Aptamers in Biotechnology by Unknown

Author:Unknown
Language: eng
Format: epub
ISBN: 9783030540616
Publisher: Springer International Publishing

3.3.4 Thermodynamics Bases of the Molecular Interaction

Electrostatic interactions, hydrogen bonding, and hydrophobic association taken together mainly generate the molecular recognition, characterized by an affinity constant of an aptamer for a given protein, like any other complex in affinity chromatography [89]. Thus the density of the aptamer-grafted ligand on solid support is critical for the binding capacity properties of the affinity sorbent. Moreover the degree of freedom of the grafted aptamer must be relatively large to reach the protein aptatope to dock there intimately. To this end it appears useful to have a flexible spacer between the oligonucleotide ligand and the solid matrix. On the other side, proteins are large constructs that surpass the mass of the oligonucleotide by factors ranging from 1 to about 3. Proteins are folded on themselves and expose generally a limited surface area, compared to the length of the amino acid sequence. This situation largely enhances the probability to have a highly specific molecular interaction happening.

Figure 5 depicts the interaction between a grafted aptamer and a protein in solution schematically. Therefore the formation of this intimate couple is only possible if complementary/synergistic association forces are present and located in the right position.

Fig. 5Representation cartoon of the molecular docking between the immobilized aptamer and the protein. The specific interaction covers a given area of the protein structural aptatope involving various regions of the aptamer. SP spacer arm, SM solid-phase medium (e.g., chromatography support). The dark red zone represents the aptatope docking region of the protein

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