I am using SELEX method to synthesize aptamers for drugs. As per literature, the concentration of oligonucleotides should decreased in successive rounds. So is it necessary to reduce concentration of target as well in successive rounds?
If yes than on what ratio?
Hi Shringika,
I think so. To isolate aptamers with high binding affinity(Low Kd), low target concentration should be used.
The average Kd value of aptamers that bind to a target under equilibrium can be analytically expressed using eq: K =[A][S]/d [AS]. where [S] is the concentration of unbound target, [A] is the concentration of unbound aptamers, and [AS] is the concentration of aptamer bound to your target.
Therefore, it becomes clear that Kd is minimized and selection efficiency is improved as [S] → 0 and as [A] → 0. In other words, using the smallest feasible amount of target and stringently removing unbound aptamers will yield the best-performing aptamer sequences ( Acc. Chem. Res. 2016, 49, 1903-1910 ). I have seen people used DNA/taget ratio from 10^3 to 10^6 to achieve efficient selection.
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