Molecular Cloning Protocols



  • EcoRI, BglII, PstI, XhoI, SpeI,XhoI,FD buffer,FD Green buffer, DNA,sterile water

Digestion temperature

  • 37℃

Time period

  1. Plasmid: 10-30min(the higher the concentration, the longer time it takes.
  2. DNA fragment:1-2h(the higher the concentration, the longer time it takes.Since it is more difficult to digest DNA than plasmid, digesting DNA requires more time.

System amount

  1. 50ul system is preferred if there is subsequent operations. If digestion is only for identification, 20ul system is used.
  2. During the double digestion, the optimum buffer system which is suitable for both enzymes should be utilized. Without such shared system, digestion of two different enzymes is usually separated.


Enzyme 1μl
10×FD Buffer or FD Green buffer2μl
DNA ≤1μg
Sterile waterup to 20μl

Gel extraction


  • Agarose Gel DNA Extraction Kit (centrifugation)

Experimental Procedure

  1. Add 500uL balance liquid(BL) to the spin column(CA2). Centrifuge at 12,000 x g for 1 min at room temperature. Discard the flow-through and put the column back to the collection tube.(optional)
  2. Excise the DNA fragment from the agarose gel and weigh it in a clean centrifuge tube (A gel slice of 100 mg approximately equals to 100 µL).
  3. Add 3 volume of sol solution(PN) to the centrifuge tube and incubate the mixture at 50℃ for 10 min with mixing the tube by tapping the bottom of the tube occationally till the gel has melted completely. Cool the tube to RT.
  4. Transfer the mixture to an spin column (CA2) within a collection tube. Centrifuge at 12,000 x g for 1 min at room temperature. Discard the flow-through and put the column back to the collection tube.
  5. Add 600 µL DNA Wash Buffer (PW) to the column and centrifuge at 12,000 x g for 1 min at room temperature. Discard the flow through and put the column back to the collection tube.
  6. Repeat step 5.
  7. Put the column back to the collection tube. Centrifuge at 12,000 x g for 2 min at room temperature to discard the PW totally. Keep the lid open for several minutes.
  8. Put the column back to the clean collection tube. Add ddH2O to the column vacantly and keep it at room temperature for 2 minutes. Centrifuge at 12,000 x g for 2 min at room temperature to collect the DNA solution.
  9. Transfer the eluted solution to CA2 and keep it at room temperature for 2minutes. Centrifuge at 12,000 x g for 2 min at room temperature.
  10. Gel electrophoresis to verify the correctness and concentration of bands.

Important Notes

  1. If the balance liquid turns turbid, incubate it at 37℃ for several minutes.
  2. When cutting the gel, keep the UV irradiation time period as short as possible, otherwise DNA would be damaged.
  3. For those DNA fragment shorter than 100bp or larger than 10kb, the sol solution volume should be increased as well as the time period for adsorption and elution.
  4. Recovery depends on the initial DNA amount and elution volume. The less the DNA, the less the elution volume, the smaller of recovery.



  • KOD-Plus-Neo
  • Tap enzymes

Experiment system

  • Experiment system with KOD enzymes (Mostly 50uL)
  • Experiment system with taq enzymes:
  • Reaction temperature:
        Two-step method:
        Denature and extension
          98℃ 10sec 
          68℃ 30sec/kb
                        × 25-45 cycles

        Three-step method:
        Denature,annealing and extension
          98℃ 10sec   
         (Tm-5)℃  30sec
          68℃  30sec/kb
                       × 25-45 cycles

Important Notes

  1. KOD enzymes should be operated in ice.
  2. Two-step method is preferred if primer Tm is relatively high.
  3. 1.2% agarose gel is used to separate 1kb-5kb DNA; 0.8% agarose gel is used to separate 3k-10k DNA; 2.5-3% agarose gel is used to separate DNA longer than 100bp.
  4. PCR reaction system varies from 20uL to 100uL. Under most cases, 20uL system is preferred as long as PCR is for identification only. However, when subsequent experiments such as tailing, digestion which require certain amount of DNA are necessary, 50uL system is usually preferred.
  5. KOD enzymes are preferred if the purpose of PCR is for gene amplification. At the same time, PCR for identification or tailing usually requires taq enzymes.

PCR Purification


  • LifeFeng DNA PCR purification kit

Experimental Procedure

  1. Transfer PCR system (< 250uL) to 1.5mL microcentrifuge tube. Add 5 volume Buffer PD and mix. Have a quick centrifugation to remove the liquid on lid.
  2. Transfer the mixture to DNA spin column (A4) and put it in a collection tube.
  3. Centrifuge at 7000g for 1 minute and replace the collection tube with a new collection tube.
  4. To wash, add 500uL Buffer WB to the spin column (A4) and centrifuge at 7000g for 1 minute. Discard the flow-through and place the column back in the same tube.
  5. Repeat step 4.
  6. Centrifuge at 12,000g for 2 minutes.
  7. Place spin column in a clean 1.5 ml microcentrifuge tube.
  8. To elute DNA, add ddwater (>30uL) to the center of the membrane. Let the column stand for 1-2 min and centrifuge the column for 1 min at 12,000g.
  9. Add elution liquid back to spin column and centrifuge at 12,000g for 1 min. ( Inoculating ddwater at 65℃ prior would improve the elution efficiency )
  10. Gel electrophoresis to verify the concentration of bands.

