Representative structures of the energetic minima of bcl2midG4-ds/TF-PNA1K heterotriplex.

Here, we report the representative structures extracted from the energetic minima  retrieved after 500ns of aMD simulations of  the heterotriplexes formed by two different peptide nucleic acids (PNA) molecular species, P3 and P4 with double helix DNA of  the G-rich tract in the  Bcl-2 gene promoter (bcl2midG4-ds).  Briefly, due to the lack of experimental structures, the bcl2midG4-ds10/TF-PNA1K heterotriplex systems were manually constructed and submitted to conventional molecular dynamics (cMD) and accelerated molecular dynamics (aMD) simulations to investigate the conformational behaviour. Specifically, two different PNA molecular species, namely P3 and P4, with different numbers and positions of N3-protonated cytosines, were investigated. Three independent cMD simulations of 1 μs each were conducted for a total simulation time of 3 μs for both P3 and P4 systems, followed by 500 ns of aMD simulations to enhance their conformational sampling. Free energy surface (FES) and principal component (PCs) analysis were generated for both P4 and P3 systems to compare the sampled conformational space and identify representative energy minima. Here, we have uploaded  the energetic minima structures of P3 and P4. Overall, these findings have implications for the future design of other TF-PNAs targeting G-rich DNA sequences, as they shed light on the importance of protonation patterns, the position of protonation sites, and the influence of PNAs on the DNA structure.