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LNA substitution for RNA in the application of modified TFO: A molecular dynamics study

Locked nucleic acid (LNA) has suggested as a potential substitute of Ribose nucleotide in the application of RNA-TFO in blood clearance in cellular processes due to early degradation of Ribose nucleotide. In this work we designed different Recombinant triplexes by substituting LNA in two different sequences of DNA and verify the stability of such type of modified triplexes and determined the binding affinity of TFO with natural DNA duplex. The molecular dynamics principles were used in the simulation. Binding free energies were determined by Molecular Mechanics Generalized Born Surface Area (MMGBSA) approach. The results of simulation suggest that substitution of LNA in DNA sequence can be used as a better substitute for RNA in application modified TFO