Team:NU Kazakhstan/Protocols




SELEX procedure

  • Binding buffer: 50mM Tris-HCl, pH 7.5, 25mM NaCL, 5 mM MgCl2, 10mM dithiothreitol (DTT);
  • Wash buffer is same as binding buffer;
  • Elution buffer: 0.4 M sodium acetate, 5mM EDTA, and 7M urea, pH 5.5;
  • MF-Millipore membrane, mixed cellulose esters, hydrophilic, 0.45 μm, 13 mm. white, plain (HAWP filter, 0.45 μm,13 mm diameter, Millipore) – 2 pcs;
  • Filter holder – 2 pcs
  • ssDNAs library was dissolved in sterile water, and concentration was 1 μg/ μl;
  • Target protein
  • Petri dish – 1 pcs
  • 6% TBE gels 1.0 mm, 10 well
  • Syringe with a needle – 2 pcs
  • glycogen (20 mg/ml); ammonium acetate (7.5 M)
  • Ethanol (100% and 75%)
  • 10*PCR buffer with MgCl2; dNTPs (2.5 mM); DL-F (20 μM); DL-R phophorylated (20 μM); Taq Polymerase; Lambda exonulcease
  • Equipments:
  • Thermocycler
  • Rotator with variable speed (15 rpm) for 1 ml tubes
  • Freezers (-20 and -80oC)
  • Centrifuge – 13000rpm
  • Buffers for SELEX
    Binding buffer/Wash buffer:
  • DTT- Dithiothreitol, Tris-HCl pH 7.5
  • Tris-HCl (50mM) – 7.88g for 1L
  • NaCl (25mM) – 1.461g for 1L
  • MgCl (5mM) – 0.476g for 1L
  • DTT (10mM) – 1.5425g for 1L
  • Elution buffer:
  • Sodium acetate (0.4M) – 32.812g for 1L
  • EDTA (5mM) – 1.86g for 1L
  • Urea (7M) pH 5.5 – 420.42g for 1L
  • Ammonium acetate (7.5M) – 578.7g for 1L/ 28.9g for 50ml
  • Procedure
    1. Pre-wetted
  • Soak membrane in sterile water for 1min and put membrane in the filter holder;
  • To eliminate DNAs that bound to the membrane, DNAs (1 μg/μl) were passed three times prior to the selection cycle through pre-wetted nitrocellulose acetate membranes in “Pop-top” filter holders;
  • 2. DNA denature
  • For the first cycle of selection, 35.5 μl (1μg/ μl) DNAs were added in 114.5 μl binding buffer solution (volume 150 μl);
  • And then were denatured at 95oC for 10 min;
  • Then were allowed to cool in thermocycler to approximately 300C (about 1.5 hours);
  • 3. Binding
    Denatured DNAs (35.5 μl, 1μg/ μl DNAs + 114.5 μl binding buffer) + 50 μl target protein (87 μg/ml) were incubated at 15 rpm on a variable speed rotor for 1 hour and 45 min at room temperature.
    4. Washing
  • Soak membrane in wash buffer (the same as binding buffer) for appr. 1 min and then put the membrane in the filter holder;
  • Aspirate the binding reaction mixture (DNAs+target) with a syringe with a needle
  • Remove the needle and inject the binding reaction mixture into the filter holder with a membrane and then inject 1 ml wash buffer solution (the same as binding buffer) and let wash buffer pass through the membrane.
  • 5. Elution
  • Heat 200ul elution buffer(0.4 M sodium acetate, 5 mM EDTA, 7M urea, pH 5.5) to 70-800C
  • Inject 200 μl of elution buffer into the filter holder to elute DNA that was retained in the filter into a fresh tube. Make sure that all liquid is out.
  • Take filter and cut into 4 pieces and put into elution buffer with DNA and put the tube to water bath at 70-80oC over the course of 5 min.
  • The elute was transferred to a fresh tube (Elute 1) and filter was eluted again as above (Elute 2)
  • 6. Precipitation
  • The elutes (1 and 2) were diluted with 200 μl H2O (each) before ethanol precipitation;
  • For precipitation: 2x6 μl glycogen (20 mg/ml) + 2x200 μl ammonium acetate (7.5 M) + 2x1 ml ethanol (100%) were incubated for 1 hour (or can leave overnight if no pellet is observed after centrifugation) at -80oC;
  • Centrifugation under 13,000 rpm at 4oC for 1 hour;
  • Carefully remove the supernatant without disturbing the pellet (S1 and S2 – keep supernatant just in case)
  • Washing the pellet with 75% ethanol solution (-20oC) (1000 μl) (add 1000 ul of ethanol and make sure the pellet came out; centrifuge for 5 min to let the pellet settle again; remove ethanol without disturbing the pellet leaving some liquid in the tube)
  • Repeat previous step one more time (2 washes of each pellet; WP1-1, WP1-2 for pellet from E1; WP2-1, WP2-2 for pellet from E2)
  • After the second wash carefully remove ethanol without disturbing the pellet with a pipette
  • Dry under the current of air in horizontal form for 2-3 minutes until it becomes transparent (maximum 5 minutes)
  • Resolve the pellet of Elute 1 in 50 μl pure water
  • After washing and drying the pellet from Elute 2, add resolved pellet from Elute 1 (50ul) into it and it is ready to do PCR.
  • 7. PCR (dsDNA)
    DNA (random library), template 1
    10*PCR buffer with MgCl25
    dNTPs (2.5 mM) 4
    DL-F (20 μM)1
    DL-R (20 μM)1
    Taq Polymerase (2.5 U) 0.5
    PCR conditions:
    95oC 5 min
    95oC 30s
    64oC 45s
    72oC 45s
    72oC 10min
    4oC Keep at
    PCR product is about 80 bp
    8. Check PCR product with 6% TBE gel
    Line 1: 1 μl marker + 7 μl loading buffer
    Line 2: 2 μl DNA library 6 1 μl loading buffer
    Line 3: 3 μl product 1 + 5 μl loading buffer
    Line 4: 3 μl product 2 + 5 μl loading buffer
    μ 20x SYBR Green is added to each well
    Gel running conditions: 200V

