Design, synthesis, conformational analysis and nucleic acid hybridisation properties of thymidyl pyrrolidine-amide oligonucleotide mimics (POM)

Abstract

Pyrrolidine-amide oligonucleotide mimics (POM) 1 were designed to be stereochemically and conformationally similar to natural nucleic acids, but with an oppositely charged, cationic backbone. Molecular modelling reveals that the lowest energy conformation of a thymidyl-POM monomer is similar to the conformation adopted by ribonucleosides. An efficient solution phase synthesis of the thymidyl POM oligomers has been developed, using both N-alkylation and acylation coupling strategies. ¹H NMR spectroscopy confirmed that the highly water soluble thymidyl-dimer, T₂-POM, preferentially adopts both a configuration about the pyrrolidine N-atom and an overall conformation in D₂O that are very similar to a typical C3′-endo nucleotide in RNA. In addition the nucleic acid hybridisation properties of a thymidyl-pentamer, T₅-POM, with an N-terminal phthalimide group were evaluated using both UV spectroscopy and surface plasmon resonance (SPR). It was found that T₅-POM exhibits very high affinity for complementary ssDNA and RNA, similar to that of a T₅-PNA oligomer. SPR experiments also showed that T₅-POM binds with high sequence fidelity to ssDNA under near physiological conditions. In addition, it was found possible to attenuate the binding affinity of T₅-POM to ssDNA and RNA by varying both the ionic strength and pH. However, the most striking feature exhibited by T₅-POM is an unprecedented kinetic binding selectivity for ssRNA over DNA.