From 2012.igem.org

Plasmid pSB1A3 was chosen as a backbone vector for cloning. The Pst I site in pSB1A3 was mutated to Afl II site to facilitate following cloning processes. Proper primers were designed and PCR-based site-directed mutageneis were carried out to generate this mutation as descbibed below.
Method:
1. Set up PCR assay tubes as described below:
Total: 25 μl
+ 0.25 μl of Ex Taq polymerase
 + 2.5 μl of 10× Taq reaction buffer
 + 2.0 μl of dNTP(2 mM)  
+ 1.0 μl of template (E.coli plasmid 817) 
+ 1.0 μl of oligonucleotide primer PtoA-F*
 + 1.0 μl of oligonucleotide primer PtoA-R* 
+ 18.25 μl of ddH2O  
*The sequences of primer pair PtoA-F and PtoA-R.
 PtoA-F 5'-CCACCTGACGTCTAAGAAAC-3'
 PtoA-R 5'-ATGATCATCGCCGGCGAATTCAGGC-3'
2. Set parameters for PCR to amplify desired products.  

Temperature	Time	Cycle
94˚C	5min	1
94˚C	1min	30
55˚C	1min	30
72˚C	1min 20sec	30
4˚C	7hrs	1

Restriction Enzyme Digestion for Verification

To verify whether PstI site in pSB1A3 was successfully mutated to AflII site, we performed restriction enzyme digestion experiments.
Bacterial plasmids are double-stranded circular DNA molecules and uncut plasmid DNA can be in any of three forms - nicked circular, linear, closed supercoiled. When run on an agarose gel one frequently will see these forms as different bands with closed supercoiled form migrates the fastest, linear form migrates the slowest, and nicked circular migrates in between. If the PStI site was successfully mutated to AflII site, we expected to see increased linear form of pSB1A3 when digested with AflII. SpeI-cut pSB1A3 was served as a positive control.
Method
1. Set up Pst I digestion in 1.5 ml eppendorf tubes as described below:
Total: 10μl
+ 0.5μl of Pst I restriction enzyme (company :Takara)
+ 1μl of 10XH buffer
+ 1μl of plasmid DNA
+ 7.5μl of ddH2O
2. Set up Afl II digestion in 1.5 ml eppendorf tubes as described below:
Total: 10μl
+ 0.5μl of Afl II restriction enzyme, (company :Takara)
+ 1μl of 10XM buffer
+ 1μl of plasmid DNA
+ 1.0μl of 0.01% BSA
+ 6.5μl of ddH2O
3. Incubate the eppendorf tubes in 37℃ water bath for 1-2 hr.  
4. Prepare 1% agarose gel in Conical flask. Weigh 0.6 g agarose and add 60 ml 1x TAE (diluted from 50x TAE). Cover the Conical flask with silver paper to avoid the loss of water vapor. Place the Conical flask in the microwave and microwave for 1 minute with a middle power. Take it out and shake gently till the solution is homogeneous,(BE CAREFUL to watch the solution closely when shake it–it superheats and can boil over and cause severe burns). Continue microwave and swirl until solution is seen clear and homogeneous with no existence of solid. After cool down the agarose gel briefly, add 3 μl of Gelred (10000x ) and mix well. Pour the agarose gel in gel casting apparatus and insert combs.
 5. By inserting the pipette tip below the TAE liquid and into the well, add 5 μl of 1kb DNA ladder solution to first (and last if desired) well, skip one well, then begin adding the 5μl of digested DNA solutions mixed with 1 μl loading buffer (6x) to the wells. 
6. Place the cover on the electrophoresis unit, plug into the power source, and turn on voltage to 120V, set time to 30 minutes, and press the start button twice,until the bubbles are seen. DNA separation can be observed as time goes on by turning off the power supply then gently removing the basin from the electrophoresis unit (be careful not to let the gel slip out of the basin) and placing on the UV transilluminator to see DNA bands.
 7. When the desired level of separation is obtained, the basin can be placed on the transilluminator for picture taking(Of the absence of transilluminator,we use camera to take pictures with the UV light ). 
8. Cut the gel of specific position and collect it in tubes that have measured weight.  
9. Use DNA Gel Extraction Ki to purify the plasmid DNA mutant-pSB1A3. RPF (SpeI/AflII-digested), GFP (SpeI/AflII-digested) fragments were ligated into this vector, which was followed by insertion of designed terminator sequences between RFP and GFP, respectively.

(Figure 1 : This figure shows that the site-directed mutagenesis succeed ,we successfully change a restriction enzyme cutting site named Pst I to Afl II. Lane 1 represents the plasmid mutant-pSB1A3, lane 2 shows that the mutant-pSB1A3 cannot be digested by restriction enzyme Spe I ,lane 3 shows that mutant-pSB1A3 can be digested by restriction enzyme Afl II.)

Media Preparation

For all experiments involving the bacterial biomass and experimentation, proper media is chosen to grow the cells. Commonly,we use Lysogeny broth media for E. coli. The following is the media compositions and their quantities.
Method:
1.Prepare the Lysogeny Broth (LB) liquid media (1 L) as indicated below:
+ Bacto-Tryptone - 10 g
+ NaCl - 10 g
+ Yeast Extract - 5 g
Add ddH2O and 5mmol/L Tris Buffer in a measuring cylinder to ensure accuracy, to make a total of 1 liter and pH is 8.0.
2.Prepare the Lysogeny Broth (LB) solid media (1 L) as indicated below:
+ Bacto-Tryptone - 10 g
+ NaCl - 10 g
+ Yeast Extract - 5 g
+ Difco Agar - 15g
Add ddH2O and 5mmol/L Tris Buffer in a measuring cylinder to ensure accuracy, to make a total of 1 liter and pH is 8.0.
3. Autoclaving
Autoclave at 121 °C for 60 minutes. After the media cooling down enough, antibiotics Ampicillin(100mg of Ampicillin per 1ml of the media) are added. At last the media are poured 15ml on each plate and become solid.Store the plate at 4℃ refrigerator.

Bacterial Transformation

Transformation is commonly used to introduce recombinant plasmid DNA into bacterial strains which can transform naturally or can be made competitive for transformation by artificial means. The purpose of this technique is to introduce a recombinant plasmid DNA into a bacterial strains and to use bacteria strains to amplify the plasmid mutant-pSB1A3 for further plasmid construction. Method
1. Take out an appropriate number of tubes that contain competent cells(100μl ) from the freezer. Immediately place the tubes on ice, so that all but the cap is surrounded by ice. Allow the cells to thaw on ice for 2-5 min.
2. Visually check the cells to see whether they have thawed and gently flick the cells 1-2 times to evenly resuspend the cells.
3. Add 10μl PCR products(mini-prep purified) to the competent cells DH-5α. Stir gently to mix and return the tube to the ice, making sure that the tube is surrounded by ice except for the cap. Repeat for additional two times for the same samples.
4. Incubate the tubes on ice for 30 min.
5. Place the tubes in a 42°C water bath for exactly 90 sec; do not shake.
6. Place the tubes on ice for 2 min to cool down.
7. Add 800 μl of room temperature LB medium to each tube.
8. Shake the tubes vigorously at 37°C for 45-60 min.
9. Centrifuge the tubes at 3K RPM for 1 min. Discard the supernatant liquor and leave 100-200 μl of the mixtures.Mix the contents and spread the whole liquid on LB agar plates containing the appropriate antibiotic ampicillin for the plasmid.
10. Place the plates on the bench for several min to allow excess liquid to be absorbed, and then invert and incubate overnight at 37°C (12-16 h).

Colony PCR for Verification

Colony PCR is used to identify and select cell colonies that have the correct plasmid inserted. The procedure is a way to do several PCR operations on cell colonies in parallel, to evaluate the results and select the corresponding positive cell colonies. After an overnight growth of E.coli, we can pick up several colonies from the plate and do a colony PCR verification. Besides, the colonies we choose and should also be stored, we can incubate these colonies in one plate after every colony has been marked.
Method
1. Prepare the sample reaction as indicated below:
Total: 25μl
+ 0.25 μl of Ex Taq polymerase (company:Takara)
+ 2.5 μl of 10× Taq reaction buffer
+ 1.0 μl of R-NPS-F*
+ 1.0 μl of G-SXA-R*
+ 1.0 μl of plasmid mutant-pSB1A3
+ 2.0 μl of dNTP( 25mM )
+ 17.25 μl of ddH2O
Note: The sequences of primers R-NPS-F , G-SXA-R
R-NPS-F 5'-TATAGCGGCCGCCTTAAGTAAGTAAGAGTATACG-3'
G-SXA-R 5'-TCTCCGACTTAAGGGATCCTATAAACGCAG-3'
2. Set parameters for PCR to amplify desired products.  

Temperature	Time	Cycle
94˚C	5min	1
94˚C	1min	30
55˚C	1min	30
72˚C	1min 20sec	30
4˚C	7hrs	1

3. Electrophorese the total system and observe the lane separation.

Cultivate the Bacteria

According to the results of the PCR detection, positive colonies are chosen and transferred them to 5ml LB liquid media ( 5μl of ampicillin added) stored in 12.5ml centrifuge tubes. Put the centrifuge tubes in 37℃ gas bath overnight.

