CH2- lengthening of the internucleotide linkage in the ApA dimer can improve its conformational compatibility with its natural polynucleotide counterpart

The complete family of ApA phosphonate analogues with the internucleotide linkage elongated by insertion of a -CH2- group was prepared and the hybridisation and structural properties of its members in interaction with polyuridylic acid were investigated using an original 2D Raman approach. Except for the conformationally restricted A(CH)pA(2'3'endo-5') modification, all of the isopolar, non-isosteric analogues form triplex-like complexes with poly(rU) at room temperature, in which two polymer strands are bound by Watson-Crick and Hoogsteen bonds to a central pseudostrand consisting of a 'chain' of A-dimers. For all of these dimers, the overall conformation of the triplexes was found to be similar according to their extracted Raman spectra. A simple semi-empirical model was introduced to explain the observed dependency of the efficiency of triplex formation on the adenine concentration. Apparently, for most of the modifications studied, the creation of a stable complex at room temperature requires the formation of a central pseudostrand, consisting of several adenine dimers. Molecular dynamics calculations were finally performed to interpret the differences in 'cooperative' behaviour between the different dimers studied. The results indicate that the exceptional properties of the Ap(CH2)A(3'-5') dimer could be caused by the 3D conformational compatibility of this modified linkage with the second (Hoogsteen) poly(rU) strand.