Aptamer

A nucleic-acid aptamer is a folded DNA or RNA molecule that binds a specified target. Its nucleotide sequence supports molecular recognition through a three-dimensional structure; the target need not be a complementary nucleic-acid strand. Here the term concerns nucleic-acid binders. Binding alone does not make the molecule a deoxyribozyme or ribozyme, since catalysis additionally requires a chemical transformation.

A motivating primary experiment by C. Tuerk and L. Gold alternated binding selection and amplification to isolate RNA ligands for bacteriophage T4 DNA polymerase. Their eight-position randomized region represented $4^8=65,536$ possible sequences. Two selected RNAs had equivalent binding constants despite differing at four positions, showing that a functional binder need not have one unique sequence.^[ref]

A simple equilibrium model makes binding affinity quantitative. For one aptamer species $A$ and ligand $L$ forming a 1:1 complex,The dissociation constant has concentration units, and the last equation uses free ligand concentration. With stipulated $K_d=10\mathrm{nM}$, free ligand at $1$, $10$ and $100\mathrm{nM}$ gives bound fractions approximately $0.091$, $0.50$ and $0.909$. Replacing free concentration with the total added amount can fail when appreciable ligand is bound.

An affinity measurement should distinguish retained or bound material from material that adheres nonspecifically or survives the detection procedure for another reason. A binding curve, a sequence comparison and a downstream functional assay provide different evidence. In vitro selection enriches candidates under its selection conditions; it does not by itself establish binding specificity or useful behavior in every sample environment.