Plasmid DNA Isolation

Use E.Z.N.A.TM Plasmid Mini I to realize plasmid DNA isolation.
Method

Transfer 5 ml of overnight culture into a 1.5-ml eppendorf tube labeled with group number.
Centrifuge the sample at max. speed of desk top centrifuge and RT for 1min to pellet the cells.
Discard the supernatant. Remove as much of the supernatant as possible without disturbing the cell pellet.
Repeat step 1 and 2 twice.
Resuspend the pellet completely in 250 ml of Solution I (containing RNase A) by vortexing the samples vigorously . No clumps should be visible in the tube.
Add 250 ml of Solution II and mix the sample by gently inverting the tube 4 to 6 times. Do not vortex or shake the sample vigorously. The bacterial suspension should begin to clear which have lysed the bacterial cells in this step. Warning: Do not stop here for more than five min, as the high pH hurts your DNA!
Add 350 ml of Solution III and mix by gently inverting the tube 4 to 6 times until a flocculent white precipitate forms. Do not shake vigorously, as it might break the genomic DNA.
Centrifuge at maximum speed for 10 min at room temperature to pellet the cell debris. You should see a white precipitate in the tube after the centrifugation.
While the samples are centrifuging, for each sample, label a clean HiBind Miniprep Column which is to assembled in a 2-ml collection tube
Apply the supernatants from step 8 to the columns.
Centrifuge at maximum speed for 1 min at RT. Discard the flow-through in the collection tube.
Add 500 ml of Buffer HB to wash the Hibind Miniprep Column. Centrifuge at maximum speed for 1 min at RT. Discard the flow-through in the collection tube.
Wash the column by adding 700 ml of DNA Wash Buffer diluted with absolute ethanol. Centrifuge at maximum speed for 1 min at room temperature and discard the flow-through.
Then centrifuge the tubes again for 2 min to remove all the moisture.
Place the column in a clean 1.5 ml eppendorf tube that is labeled with the plasmid name and group number. To elute the DNA, add 50 ml of Elution Buffer to the center of each column. Let the samples stand for 2 or more minutes at RT, and then centrifuge for 1 min. The sample in the centrifuge tube (bottom) is your plasmid DNA.
Discard the column and save the sample in the eppendorf tube by placing it in the freezer (-20°C).

Restriction Enzyme Digestion and Electrophoresis

Because the colony PCR test is so sensitive and affect markedly by environment factors. So we do a restriction enzyme digestion to ensure that the isolated plasmid is the site-directed mutated plasmid.
Method
1. Prepare the control reaction as indicated below:
Total: 10μl
+ 0.5μl of Pst I restriction enzyme(company :Takara)
+ 1μl of 10XH buffer
+ 1μl of plasmid DNA
+ 7.5μl of ddH2O
2. Prepare the sample reaction as indicated below:
Total: 10μl
+ 0.5μl of Afl II restriction enzyme, (company :Takara)
+ 1μl of 10XM buffer
+ 1μl of plasmid DNA
+ 1.0μl of 0.01% BSA
+ 6.5μl of ddH2O
3. Electrophorese the total system and observe the lane separation.

Polymerase Chain Reaction(GFP & RFP) and Electrophoresis

GFP and RFP DNA fragments are the insert which need to be ligate to the plasmid mutant-pSB1A3. Do a PCR amplification can get enough quantities for the following reactions.
Method
１．Prepare the sample reaction as indicated below:
Total: 100μl ( PCR amplification of GFP fragments）
+ 1.0μl of Taq DNA polymerase,#EP0402
+ 10μl of 10XTaq buffer
+ 10μl of MgCl2(25mM)
+ 10μl of dNTP(2mM)
+ 2μl of G-SXA-R*
+ 2μl of G-SXA-F*
+ 4μl of DNA template
+ 61μl of ddH2O
Total: 100μl（PCR amplification of RFP fragments）
+ 1.0μl of Taq DNA polymerase, EP0402
+ 10μl of 10XTaq buffer
+ 10μl of MgCl2(25mM)
+ 10μl of dNTP(2mM)
+ 2μl of R-NPS-R*
+ 2μl of R-NPS-F*
+ 4μl of DNA template
+ 61μl of ddH2O
Note: The sequences of primers R-NPS-F , R-NPS-R , G-SXA-F ,G-SXA-R
R-NPS-F 5'-TATAGCGGCCGCCTTAAGTAAGTAAGAGTATACG-3'
R-NPS-R 5'-CGGAGACTAGTCTGCAGATCACATAAGTAAAGTGATAATC-3'
G-SXA-F 5'-CTAGACTAGTTCTAGAGGCGGACTCACTATAGA-3'
G-SXA-R 5'-TCTCCGACTTAAGGGATCCTATAAACGCAG-3'
2. Set parameters for PCR to amplify desired products.  

Temperature	Time	Cycle
94˚C	5min	1
94˚C	1min	30
55˚C	1min	30
72˚C	1min 20sec	30
4˚C	7hrs	1

3. Use DNA Gel Extraction Kit to purify the GFP and RFP DNA fragments after the Electrophoresis.

(Figure 2 : This figure shows that The PCR reaction system can amplify large quantities of GFP and RFP DNA fragments. The digestion based on the GFP and RFP DNA fragments can be done to prepare for the ligation. Lane 1 represents the template E.coli 817 can amplify the GFP and RFP DNA fragments , lane 2 represents the template E.coli 817(355.5) can also amplify the GFP and RFP DNA fragments.)

Double Restriction Enzyme Digestion and Electrophoresis.

Use specific restriction enzymes to digest plasmid mutant-pSB1A3,GFP and RFP to get sticky ends and purify the DNA fragment after the Electrophoresis.
Method:
1. Digestion of plasmid mutant-pSB1A3
Prepare the sample reaction as indicated below:
Total: 50μl
+ 3.0μl of Not I restriction enzyme, #ER0591
+ 3.0μl of Afl II restriction enzyme, #ER0831
+ 5.0μl of 10X buffer O
+ 1.0μl of mutant-pSB1A3 plasmid
+ 37.0μl of ddH2O
2. Digestion of PCR product GFP
Prepare the sample reaction as indicated below:
Total: 50μl
+ 3.0μl of Not I restriction enzyme, #ER0591
+ 3.0μl of Spe I restriction enzyme, #ER1251
+ 5μl of 10X buffer Tango
+ 10μl of PCR products GFP
+ 29μl of ddH2O
3. Digestion of PCR product RFP
Prepare the sample reaction as indicated below:
Total: 50μl
+ 3.0μl of Afl II restriction enzyme, #ER0831
+ 3.0μl of Spe I restriction enzyme, #ER1251
+ 5μl of 10X buffer Tango
+ 10μl of PCR products RFP
+ 29μl of ddH2O
4. Put the tubes in 37℃ environment for 4-8 hours
5. Use DNA Gel Extraction Kit to purify the mutant-pSB1A3 fragment, GFP and RFP after digestion and named them by mutant-pSB1A3 (NA) ,GFP(NS) and RFP(AS) after the Electrophoresis.

Ligation

Ligation is the process that target DNA gene is inserted into a plasmid. Both the vector and insert are prepared to have the sticky ends. These two kinds of DNA pieces are placed in a reaction tube and the proper DNA ligase, buffer, and cofactors are added for the reaction to take place. When done properly, the ligation will result in a successful combination of the insert and plasmid into one plasmid.Based on the digestion of mutant-pSB1A3,GFP and RFP DNA fragments,also ligation can be done. We ligate mutant-pSB1A3 vector and sticky GFP and RFP DNA fragments to construct an new plasmid mutant-pSB1A3-GR.
1. Prepare the control reaction as indicated below:
Total: 10μl
+ 1.0μl of plasmid mutant-pSB1A3 (NA)
+ 3.0μl of GFP(NS)
+ 3.0μl of RFP(AS)
+ 2.0μl of T4 DNA Ligase,#EL0011
+ 1.0μl of 10XT4 Ligase buffer
Note: GFP(NS) means the product of GFP DNA fragments digested by restriction enzyme Not I and Spe I.
2. Prepare the sample reaction as indicated below:
Total: 10μl
+ 1.0μl of plasmid mutant-pSB1A3 (NA)
+ 2.0μl of T4 DNA Ligase, #EL0011
+ 1.0μl of 10XT4 Ligase buffer
+ 6.0μl of ddH2O
3. Put the tubes in 22℃ water bath, react for 8-12 hours.

Bacterial Transformation

Transform the ligation products into the DH-5α competent cells, put the plate on 37℃ gas bath for 12-16 hours.

Bacterial Colony PCR

Colony PCR is used to identify and select cell colonies that have the correct plasmid insert. This procedure is a way to do several PCR operations on cell colonies in parallel, to evaluate the results and select the corresponding good cell colonies. After an overnight growth of E.coli, we can pick up some colonies from the plate and do a colony PCR verification. Besides, the colonies we choose and should also be stored, we can incubate these colonies in one plate after every colony has been marked.
Method
1. Prepare the sample reaction as indicated below:
Total: 20μl
+ 0.25 μl of Ex Taq polymerase,#EP0402
+ 2.0 μl of 10× Taq reaction buffer
+ 1.0 μl of R-NPS-F*
+ 1.0 μl of G-SXA-R*
+ 5.0 μl of bacterial colony
+ 2.0 μl of dNTP( 25mM )
+ 8.75 μl of ddH2O
Note: The sequences of primers R-NPS-F , R-NPS-R , G-SXA-F ,G-SXA-R
R-NPS-F 5'-TATAGCGGCCGCCTTAAGTAAGTAAGAGTATACG-3'
R-NPS-R 5'-CGGAGACTAGTCTGCAGATCACATAAGTAAAGTGATAATC-3'
G-SXA-F 5'-CTAGACTAGTTCTAGAGGCGGACTCACTATAGA-3'
G-SXA-R 5'-TCTCCGACTTAAGGGATCCTATAAACGCAG-3'
2. Set parameters for PCR to amplify desired products.  

