DNA triplex with conformationally locked sugar disintegrates to duplex: Insights from molecular simulations

Abstract

DNA triplex is a popular, higher-order structural arrangement with several biological importance. In the present article, we examined the impact of replacing regular deoxyribose sugar by conformationally locked sugar on the structure/stability of a DNA triplex. We individually modified single strands of DNA triplex (3′-5′ strand/5′-3′ strand) and observed the consequences in terms of the overall structural integrity and energetics using all-atom explicit-solvent Gaussian accelerated molecular dynamics simulations at biological salt concentration. As anticipated, the control DNA triplex maintained the structural integrity throughout the simulations. However, it is striking to note that a duplex evolved from both the modified systems (3′-5′ modified triplex as well as 5′-3′ modified triplex). The resultant duplexes in both cases contain a modified strand and a regular strand, whereas the third strand (regular ssDNA) left the binding site entirely. We observed that the modified ssDNA binds to the regular ssDNA with high affinities in both the hybrid duplexes (∼−64 kcal/mol), significantly higher than the regular ssDNA – regular ssDNA interaction (∼−52 kcal/mol). The remarkable binding of modified ssDNA to regular ssDNA can be utilized to design new antisense oligonucleotides, and the role of such modified oligonucleotides in anticancer therapy is foreseen.