Because a key feature associated with the recognition of a target by an aptamer is a conformational transition (or folding) from loose random coil to a compact tertiary structure, can you recommend using any spacer between gold particles and the aptamer?
For example, I know the example of using (dT)10 associated with the aptamer. Can another spacer sequence be used? How about using core sequence of the aptamer alone vs. aptamer sequence with flanked constant regions after SELEX?
Thank you.
In the literature, polyA, or polyT is the most frequently used. In my experience, the optimized space arm length is 9-12 nt of dA or dT, and please mfold your prolonged sequence to make sure that the arm is not form a spedific secondary structures such as stem or knot with the aptamer. Good luck.
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