Aptamers Aptamers are single-stranded DNA or RNA molecules. Depending on their sequence they can adopt a variety of shapes since complementary bases form hydrogen bonds in solution. Different compounds, from large proteins to small molecules, can form complexes with aptamers with dissociation constants as low as a few nM. In contrast to the familiar enzyme-substrate “lock and key” interactions, the binding between the target and aptamer is not a simple geometrical fit. Other interactions, such as hydrophobic attraction and  stacking can play a significant role as well. Aptamers are usually produced in a process known as SELEX [1]. Briefly, the process involves: 1) Synthesizing a large pool of oligonucleotides of random sequence but with constant regions at both ends (these regions are required for the Polymerase Chain Reaction (PCR) in step 5). 2) Exposing the pool of oligonucleotides to surface immobilized targets. 3) Washing away and discarding the sequences that have not bound. 4) Eluting the bound oligonucleotides from the solid support. 5) Amplifying the eluted oligonucleotides using PCR. After PCR amplification, all the above steps are repeated with the enriched oligonucleotide pool, refining the pool of oligonucleotides to select the ones with high binding affinity to the target. Usually several rounds of SELEX are required before aptamers with low dissociation constants are found. In this project, two DNA aptamers from the aptamer database were selected. They have been reported to bind to lysozyme with dissociation constants in the nanomolar range. For more information on the aptamers used in the project, please refer to the Lab Book section of this website. References: [1] Orava, E. Cicmil, N. Gariépy, J. Delivering Cargoes into Cancer Cells Using DNA Aptamers Targeting Internalized Surface Portals, Biochimica et Biophysica Acta (BBA) – Biomembranes, 1798, 2010, 2190.