Temperature	Time	Cycle
94˚C	13.5min	1
94˚C	1min	30
55˚C	1min	30
72˚C	1min 20sec	30
4˚C	7hrs	1

3. Electrophorese the total system and observe the lane separation.

(Figure 3: The lane on the figure are 2k DNA fragments, it shows the GFP and RFP DNA fragments are ligated to the vectors which were isolated from the bacterial colonies.)

Cultivate the Bacteria

According to the results of the PCR detection, we choose positive colonies and transfer them to 5ml LB liquid media ( 5μl of ampicillin has added) stored in 12.5ml centrifuge tubes. Put the centrifuge tubes in 37℃ gas bath overnight.

Plasmid DNA Isolation

Use E.Z.N.A.TM Plasmid Mini I to isolate the constructed plasmid mutant-pSB1A3-GR.

Restriction Enzyme Digestion and Electrophoresis

From the last step, we got the certain quantities of isolated plasmids. In this step, we do two restriction enzyme digestion reactions, one to prove that the plasmid is construct correctly ( mutant-pSB1A3-GR ), one to get sticky ends preparing for the ligation.
Method 1.Restriction Enzyme Digestion to prove that plasmid is constructed correctly 1.1. Prepare the sample reaction as indicated below:
Total: 10μl
+ 1.0μl of Not I restriction enzyme,#ER0591
+ 1.0μl of Spe I restriction enzyme,#ER1251
+ 2.0μl of Buffer Tango( 10X )
+ 1.5μl of plasmid mutant-pSB1A3-GR
+ 14.5μl of ddH2O
1.2. Electrophorese the total system and observe the lane separation.
2. Restriction Enzyme Digestion to get sticky ends preparing for the ligation.
2.1. Prepare the sample reaction as indicated below:
Total: 50μl
+ 5.0μl of Pst I restriction enzyme, #ER0611
+ 5.0μl of Xba I restriction enzyme, #ER0681
+ 3.0μl of Buffer Tango( 10X )
+ 5.0μl of plasmid mutant-pSB1A3-GR
+ 32.0μl of ddH2O
2.2. Electrophorese the total system and observe the lane separation.
2.3. Cut the gel of specific position and collect it in tubes that have measured weight.
2.4. Use DNA Gel Extraction Ki to purify the plasmid DNA mutant-pSB1A3-GR(PX) .
Note: Mutant-pSB1A3-GR(PX) means plasmid Mutant-pSB1A3-GR digested by Pst I and Xba I. (Figure 4 : The double digestion of mutant-pSB1A3 forms a linear DNA fragments and it runs slower than circle DNA fragments. This suggest that the double digestion of mutant-pSB1A3 works in a high efficiency, and desired sticky ends are formed.1,3,5 are plasmids digested by restriction enzyme Pst I and Xba I from different colonies, 2,5,6 are pure plasmid mutant-pSB1A3-GR, 7 is the plasmid mutant-pSB1A3. )

Ligation

Ligation is the process that target DNA gene is inserted into a plasmid. Both the vector and insert are prepared to have the sticky ends. These two kinds of DNA pieces are placed in a reaction tube and the proper DNA ligase, buffer, and cofactors are added for the reaction to take place. When done properly, the ligation will result in a successful combination of the insert and plasmid into one plasmid.Based on the digestion of mutant-pSB1A3-GR, terminator DNA fragments,ligation can be done. We ligate mutant-pSB1A3-GR vector and sticky terminator DNA fragments to construct an new plasmid mutant-pSB1A3-GR-t.By detecting the quantities of GFP and RFP, terminator efficiency can be calculated.
1. Prepare the control reaction as indicated below:
Total: 10μl
+ 1.0μl of plasmid mutant-pSB1A3 (NA)
+ 6.0μl of terminator
+ 2.0μl of T4 DNA Ligase , #EL0011
+ 1.0μl of 10XT4 Ligase buffer
2. Put the tubes in 22℃ water bath, react for 8-12 hours.

Bacteria transformation

Transform the ligation products into the DH-5α competent cells, put the plate on 37℃ gas bath for 12-16 hours.

Cultivate the Bacteria

According to the results of the PCR detection, we choose positive colonies and transfer them to 5ml LB liquid media ( 5μl of ampicillin has added) stored in 12.5ml centrifuge tubes. Put the centrifuge tubes in 37℃ gas bath overnight.

Flow Cytometer Analysis

Flow cytometry is a laser based, biophysical technology employed in cell counting, sorting, biomarker detection and protein engineering, by suspending cells in a stream of fluid and passing them by an electronic detection apparatus. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of up to thousands of particles per second.
Each fluorophore has a characteristic peak excitation and emission wavelength, and the emission spectra often overlap. Consequently, the combination of labels which can be used depends on the wavelength of the lamp(s) or laser(s) used to excite the fluorochromes and on the detectors available. It is practical that the expression of RFP and GFP can be measured at the same time.
Method:
1. Materials:
  1.1. NaCl solution( 0.9% ,M/V)
  1.2. 75% ethanol
2. Procedures:
  2.1. Bacterium are harvested by centrifuge at 10000g for 30s, then discard the supernatant. Repeat this step again until we got adequate bacterium.
  2.2. Suspend the bacterium With NaCl solution(0.9%) and vibrate the centrifuge tubes until the bacterium are distributed homogeneous.
  2.3. Load the bacteria containing pSB1A3 to Flow Cytometer (Beckman), set the parameters. Measure the GFP-FL1 and RFP-FL2 by Cytometer.

Fluorescence Microscope

A fluorescence microscope is an optical microscope that uses fluorescence and phosphorescence reflection and absorption to study properties of organic or inorganic substances and generate an image.Fluorescence microscope detection are used to confirm the expression of GFP and RFP which are illuminated with light of a wavelength which excites fluorescence in the sample.
Method
Add 10μl of bacteria solution to micro slide and cover with coverslip. Placed the micro slide on the Fluorescence Microscope. Set parameters to detect GFP and RFP.
Generate an image of fluorescence protein and save it.

