Difference between revisions of "Team:NCKU Tainan/Protocol"

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                                 </br>
 
                                 </br>
 
                                 <div class="row">
 
                                 <div class="row">
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                                     <a class="btn col-md-12" data-toggle="collapse" href="#Extraction"
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                                     <a class="btn col-md-12" data-toggle="collapse" href="#Extraction" role="button"
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                                        role="button" aria-expanded="false" aria-controls="multiCollapseExample1">
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                                        aria-expanded="false" aria-controls="multiCollapseExample1">
 
                                         PCR Clean-Up & Gel Extraction
 
                                         PCR Clean-Up & Gel Extraction
 
                                         <i class="fa fa-arrow-down fa-10" aria-hidden="true"></i>
 
                                         <i class="fa fa-arrow-down fa-10" aria-hidden="true"></i>
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                                 <div class="collapse multi-collapse" id="Extraction">
 
                                 <div class="collapse multi-collapse" id="Extraction">
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                                     <p class="pcontent">
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                                        <h3>Gel Dissociation</h3></br>
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                                     <h3>Gel Dissociation</h3></br>
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                                        1. Gel Extraction</br></br>
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                                    <p class="pcontent">1. Gel Extraction</br></br>
 
                                         a. Excised the DNA fragment from the agarose gel.</br></br>
 
                                         a. Excised the DNA fragment from the agarose gel.</br></br>
 
                                         b. Transferred up to 300 mg of the gel slice to a 1.5 ml microcentrifuge tube.</br></br>
 
                                         b. Transferred up to 300 mg of the gel slice to a 1.5 ml microcentrifuge tube.</br></br>
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                                         d. During the incubation, mixed by vortexing the tube every 2~3 minutes.</br></br>
 
                                         d. During the incubation, mixed by vortexing the tube every 2~3 minutes.</br></br>
 
                                         e. Cooled the dissolved sample mixture to the room temperature.</br></br>
 
                                         e. Cooled the dissolved sample mixture to the room temperature.</br></br>
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                                        <h3>DNA Binding</h3></br>
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                                    </p>
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                                        2. Placed a PG Column in a Collection Tube. Apply the supernatant to the PG
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                                    <h3>DNA Binding</h3></br>
 +
                                    <p class="pcontent">2. Placed a PG Column in a Collection Tube. Apply the
 +
                                        supernatant to the PG
 
                                         Column
 
                                         Column
 
                                         by decanting or pipetting.</br></br>
 
                                         by decanting or pipetting.</br></br>
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                                         4. Discarded the flow-through and place the PG Column back into the same
 
                                         4. Discarded the flow-through and place the PG Column back into the same
 
                                         collection
 
                                         collection
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                                         tube.</br></br>
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                                         tube.</br></br></p>
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                                        <h3>Wash</h3></br>
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                                    <h3>Wash</h3></br>
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                                        6. Added 400 μl of the Buffer W1 into the PG Column.</br></br>
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                                    <p class="pcontent">6. Added 400 μl of the Buffer W1 into the PG Column.</br></br>
 
                                         7. Centrifuged at 16,000 xg for 30 seconds.</br></br>
 
                                         7. Centrifuged at 16,000 xg for 30 seconds.</br></br>
 
                                         8. Discarded the flow-through and place the PG Column back into the same
 
                                         8. Discarded the flow-through and place the PG Column back into the same
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                                         collection tube.</br></br>
 
                                         collection tube.</br></br>
 
                                         12. Centrifuged at 16,000 xg again for 2 minutes to remove the residual Buffer
 
                                         12. Centrifuged at 16,000 xg again for 2 minutes to remove the residual Buffer
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                                         W2.</br></br>
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                                         W2.</br></br></p>
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                                        <h3>Elution</h3></br>
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                                    <h3>Elution</h3></br>
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                                        13. To elute the DNA, placed the PG Column in a clean 1.5 ml microcentrifuge
+
                                    <p class="pcontent">13. To elute the DNA, placed the PG Column in a clean 1.5 ml
 +
                                        microcentrifuge
 