    Cloning and transformation

  • Resuspended DNA (Resuspend well in 10ul dH20, pipette up and down several times, let sit for a few minutes) Competent cells (50ul per transformation)
  • Ice (in ice bucket/container)
  • 2ml tube (1 per a transformation')
  • 42ºC water bath
  • SOC media (check for contamination!)
  • Petri dishes with LB agar and appropriate antibiotic (2 per transformation)
  • glass beads or spreader
  • 37ºC incubator
  • 10pg/ul RFP Control (pSB1A3 w/ BBa_J04450)
    1. Procedure:
    2. Start thawing the competent cells on ice.
    3. Add 50 µL of thawed competent cells into pre-chilled 2ml tube, and another 50µL into a 2ml tube, labelled for your control.
    4. Add 1 - 2 µL of the resuspended DNA to the 2ml tube. Pipet up and down a few times, gently. Make sure to keep the competent cells on ice.
    5. Add 1 µL of the RFP Control to your control transformation.
    6. Close tubes and incubate the cells on ice for 30 minutes.
    7. Heat shock the cells by immersion in a pre-heated water bath at 42ºC for 60 seconds.
    8. Incubate the cells on ice for 5 minutes.
    9. Add 200 μl of SOC media (make sure that the broth does not contain antibiotics and is not contaminated) to each transformation
    10. Incubate the cells at 37ºC for 2 hours while the tubes are rotating or shaking. Important: 2 hour recovery time helps in transformation efficiency, especially for plasmid backbones with antibiotic resistance other than ampicillin.
    11. Label two petri dishes with LB agar and the appropriate antibiotic(s) with the part number, plasmid backbone, and antibiotic resistance. Plate 20 µl and 200 µl of the transformation onto the dishes, and spread. This helps ensure that you will be able to pick out a single colony.
    12. For the control, label two petri dishes with LB agar (AMP). Plate 20 µl and 200 µl of the transformation onto the dishes, and spread.
    13. Incubate the plates at 37ºC for 12-14 hours, making sure the agar side of the plate is up. If incubated for too long the antibiotics start to break down and un-transformed cells will begin to grow. This is especially true for ampicillin - because the resistance enzyme is excreted by the bacteria, and inactivates the antibiotic outside of the bacteria.
    14. You can pick a single colony, make a glycerol stock, grow up a cell culture and miniprep.
    15. Count the colonies on the 20 μl control plate and calculate your competent cell efficiency.

    DOT ELISA for biotynilated CEA

  • Nitrocellulose membrane
  • Streptavidin-HRP
  • Blocking buffer
    1. Procedure
    2. Place 7.5 ul drop of anti-CEA antibody on nitrocellulose membrane (make 3 concentrations: 1:200, 1:400, and 1:800). Also put positive (Biotynilated marker) and negative (PBS) controls
    3. Allow to air dry on paper towel.
    4. Soak membrane in blocking buffer for 45 min.
    5. Remove membrane from blocking buffer and allow to air dry on paper towel.
    6. Coat membrane in biotynylated CEA for 30 min.
    7. Wash membrane 3-4 times in 1X KPL wash solution.
    8. Allow to air dry on paper towel.
    9. Coat membrane in BCIP/NBT for 15 min in dark. Once color change can clearly be seen stop reaction with di water.
    10. Allow membrane to air dry on paper towel in the dark before taking picure.


    Materials and reagents
  • Protein marker
  • 10% Ammonium persulfate
  • 10% SDS
  • 40% Acrylamide/Bis
  • b-mercaptoethanol
  • Tris HCl
  • Glycine
  • EDTA
  • Glycerol
  • Isopropanol
    1. Buffers:
    2. 10XRunning buffer:
    3. Tris base - 30.3 g
      Glycine - 144 g
      SDS - 10 g
      Completely dissolve in 800 ml of di water and then add more di water up to 1 L.
    4. 2XSDS protein sample buffer:
    5. 1M Tris HCl - 1.25 ml
      10% SDS - 4 ml
      Glycerol - 2 ml
      0.5M EDTA - 0.5 ml
      Bromophenol Blue - 4 mg
      14.3 M b-mercaptoethanol - 0.2 ml
      Water - add to total volume of 10 ml
    1. Make 10% SDS PAGE gel with 4% stacking gel
    2. Prepare samples by adding the same amount of 2x protein sample buffer to each protein sample, then, mix and boil at 95degC for 10 min.
    3. Spin the samples at maximum speed for 1 min.
    4. Run the samples in 1X electrophoresis Running buffer at voltage from 100V to 150V.
    5. Use Coomasies blue staining to visualize the proteins.