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                                      <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/introduction">Overview</a></li>
                                      <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm">Algorithm</a></li>
-                                     <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/achievements">Achievements</a></li>
+                                     <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/achievements">Results</a></li>
                                      <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/Download">Download</a></li>
                                      <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/comment">Comment</a></li>
@@ Line 490: / Line 490: @@
 <p><a href="#Flow">20.  Flow Cytometer Analysis</a></p>
 <p><a href="#Fluorescence">21.  Fluorescence Microscope </a></p>
-<br>
+<br/>
-<a name="Site-Directed_Mutagenesis" ></a></font>
+<h1></h1>
+<p>
+<a name="Site-Directed_Mutagenesis" ></a>
 <h3><font face="Arial, Helvetica"><b><font color="#0000FF">Site-Directed Mutagenesis</font></b></font></h3>
-<font face="Arial, Helvetica">
-<p>Plasmid pSB1A3 was chosen as a backbone vector for cloning. The Pst I site in pSB1A3 was mutated to Afl II site to facilitate following cloning processes. Proper primers were designed and PCR-based site-directed mutageneis were carried out to generate this mutation as descbibed below.  </p>
-<p><strong>Method:</strong></p>
+Plasmid pSB1A3 was chosen as a backbone vector for cloning. The Pst I site in pSB1A3 was mutated to Afl II site to facilitate following cloning processes. Proper primers were designed and PCR-based site-directed mutageneis were carried out to generate this mutation as descbibed below.  <br/>
-<p>1.  Set up PCR assay tubes as described below:
+<!--<p>要到很后面才能找到他的结束-->
+<strong>Method:</strong><br/>
+.  Set up PCR assay tubes as described below:
 <br/>
 Total: 25 μl<br />
@@ Line 511: / Line 515: @@
  PtoA-F  5'-CCACCTGACGTCTAAGAAAC-3'<br />
  PtoA-R  5'-ATGATCATCGCCGGCGAATTCAGGC-3' <br />
-</p>
-  <p> 2.    Set parameters for PCR to amplify desired products.  </p>
+.    Set parameters for PCR to amplify desired products.  <br/>
 <table>
@@ Line 519: / Line 523: @@
 </tr>
 <tr>
-   <td>94˚C</td> <td>13.5min</td> <td>1</td>
+   <td>94˚C</td> <td>5min</td> <td>1</td>
 </tr>
 <tr>
@@ Line 534: / Line 538: @@
 </tr>
 </table>
+<!--那个p的结束，下同-->
+</p>
+<br/>
+<p>
 <font face="Arial, Helvetica">
-               <p><br>
-                 <a name="Restriction" ></a>              </p>
+                 <a name="Restriction" ></a>
 </font>
 <h3><font face="Arial, Helvetica"><b><font color="#0000FF">Restriction Enzyme Digestion for Verification</font></b></font></h3>
-<p align="left">To verify whether PstI site in pSB1A3 was successfully mutated to AflII site, we performed restriction enzyme digestion experiments. </p>
+To verify whether PstI site in pSB1A3 was successfully mutated to AflII site, we performed restriction enzyme digestion experiments. <br/>
-<p>Bacterial plasmids are double-stranded circular DNA molecules and uncut plasmid DNA can be in any of three forms - nicked circular, linear, closed supercoiled. When run on an agarose gel one frequently will see these forms as different bands with closed supercoiled form migrates the fastest, linear form migrates the slowest, and nicked circular migrates in between. If the PStI site was successfully mutated to AflII site, we expected to see increased linear form of pSB1A3 when digested with AflII. SpeI-cut pSB1A3 was served as a positive control. </p><br />
+Bacterial plasmids are double-stranded circular DNA molecules and uncut plasmid DNA can be in any of three forms - nicked circular, linear, closed supercoiled. When run on an agarose gel one frequently will see these forms as different bands with closed supercoiled form migrates the fastest, linear form migrates the slowest, and nicked circular migrates in between. If the PStI site was successfully mutated to AflII site, we expected to see increased linear form of pSB1A3 when digested with AflII. SpeI-cut pSB1A3 was served as a positive control. <br />
      <strong>Method</strong><br />
 .  Set up Pst I digestion in 1.5 ml eppendorf tubes as described below:<br />
@@ Line 562: / Line 572: @@
 .  When the desired level of separation is obtained, the basin can be placed on the transilluminator for picture taking(Of the absence of transilluminator,we use camera to take pictures with the UV light ). <br/>
 .  Cut the gel of specific position and collect it in tubes that have measured weight.  <br/>
-.  Use DNA Gel Extraction Ki to purify the plasmid DNA mutant-psb1a3.
+.  Use DNA Gel Extraction Ki to purify the plasmid DNA mutant-pSB1A3.
 RPF (SpeI/AflII-digested), GFP (SpeI/AflII-digested) fragments were ligated into this vector, which was followed by insertion of designed terminator sequences between RFP and GFP, respectively.</p>
 <font face="Arial, Helvetica">
-<p> <img src="https://static.igem.org/mediawiki/2012/5/59/11.png" alt="" class="img_fl img_border" align="left"/> </p>
+<img src="https://static.igem.org/mediawiki/2012/5/59/11.png" alt="" class="img_fl img_border" align="left"/>
 <br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/>
-<p>(Figure 1  : This figure shows that the site-directed mutagenesis succeed ,we successfully  change a restriction enzyme cutting site named Pst I to Afl II. Lane 1  represents the plasmid mutant-psb1a3,  lane 2 shows that the mutant-psb1a3  cannot be digested by restriction enzyme Spe I ,lane 3 shows that mutant-psb1a3 can be digested by restriction enzyme Afl  II.) </p>
+(Figure 1  : This figure shows that the site-directed mutagenesis succeed ,we successfully  change a restriction enzyme cutting site named Pst I to Afl II. Lane 1  represents the plasmid mutant-pSB1A3,  lane 2 shows that the mutant-pSB1A3  cannot be digested by restriction enzyme Spe I ,lane 3 shows that mutant-pSB1A3 can be digested by restriction enzyme Afl  II.)
+</p>
+<br/>
-   <a name="Media"></a></font>
+<p>
+   <a name="Media"></a>
 <h3><font face="Arial, Helvetica"><b><font color="#0000FF">Media Preparation</font></b></font></h3>
-<p align="left">For all experiments  involving the bacterial biomass and experimentation, proper media is chosen to grow  the cells. Commonly,we use Lysogeny broth media for <em>E. coli</em>. The following is the media compositions and their  quantities.<br />
+For all experiments  involving the bacterial biomass and experimentation, proper media is chosen to grow  the cells. Commonly,we use Lysogeny broth media for <em>E. coli</em>. The following is the media compositions and their  quantities.<br />
-    <strong>Lysogeny Broth (LB) liquid media (1   L)</strong><br />
+<strong>Method:</strong><br/>
-  Bacto-Tryptone - 10 g<br>
-  NaCl - 10 g<br>
+.Prepare the Lysogeny Broth (LB) liquid media (1 L) as indicated below:	<br/>
-  Yeast Extract - 5 g<br>
++ Bacto-Tryptone - 10 g<br/>
-<p align="left">Add  ddH2O and 5mmol/L Tris Buffer in a  measuring cylinder to ensure accuracy, to make a total of 1 liter and pH is 8.0. <br />
++ NaCl - 10 g<br/>
-    <strong>Lysogeny Broth (LB) solid media (1   L)</strong><br />
++ Yeast Extract - 5 g<br/>
-  Bacto-Tryptone - 10 g<br>
+Add ddH2O and 5mmol/L Tris Buffer in a measuring cylinder to ensure accuracy, to make a total of 1 liter and pH is 8.0.<br/>
-  NaCl - 10 g<br>
+.Prepare the Lysogeny Broth (LB) solid media (1 L) as indicated below:<br/>
-  Yeast Extract - 5 g<br>
++ Bacto-Tryptone - 10 g<br/>
-  Difco Agar - 15g</li><br>
++ NaCl - 10 g<br/>
-<p align="left">Add  ddH2O and 5mmol/L Tris Buffer in a  measuring cylinder to ensure accuracy, to make a total of 1 liter and pH is 8.0. <br />
++ Yeast Extract - 5 g<br/>
-    <strong>Autoclaving</strong> </p>
++ Difco Agar - 15g<br/>
-<ol>
+Add ddH2O and 5mmol/L Tris Buffer in a measuring cylinder to ensure accuracy, to make a total of 1 liter and pH is 8.0.<br/>
-<ul>
+. Autoclaving<br/>
-  <li>Autoclave at 121 °C for 60 minutes. After the media cooling down enough, antibiotics Ampicillin(100mg  of Ampicillin per 1ml of the media) are added. At last the media are poured 15ml  on each plate and become solid.Store the plate at 4℃ refrigerator. </li>
+Autoclave at 121 °C for 60 minutes. After the media cooling down enough, antibiotics Ampicillin(100mg of Ampicillin per 1ml of the media) are added. At last the media are poured 15ml on each plate and become solid.Store the plate at 4℃ refrigerator.
-</ul>
+ </p>
-</ol>
+<br/>
+<p>
 <font face="Arial, Helvetica">
-<p>&nbsp;</p>
-<br>
    <a name="Bacterial"></a></font>
 <h3><font face="Arial, Helvetica"><b><font color="#0000FF">Bacterial Transformation</font></b></font></h3>
-<font face="Arial, Helvetica">
-<p>Introduction of exogenous DNA into cells using  non-viral methods is called “Transformation”.Transformation is  commonly used to introduce recombinant plasmid DNA into bacterial strains which  can transform naturally or can be made competitive for transformation by  artificial means.<br />
