I am asked to construct an aptamer library of exactly 1024 members, each with a unique V.
I have two questions regarding this; firstly, is it wrong to construct an aptamer library using a column with the target protein, then amplify the product with PCR and repeat selection?
The answer which we were given for this question states that:
"I would begin by looking at which amino acids are involved in the natural binding of protein substrates to the target protein. Knowing the amino acids involved in binding, nucleotides with similar properties can be incorportated at their equal postitions. I would vary the portions of the V region which bind the target protein to yield different oligos.
I would then synthesize a primer containing a T7 RNA polymerase promoter. DNA polymerase can use this as a primer to make dsDNA incorporating the promoter. It is then possible for RNA pol to bind and synthesize RNA strands, the aptamers."
I don't understand the first part about the amino acids and it doesn't answer how to make the library of exactly 1024 members? All help is appreciated!