Triplet-wise computational analysis of recombinant triplex formed by LNA-TFO

Abstract

Triplex is short time vital structures of nucleic acidsformed in many biological processes. The study of triplex structure not only limited to explanation of vital processes but also extended up to its usefulness as biotechnical tools, gene-engineering and bio-nanotechnology. Such enormous application of triplex structure demands TFO(triplex-forming oligonucleotides) with greater binding affinity and stability. In this respect modification in oligonucleotides as LNA(Locked Nucleic Acids), locked sugar in RNA like C3’-endo conformation as RNA form more stable triplex but its application limited in biological environment due to blood clearance. Thus, here in this study, a 15-mer triplex was designed and molecular dynamics of 50ns run to see stability during simulation and QM/MM was done for triplet wise decomposition energy analysis with PM3 and PM6 methodology. The result of study exhibits that LNA triplets play essential role in the form of triplet and binds with greater affinity.Triplex is short time vital structures of nucleic acidsformed in many biological processes. The study of triplex structure not only limited to explanation of vital processes but also extended up to its usefulness as biotechnical tools, gene-engineering and bio-nanotechnology. Such enormous application of triplex structure demands TFO(triplex-forming oligonucleotides) with greater binding affinity and stability. In this respect modification in oligonucleotides as LNA(Locked Nucleic Acids), locked sugar in RNA like C3’-endo conformation as RNA form more stable triplex but its application limited in biological environment due to blood clearance. Thus, here in this study, a 15-mer triplex was designed and molecular dynamics of 50ns run to see stability during simulation and QM/MM was done for triplet wise decomposition energy analysis with PM3 and PM6 methodology. The result of study exhibits that LNA triplets play essential role in the form of triplet and binds with greater affinity.