+Transformation is commonly used to introduce recombinant plasmid DNA into bacterial strains which can transform naturally or can be made competitive for transformation by artificial means. The purpose of this technique is to introduce a recombinant plasmid DNA into a bacterial strains and to use bacteria strains to amplify the plasmid mutant-pSB1A3 for further plasmid construction.
-  Depending on the expected transformation  efficiency, there are two main types of competent cells that can be used for  transformation.<br />
-.Chemically competent cells<br />
-  Chemically induced competent cells are calcium  chloride-treated to facilitate attachment of the plasmid DNA to the competent  cell membrane. During chemical transformation, the cells are heat-shocked in a  water bath; which opens the pores of the cell membrane allowing entry of  plasmid DNA from the buffer. <br />
-.Electrocompetent cells<br />
-  Electrocompetent cells are prepared for  transformation using electroporation, a method that uses an electrical pulse to  create pores through which genetic material enters the cells. This method usually  has high transformation efficiency. <br />
    <strong>Method</strong><br />
 . Take out an  appropriate number of tubes that contain competent cells(100μl ) from the freezer. Immediately place the tubes on ice, so that all  but the cap is surrounded by ice. Allow the cells to thaw on ice for 2-5 min.<br />
@@ Line 609: / Line 617: @@
 . Place the tubes  in a 42°C  water bath for exactly 90 sec; do not shake.<br />
 . Place the tubes  on ice for 2 min to cool down.<br />
-. Add 800 l of room temperature LB medium to each tube.<br />
+. Add 800 μl of room temperature LB medium to each tube.<br />
-. Shake the tubes  vigorously at 37<a name="OLE_LINK2" id="OLE_LINK2"></a><a name="OLE_LINK1" id="OLE_LINK1">°C</a> for 45-60 min.<br />
+. Shake the tubes  vigorously at 37°C for 45-60 min.<br />
 . Centrifuge the  tubes at 3K RPM for 1 min. Discard the supernatant liquor and leave 100-200 μl of the mixtures.Mix the contents and spread  the whole liquid on LB agar plates containing the appropriate antibiotic ampicillin  for the plasmid.<br />
-. Place the  plates on the bench for several min to allow excess liquid to be absorbed, and  then invert and incubate overnight at 37°C (12-16 h).</p>
+. Place the  plates on the bench for several min to allow excess liquid to be absorbed, and  then invert and incubate overnight at 37°C (12-16 h).
-<br>
+<br/>
-   <a name="Colony"></a></font>
+</p>
+<p>
+   <a name="Colony"></a>
 <h3><font face="Arial, Helvetica"><b><font color="#0000FF">Colony PCR for Verification</font> </b></font></h3>
-<font face="Arial, Helvetica">
-<P>Colony PCR is used  to identify and select cell colonies that have the correct plasmid inserted.  The procedure is a way to do several PCR operations on cell colonies in  parallel, to evaluate the results and select the corresponding good cell  colonies. After an overnight growth of E.coli, we can pick up several colonies  from the plate and do a colony PCR verification. Besides, the colonies we  choose and should also be stored, we can incubate these colonies in one plate  after every colony has been marked.<br />
+Colony PCR is used to identify and select cell colonies that have the correct plasmid inserted. The procedure is a way to do several PCR operations on cell colonies in parallel, to evaluate the results and select the corresponding positive cell colonies. After an overnight growth of E.coli, we can pick up several colonies from the plate and do a colony PCR verification. Besides, the colonies we choose and should also be stored, we can incubate these colonies in one plate after every colony has been marked.<br/>
    <strong>Method</strong><br />
 . Prepare the sample reaction as  indicated below:<br />
@@ Line 623: / Line 635: @@
        +  0.25 μl of Ex Taq polymerase (company:Takara)<br />
        +  2.5 μl of 10× Taq reaction buffer<br />
-      +  1.0 μl of R-NPS-F <br />
+       +  1.0 μl of R-NPS-F*<br />
-       +  1.0 μl of G-SXA-R<br />
+       +  1.0 μl of G-SXA-R*<br />
-       +  1.0 μl of plasmid mutant-psb1a3<br />
+       +  1.0 μl of plasmid mutant-pSB1A3<br />
        +  2.0 μl of dNTP( 25mM  ) <br />
        +  17.25 μl of ddH2O <br />
-.  Procedures on the thermocycler are listed below:<br />
+Note: The sequences of primers R-NPS-F  , G-SXA-R <br />
-    ① 94˚C for 5 min<br />
+R-NPS-F   5'-TATAGCGGCCGCCTTAAGTAAGTAAGAGTATACG-3'  <br />
-      ② 30 cycle<br />
+G-SXA-R   5'-TCTCCGACTTAAGGGATCCTATAAACGCAG-3'<br />
-       a. 94˚C for 1 min<br />
-        b. 55˚C for 1 min<br />
+.    Set parameters for PCR to amplify desired products.
-         c. 72˚C for 1 min20sec<br />
-      ③ 4℃ for 7 hours <br />
+<table>
-.   Electrophorese the total system and observe the lane separation. </P>
+<tr>
-<br>
+  <td>Temperature</td> <td>Time</td> <td>Cycle</td>
-   <a name="Culture"></a></font>
+</tr>
+<tr>
+  <td>94˚C</td> <td>5min</td> <td>1</td>
+</tr>
+<tr>
+  <td>94˚C</td> <td>1min</td> <td>30</td>
+</tr>
+<tr>
+  <td>55˚C</td> <td>1min</td> <td>30</td>
+</tr>
+<tr>
+  <td>72˚C</td> <td>1min 20sec</td> <td>30</td>
+</tr>
+<tr>
+  <td>4˚C</td> <td>7hrs</td> <td>1</td>
+</tr>
+</table>
+.   Electrophorese the total system and observe the lane separation.
+</p>
+<br/>
+<p>
+   <a name="Culture"></a>
 <h3><font color="#0000FF" face="Arial, Helvetica"><b>Cultivate the Bacteria</b></font></h3>
-               <font face="Arial, Helvetica"><p>According  to the results of the   PCR detection,  positive colonies are chosen and transferred them to 5ml LB liquid media ( 5μl of ampicillin added) stored in  12.5ml centrifuge tubes. Put the  centrifuge tubes in 37℃ gas bath  overnight. </p>
+               According  to the results of the   PCR detection,  positive colonies are chosen and transferred them to 5ml LB liquid media ( 5μl of ampicillin added) stored in  12.5ml centrifuge tubes. Put the  centrifuge tubes in 37℃ gas bath  overnight.
-  <br>
+</p>
+<br/>
+<p>
    <a name="Plasmid"></a>
-             <h3><b>Plasmid DNA Isolation</b></h3>
+       <h3><font color="#0000FF" face="Arial, Helvetica"><b>Plasmid DNA Isolation</b></font></h3>
-              <p>Use E.Z.N.A.TM  Plasmid Mini I to realize plasmid DNA isolation.<br />
+              Use E.Z.N.A.TM  Plasmid Mini I to realize plasmid DNA isolation.<br />
-                <strong>Method</strong></p>
+                <strong>Method</strong><br/>
-              <ul>
-              <ul>
+              <ol>
                 <li>Transfer 5 ml of overnight culture into a  1.5-ml eppendorf tube labeled with group number.  </li>
                 <li>Centrifuge the sample at max. speed of desk  top centrifuge and RT for 1min to pellet the cells.</li>
@@ Line 663: / Line 702: @@
                 <li>Place the column in a clean 1.5 ml  eppendorf tube that is labeled with the plasmid name and group number. To elute  the DNA, add 50 ml of Elution Buffer  to the center of each column. Let the samples stand for 2 or more minutes at  RT, and then centrifuge for 1 min. The sample in the centrifuge tube (bottom)  is your plasmid DNA. </li>
                 <li>Discard the column and save the sample in  the eppendorf tube by placing it in the freezer (-20°C).  </li>
-              </ul></ul>
+              </ol>
-              <a name="#Restriction_2" ></a>         </font>
+</p>
+<p>
+              <a name="#Restriction_2" ></a>
           <h3><font face="Arial, Helvetica"><b><font color="#0000FF">Restriction Enzyme Digestion and Electrophoresis</font></b></font></h3>
-               <font face="Arial, Helvetica">
-<p>Because  the colony PCR test is so sensitive and affect markedly by environment factors.  So we do a restriction enzyme digestion to ensure that the isolated plasmid is  the site-directed mutated plasmid.<br />
+Because  the colony PCR test is so sensitive and affect markedly by environment factors.  So we do a restriction enzyme digestion to ensure that the isolated plasmid is  the site-directed mutated plasmid.<br />
      <strong>Method</strong><br />
 .  Prepare the control  reaction as indicated below:<br />
@@ Line 682: / Line 724: @@
       + 1.0μl of 0.01% BSA<br />
       + 6.5μl of ddH2O <br />
-.   Electrophorese the total system and observe the lane separation.</p>
+.   Electrophorese the total system and observe the lane separation.
-<br>
+</p>
-   <a name="Amplify"></a>              </font>
+<br/>
+<p>
+   <a name="Amplify"></a>
             <h3><font face="Arial, Helvetica"><b><font color="#0000FF">Polymerase Chain  Reaction(GFP &amp; RFP) and Electrophoresis</font></b></font></h3>
-               <font face="Arial, Helvetica">
-               <p>GFP and RFP DNA fragments are the insert  which need to be ligate to the plasmid mutant-psb1a3. Do a PCR amplification can get enough quantities  for the following reactions.<br />
+               GFP and RFP DNA fragments are the insert  which need to be ligate to the plasmid mutant-pSB1A3. Do a PCR amplification can get enough quantities  for the following reactions.<br />
      <strong>Method </strong><br />
 １．Prepare the sample reaction as  indicated below:<br />
-Total: 100μl ( PCR <a name="OLE_LINK37" id="OLE_LINK37"></a><a name="OLE_LINK36" id="OLE_LINK36">amplification</a> of GFP fragments） <br />
