1H NMR Study on the pH‐Dependent Polymorphism of a DNA Triplex with Oligonucleoside Methylphosphonate Analogues

Abstract Triplex formation in various stoichiometric mixtures of oligonucleoside methylphosphonates d‐Ap(GpAp)7G (A) and d‐Cp(TpCp)7 (B) (p = methylphosphonate) was studied by measuring the NH‐N hydrogen bonded NMR resonance in relation to temperature and pH. Only a duplex or a triplex was observed for the mixture at pH 6.8 or 3.83 respectively, but both duplex and triplex coexist at pH 4.75. Thus the polymorphism of the mixture is close related to the pKa (4.30) for protonation of B. The triplex starts to dissociate when pH < 2. All data indicate that the duplex and triplex formed by A and B are less stable than those formed by d‐A‐(G‐A‐)7G (C) and d‐C‐(T‐C‐)7T (D) (‐ = phosphodiester). The conformation of the triplex A·B2 is the same at pH 3.83 as that of the corresponding triplex C·D2 at pH 4.50, but different at pH 4.75. Thus, the A·B2 triplex must be able to exist in various conformations, depending on the acidity of the solution. Furthermore, no diastereoisomeric effect was observable on duplex and triplex formation as similar chemical shifts of all NH resonances from C+, G, and T bases were recorded from a mixture of myriad steric isomers.