Computational improvement of the aptamer

The target of this protocol is to improve the union affinity between the protein and the aptamer, obtained by the process that had been explained previously, by bioinformatics methods.

To carry out this affinity improvement, you can start from only 2 elements: the DNA aptamer sequence and the name or preferably the amino acid protein sequence. However, any extra information that you could find in previous studies could be so helpful to save time and reduce the margin of cumulative error. The complete protocol have four different sections:

• • Obtaining the 3D protein structure.

• • Obtaining the 3D aptamer structure (most critical point).

• • Search of the binding site between protein and aptamer through a docking process.

• • Study of the union and proposal of mutation in the sequence.

It is very important to understand that this process not guarantee a better result. However it gives the opportunity of improve the aptamer obtained. Although there are so much works with proteins structures and the interaction between each other’s, there are almost no studies that work with nucleic acids in simulation or structure prediction terms beyond double strand helix. Therefore any final result obtained should be checked in the laboratory, either to confirm or discard the new sequence obtained.