+Total: 100μl ( PCR amplification of GFP fragments） <br />
      + 1.0μl of Taq DNA  polymerase,#EP0402<br />
      + 10μl of 10XTaq buffer <br />
      + 10μl of MgCl2(25mM)<br />
      + 10μl of dNTP(2mM)<br />
-     + 2μl of G-SXA-R <br />
+     + 2μl of G-SXA-R* <br />
-     + 2μl of G-SXA-F<br />
+     + 2μl of G-SXA-F*<br />
      + 4μl of DNA template<br />
      + 61μl of ddH2O <br />
@@ Line 704: / Line 749: @@
      + 10μl of MgCl2(25mM)<br />
      + 10μl of dNTP(2mM)<br />
-     + 2μl of R-NPS-R <br />
+     + 2μl of R-NPS-R* <br />
-     + 2μl of R-NPS-F<br />
+     + 2μl of R-NPS-F*<br />
      + 4μl of DNA template<br />
      + 61μl of ddH2O <br />
-Note:   Here listed the sequences of primers.<br />
+Note: The sequences of primers R-NPS-F , R-NPS-R , G-SXA-F ,G-SXA-R <br />
 R-NPS-F   5'-TATAGCGGCCGCCTTAAGTAAGTAAGAGTATACG-3'  <br />
 R-NPS-R   5'-CGGAGACTAGTCTGCAGATCACATAAGTAAAGTGATAATC-3' <br />
 G-SXA-F   5'-CTAGACTAGTTCTAGAGGCGGACTCACTATAGA-3'  <br />
-G-SXA-R   5'-CCGACTTAAGGGATCCTATAAACGCAG-3'<br />
+G-SXA-R   5'-TCTCCGACTTAAGGGATCCTATAAACGCAG-3'<br />
-２．Procedures on the thermocycler are listed below:<br />
-     ① 94˚C for 5 min<br />
+.    Set parameters for PCR to amplify desired products.  <br/>
-      ② 30 cycle<br />
-       a. 94˚C for 1 min<br />
+<table>
-        b. 55˚C for 1 min<br />
+<tr>
-         c. 72˚C for 1 min20sec<br />
+  <td>Temperature</td> <td>Time</td> <td>Cycle</td>
-      ③ 4℃ for 7 hours </p>
+</tr>
-              </font>
+<tr>
-              <ul>
+  <td>94˚C</td> <td>5min</td> <td>1</td>
-                <li>Use  DNA Gel Extraction Kit  to purify the GFP and RFP DNA fragments after the Electrophoresis.</li>
+</tr>
-              </ul>
+<tr>
-               <p align="left"><strong>Figure</strong></p>
+  <td>94˚C</td> <td>1min</td> <td>30</td>
-              <p><font face="Arial, Helvetica"><img src="https://static.igem.org/mediawiki/2012/7/72/111.png" alt="" class="img_fl img_border" />  </font></p>
+</tr>
-              <p>(Figure 2  : This figure shows that The PCR reaction system can amplify large quantities  of GFP and RFP DNA fragments. The digestion based on the GFP and RFP DNA  fragments can be done to prepare for the ligation. Lane 1 represents the  template E.coli 817 can amplify the GFP and RFP DNA fragments , lane 2  represents the template E.coli 817(355.5) can also amplify the GFP and RFP DNA  fragments.) <font face="Arial, Helvetica"><br>
+<tr>
+  <td>55˚C</td> <td>1min</td> <td>30</td>
+</tr>
+<tr>
+  <td>72˚C</td> <td>1min 20sec</td> <td>30</td>
+</tr>
+<tr>
+  <td>4˚C</td> <td>7hrs</td> <td>1</td>
+</tr>
+</table>
+. Use  DNA Gel Extraction Kit  to purify the GFP and RFP DNA fragments after the Electrophoresis.
+               <font face="Arial, Helvetica"><img src="https://static.igem.org/mediawiki/2012/7/72/111.png" alt="" class="img_fl img_border" align="left"/>  </font>
+<br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/>
+              (Figure 2  : This figure shows that The PCR reaction system can amplify large quantities  of GFP and RFP DNA fragments. The digestion based on the GFP and RFP DNA  fragments can be done to prepare for the ligation. Lane 1 represents the  template E.coli 817 can amplify the GFP and RFP DNA fragments , lane 2  represents the template E.coli 817(355.5) can also amplify the GFP and RFP DNA  fragments.)<br/><br/>
+</p>
+<br/>
+<p>
+ <font face="Arial, Helvetica"><br/>
                    <a name="Restriction_Enzyme"></a>
-               </font></p>
+               </font>
-               <font face="Arial, Helvetica">              </font>
           <h3><font face="Arial, Helvetica"><b><font color="#0000FF">Double Restriction  Enzyme Digestion and Electrophoresis.</font></b></font></h3>
                <font face="Arial, Helvetica">
-               <p>Use specific restriction enzymes to digest  plasmid mutant-psb1a3,GFP and  RFP to get sticky ends and purify the DNA fragment after the Electrophoresis.<br />
+               Use specific restriction enzymes to digest  plasmid mutant-pSB1A3,GFP and  RFP to get sticky ends and purify the DNA fragment after the Electrophoresis.<br />
-                <strong>Method:</strong></p>
+               <strong>Method:</strong><br/>
                </font>
-               <ul>
-                <li> Digestion of plasmid mutant-psb1a3 </li>
+. Digestion of plasmid mutant-pSB1A3 <br/>
-               </ul>
+               Prepare the sample reaction as indicated below:<br />
-              <p>Prepare the sample reaction as indicated below:<br />
                  Total: 50μl <br />
                  + 3.0μl of Not I restriction enzyme, #ER0591<br />
                  + 3.0μl of Afl II restriction enzyme, #ER0831<br />
                  + 5.0μl of 10X buffer O <br />
-                 + 1.0μl of mutant-psb1a3 plasmid <br />
+                 + 1.0μl of mutant-pSB1A3 plasmid <br />
                  + 37.0μl of ddH2O<br />
 .  Digestion of PCR  product GFP<br />
                  Prepare the sample reaction as indicated below:<br />
@@ Line 753: / Line 820: @@
                  + 10μl of PCR products GFP<br />
                  + 29μl of ddH2O<br />
 .  Digestion of PCR  product RFP<br />
                  Prepare the sample reaction as indicated below:<br />
@@ Line 761: / Line 829: @@
                  + 10μl of PCR products RFP<br />
                  + 29μl of ddH2O<br />
 .    Put the  tubes in 37℃ environment for 4-8 hours <br />
-.   Use DNA Gel Extraction Kit to purify the  mutant-psb1a3 fragment,  GFP and RFP after digestion and named them by mutant-psb1a3 (NA) ,GFP(NS) and RFP(AS) after the  Electrophoresis.</p>
-               <font face="Arial, Helvetica"><br>
+.   Use DNA Gel Extraction Kit to purify the  mutant-pSB1A3 fragment,  GFP and RFP after digestion and named them by mutant-pSB1A3 (NA) ,GFP(NS) and RFP(AS) after the  Electrophoresis.
+</p>
+<br/>
+<p>
+               <font face="Arial, Helvetica">
                <a name="Ligayion"></a>              </font>
           <h3><font face="Arial, Helvetica"><b><font color="#0000FF">Ligation</font></b></font></h3>
-               <font face="Arial, Helvetica">
-               <p>Ligation is the process that target DNA gene is inserted  into a plasmid. Both the vector and insert are prepared to have the sticky ends.  These two kinds of DNA pieces are placed in a reaction tube and the proper DNA  ligase, buffer, and cofactors are added for the reaction to take place. When  done properly, the ligation will result in a successful combination of the  insert and plasmid into one plasmid.Based on the digestion of mutant-psb1a3,GFP and RFP DNA fragments,also ligation  can be done. We ligate mutant-psb1a3  vector and sticky GFP and RFP DNA fragments to construct an new plasmid  mutant-psb1a3-GR.  <br />
+               Ligation is the process that target DNA gene is inserted  into a plasmid. Both the vector and insert are prepared to have the sticky ends.  These two kinds of DNA pieces are placed in a reaction tube and the proper DNA  ligase, buffer, and cofactors are added for the reaction to take place. When  done properly, the ligation will result in a successful combination of the  insert and plasmid into one plasmid.Based on the digestion of mutant-pSB1A3,GFP and RFP DNA fragments,also ligation  can be done. We ligate mutant-pSB1A3  vector and sticky GFP and RFP DNA fragments to construct an new plasmid  mutant-pSB1A3-GR.  <br />
 .  Prepare the control  reaction as indicated below:<br />
                  Total: 10μl <br />
-                 + 1.0μl of plasmid mutant-psb1a3  (NA) <br />
+                 + 1.0μl of plasmid mutant-pSB1A3  (NA) <br />
                  + 3.0μl of GFP(NS) <br />
                  + 3.0μl of RFP(AS) <br />
@@ Line 778: / Line 853: @@
 .  Prepare the sample  reaction as indicated below:<br />
                  Total: 10μl <br />
-                 + 1.0μl of plasmid mutant-psb1a3  (NA) <br />
+                 + 1.0μl of plasmid mutant-pSB1A3  (NA) <br />
                  + 2.0μl of T4  DNA Ligase, #EL0011   <br />
                  + 1.0μl of 10XT4  Ligase buffer<br />
                  + 6.0μl of ddH2O<br />
-.  Put  the tubes in 22℃ water bath, react for 8-12 hours. <br>
+.  Put  the tubes in 22℃ water bath, react for 8-12 hours.
-               <a name="Bacterial_Transformation"></a>              </font>
+</p> <br/>
+<p>
+               <a name="Bacterial_Transformation"></a>
           <h3><font face="Arial, Helvetica"><b><font color="#0000FF">Bacterial Transformation</font></b></font></h3>
                <font face="Arial, Helvetica">
-               <p>Transform the ligation products into  the DH-5α competent cells, put the plate on 37℃ gas bath for 12-16  hours. </p>
+               Transform the ligation products into  the DH-5α competent cells, put the plate on 37℃ gas bath for 12-16  hours.
-               <br>
+</p>
+               <br/>
+<p>
                <a name="Bacterial_Colony"></a>              </font>
           <h3><font face="Arial, Helvetica"><b><font color="#0000FF">Bacterial Colony PCR</font></b> </font></h3>
-               <font face="Arial, Helvetica">
