Study of PNA-Protein Biomolecular Interactions

Peptide Nucleic Acids (PNAs) are synthetic analogues of DNA characterized by a pseudopeptide, achiral and neutral backbone, and by DNA nucleobases. PNAs were originally developed and studied to bind complementary RNA and DNA with high affinity and selectivity. However, being multifunctional molecules, they can interact with various biopolymers, including proteins. Nevertheless, the study of interactions between PNAs and proteins is limited. We used a PNA aptamer that binds the protein cardiac troponin I (cTnI) with picomolar affinity as a case study to investigate PNA–protein interactions, both computationally and experimentally. We designed and synthesized several variants of this PNA aptamer, shorter and with different terminal groups. We tested their ability to bind cTnI using surface plasmon resonance and graphene field-effect transistor sensors, as well as different functionalization chemistries. We used molecular dynamics simulations to assess the structure of the PNA aptamers in solution and molecular docking to characterize their binding to cTnI. We also explored PNA–protein binding mediated by small molecules within the Ribonuclease Targeting Chimera framework. We functionalized a PNA strand with an RNase L ligand and tested the ability of the chimera to recruit RNase L on a fiber optic-SPR sensor. Finally, we designed and coded a pipeline for in silico ligand screening to identify putative RNase L ligands with optimized affinity.