                                         tube.</br></br>
 
                                         tube.</br></br>
 
                                         14. Added 50 μl of the H2O (pH is between 7.0 and 8.5) to the center of each PG
 
                                         14. Added 50 μl of the H2O (pH is between 7.0 and 8.5) to the center of each PG
 
                                         Column, let it stand for at least 2 minutes, and centrifuge at 16,000 xg for 2
 
                                         Column, let it stand for at least 2 minutes, and centrifuge at 16,000 xg for 2
−
                                         min.</br></br>
+
                                         min.</br></br></p>
 
                                     </p>
 
                                     </p>
  

Revision as of 15:51, 21 September 2018

Protocol




1. Gently mix the following reaction by pipetting and centrifuge briefly.

　 　 　 　 　 　 　 　 　 　 　 　 　 　 　
20 μl system 50 μl system
Template12～20 ng 30～50 ng
Forward primer1.0 μl 2.5 μl
Reverse primer1.0 μl 2.5 μl
dNTP1.6 μl 4.0 μl
10x Buffer2.0 μl 5.0 μl


Program of KOD DNA polymerase

　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　
TemperatureTime
94 ℃3 min. 25～30 cycles
94 ℃
(Denaturation)		40 sec
57.5 ℃
(Annealing)		30 sec
72 ℃
(Extension)		Depend on sequence size
(2 kbp/min. for Taq)
72 ℃5 min.
4 ℃∞


2. Confirm the size of the digested product by gel electrophoresis.

3. Gel purification of the target size.




1. Digestion (vector)

　 　 　 　 　 　 　 　 　 　 　 　 　 　 　
Plasmid200 ng 1000 ng
EcoRI / SpeI0.2 μl 1 μl
XbaI / PstI0.2 μl 1 μl
CutSmart Buffer2 μl 5 μl
ddH2OUp to 20 μl Up to 50 μl
Digestion at 37℃ for 2.5hr.

2. Digestion (insert)

　 　 　 　 　 　 　 　 　 　 　 　 　 　 　
Plasmid200 ng 1000 ng
EcoRI / XbaI0.2 μl 1 μl
SpeI / PstI0.2 μl 1 μl
CutSmart Buffer2 μl 5 μl
ddH2OUp to 20 μl Up to 50 μl
Digestion at 37℃ for 2.5hr.

3.Confirm the size of the digested product by gel electrophoresis.

4. Gel purification of the target size.

5. Ligation

　 　 　 　 　 　 　
Vector (2 kbp)molar ratio = 1:3
(can up to 1:10 depending on the DNA sizes)
Insert (1.5 kbp)
Quick Ligase Reaction Buffer (2X)* 10 μl
Quick Ligase 1 μl
ddH2O Up to 20 μl

6. Transform the product by heat shock.


Gel Dissociation


1. Gel Extraction

a. Excised the DNA fragment from the agarose gel.

b. Transferred up to 300 mg of the gel slice to a 1.5 ml microcentrifuge tube.

c. Added 500 μl of the Gel/PCR Bufffer to the sample and mixed by vortex.

Incubate


at 55~60℃ for 10 minutes (or until the gel slice has completely dissolved).

d. During the incubation, mixed by vortexing the tube every 2~3 minutes.

e. Cooled the dissolved sample mixture to the room temperature.

DNA Binding


2. Placed a PG Column in a Collection Tube. Apply the supernatant to the PG Column by decanting or pipetting.

3. Centrifuged at 16,000 xg for 30 seconds.

4. Discarded the flow-through and place the PG Column back into the same collection tube.

Wash


6. Added 400 μl of the Buffer W1 into the PG Column.

7. Centrifuged at 16,000 xg for 30 seconds.

8. Discarded the flow-through and place the PG Column back into the same collection tube.

9. Added 600 μl of the Buffer W2 (ethanol added) into the PG Column.

10. Centrifuged at 16,000 xg for 30 seconds.

11. Discarded the flow-through and place the PG Column back into the same collection tube.

12. Centrifuged at 16,000 xg again for 2 minutes to remove the residual Buffer W2.

Elution


13. To elute the DNA, placed the PG Column in a clean 1.5 ml microcentrifuge tube.

14. Added 50 μl of the H2O (pH is between 7.0 and 8.5) to the center of each PG Column, let it stand for at least 2 minutes, and centrifuge at 16,000 xg for 2 min.