Team:HokkaidoU Japan/Notebook/Week 1

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Contents

July 2nd

On your mark...

July 3rd

Get set...

July 4th

Transformation
Transformation of BBa_B0015(dT), B0034(RBS), I179005(pT7), K346007(Ag43), and K542009(pLacI-RBS-Ag43) in DH5α
  1. Added each DNA solutions (1ul) into DH5α comeptent cell and standed on ice in 30 min.
  2. Cultivated on LBA(dt,RBS,T7) and LBC(Ag43, pLacI-RBS-Ag43). E.coli cultivate in LBC was pre-cultivated in 2 hrs. pT7 was 21hrs and Others were 20hrs cultivated

July 5th

Transformation
K346007(Ag43) was failed to cultivate on LBC plate. Transformation of K346007(Ag43) in DH5α.
  1. Add DNA solution(1ul) into DH5α comeptent cell and stand on ice in 30 min.
  2. Pre-cultivated in 2hrs.
  3. Cultivated on LBC in 21hrs.
Single colony isolation
Single colony isolation of BBa_B0015, B0034, I179005 and K542009.
  1. Picked up one colony.
  2. Cultivation on LBA(dt,RBS,T7) and LBC(pLacI-RBS-Ag43) in 14hrs30mins
BBa_K542009 was Ag43 only part! And the part didn't have Biobrick suffix.

July 6th

Liquid culture
Liquid culture in LBA(dT,RBS,pT7) and LBC(pLacI-RBS-Ag43)
  1. Picked up two colonies from each plates.
  2. One colony was dipped in 1ml LB (A or C), and other colony was dipped in 2ml LB(A or C). 1ml is for glycerol stocks and 2ml is for mini-prep.
  3. 16hrs Cultivation

Single colony isolation
  1. Single colony isolation of K346007(Ag43).

July 7th

Liquid culture
Liquid culture in LBC(Ag43).
  1. Picked up two colonies from each plates.
  2. Both of colonies were dipped in 2ml LBC, and then we cultivate them in 38℃.
However, one of them cultivated only 8 hours. It's for glycerol stock.
3A assembly!
Assembled pT7, RBS and pSB1C3 by 3A assembly. This 3A assembly is our first try!
mini-prep
  1. mini-prep of dT,RBS,pT7 and pLacI-RBS-Ag43.
  2. Elution in 50ul buffer

Glycerol stock
Made glycerol stocks of dT,RBS,pT7 and pLacI-RBS-Ag43.
  1. Parts written above were cultivated in LBA(dT,RBS,pT7) and LBC(pLacI-RBS-Ag43) 1ml in 16hrs 30min.
  2. Add glycerol and Freeze at -80C

Electrophoresis
Electrophoresis to predict concentration of mini-prep products(dT,RBS,pT7 and pLacI-RBS-Ag43).
  1. Used 1% agarose gel.
  2. Pre-migration.
  3. Migrated 1.2ul of DNA solutions (1ul is mini-prep products and 0.2ul is Loading Dye) in 35min.
  4. Took a photograph of 1% agarose gel that finished electrophoresis.
Erectrophoresis result


Digestion


Digestion of I719005, B0034 and pSB1K3

Digestion recipe

All parts were reacted in 30ul solution.

  • I719005(40ng/ul)
DNA solution 12.5ul
EcoRI 1ul
SpeI 1ul
10xH Buffer 3ul
DW 12.5ul


  • B0034(40ng/ul)
DNA solution 12.5ul
XbaI 1ul
PstI 1ul
10xM Buffer 3ul
DW 12.5ul


  • pSB1K3(25ng/ul)
DNA solution 12ul
EcoRI 1ul
PstI 1ul
10xH Buffer 3ul
DW 13ul


Ethanol precipitation

For rising concentration of DNA solution which use for Ligation and removing restriction enzyme.

  1. Added 3ul of NaoAc, 1.5ul of glycogen and 75ul of 100% ethanol.
  2. Centrifuged in 14000rpm, 30min at 4C.
  3. Remove supernatant and added 220ul of 70% ethanol.
  4. Centrifuged in 15000rpm, 15min at 4C.
  5. Remove supernatant and air drying in room temperature then added 10ul of DW.


Ligation

All DNA solutions were digested. 3A assembly protocol required Ligation reaction should be in total 25ul solution.

Ligation Mighty Mix 12.5ul
pT7 2ul
RBS 2ul
pSB1K3 2ul
DW 6.5ul
Total 25ul

Ligation reaction recipe was written below.

Degree Minute
16 30
65 10
4 Hold


ligation was finished. But now pm10:00. 2.5hrs needs for doing transformation. Transformation would finish at am:0:30.

