Dynamics of terminal fraying–peeling and hydrogen bonds dictates the sequential vs. cooperative melting pathways of nanoscale DNA and PNA triplexes

Abstract

Peptide nucleic acids (PNAs) are charge-neutral synthetic DNA/RNA analogues. In many aspects of biology and biotechnology, the details of DNA and PNA melting reaction coordinates are crucial, and their associative/dissociative details remain inadequately understood. In the current study, we have attempted to gain insights into comparative melting pathways and binding affinity of iso-sequences of an 18-mer PNA–DNA–PNA triplex and the analogous DNA–DNA–DNA triplex, and DNA–DNA and PNA–DNA duplexes. It is intriguing that while the DNA–DNA–DNA triplex melts in two sequential steps, the PNA–DNA–PNA triplex melts in a single step and the mechanistic aspects for this difference are still not clear. We report an all-atom molecular dynamics simulation of both complexes in the temperature range of 300 to 500 K with 20 K intervals. Based on the trajectory analysis, we provide evidence that the association and dissociation are dictated by the differences in fraying–peeling effects from either terminus to the center in a zipper pattern among the PNA–DNA–PNA triplex and DNA–DNA–DNA triplexes. These are shown to be governed by the different characteristics of H-bonding, RMSD, and Free Energy Landscape (FEL) as analyzed by PCA, leading to the DNA–DNA–DNA triplex exhibiting sequential melting, while the PNA–DNA–PNA triplex shows cooperative melting of the whole fragment in a single-step. The PNA–DNA–PNA triplex base pairs are thermodynamically more stable than the DNA–DNA–DNA triplex, with the binding affinity of PNA–TFO to the PNA : DNA duplex being higher than that of DNA–TFO to the DNA : DNA duplex. The investigation of the association/dissociation of PNA–TFO to the PNA–DNA duplex has relevance and importance in the emerging effective applications of oligonucleotide therapy.