-               <p>Colony PCR is used  to identify and select cell colonies that have the correct plasmid insert. This  procedure is a way to do several PCR operations on cell colonies in parallel,  to evaluate the results and select the corresponding good cell colonies. After an  overnight growth of E.coli, we can pick up some colonies from the plate and do  a colony PCR verification. Besides, the colonies we choose and should also be  stored, we can incubate these colonies in one plate after every colony has been  marked.<br />
+               Colony PCR is used  to identify and select cell colonies that have the correct plasmid insert. This  procedure is a way to do several PCR operations on cell colonies in parallel,  to evaluate the results and select the corresponding good cell colonies. After an  overnight growth of E.coli, we can pick up some colonies from the plate and do  a colony PCR verification. Besides, the colonies we choose and should also be  stored, we can incubate these colonies in one plate after every colony has been  marked.<br />
                  <strong>Method</strong><br />
 . Prepare the sample reaction as  indicated below:<br />
@@ Line 797: / Line 878: @@
       +  0.25 μl of Ex Taq polymerase,#EP0402 <br />
       +  2.0 μl of 10× Taq reaction buffer<br />
-      +  1.0 μl of R-NPS-F <br />
+      +  1.0 μl of R-NPS-F* <br />
-      +  1.0 μl of G-SXA-R<br />
+      +  1.0 μl of G-SXA-R*<br />
       +  5.0 μl of bacterial colony<br />
       +  2.0 μl of dNTP( 25mM  ) <br />
       +  8.75 μl of ddH2O <br />
-Note: Here listed the sequence of  primers.<br />
+Note: The sequences of primers R-NPS-F , R-NPS-R , G-SXA-F ,G-SXA-R <br />
- R-NPS-F   5'-TATAGCGGCCGCCTTAAGTAAGTAAGAGTATACG-3'  <br />
+R-NPS-F   5'-TATAGCGGCCGCCTTAAGTAAGTAAGAGTATACG-3'  <br />
-R-NPS-R    5'-CGGAGACTAGTCTGCAGATCACATAAGTAAAGTGATAATC-3' <br />
+R-NPS-R   5'-CGGAGACTAGTCTGCAGATCACATAAGTAAAGTGATAATC-3' <br />
-G-SXA-F    5'-CTAGACTAGTTCTAGAGGCGGACTCACTATAGA-3'  <br />
+G-SXA-F   5'-CTAGACTAGTTCTAGAGGCGGACTCACTATAGA-3'  <br />
-G-SXA-R    5'-CCGACTTAAGGGATCCTATAAACGCAG-3'<br />
+G-SXA-R   5'-TCTCCGACTTAAGGGATCCTATAAACGCAG-3'<br />
-.  Procedures on the thermocycler are listed below:<br />
-     ① 94˚C for 5 min<br />
+.    Set parameters for PCR to amplify desired products.  <br/>
-      ② 30 cycle<br />
+<table>
-       a. 94˚C for 1 min<br />
+<tr>
-        b. 55˚C for 1 min<br />
+  <td>Temperature</td> <td>Time</td> <td>Cycle</td>
-         c. 72˚C for 1 min20sec<br />
+</tr>
-      ③ 4℃ for 7 hours </p>
+<tr>
-              </font>
+  <td>94˚C</td> <td>13.5min</td> <td>1</td>
-              <ul>
+</tr>
-                <li> Electrophorese the  total system and observe the lane separation. </li>
+<tr>
-              </ul>
+  <td>94˚C</td> <td>1min</td> <td>30</td>
-              <p><strong>Figure</strong></p>
+</tr>
-               <p> <img src="https://static.igem.org/mediawiki/2012/0/07/1111.png" alt="" class="img_fl img_border" /> </p>
+<tr>
-              <p>(Figure 3: The lane on the figure are 2k  fragments, it shows the GFP and RFP are ligated to the vectors which was  isolated from the bacterial colonies.) </p>
+  <td>55˚C</td> <td>1min</td> <td>30</td>
-               <p><font face="Arial, Helvetica"><br>
+</tr>
+<tr>
+  <td>72˚C</td> <td>1min 20sec</td> <td>30</td>
+</tr>
+<tr>
+  <td>4˚C</td> <td>7hrs</td> <td>1</td>
+</tr>
+</table>
+. Electrophorese the  total system and observe the lane separation. <br/>
+               <img src="https://static.igem.org/mediawiki/2012/0/07/1111.png" alt="" class="img_fl img_border" align="left"/>
+<br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/>
+              (Figure 3: The lane on the figure are 2k DNA fragments, it shows the GFP and RFP DNA fragments are ligated to the vectors which were isolated from the bacterial colonies.)
+</p>
+<br/>
+               <p>
+<font face="Arial, Helvetica">
                    <a name="Culture_the"></a>
-              </font></p>
-              <font face="Arial, Helvetica">
                </font>
                <h3><font color="#0000FF" face="Arial, Helvetica"><b>Cultivate the Bacteria</b></font></h3>
-               <font face="Arial, Helvetica"><p>According to the results of the   PCR detection, we choose positive colonies and  transfer them to 5ml LB liquid media ( 5μl of ampicillin has added) stored  in 12.5ml centrifuge tubes. Put the centrifuge tubes in 37℃  gas bath overnight. </p>
+               According to the results of the   PCR detection, we choose positive colonies and  transfer them to 5ml LB liquid media ( 5μl of ampicillin has added) stored  in 12.5ml centrifuge tubes. Put the centrifuge tubes in 37℃  gas bath overnight.
-              <p><font face="Arial, Helvetica"><a name="Plasmid_DNA"></a> </font></p>
+</p>
-              <font face="Arial, Helvetica"> </font> </font>
+<br/>
+<p>
+              <font face="Arial, Helvetica"><a name="Plasmid_DNA"></a> </font>
                <h3><font color="#0000FF" face="Arial, Helvetica"><b>Plasmid DNA Isolation</b></font></h3>
-               <p><font face="Arial, Helvetica">Use E.Z.N.A.TM Plasmid Mini I to isolate the constructed plasmid mutant-psb1a3-GR. </font></p>
+               <font face="Arial, Helvetica">Use E.Z.N.A.TM Plasmid Mini I to isolate the constructed plasmid mutant-pSB1A3-GR. </font>
-              <p><font face="Arial, Helvetica"><a name="Restriction_Enzyme" ></a> </font></p>
+</p>
+<br/>
+<p>
+              <font face="Arial, Helvetica"><a name="Restriction_Enzyme" ></a> </font>
                <font face="Arial, Helvetica"> </font>
                <h3><font color="#0000FF" face="Arial, Helvetica"><b>Restriction Enzyme  Digestion and Electrophoresis</b></font></h3>
-               <p>From the last step, we got the certain  quantities of isolated plasmids. In this step, we do two restriction enzyme  digestion reactions, one to prove that the plasmid is construct correctly (  mutant-psb1a3-GR ), one  to get sticky ends preparing for the ligation.<br />
+               From the last step, we got the certain  quantities of isolated plasmids. In this step, we do two restriction enzyme  digestion reactions, one to prove that the plasmid is construct correctly (  mutant-pSB1A3-GR ), one  to get sticky ends preparing for the ligation.<br />
-                 <strong>Method</strong></p>
+                 <strong>Method</strong>
-               <ul>
+.Restriction Enzyme Digestion to prove that plasmid is  constructed correctly
-                <li><strong>Restriction Enzyme Digestion to prove that plasmid is  constructed correctly</strong></li>
-               </ul>
+.1.  Prepare the sample  reaction as indicated below:<br />
-               <p align="left">a.  Prepare the sample  reaction as indicated below:<br />
                  Total: 10μl<br />
                  + 1.0μl of Not I  restriction enzyme,#ER0591<br />
                  + 1.0μl of Spe I  restriction enzyme,#ER1251     <br />
                  + 2.0μl of Buffer Tango( 10X )<br />
-                 + 1.5μl of plasmid  mutant-psb1a3-GR<br />
+                 + 1.5μl of plasmid  mutant-pSB1A3-GR<br />
                  + 14.5μl of ddH2O <br />
-                 b.   Electrophorese the total system and observe the lane separation. </p>
+.2.   Electrophorese the total system and observe the lane separation. <br/>
-               <ul>
-                <li><strong>Restriction Enzyme Digestion to get sticky ends preparing  for the ligation.</strong></li>
+. Restriction Enzyme Digestion to get sticky ends preparing  for the ligation.<br/>
-              </ul>
-               <p align="left">a.  Prepare the sample  reaction as indicated below:<br />
+.1.  Prepare the sample  reaction as indicated below:<br />
                  Total: 50μl<br />
                  + 5.0μl of Pst I  restriction enzyme, #ER0611<br />
                  + 5.0μl of Xba I restriction enzyme, #ER0681    <br />
                  + 3.0μl of Buffer Tango( 10X )<br />
-                 + 5.0μl of plasmid  mutant-psb1a3-GR<br />
+                 + 5.0μl of plasmid  mutant-pSB1A3-GR<br />
                  + 32.0μl of ddH2O <br />
-                 b.   Electrophorese the total system and observe the lane separation.<br />
+.2.   Electrophorese the total system and observe the lane separation.<br />
-                 c.   Cut the gel of specific position and collect it in tubes that have  measured weight. <br />
+.3.   Cut the gel of specific position and collect it in tubes that have  measured weight. <br />
-                 d. Use DNA  Gel Extraction Ki to purify the plasmid  DNA mutant-psb1a3-GR(PX) .<br />
+.4. Use DNA  Gel Extraction Ki to purify the plasmid  DNA mutant-pSB1A3-GR(PX) .<br />
-                 Note: Mutant-psb1a3-GR(PX) means plasmid Mutant-psb1a3-GR digested by Pst I and Xba I.</p>
+                 Note: Mutant-pSB1A3-GR(PX) means plasmid Mutant-pSB1A3-GR digested by Pst I and Xba I.
-              <p><strong>Figure</strong></p>
-              <p align="left"><strong><img src="https://static.igem.org/mediawiki/2012/d/d8/11111.png" alt="" class="img_fl img_border" /></strong></p>
