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Suppose there were DNA or RNA aptamers that bind specifically to a certain terminal amino acid residue. Let's name it aaSA (amino acid specific aptamer). For example, the aptamer binding to terminal methionine residue is named as MetSA.

If such 20 aaSA all existed, then they could be applied to identify the terminal amino acid of a peptide. Concretedly, the peptide sample is immobilized to a solid surface, then all 20 aaSA are introduced and bind to the terminal residue. Extra unbinding aaSA will be washed away, and the binding aaSA will be separated later by another approach (like heating). And by sequencing the binding aaSA we can know the terminal residue of the peptide.

Either N-terminal or C-terminal is OK.

I know mass spectrometry is much more powerful in this task than the method I have supposed. But I still want to know if such aptamer exists or not.

I have searched in Google and Google Scholar, only to find aptamers binding to some intact proteins (rather than short peptides with terminal exposed). The binding site is unknown, possibly not in the terminal.

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  • $\begingroup$ I'm not quite sure what you're asking about. If you're just talking about peptides, then N- or C-terminal sequencing is much easier and more accurate than the method you describe. For large proteins, they're still easier, as the terminal peptides may not even be available to an aptamer in the protein's native conformation. $\endgroup$ – MattDMo Mar 6 '16 at 18:47
  • $\begingroup$ @MattDMo Thank you for your comment. I have learned many well-developed N- or C-terminal analysis method in biochemistry class such as DNS, PITC, hydrazinolysis and amino/carboxy peptidase. I'm not proposing the first peptide terminal analysis method but just an alternative. Despite this, I think the method by aptamers may still have some advantages. For example, if the peptide is in trace amount, the signal produced by other methods may be too weak to be detected accurately. But for aptamers, they are nucleic acid and can be amplified. $\endgroup$ – Wei Feng Mar 7 '16 at 7:05
  • $\begingroup$ @MattDMo And after searching in the Google, I found it seemed that nobody had done it. So I'm wondering if I have read enough paper or someone already did it. $\endgroup$ – Wei Feng Mar 7 '16 at 7:11
  • $\begingroup$ Two places I'd definitely recommend looking are the US and EU patent and trademark office websites. If someone has developed something like this, they almost surely have filed for patent protection. If you end up doing it, you should get a lawyer and patent ASAP. $\endgroup$ – MattDMo Mar 7 '16 at 14:47

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