Structural insight into locked nucleic acid based novel antisense modifications: A DFT calculations at monomer and MD simulations at oligomer level

Abstract

In the present study, five novel LNA based antisense modifications have been proposed. A conformational search was carried out using TANGO, followed by geometry optimization using MOPAC. Based on their electronic energies the most stable conformation for each modification was identified. Further, DFT based full geometry optimization on the most stable conformations at the gas phase B3LYP/6-31G(d,p) using a Gaussian03 and single point energy calculations on the optimized structures at the solvent phase B3LYP/6-311G(d,p) level of theory were done to derive their quantum chemical descriptors using the Gaussian09. A comparison of global reactivity descriptors confirmed that the LNA based modifications were the most reactive. Base-pair stability was recorded by observing the binding energies and base-pairing conformations of modified GC base pairs at the B3LYP/6-311G(d,p) level of theory. Molecular dynamics simulations have been performed at the oligomer duplex level by incorporating individual modifications on 20-mer RNA-RNA duplexes using AMBER16. Free energy calculations of duplex structures suggested that incorporation of A2 modification into the RNA-RNA duplex increased the duplex binding affinity similar to LNA. Whereas, the A3 modification showed less binding compared to LNA but improved binding compared to MOE. This computational approach using quantum chemical methods may be very useful to propose better modifications than the existing ones before performing the experiments in the area of antisense technology.