-               <p>(Figure 4 : The double  digestion of mutant-psb1a3  forms a linear DNA fragments and it runs slower than circle DNA fragments. This  suggest that the double digestion of mutant-psb1a3 works in a high efficiency, and desired sticky  ends are formed.1,3,5  are plasmids  digested by restriction enzyme Pst I and Xba I from different colonies, 2,5,6  are pure plasmid mutant-psb1a3-GR,  7 is the plasmid mutant-psb1a3.  )</p>
+             <strong><img src="https://static.igem.org/mediawiki/2012/d/d8/11111.png" alt="" class="img_fl img_border" align="left" /></strong>
-              <p align="left">&nbsp;</p>
+               (Figure 4 : The double  digestion of mutant-pSB1A3  forms a linear DNA fragments and it runs slower than circle DNA fragments. This  suggest that the double digestion of mutant-pSB1A3 works in a high efficiency, and desired sticky  ends are formed.1,3,5  are plasmids  digested by restriction enzyme Pst I and Xba I from different colonies, 2,5,6  are pure plasmid mutant-pSB1A3-GR,  7 is the plasmid mutant-pSB1A3.  )
-               <p><font face="Arial, Helvetica"><a name="Ligation1" ></a> </font></p>
+ </p>
+<br/>
+               <p>
+<font face="Arial, Helvetica"><a name="Ligation1" ></a> </font>
                <font face="Arial, Helvetica"> </font>
                <h3><font color="#0000FF" face="Arial, Helvetica"><b>Ligation</b></font></h3>
-               <p>Ligation is the process that target DNA gene is inserted  into a plasmid. Both the vector and insert are prepared to have the sticky ends.  These two kinds of DNA pieces are placed in a reaction tube and the proper DNA  ligase, buffer, and cofactors are added for the reaction to take place. When done  properly, the ligation will result in a successful combination of the insert  and plasmid into one plasmid.Based on the digestion of mutant-psb1a3-GR, terminator DNA fragments,ligation can  be done. We ligate mutant-psb1a3-GR  vector and sticky terminator DNA fragments to construct an new plasmid  mutant-psb1a3-GR-t.By  detecting the quantities of GFP and RFP, terminator efficiency can be  calculated. <br />
+               Ligation is the process that target DNA gene is inserted  into a plasmid. Both the vector and insert are prepared to have the sticky ends.  These two kinds of DNA pieces are placed in a reaction tube and the proper DNA  ligase, buffer, and cofactors are added for the reaction to take place. When done  properly, the ligation will result in a successful combination of the insert  and plasmid into one plasmid.Based on the digestion of mutant-pSB1A3-GR, terminator DNA fragments,ligation can  be done. We ligate mutant-pSB1A3-GR  vector and sticky terminator DNA fragments to construct an new plasmid  mutant-pSB1A3-GR-t.By  detecting the quantities of GFP and RFP, terminator efficiency can be  calculated. <br />
 .  Prepare the control  reaction as indicated below:<br />
 Total: 10μl <br />
-       + 1.0μl of plasmid mutant-psb1a3  (NA) <br />
+       + 1.0μl of plasmid mutant-pSB1A3  (NA) <br />
        + 6.0μl of terminator<br />
        + 2.0μl of T4  DNA Ligase , #EL0011 <br />
        + 1.0μl of 10XT4  Ligase buffer<br />
-.  Put  the tubes in 22℃ water bath, react for 8-12 hours. </p>
+.  Put  the tubes in 22℃ water bath, react for 8-12 hours.
-              <p><font face="Arial, Helvetica"><a name="Bacteria" id="Culture_the"></a> </font></p>
+</p>
+<br/>
+<p>
+          <font face="Arial, Helvetica"><a name="Bacteria" id="Culture_the"></a> </font>
                <font face="Arial, Helvetica"> </font>
                <h3><font color="#0000FF" face="Arial, Helvetica"><b>Bacteria  transformation</b></font></h3>
-               <p>Transform the ligation products into  the DH-5α competent cells, put the plate on 37℃ gas bath for 12-16  hours. </p>
+               Transform the ligation products into  the DH-5α competent cells, put the plate on 37℃ gas bath for 12-16  hours.
-              <p><font face="Arial, Helvetica"><a name="Cultivate"></a> </font></p>
+</p><br/>
+<p>
+              <font face="Arial, Helvetica"><a name="Cultivate"></a> </font>
                <font face="Arial, Helvetica"> </font>
                <h3><font color="#0000FF" face="Arial, Helvetica"><b>Cultivate the Bacteria</b></font></h3>
-               <p>According to the results of the   PCR detection, we choose positive colonies and  transfer them to 5ml LB liquid media ( 5μl of ampicillin has added)  stored in 12.5ml centrifuge tubes. Put the  centrifuge tubes in 37℃ gas bath  overnight. </p>
+               According to the results of the   PCR detection, we choose positive colonies and  transfer them to 5ml LB liquid media ( 5μl of ampicillin has added)  stored in 12.5ml centrifuge tubes. Put the  centrifuge tubes in 37℃ gas bath  overnight.
-               <p><font face="Arial, Helvetica"><a name="Flow" ></a> </font></p>
+</p> <br/>
+               <p>
+<font face="Arial, Helvetica"><a name="Flow" ></a> </font>
                <font face="Arial, Helvetica"> </font>
-               <h3><font color="#0000FF" face="Arial, Helvetica"><b>Flow Cytometer  Analysis</b></font></h3>
+               <h3><font color="#0000FF" face="Arial, Helvetica"><b>Flow Cytometer Analysis</b></font></h3>
-               <p>  1. NaCl solution(  0.9% )<br />
+               Flow cytometry is a laser based, biophysical technology employed in cell counting, sorting, biomarker detection and protein engineering, by suspending cells in a stream of fluid and passing them by an electronic detection apparatus. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of up to thousands of particles per second. <br/>
-. 75% Methanol<br />
+   Each fluorophore has a characteristic peak excitation and emission wavelength, and the emission spectra often overlap. Consequently, the combination of labels which can be used depends on the wavelength of the lamp(s) or laser(s) used to excite the fluorochromes and on the detectors available. It is practical that the expression of RFP and GFP can be measured at the same time.<br/>
-                B.  Procedures:<br />
+<strong>Method:</strong><br/>
-. Transfer overnight suspension culture to 1.5ml centrifuge  tubes and centrifuge at 12000RPM for 30s. Pour the supernatant and add  overnight suspension culture and centrifuge again until enough bacteria has  been collected. <br />
+. Materials:<br/>
-.  Use NaCl  solution(0.9%) to mix the bacteria and vibrate the centrifuge tubes until the  bacteria distributed uniformly.<br />
+&nbsp;&nbsp;1.1. NaCl solution( 0.9% ,M/V)<br/>
-.  Put the centrifuge  tubes into the Flow Cytometer and set  parameters and run the program.</p>
+&nbsp;&nbsp;1.2. 75% ethanol<br/>
-              <p>&nbsp;</p>
+. Procedures:<br/>
-               <p><font face="Arial, Helvetica"><a name="Fluorescence"></a> </font></p>
+&nbsp;&nbsp;2.1. Bacterium are harvested by centrifuge at 10000g for 30s, then discard the supernatant. Repeat this step again until we got adequate bacterium.<br/>
+&nbsp;&nbsp;2.2. Suspend the bacterium With NaCl solution(0.9%) and vibrate the centrifuge tubes until the bacterium are distributed homogeneous.<br/>
+&nbsp;&nbsp;2.3. Load the bacteria containing pSB1A3 to Flow Cytometer (Beckman), set the parameters. Measure the GFP-FL1 and RFP-FL2 by Cytometer.
+</p>
+<br/>
+               <p>
+<font face="Arial, Helvetica"><a name="Fluorescence"></a> </font>
                <font face="Arial, Helvetica"> </font>
                <h3><font color="#0000FF" face="Arial, Helvetica"><b>Fluorescence  Microscope</b></font></h3>
-              <p><strong>Method</strong><br />
+A fluorescence microscope is an optical microscope that uses fluorescence and phosphorescence  reflection and absorption to study properties of organic or inorganic substances and generate an image.Fluorescence microscope detection are used to confirm the expression of GFP and RFP which are illuminated with light of a wavelength which excites fluorescence in the sample.
-Add 10μl of former bacteria solution to  micro slide and cover with coverslip.Then placed it on the Fluorescence  Microscope with 488nm light activating and observe the GFP and RFP. </p>
+<br/>
-<br>
+              <strong>Method</strong><br />
+Add 10μl of bacteria solution to micro slide and cover with coverslip.
+Placed the micro slide on the Fluorescence Microscope. Set parameters to detect GFP and RFP. <br/>
+Generate an image of fluorescence protein and save it.
+</p>
+<br/>
                  </article>

Team:SUSTC-Shenzhen-B/protocol1

From 2012.igem.org

Latest revision as of 21:47, 26 October 2012

Lab Protocol

Site-Directed Mutagenesis

Restriction Enzyme Digestion for Verification

Media Preparation

Bacterial Transformation

Colony PCR for Verification

Cultivate the Bacteria

Plasmid DNA Isolation

Restriction Enzyme Digestion and Electrophoresis

Polymerase Chain Reaction(GFP & RFP) and Electrophoresis

Double Restriction Enzyme Digestion and Electrophoresis.

Ligation

Bacterial Transformation

Bacterial Colony PCR

Cultivate the Bacteria

Plasmid DNA Isolation

Restriction Enzyme Digestion and Electrophoresis

Ligation

Bacteria transformation

Cultivate the Bacteria

Flow Cytometer Analysis

Fluorescence Microscope