My peptide is 26 amino acids long (mol wt : around 2850 g/mol), largely hydrophobic but soluble in water (>250mg/ml), and is known to be a cell-penetrating peptide. I want to track its localisation in cell by labeling it with a succinimidyl ester of Alexa fluor 488. I am thinking of labelling the N-terminus. There are 3 other lysine residues. How to block these? Could some one help and give me a detailed protocol on how to do this as well as remove the unlabelled peptide and dye molecules and how to confirm the labelling?
You can you can follow The protocolos and check the references in Hermanson's Bioconjugate Techniques. Very good manual. Anyhow, it's going to be difficult getting specific N-terminal labeling without modifying the Lys side chains. Perhaps you could separate the products by HPLC, but then you are faced with the problem of knowing where is the peptide modified in each case. Bottom line, I believe you're better off labeling the peptide in the solid phase.
http://www.sciencedirect.com/science/book/9780123822390
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