C3), torA-GFP-DT and pspA-DT

Quick Taq	VF	VR	MilliQ	total
25	1	1	23	50

E.coli in liquid culture that had pspA(pSB1C3) also expressed RFP.

Restriction

pspA	EcoR1	Spe1	BufferM	BSA	MilliQ	total
5	0.3	0.3	3	0.3	21.1	30

And then we did ethanol precipitation

Ethanol precipitation

pspA 11.5ng/µL.

Miniprep

Lacp+pSB3C5-8 77.9µg/mL
Lacp+pSB3C5-10 69.0µg/mL
Kil+DT-4 58.0µg/mL
Kil+DT-7 15.2µg/mL

Restriction

Lacp+pSB3C5-8	Spe1	Pst1	Buffer2	BSA	MilliQ	total
20	0.5	0.5	3	0.5	5.5	30

Kil+DT-4	Xba1	Pst1	Buffer2	BSA	MilliQ	total
20	0.5	0.5	3	0.5	5.5	30

at 37℃ for 1.5 hours
And then we did Gel extraction.

Gel Extraction

Lacp+pSB3C5-8 40.4µg/mL
Kil+DT-4 26.8µg/mL

March 26

Miniprep

torA(pSB1C3) 18.5[ng/µL]
torA-GFP-DT 20.0[ng/µL]

Restriction

torA(pSB1C3)	EcoR1	Pst1	BufferH	BSA	MilliQ	total
5	0.2	0.2	2	0.2	12.4	20
5	0.2	0	2	0.2	12.6	20

torA-GFP-DT	EcoR1	Xba1	Pst1	BufferH	BufferM	BSA	MilliQ	total
5	0.2	0	0.2	2	0	0.2	12.4	20
5	0.2	0	0	2	0	0.2	12.6	20
20	0	0.2	0.2	0	3	0.3	6.3	30

We did Gel extraction and then got ??? 28.7[ng/µL]

Ligation

Lacp (pSB3C5)	torA-GFP-DT	Ligation High Ver.2	total
1	5	3	9

• Lacp : 22fmol
  
• torA-GFP-DT : 197fmol
  

pspA	pSB1C3	Ligation High Ver.2	total
10	1	5	16

pspA	DT	Ligation High Ver.2	total
10	1	5	16

• pspA : 180fmol
  
• pSB1C3 : 18fmol
  
• DT : 16fmol
  

LacP(pSB3C5)	Kil-DT	Ligation High Ver.2	total
1	5	3	9

for 2 hours at 16℃

Transformation

Lacp-Kil-DT	competent cell	total
1	10	11

March 27

Miniprep

We retryed miniprep of torA(pSB1C3).
We got torA and its concentration was 39.3[ng/µL].

Transformation

Name	Well	Sample	Competent Cells	Total	Plate	Colony
BBa_K117004	14J(2011 plate2)	5	20	?	?	?

We added 100[µL] of culture medium before we started culturing the E.coli.

Screening PCR

Quick Taq	VF2	VR	MilliQ	Total
25	1	1	23	50

Lacp-torA-GFP-DT 1, 3, 5, 6, 8, 9 was successful.
pspA-DT was failed.
E.coli that had pspA(pSB1C3) did not make any colony.
Lacp-Kil-DT 1,2,3,4,5,6,7,8 was failed.

Liquid culture

Lacp-torA-GFP-DT