Pyrrolidino DNA with Bases Corresponding to the 2‐Oxo Deletion Mutants of Thymine and Cytosine: Synthesis and Triplex‐Forming Properties

Abstract

Abstract The dual recognition properties of pyrrolidino DNA species as parallel triplex‐forming oligonucleotides were previously found to be strongly dependent upon the nature of the pyrimidine bases. In the structure–activity study presented here we were able to exclude this differential binding being due to their 2‐oxo function. We had previously reported on the incorporation of pyrrolidino C ‐nucleosides into triplex‐forming 2′‐deoxyoligonucleotides (TFOs). The basic nitrogen atom that replaces the 4′‐oxygen atom of the 2′‐deoxysugar in such modified units introduces a positive charge in the third strand, and this is able to produce favourable electrostatic interaction with the negatively charged DNA target duplex. A first series of pyrrolidino pseudonucleosides with the bases isocytosine and uracil proved successful for GC base‐pair recognition, but was unsuccessful for AT base‐pair recognition within the parallel triplex binding motif. Here we report on the synthesis of the two novel 2′‐deoxypyrrolidino nucleosides carrying the bases pyridin‐2‐one and 2‐aminopyridine, their phosphoramidite building blocks and theirincorporation into TFOs. Pyrrolidinylpyridin‐2‐one (dp2P) and ‐2‐aminopyridine (dp2AP), prepared as part of a structure–activity profiling of pyrrolidino DNA in triplex binding, are deletion mutants of T and C, respectively. We found by T m measurements that neither modification increased triplex binding efficiency relative to the iso‐C‐ and ‐U‐containing pyrrolidino TFOs. These experiments clearly show that the C4 carbonyl function, although important for triplex binding through indirect contributions in general, is not responsible for the differential binding of the latter two aminonucleosides and suggest that TFO conformation is more important. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)