Influence of PNA containing 8-aza-7-deazaadenine on structure stability and binding affinity of PNA.DNA duplex: insights from thermodynamics, counter ion, hydration and molecular dynamics analysis

This paper describes the synthesis of a novel 8-aza-7-deazapurin-2,6-diamine (DPP)-containing peptide nucleic acid (PNA) monomer and Boc protecting group-based oligomerization of PNA, replacing adenine (A) with DPP monomers in the PNA strand. The PNA oligomers were synthesized against the biologically relevant SV40 promoter region (2494-AATTTTTTTTATTTA-2508) of pEGFP-N3 plasmid. The DPP-PNA.DNA duplex showed enhanced stability as compared to normal duplex (A-PNA.DNA). The electronic distribution of DPP monomer suggested that DPP had better electron donor properties over 2,6-diamino purine. UV melting and thermodynamic analysis revealed that the PNA oligomer containing a diaminopyrazolo(3,4-d) pyrimidine moiety (DPP) stabilized the PNA.DNA hybrids compared to A-PNA.DNA. DPP-PNA.DNA duplex showed higher water activity (Delta n(w) = 38.5) in comparison to A-PNA.DNA duplex (Delta n(w) = 14.5). The 50 ns molecular dynamics simulations of PNA.DNA duplex containing DPP or unmodified nucleobase-A showed average H-bond distances in the DPP-dT base pair of 2.90 angstrom (O...H-N bond) and 2.91 angstrom (N...H-N bond), which were comparably shorter than in the A-dT base pair, in which the average distances were 3.18 angstrom (O...H-N bond) and 2.97 angstrom (N...H-N bond), and there was one additional H-bond in the DPP-dT base pair of around 2.98 angstrom (O2...H-N2 bond), supporting the higher stability of DPP-PNA.DNA. The analysis of molecular dynamics simulation data showed that the system binding free energy increased at a rate of approximately -4.5 kcal mol(-1) per DPP base of the PNA.DNA duplex. In summary, increased thermal stability, stronger hydrogen bonding and more stable conformation in the DPP-PNA.DNA duplex make it a better candidate as antisense/ antigene therapeutic agents.