intavis AG Bioanalytical Instruments

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1 Fmoc resin cleavage and workup When the synthesis on the MultiPep has been finished the resin contains a fully assembled peptide with some protected side chains. Cleavage refers to the final removal of the peptide from the resin as well as selective removal of amino acid side chain protecting groups. This process is performed with Trifluoroacetic acid (TFA) and scavengers. Some of the amino acid side chains are sensitive to chemical reactions and the groups liberated are very reactive. Therefore the cleavage cocktail is made up with scavenger reagents. Scavengers are used to surround the amino acid side chain protecting groups and prevent them from reattaching to the peptide. There are numerous cleavage cocktails but only a general-purpose one is used below. The cocktail recommended here works well with the protection groups listed in our amino acid table. Before performing the cleavage, the resin should be thoroughly washed with DCM to remove all traces of DMF. Residual basic DMF can inhibit TFA acidolysis. Dry the peptide resin under high vacuum for 4 h, or preferably over night over KOH. After cleavage the peptide is precipitated with cold ether, collected and washed again with ether. Then it is dissolved in water or an aqueous solution and lyophilized. Various amino acid side chain protecting groups require different scavengers to be added to the TFA cleavage mix. Cleavage cocktail General cleavage cocktail Peptides containing all amino acids best for peptides with R, C, M, W Peptides containing all amino acids except R and/or W General Mixture A 92.5% TFA 2.5% water 5.0% TIS Mixture B 82.5 % TFA 5.0 % water 5.0 % thioanisol 5.0 % phenol 2.5 % EDT Mixture C 94 % TFA 2.5 % water 1.0 % TIS 2.5 % EDT Reference EMD Biosciences Technical Note, "Fmoc Resin Cleavage and Deprotection"

2 Synthesis Work-up Columns Hazardous Chemicals! General Purpose Cleavage Cocktail 92.5 % (v/v) trifluoroacetic acid, TFA 5 % (v/v) triisopropyl silane 2.5 % (v/v) water Trifluoroacetic acid (TFA) is a very strong volatile acid and ether is highly flammable. The entire cleavage and work up must be executed in a fume hood. Safety glasses, gloves and lab coat are mandatory at this stage. All waste must be disposed of according to national regulations. 1. Take the columns out of the holder and label them carefully. Put them in a vacuum dessicator or connect them to a source of nitrogen and remove all traces of ethanol. If possible, weigh the columns and determine the gross yield by comparison with the starting weight. (Weigh column, frit and resin aliquot with container before starting). 2. Transfer the resin and both frits to a polypropylene screw cap vial or a glass flask by pushing from the bottom with a blunt toothpick. You will need about 1 ml of TFA per mg of resin and at least the 5-fold volume of ether. To cleave 100 Jmoles peptide a 50 ml FALCON tube is recommended. 3. Prepare the appropriate cleavage cocktail (see composition below) and add it to the resin or add scavengers first, followed by the TFA. Gently swirl the tube to mix resin and TFA. Do not fully close the tube as during the first minutes some protection groups are released as a gas. Let the solution stand for 3 hours, swirling it every now and then, especially during the first 5 minutes. 4. Pour about the five-fold volume of ice-cold ether on the cleavage mixture and stir or shake. We recommend to use tert-butyl-methyl-ether. The solution will warm up and has to be cooled on ice. Let the precipitate settle, decant most of the clear ether and wash the precipitate with fresh ether 2 to 3 times. We provide single use filter tubes to filter the peptide from the ether. If you have an explosion-proof cooled centrifuge you can also spin down the precipitated peptide. It is hazardous and highly illegal to spin ether solutions in a normal centrifuge! 5. Dissolve the precipitated peptide. Filter the resin particles from the solution using the spent synthesis column or the filtration column used to isolate the precipitate. Freeze the solution, decant residual ether and lyophilize. Most peptides will be soluble in water. If this fails, freeze the suspension and decant the ether. Evaporate residual ether and add up to 30 % acetonitrile. If this also fails to dissolve the peptide, freeze it again and lyophilize. Try to dissolve the peptide in water again. If it is a very acidic sequence, addition of a few drops of diluted ammonia may help. Otherwise add acetonitrile again. Some peptides are insoluble under these conditions and very difficult to handle.

