Chemical Synthesis of ImpA (adenosine 5'-phosphorimidazolide)

Posted by ychoi
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Based on 26.4.4 Current Protocols in Molecular Biology 2005.

This protocol is used to synthesize ImpA which is required to make the intermediate reaction product of RNA/DNA ligases.  This is desirable when the target molecule has a 5'-phosphate because use of an activated linker oligo allows ligation without ATP and avoids self-circularization of the molecule of interest.

Work must be done in a fume hood.



Reagent Supplier Product # CAS #
Adenosine 5 -monophosphoric acid (5 -AMP) MP Biomedical 210008001 18422-05-4
Dimethylformamide (DMF) Sigma D-4551 68-12-2
Triphenylphosphine Sigma T84409 603-35-0
2,2 -Dipyridyldisulfide Sigma/Fluka 43791 2127-03-9
Imidazole Sigma I2399 288-32-4
Triethylamine Sigma T0886 121-44-8
Sodium perchlorate Sigma 410241 7601-89-0 
Acetone Sigma 154598 67-64-1
Anhydrous ethyl ether Sigma 346136 60-29-7
Thin layer chromatography (TLC) cellulose plates with a 254-nm fluorescence indicator (cellulose-F TLC) Analtech 06011  
(NH4)2SO4 Sigma A4418 7783-20-2
100% ethanol Gold Shield    
MgCl2 Hexahydrate Enzyme Grade Fisher BP214-500 7791-18-6
glycerol Fisher BP229-1 56-81-5
HEPES VWR VWR1481-04 7365-45-9
acetylated bovine serum albumin Sigma B8894 9048-46-8



Synthesize ImpA

1. Dissolve 174 mg (0.5 mmol) of 5'-AMP in 15 ml DMF. Keep a 50-μl aliquot for TLC analysis.

2. Dissolve 262 mg (1 mmol) of triphenylphosphine, 220 mg (1 mmol) of 2,2'-dipyridyldisulfide, and 170 mg (2.5 mmol) of imidazole in 15 ml DMF and 0.9 ml (2.5 mmol) triethylamine.  Keep a 50-μl aliquot for TLC analysis.
3. Add the AMP solution dropwise to a vigorously stirred triphenylphosphine containing solution. Cover beaker and stir for 1.5 hr at room temperature under fume hood.

Purify ImpA

4. Precipitate the ImpA by adding the reaction mixture dropwise into a vigorously stirred solution of 1.1 g (9 mmol) sodium perchlorate, 115 ml acetone, and 55 ml anhydrous ethyl ether.

5. Let the precipitate settle to the bottom of the beaker for 1 hr and decant 150 ml of the supernatant without perturbing the precipitate.
A large glass pipet connected to a pipetting aid may also be used to aspirate off the supernatant.
6. Once the volume has been reduced to 20 ml, resuspend the precipitate with the residual supernatant and transfer the suspension to 30-ml Corex tubes. Transfer the residual precipitate by rinsing the beaker with small volumes (5 ml) of acetone.
Collect the precipitate by centrifuging 10 min at 3000 × g (5000 rpm with a Sorvall SS34 rotor), room temperature.
7. Remove the supernatant and wash the pellet two times by resuspending it with 10 ml acetone and then centrifuge 5 min at 3000 × g, room temperature.
8. Resuspend the pellet in 10 ml anhydrous ethyl ether and centrifuge 20 min at 3000 × g, room temperature. Dry the pellet overnight in a vacuum oven at 40C.
9. Store the dried powder up to 3 weeks at -20C protected from humidity.
The yield of ImpA is 80 mg. The molecular weight of ImpA is 396.28 g/mol.

Perform quality control of synthesized ImpA

10. Soak cellulose-F TLC plates in 10% saturated aqueous (NH4)2SO4 and dry the TLC plates in open air for 1 hr or blow dry.
11. Dissolve 1 mg ImpA in 50 μl water and spot the sample on pre-treated TLC plates with aliquots of the AMP solution and triphenylphosphine solutions using glass capillaries. Develop the TLC by using 80% ethanol and visualize the spots under 254-nm UV light.
The AMP should have the lowest retention factor (Rf = 0.26), ImpA should run faster (Rf = 0.4), and the components of the triphenylphosphine solution all run near the solvent front.