I can find several papers that give me a guide for choosing a suitable aptamer sequence 1. But how to find a property aptamer sequence 2(partially complementary to sequence 1)?
I think you can create a set of complementary sequences of aptamer sequence 1 and find their binding affinity using docking simulations. In this way, you can compare binding affinity of sequence 1 for complementary sequences and VEGF. Hence, you can find a complementary sequence having lesser binding affinity in comparison to VEGF.