We all know that in this method the PTH reacts with the first amino acid (aa) from the N-terminal to the peptide and separates from it giving PTH-aa so that we can know the amino acids sequence in the peptide.

The question is what prevents the PTH from reacting with the second amino acid after it separates with the first amino acid in the same time and phase? Because if it does we can't distinguish between the first and second amino acid residue in the sequence.

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    $\begingroup$ Welcome to Biology SE! Just to improve your wording here - if we all knew what Edman did you wouldn't need to explain. Don't expect everyone to be a Biochemist working on proteins. also - prevent acronyms like aa. Don't apologize. Just ask the question. $\endgroup$ – AliceD Mar 19 '15 at 13:13
  • $\begingroup$ And isn't the answer linked to the chain termination methods in DNA sequencing like the Sanger method? en.wikipedia.org/wiki/Sanger_sequencing $\endgroup$ – AliceD Mar 19 '15 at 13:17

The short answer is that the Edman degradation is a multi-step process. The Wikipedia page has a decent picture of the mechanism. In practice, the peptide is reacted with phenylisothiocyanate (PTH) under mildly basic conditions to give a thiourea, which is stable. The excess PTH is separated from the thiourea intermediate. The thiourea is then treated with acid to cleave the N-terminal residue from the peptide. The PTH is no longer present, so there's no concern about reacting with the second residue.

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