Withdraw!!!!

July 8th

  • (pT7 + RBS)
Transformation
Transformation for pT7+RBS+pSB1K3
  1. Added DNA soltions (Ligation products) 1ul to DH5α compitent cell.
  2. Stood on ice in 30min.
  3. Added 600ul of LB to transformed DH5α solution.
  4. Pre-cultivate in 2hrs
  5. Splead 300ul of LB&DH5α solution to LBK.
  6. Cultivated

  • K346007(Ag43)
mini-prep
mini-prep for Liquid culture product of K346007(Ag43)
  1. Used FastGene Plasmid Mini Kit(Nippon Genetics)
  2. Elutioned in 50ul
  3. First we eluted in colection tube. then moved in Eppendorf tube.
Erectrophoresis
Erectrophoresis for mini-prep product(Ag43).
  1. Prepared 1% Agalose gel and added EtBr then pre-migration in 30min.
  2. 1ul 1kb ladder, 1.2ul mini-prep product(1ul is DNA solution and 0.2ul is loading dye) added then migtrated
mini-prep result (With ligation result of pT7+RBS+pSB1K3) HokkaidoU2012 120708 K346007 miniprep and pt7 rbs.jpg
Glycerol stock
Made glycerol stock of K346007 (Ag43).
  1. Parts written above were cultivated in LBC.
  2. Added glycerol and Freezed at -80C
  • (Ag43 + dT)
Assembling K346007(Ag43) + B0015(dT) with 2-piece assembly(Biobrisk standard assembly)
Digestion
Digested Ag43 and dT in solution by recipes Written below. Insert DNA required too much weight and volume(volume was calculated from concentration of DNA mini-prep product)from our calculation. There are no insurance of succession of digestion.
  • Ag43(Insert)
5190bp(Ag43 + pSB1C3) DW
DNA solution 48ul
EcoRI 1ul
SpeI 1ul
10xH buffer 6ul
4ul
Total 60ul


  • dT(Vector)

3318bp(Ag43 + pSB1AK3)

DNA solution 8ul
EcoRI 1ul
XbaI 1ul
10xM buffer 2ul
DW 8ul
Total 20ul


Digestion result image


HokkaidoU2012 120708 dt K346007 digestion umeuchi.jpg


K346007(Ag43) was 5190bp before digestion (Biobrick prefix + Ag43 + Biobrick suffix + pSB1C3). After digestion, Ag43 and pSB1C3 was separated and became fragments about 3120bp(Ag43) and 2070bp(pSB1C3). Gel image above shows there are two fragments, one fragment is about 2000bp other fragment is 3000bp. Digestion would be succeeded. About Vector(Boo15:dT), the DNA was circular so DNA migrated more far than Linear DNA. d+ (Circular DNA) migrated little more far than d- (Linear DNA). so we think digestion was succeeded.


Ethanol precipitation

Ethanol precipitation for gel extraction products(K346007(Ag43) and B0015(dT))

  1. Added 5ul of NaoAc , 1.5ul of glycogen and 125ul of 100% ethanol to 50ul DNA solutions.
  2. Centrifuged in 15000rpm, 10min at 4C.
  3. Remove supernatant and added 220ul of 70% ethanol.
  4. Centrifuged in 15000rpm, 5min at 4C.
  5. Remove supernatant and air drying in room temperature then added 10ul of DW.
Ligation

All DNA solutions were digested. Used Ligation Mighty Mix(TakaraBio)

Ligation Mighty Mix 5ul
Insert: Ag43 2ul
Vector: dT 2ul
DW 1ul
Total 10ul


Ligation reaction recipe was written below.

Degree Minute
16 30
65 10
4 Hold


Electrophoresis

Confirmation of succession of ligation.

  1. Prepared 1% Agalose gel and added EtBr then pre-migration in 30min.
  2. Added 1kb ladder, Ligation product(1ul) and digestion products (control:each solutions 1ul).
  3. Migtrated in 30min.

Electrophoresis results


HokkaidoU2012 120708 K346007-dT ligation.jpg


Transformation

Transformation for K346007(Ag43)+B0015(dT) on pSB1AK3.

  1. Added DNA soltions (Ligation products) 1ul to DH5α compitent cell.
  2. Stood on ice in 30min.
  3. Added 600ul of LB to transformed DH5α solution.
  4. From 700 solution(100ul is DH5α and 600ul is LB), 100ul add to 900ul of LB(x10 solution)
  5. Spread 300ul from 600(700-100)ul and 1000ul of LB&DH5α solution to each LBA plates.
  6. Cultivated.


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