3 6. Weigh the peptide to determine the final yield. With some losses during synthesis, cleavage and work up you should expect a final yield of approx. 70 to 80 %, depending on the nature of the peptide. 7. Analyze your peptides by reversed-phase HPLC and mass spectrometry. As there are numerous potential problems during synthesis and work-up it is highly recommended to check the peptides before using them in biological assays. Peptide Isolation After cleavage from the resin the peptide is obtained as a solution in trifluoroacetic acid. It can be isolated by evaporation of the acid or precipitation with cold ether. A third method is repeated extraction into water. All methods have serious drawbacks: Evaporation in a rotary evaporator is tedious. After evaporation the residue must be extracted with ether to remove scavengers and protection groups and then filtered from the ether solution. The method is very labour and time consuming. Precipitation with ether is very elegant, but requires separation of the precipitate from the solution. The precipitate usually is too fine to be filtrated properly. It can be centrifuged down and the ether decanted. This procedure requires an explosion proof centrifuge or a process otherwise protected against ignition of ether vapour. Check the applicable safety regulations. Extraction of the peptide into water is difficult because the procedure does not effectively remove the TFA. It works for easily water-soluble peptides only. After about ten rounds of extraction most of the TFA should be removed and the peptide solution can be lyophilized.

4 Synthesis Work-up Plates Hazardous Chemicals! General Purpose Cleavage Cocktail 92.5 % (v/v) trifluoroacetic acid, TFA 5 % (v/v) triisopropyl silane 2.5 % (v/v) water Trifluoroacetic acid (TFA) is a very strong volatile acid and ether is highly flammable. The entire cleavage and work up must be executed in a fume hood. Safety glasses, gloves and lab coat are mandatory at this stage. All waste must be disposed of according to national regulations. 1. Take the reaction plates out of the vacuum holder and label them carefully. Before performing the cleavage, the resin should be thoroughly washed with DCM to remove all traces of DMF. Put them in a vacuum desiccator to dry the resin completely before you begin the cleavage. 2. Place the reaction plate on top of a deep well plate inside our vacuum cleavage tray. The deep well plate will collect the TFA peptide solution during the procedure. Different deep well plates can be used. The volume ranges from 1.2 to 2.0 ml per well. 3. Prepare the appropriate cleavage cocktail (see composition above) and add it in small aliquots using a multi channel pipette to the resin. Add 200 Jl of the TFA cocktail to the resin. Wait 10 minutes and add 100 Jl of the TFA cocktail to the resin. Wait 20 minutes and add 100 Jl of the TFA cocktail to the resin. Wait 60 minutes and add 100 Jl of the TFA cocktail to the resin. The final volume in the collection plate can be up to 500 Jl of TFA peptide solution. Wait another 90 minutes to complete the cleavage. Wash the resin with 100 Jl need TFA and apply vacuum to the cleavage devise and collect the TFA completely in the collection plate. 4. Use a speed-vac with plate holder to evaporate the TFA solution. The procedure runs for 30 minutes, at RT and the vacuum is set to 2 mbar. To use a trap at 80 C is mandatory. If a plate holder is not available transfer the TFA solution from the plate into 2 ml vials with caps and evaporate the TFA. Alternatively leave the plate overnight under a hood without a cover. This will reduce the volume down to 200 Jl just by TFA evaporation. 5. Add 1000 Jl of ice cold ether into each well of the plate and shake gently. Leave the plate in the freezer over night. If you have an explosion-proof cooled centrifuge you can spin down the precipitated peptide. We recommend to use tert-butyl-methyl-ether. It is hazardous and highly illegal to spin ether solutions in a normal centrifuge! Centrifuge the

5 plate or the vials for 10 minutes at 4 C and 5000 RPM. Take up the supernatant and wash the pellet with fresh ether 2 to 3 times. Finally take up the ether and dry the precipitated peptide under a hood over night or use a vacuum desiccator and remove all traces of ether. 6. Dissolve the precipitated peptide. Most peptides will be water-soluble. If this fails, freeze the suspension. Evaporate residual ether and add up to 30 % acetonitrile. If this also fails to dissolve the peptide, freeze it again and lyophilise it. Try to dissolve the peptide in water again. If it is a very acidic sequence, addition of a few drops of diluted ammonia may help. Otherwise add acetonitrile again. Some peptides are insoluble under these conditions and very difficult to handle. Weigh the peptide to determine the final yield. With some losses during synthesis, cleavage and work up you should expect a final yield of approx. 70 to 80 %, depending on the nature of the peptide. Analyze your peptides by reversed-phase HPLC and mass spectrometry. As there are numerous potential problems during synthesis and work-up it is highly recommended to check the peptides before using them in biological assays.