Binding interaction analysis of RNA aptamer-Fc region of human immunoglobulin G using fragment molecular orbital calculation

To understand the high affinity and specificity of an RNA aptamer against Fc region of human immunoglobulin G1 (hFc1), we analyzed the binding profiles of the RNA aptamer-hFc1 complex by studying its interaction using ab initio fragment molecular orbital calculations. Our calculations revealed that base-flipped G7 nucleotide is critical for hFc1 binding due to its robust interaction energy with hFc1 in the phosphate and base groups. It was suggested that G7 nucleotide renders a high degree of shape complementarity with the hFc1 molecule surface. This study provides physicochemical insights into the binding of the RNA aptamer to hFc1.