Important Notes

  • Buffer PD contains irritant compounds, thus be careful not to avoid contamination of skin.

DNA Ligation

Experimental Procedures

  1. Set up the following reaction in a microcentrifuge tube on ice.
  2. Gently mix the reaction by pipetting up and down and microfuge briefly.
  3. For cohesive (sticky) ends, incubate at 16°C overnight or room temperature for 10 minutes.
  4. For blunt ends or single base overhangs, incubate at 16°C overnight or room temperature for 2 hours
  5. Chill on ice and transform 1-5 μl of the reaction into 50 μl competent cells.

Ligation System

10X T4 DNA Ligase Buffer 2 μl
Vector DNA 0.025 pmol
Insert DNA 0.076 pmol
T4 DNA Ligase 1μl
Nuclease-free water to 20 μl

Bacteria Culture


  1. DH5a (F- endA1 glnV44 thi-1 recA1 relA1 gyrA96 deoR nupG Φ80dlacZΔM15 Δ(lacZYA-argF)U169, hsdR17(rK- mK+), λ–)use for cloning
  2. BL21(DE3) (fhuA2 [lon] ompT gal (λ DE3) [dcm] ∆hsdS,λ DE3 = λ sBamHIo ∆EcoRI-B int::(lacI::PlacUV5::T7 gene1) i21 ∆nin5) use for expressing


LB Medium

NaCl 10g
Tryptone 10g
Yeast Extract 5 g
Water up to 1000mL

SOB Medium

Tryptone 20g
Yeast extract 5g
NaCl 0.5g
1M KCl 2.5ml
ddH2O up to 1000 ml
Adjust pH to 7.0 with 10N NaOH, autoclave to sterilize, and add 10 ml of 1 M MgCl2 before use


Storage Use
Kana 50 mg/ml(Water) 50 μg/ml
Amp50 mg/ml(Water)50 μg/ml
Tet10 mg/ml (Alcohol)10 μg/ml
Cm34 mg/ml (Alcohol)68 μg/ml


  1. Remove competent cells from freezer and allow to thaw
  2. Add 3-5 μl of DNA to the cells
  3. Incubate on ice for 30 min
  4. Heat shock the cells at 37°C for 1.5 mins
  5. Add 500 μl of SOB medium, and incubate in a shaker at 37°C for 1 hour
  6. Centrifuge for 3 min at 3,000 g, remove and keep 100 μl of the supernatant, and pour away the rest
  7. Re-suspend the pellet in the 100 μl of supernatant that was removed earlier
  8. Spread All onto one plate with corresponding antibotics, and then pour the rest onto another. Incubate the plates overnight at 37°C.

Violacein Protocols

Induction and Extraction

  1. Incubate the monoclonal from medium in a shaker at 37°C overnight
  2. Add 0.1% Arabinose, 1mM Ferrous ammonium sulfate and 40 μM to start induction for another 6 hours
  3. Centrifuge for 1 min at 10000rpm, remove the LB Medium
  4. Add 800 μL 10%SDS and break cells using ultrasound
  5. Add 800 μL ethyl acetate to extract violacein/deoxyviolacein
  6. Use rotovap to concentrate violacein and resuspend with methanol


  • Column: C18, 15cm
  • Mobile phase: 75% methanol, 25% ddH2O
  • Injection volume: 20 μL
  • Speed: 0.5 mL/min
  • Detection: 230 nm

Fatty Acid Protocols

  1. Transfer a fresh transformed colony to 5ml LB liquid medium and shake at 37℃ overnight(12h).
  2. Add seed broth to 50-100ml LB medium(volume ratio is 3% and loaded liquid is 20%) and shake until the OD600 reaches 0.6 or so. Add inducer of appropriate concentration to induce gene expression.
  3. Continue shake culture for another 20h. Contrifuge at 8,000 for 5min. Collect supernatant and bacteria sediment respectively (prepare 3 parallel samples, each 10ml).
  4. Extract the supernatant by chloroform-methanol(2:1) solution of the same volume (shake for 5min) place until stratification. Dry the lower organic layer at 50℃ for about 24h. Suspend the bacteria by 1ml ddH2O. Add 20ml chloroform-methanol solution and extract for another 2 times.(Attention: weigh the empty flask before drying).
  5. Weigh the crude extract and record the results. (For reference only)
  6. Dissolve the crude extract with 1ml methanol and add 2ml tetrafluoroboron. Methyl esterificate at 60℃ for 30min. After the reagent cools down, add 2ml N-hexane and extract for 2 times. Collect the upper layer and dry overnight at 50℃ (weigh the empty flask before drying as well).
  7. Add the crude bacteria extract to 1ml chloroform-methanol(2:1) solution and shake by vortex to extract the total lipid of the cells. Add 2ml methanol-water(4:1) as saponification reagent. Saponificate in 60℃ water bath for 1h. Then esterificate as the 6th step.
  8. Dissolve the obtained fatty acidmethyl ester(FAME)mixture with N-hexane(2mg/ml). Take 1ml sample for test.
  9. GC-MS condition:
Sample injector temperature: 250℃;
Detector temperature: 280℃;
Temperature programming: begin at 100℃ and last 2min. Warm to 250℃ at the rate of 10℃/min and last 5min.
Use C15 FAME as the interior label for quantification. (Quantity of C15 FAME depends on the sample concentration)