Reduction of interstrand charge repulsion of DNA duplexes by salts and by neutral phosphotriesters – Contrary effects for harnessing duplex formation

To exploit the formation of DNA duplexes, the charge repulsion between complementary DNA strands can be reduced by adding salts or by replacing the negatively charged natural phosphodiester linkage(s) with charge-neutral methyl phosphotriester(s) (MPTE) linkage(s) of the synthetic nDNA oligonucleotides. Recently, we reported prominent improvements of detecting target nucleic acids with nDNA probes on liquid-phase PCR and solid/liquid-interface biosensing. To understand the observed improvements from thermodynamics perspectives, we studied the formation and stability of the double-stranded DNA (dsDNA) containing nDNA and/or natural DNA. With the natural DNA oligonucleotides, increment of Na⁺ cations caused unexpected reductions of favorable enthaply (ΔH) of duplex formation and expected increases of favorable free energy (ΔG) and temperature of melting transition (T_m). With one nDNA in duplex formation, the increase of Na⁺ yielded extra faborable ΔH, yet unfavorable ΔG and T_m. Possibly, Na⁺ cations (> 50 mM) promote the formation of dsDNA through the endothermic release of DNA (and nDNA)-hydrating water molecules more than through the reduction of inter-strand repulsions. The methyl groups of MPTE of nDNA also destabilize the DNA duplexes by hindering the formation of standard double helices. These novel findings explain the duplex-destabilization property of nDNA which enables its discrimination of single-nucleotide polymorphisms.