SELEX

Bill Of Materials: You could see a complete BoM here (upload the bill).

Amount of time: 1 day

Total costs: 100 €.

DIY nitrocellulose column manufacture

1. Download the columns of the stl files from our github repository.

2. 3D print the stl models in PETG. For more information about the reasons why we choose this material see the results page.

ADVICE: We have found the following parameters as the optimal ones printing with a Prusa i3 machine:

-Filaments diameter of 1.75mm

-Nozzle at 230ºC. Base 80ºC with Nelly hairspray. (CAUTION: The brand of the headspray must be Nelly.



3. Separate the 3D printed structures from the printer base. Remove the excess of printed material.

4. Treat the columns with dichloromethane until the surface gets smooth.



ADVICE: For us it have worked putting the columns in glass jar, above a cardboard pedestal. Then cover the base of the jar with dicloromethane without touching the 3D printed files. Put the jard on the 3D printed hotbed at 80ºC for 20 minutes.

5. Wash the columns three times in deionized water to clean them from dicloromethane.

6. Put the columns in sterilizing solution (0,1N NaOH, 1% (m/v) EDTA) to inactivate DNAses and remove other pollutants. Keep overnight at room temperature.

7. Keep in milliQ water until its use.

Designing and ordering the initial library

Amount of time: 20 mins

Total costs: 100 € (Without been sponsored)

8. Design your library as a DNA of 30-40 random nucleotides flanked by constant extremes of 12-18 nucleotides. Use HPLC purification. Also order the primers for this constant edges.

ADVICE: For us, IDT have worked well as a DNA provider. They are also iGEM sponsor at our year, so this libraries could be free for igem teams.

ADVICE: The following sequence have fit well to us:.



Prepare the library pool

9. Resuspend 2 nmol de la library pool on 200 µl of Binding Buffer (Tris-HCl PH= 7,4 20 mM; MgCl21mM; NaCl 150mM; KCl 5 mM).

10. Denatured the library by heating it at 90ºC for 10 min and immediately cold it on ice for another 10 min.

11. Wash in distilled water and mount the nitrocellulose column by cutting a small square of the membrane and then pre-wet it with the BB.

CAUTION: The colums break easily, so do not aplyy too much force on them.

12. To get rid of the DNA that unespecifically binds to the system, apply the library through a nitrocellulose membrane and centrifuge 1 min at 8000 rpm. Quantify the DNA that does not bind unspeficically and note it as the initial DNA.

Protein-Aptamer incubation

13. Incubate the flowthrough with the protein of interest during 1 hour.

14. Apply the DNA to a new nitrocellulose membrane as in step 3.

15. Wash the membrane four times with 300 µl of BB, like on step 3.

16. Recover the membrane and transfer it to a new Eppendorf tube without letting it dry.

Denatured the protein and elute the selected DNAs

17. Add 400µL of FES and 500 µL of phenol and mix in a thermomixer at 1.400 rpm for 10 min.

18. Transfer the liquid to a new tube and repeat the step 8 but this time with 200 µl of each regeant.

19. Mix the two samples and add 200 µl of Milli-Q wáter to allow the phase separation and centrifuge 10 min at 16100 g.

20. Transfer the aqueous phase (upper) to a new 2 ml tube and PCI extract the DNA.

PAUSE POINT: You can leave the PCI precipitation overnight.

Library amplification

21. Prepare the PCR mixture for a final volume of 50 µl per reaction and a final primer concentration of 0,8 µM.

22. Perform the amplification with the following amplification conditions (adjust according to the primers used):



23. Prepare an agarose gel at 3%. Load the samples and perform the electrophoresis at 90V for 50 min.

24. Remove the gel and observe the bands under UV light.

25. It is needed at least 1 ug to continue with the next round. If it not accomplish , a further amplification is needed.