Structural basis of biotin–RNA aptamer binding: a theoretical study

Molecular dynamics simulation of biotin–RNA aptamer in absence of its ligand, as well as semiempirical quantum-chemical calculations of its biotin-binding pocket in the presence of biotin have been performed. The global 3D architecture of the aptamer seems to be guided mainly by its primary and secondary structure, whereas a local structural adjustment of its biotin-binding pocket ought to proceed largely due to biotin-binding process. Physico-chemical grounds for much lower RNA–biotin affinity (as compared to that of avidin-like proteins) are discussed using calculated frontier molecular orbital contours of the RNA and protein complexes in question.