I have a system, in which amino acids are bound to the matrix (with C-alpha-R) group. All amino acids have free amino and carboxylic groups. I need to add one layer of amino acids on the top of that (preferentially polypeptide bond).
Why dont you synthesize dipeptides/tripeptides and then immobilize them to the matrix!
Thanks for your suggestion Dr. Shing. But I need to connect two matrix either directly (using peptide bonds of bound amino acids) or I may need to add one more layer of amino acids to facilitate the matrix binding. So my system will work if it would appear like a sandwich (both side matrix and in between peptide bonds working as linkers.
Is it safe to assume that the matrix is similar to a solid-phase peptide resin, in which the peptide can be built upon? If that is the case, you should be able to just conjugate amino acids to the matrix using HATU/DIPEA coupling, then wash remaining reagents and amino acids away from the matrix. You would then deprotect the amino acid you just added (assuming they are FMOC protected), wash, then couple the next amino acid, and so forth... Not sure how you would test the matrix for completion of the amide bond formation. It's very easy to do with resin beads and picryl sulfonic acid (PSA) testing, but in your case you might have to come up with something else.
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